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Merge branch 'master' into lammps-icms
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Authored by Axel Kohlmeyer <akohlmey@gmail.com> on Oct 12 2012, 14:46.

Description

Merge branch 'master' into lammps-icms

Resolved Conflicts:
doc/Eqs/pair_gauss.jpg
lib/cuda/Makefile.common
lib/cuda/Makefile.defaults
lib/cuda/Makefile.lammps
lib/cuda/cuda_wrapper_cu.h
lib/cuda/pair_cg_cmm_coul_cut_cuda.cu
lib/cuda/pair_cg_cmm_coul_cut_cuda_cu.h
lib/cuda/pair_cg_cmm_coul_debye_cuda.cu
lib/cuda/pair_cg_cmm_coul_debye_cuda_cu.h
lib/cuda/pair_cg_cmm_coul_long_cuda.cu
lib/cuda/pair_cg_cmm_coul_long_cuda_cu.h
lib/cuda/pair_cg_cmm_cuda.cu
lib/cuda/pair_cg_cmm_cuda_cu.h
lib/cuda/pair_cg_cmm_cuda_kernel_nc.cu

Details

Committed
Axel Kohlmeyer <akohlmey@gmail.com>Oct 12 2012, 14:46
Pushed
jungeOct 6 2016, 16:49
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rLAMMPS38ce57cd4a61: git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8948 f3b2605a-c512-4ea7…
rLAMMPSaf6cef97bf45: Merge branch 'master' into lammps-icms
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Axel Kohlmeyer <akohlmey@gmail.com> committed rLAMMPS9a0e9670fb05: Merge branch 'master' into lammps-icms (authored by Axel Kohlmeyer <akohlmey@gmail.com>).Oct 12 2012, 14:46

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This commit merges a very large number of changes. Only the first 50 are shown.
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Changes (848)
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Path
Adoc/Eqs/pair_coul_dsf.jpg
Adoc/Eqs/pair_coul_dsf.tex
Mdoc/Eqs/pair_gauss.tex
Mdoc/Section_accelerate.html
Mdoc/Section_accelerate.txt
Mdoc/Section_commands.html
Mdoc/Section_commands.txt
Mdoc/Section_intro.html
Mdoc/Section_intro.txt
Mdoc/Section_packages.html
Mdoc/Section_packages.txt
Mdoc/Section_tools.html
Mdoc/Section_tools.txt
Mdoc/communicate.html
Mdoc/communicate.txt
Mdoc/fix_ave_atom.html
Mdoc/fix_ave_atom.txt
Mdoc/fix_efield.html
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Mdoc/fix_wall.html
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Mdoc/kspace_modify.html
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Mdoc/kspace_style.html
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Mdoc/neigh_modify.html
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Mdoc/package.html
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Ddoc/pair_buck_coul.html
Ddoc/pair_buck_coul.txt
Adoc/pair_buck_long.html
Adoc/pair_buck_long.txt
Mdoc/pair_charmm.html
Mdoc/pair_charmm.txt
Mdoc/pair_class2.html
Mdoc/pair_class2.txt
Mdoc/pair_coul.html
Mdoc/pair_coul.txt
Mdoc/pair_gauss.html
Mdoc/pair_gauss.txt
Mdoc/pair_gayberne.html
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Mdoc/pair_lj.html
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Ddoc/pair_lj_coul.html
Ddoc/pair_lj_coul.txt
Adoc/pair_lj_long.html
Adoc/pair_lj_long.txt
Mdoc/read_restart.html
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Mdoc/replicate.html
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Mlib/cuda/Makefile.common
Mlib/cuda/atom_vec_angle_cuda.cu
Mlib/cuda/atom_vec_angle_cuda_cu.h
Mlib/cuda/atom_vec_atomic_cuda.cu
Mlib/cuda/atom_vec_atomic_cuda_cu.h
Mlib/cuda/atom_vec_charge_cuda.cu
Mlib/cuda/atom_vec_charge_cuda_cu.h
Mlib/cuda/atom_vec_cuda.cu
Mlib/cuda/atom_vec_cuda_kernel.cu
Mlib/cuda/atom_vec_full_cuda.cu
Mlib/cuda/atom_vec_full_cuda_cu.h
Dlib/cuda/binning.cu
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Mlib/cuda/comm_cuda.cu
Mlib/cuda/comm_cuda_cu.h
Mlib/cuda/comm_cuda_kernel.cu
Mlib/cuda/compute_temp_cuda.cu
Mlib/cuda/compute_temp_cuda_cu.h
Mlib/cuda/compute_temp_cuda_kernel.cu
Mlib/cuda/compute_temp_partial_cuda.cu
Mlib/cuda/compute_temp_partial_cuda_cu.h
Mlib/cuda/compute_temp_partial_cuda_kernel.cu
Mlib/cuda/crm_cuda_utils.cu
Mlib/cuda/cuda.cu
Mlib/cuda/cuda_common.h
Mlib/cuda/cuda_data.cu
Mlib/cuda/cuda_data_cu.h
Mlib/cuda/cuda_data_kernel.cu
Mlib/cuda/cuda_pair.cu
Mlib/cuda/cuda_pair_cu.h
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/cuda_wrapper.cu
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Mlib/cuda/domain.cu
Mlib/cuda/domain_cu.h
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Mlib/cuda/fft3d_cuda.cu
Mlib/cuda/fft3d_cuda_cu.h
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Mlib/cuda/fix_addforce_cuda.cu
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Mlib/cuda/fix_aveforce_cuda.cu
Mlib/cuda/fix_aveforce_cuda_cu.h
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Mlib/cuda/fix_enforce2d_cuda.cu
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Mlib/cuda/fix_freeze_cuda.cu
Mlib/cuda/fix_freeze_cuda_cu.h
Mlib/cuda/fix_freeze_cuda_kernel.cu
Mlib/cuda/fix_gravity_cuda.cu
Mlib/cuda/fix_gravity_cuda_cu.h
Mlib/cuda/fix_gravity_cuda_kernel.cu
Mlib/cuda/fix_nh_cuda.cu
Mlib/cuda/fix_nh_cuda_cu.h
Mlib/cuda/fix_nh_cuda_kernel.cu
Mlib/cuda/fix_nve_cuda.cu
Mlib/cuda/fix_nve_cuda_cu.h
Mlib/cuda/fix_nve_cuda_kernel.cu
Mlib/cuda/fix_set_force_cuda.cu
Mlib/cuda/fix_set_force_cuda_cu.h
Mlib/cuda/fix_set_force_cuda_kernel.cu
Mlib/cuda/fix_shake_cuda.cu
Mlib/cuda/fix_shake_cuda_cu.h
Mlib/cuda/fix_shake_cuda_kernel.cu
Mlib/cuda/fix_temp_berendsen_cuda.cu
Mlib/cuda/fix_temp_berendsen_cuda_cu.h
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Mlib/cuda/fix_temp_rescale_cuda.cu
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Mlib/cuda/fix_temp_rescale_limit_cuda.cu
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Mlib/cuda/fix_temp_rescale_limit_cuda_kernel.cu
Mlib/cuda/fix_viscous_cuda.cu
Mlib/cuda/fix_viscous_cuda_cu.h
Mlib/cuda/fix_viscous_cuda_kernel.cu
Mlib/cuda/neighbor.cu
Mlib/cuda/neighbor_cu.h
Mlib/cuda/neighbor_kernel.cu
Mlib/cuda/pair_born_coul_long_cuda.cu
Mlib/cuda/pair_born_coul_long_cuda_cu.h
Mlib/cuda/pair_born_coul_long_cuda_kernel_nc.cu
Mlib/cuda/pair_buck_coul_cut_cuda.cu
Mlib/cuda/pair_buck_coul_cut_cuda_cu.h
Mlib/cuda/pair_buck_coul_long_cuda.cu
Mlib/cuda/pair_buck_coul_long_cuda_cu.h
Mlib/cuda/pair_buck_cuda.cu
Mlib/cuda/pair_buck_cuda_cu.h
Mlib/cuda/pair_buck_cuda_kernel_nc.cu
Mlib/cuda/pair_eam_cuda.cu
Mlib/cuda/pair_eam_cuda_cu.h
Mlib/cuda/pair_eam_cuda_kernel_nc.cu
Mlib/cuda/pair_gran_hooke_cuda.cu
Mlib/cuda/pair_gran_hooke_cuda_cu.h
Mlib/cuda/pair_gran_hooke_cuda_kernel_nc.cu
Mlib/cuda/pair_lj96_cut_cuda.cu
Mlib/cuda/pair_lj96_cut_cuda_cu.h
Mlib/cuda/pair_lj96_cut_cuda_kernel_nc.cu
Mlib/cuda/pair_lj_charmm_coul_charmm_cuda.cu
Mlib/cuda/pair_lj_charmm_coul_charmm_cuda_cu.h
Mlib/cuda/pair_lj_charmm_coul_charmm_cuda_kernel_nc.cu
Mlib/cuda/pair_lj_charmm_coul_charmm_implicit_cuda.cu
Mlib/cuda/pair_lj_charmm_coul_charmm_implicit_cuda_cu.h
Mlib/cuda/pair_lj_charmm_coul_charmm_implicit_cuda_kernel_nc.cu
Mlib/cuda/pair_lj_charmm_coul_long_cuda.cu
Mlib/cuda/pair_lj_charmm_coul_long_cuda_cu.h
Mlib/cuda/pair_lj_class2_coul_cut_cuda.cu
Mlib/cuda/pair_lj_class2_coul_cut_cuda_cu.h
Mlib/cuda/pair_lj_class2_coul_long_cuda.cu
Mlib/cuda/pair_lj_class2_coul_long_cuda_cu.h
Mlib/cuda/pair_lj_class2_cuda.cu
Mlib/cuda/pair_lj_class2_cuda_cu.h
Mlib/cuda/pair_lj_class2_cuda_kernel_nc.cu
Mlib/cuda/pair_lj_cut_coul_cut_cuda.cu
Mlib/cuda/pair_lj_cut_coul_cut_cuda_cu.h
Mlib/cuda/pair_lj_cut_coul_debye_cuda.cu
Mlib/cuda/pair_lj_cut_coul_debye_cuda_cu.h
Mlib/cuda/pair_lj_cut_coul_long_cuda.cu
Mlib/cuda/pair_lj_cut_coul_long_cuda_cu.h
Mlib/cuda/pair_lj_cut_cuda.cu
Mlib/cuda/pair_lj_cut_cuda_cu.h
Mlib/cuda/pair_lj_cut_cuda_kernel_nc.cu
Mlib/cuda/pair_lj_cut_experimental_cuda.cu
Mlib/cuda/pair_lj_cut_experimental_cuda_cu.h
Mlib/cuda/pair_lj_expand_cuda.cu
Mlib/cuda/pair_lj_expand_cuda_cu.h
Mlib/cuda/pair_lj_expand_cuda_kernel_nc.cu
Mlib/cuda/pair_lj_gromacs_coul_gromacs_cuda.cu
Mlib/cuda/pair_lj_gromacs_coul_gromacs_cuda_cu.h
Mlib/cuda/pair_lj_gromacs_coul_gromacs_cuda_kernel_nc.cu
Mlib/cuda/pair_lj_gromacs_cuda.cu
Mlib/cuda/pair_lj_gromacs_cuda_cu.h
Mlib/cuda/pair_lj_gromacs_cuda_kernel_nc.cu
Mlib/cuda/pair_lj_sdk_coul_cut_cuda.cu
Mlib/cuda/pair_lj_sdk_coul_cut_cuda_cu.h
Mlib/cuda/pair_lj_sdk_coul_debye_cuda.cu
Mlib/cuda/pair_lj_sdk_coul_debye_cuda_cu.h
Mlib/cuda/pair_lj_sdk_coul_long_cuda.cu
Mlib/cuda/pair_lj_sdk_coul_long_cuda_cu.h
Mlib/cuda/pair_lj_sdk_cuda.cu
Mlib/cuda/pair_lj_sdk_cuda_cu.h
Mlib/cuda/pair_lj_sdk_cuda_kernel_nc.cu
Mlib/cuda/pair_lj_smooth_cuda.cu
Mlib/cuda/pair_lj_smooth_cuda_cu.h
Mlib/cuda/pair_lj_smooth_cuda_kernel_nc.cu
Mlib/cuda/pair_manybody_const.h
Mlib/cuda/pair_morse_coul_long_cuda.cu
Mlib/cuda/pair_morse_coul_long_cuda_cu.h
Mlib/cuda/pair_morse_coul_long_cuda_kernel_nc.cu
Mlib/cuda/pair_morse_cuda.cu
Mlib/cuda/pair_morse_cuda_cu.h
Mlib/cuda/pair_morse_cuda_kernel_nc.cu
Mlib/cuda/pair_sw_cuda.cu
Mlib/cuda/pair_sw_cuda_cu.h
Mlib/cuda/pair_sw_cuda_kernel_nc.cu
Mlib/cuda/pair_tersoff_cuda.cu
Mlib/cuda/pair_tersoff_cuda_cu.h
Mlib/cuda/pair_tersoff_cuda_kernel_nc.cu
Mlib/cuda/pair_virial_compute_cu.h
Mlib/cuda/pppm_cuda.cu
Mlib/cuda/pppm_cuda_cu.h
Mlib/cuda/pppm_cuda_kernel.cu
Mlib/gpu/Nvidia.makefile
Mlib/gpu/Opencl.makefile
Mlib/gpu/lal_atom.cu
Mlib/gpu/lal_aux_fun1.h
Mlib/gpu/lal_base_atomic.cpp
Mlib/gpu/lal_base_charge.cpp
Mlib/gpu/lal_base_dipole.cpp
Mlib/gpu/lal_base_ellipsoid.cpp
Mlib/gpu/lal_born.cu
Mlib/gpu/lal_born_coul_long.cu
Mlib/gpu/lal_born_coul_wolf.cu
Mlib/gpu/lal_buck.cu
Mlib/gpu/lal_buck_coul.cu
Mlib/gpu/lal_buck_coul_long.cu
Mlib/gpu/lal_cg_cmm.cu
Mlib/gpu/lal_cg_cmm_long.cu
Mlib/gpu/lal_charmm_long.cu
Mlib/gpu/lal_colloid.cu
Mlib/gpu/lal_coul_dsf.cu
Mlib/gpu/lal_coul_long.cu
Mlib/gpu/lal_device.cpp
Mlib/gpu/lal_device.cu
Mlib/gpu/lal_device.h
Mlib/gpu/lal_dipole_lj.cu
Mlib/gpu/lal_dipole_lj_sf.cu
Mlib/gpu/lal_eam.cpp
Mlib/gpu/lal_eam.cu
Mlib/gpu/lal_eam.h
Mlib/gpu/lal_eam_ext.cpp
Mlib/gpu/lal_ellipsoid_extra.h
Mlib/gpu/lal_ellipsoid_nbor.cu
Mlib/gpu/lal_gauss.cu
Mlib/gpu/lal_gayberne.cu
Mlib/gpu/lal_gayberne_lj.cu
Mlib/gpu/lal_lj.cu
Mlib/gpu/lal_lj96.cu
Mlib/gpu/lal_lj_class2_long.cu
Mlib/gpu/lal_lj_coul.cu
Mlib/gpu/lal_lj_coul_debye.cu
Mlib/gpu/lal_lj_coul_long.cu
Mlib/gpu/lal_lj_dsf.cu
Mlib/gpu/lal_lj_expand.cu
Mlib/gpu/lal_morse.cu
Mlib/gpu/lal_neighbor_cpu.cu
Mlib/gpu/lal_neighbor_gpu.cu
Mlib/gpu/lal_pppm.cu
Mlib/gpu/lal_preprocessor.h
Mlib/gpu/lal_re_squared.cu
Mlib/gpu/lal_re_squared_lj.cu
Mlib/gpu/lal_table.cu
Mlib/gpu/lal_yukawa.cu
Mlib/gpu/lal_yukawa_colloid.cpp
Mlib/gpu/lal_yukawa_colloid.cu
Msrc/CLASS2/pair_lj_class2.cpp
Msrc/CLASS2/pair_lj_class2_coul_cut.cpp
Msrc/CLASS2/pair_lj_class2_coul_long.cpp
Msrc/GPU/Install.sh
Msrc/GPU/Package.sh
Msrc/GPU/pair_born_coul_wolf_gpu.cpp
Asrc/GPU/pair_coul_dsf_gpu.cpp
Asrc/GPU/pair_coul_dsf_gpu.h
Msrc/GPU/pair_eam_alloy_gpu.cpp
Msrc/GPU/pair_eam_fs_gpu.cpp
Msrc/GPU/pair_eam_gpu.cpp
Asrc/GPU/pair_lj_cut_coul_dsf_gpu.cpp
Asrc/GPU/pair_lj_cut_coul_dsf_gpu.h
Msrc/KSPACE/Install.sh
Msrc/KSPACE/ewald.cpp
Asrc/KSPACE/ewald_disp.cpp
Asrc/KSPACE/ewald_disp.h
Vsrc/{KSPACE ← USER-EWALDN}/math_complex.h
Vsrc/{KSPACE ← USER-EWALDN}/math_vector.h
Msrc/KSPACE/msm.cpp
Msrc/KSPACE/msm.h
Msrc/KSPACE/pair_born_coul_long.cpp
Msrc/KSPACE/pair_born_coul_msm.cpp
Msrc/KSPACE/pair_buck_coul_long.cpp
Msrc/KSPACE/pair_buck_coul_msm.cpp
Asrc/KSPACE/pair_buck_long_coul_long.cpp
Asrc/KSPACE/pair_buck_long_coul_long.h
Msrc/KSPACE/pair_coul_long.cpp
Msrc/KSPACE/pair_coul_msm.cpp
Msrc/KSPACE/pair_lj_charmm_coul_long.cpp
Msrc/KSPACE/pair_lj_charmm_coul_msm.cpp
Msrc/KSPACE/pair_lj_cut_coul_long.cpp
Dsrc/KSPACE/pair_lj_cut_coul_long_tip4p.cpp
Dsrc/KSPACE/pair_lj_cut_coul_long_tip4p.h
Msrc/KSPACE/pair_lj_cut_coul_msm.cpp
Asrc/KSPACE/pair_lj_cut_tip4p_long.cpp
Asrc/KSPACE/pair_lj_cut_tip4p_long.h
Asrc/KSPACE/pair_lj_long_coul_long.cpp
Asrc/KSPACE/pair_lj_long_coul_long.h
Asrc/KSPACE/pair_lj_long_tip4p_long.cpp
Asrc/KSPACE/pair_lj_long_tip4p_long.h
Msrc/KSPACE/pppm.cpp
Msrc/KSPACE/pppm.h
Asrc/KSPACE/pppm_disp.cpp
Asrc/KSPACE/pppm_disp.h
Asrc/KSPACE/pppm_disp_tip4p.cpp
Asrc/KSPACE/pppm_disp_tip4p.h
Msrc/KSPACE/pppm_old.cpp
Msrc/KSPACE/pppm_tip4p.cpp
Msrc/Makefile
Msrc/OPT/Install.sh
Dsrc/OPT/pair_lj_cut_coul_long_tip4p_opt.cpp
Dsrc/OPT/pair_lj_cut_coul_long_tip4p_opt.h
Asrc/OPT/pair_lj_cut_tip4p_long_opt.cpp
Asrc/OPT/pair_lj_cut_tip4p_long_opt.h
Msrc/REPLICA/fix_event.cpp
Msrc/REPLICA/tad.cpp
Msrc/USER-CG-CMM/pair_cg_cmm_coul_long.cpp
Msrc/USER-CG-CMM/pair_cmm_common.cpp
Msrc/USER-CG-CMM/pair_lj_sdk.cpp
Msrc/USER-CG-CMM/pair_lj_sdk_coul_long.cpp
Msrc/USER-CUDA/cuda.cpp
Dsrc/USER-EWALDN
Dsrc/USER-EWALDN/Install.sh
Dsrc/USER-EWALDN/README
Dsrc/USER-EWALDN/ewald_n.cpp
Dsrc/USER-EWALDN/ewald_n.h
Vsrc/{USER-EWALDN → KSPACE}/math_complex.h
Vsrc/{USER-EWALDN → KSPACE}/math_vector.h
Dsrc/USER-EWALDN/pair_buck_coul.cpp
Dsrc/USER-EWALDN/pair_buck_coul.h
Dsrc/USER-EWALDN/pair_lj_coul.cpp
Dsrc/USER-EWALDN/pair_lj_coul.h
Msrc/USER-MISC/pair_edip.cpp
Msrc/USER-MISC/pair_gauss_cut.cpp
Dsrc/USER-OMP/pair_buck_coul_omp.cpp
Dsrc/USER-OMP/pair_buck_coul_omp.h
Asrc/USER-OMP/pair_buck_long_coul_long_omp.cpp
Asrc/USER-OMP/pair_buck_long_coul_long_omp.h
Asrc/USER-OMP/pair_lj_charmm_coul_long_proxy_omp.cpp
Asrc/USER-OMP/pair_lj_charmm_coul_long_proxy_omp.h
Dsrc/USER-OMP/pair_lj_charmm_coul_pppm_omp.cpp
Dsrc/USER-OMP/pair_lj_charmm_coul_pppm_omp.h
Asrc/USER-OMP/pair_lj_class2_coul_long_proxy_omp.cpp
Asrc/USER-OMP/pair_lj_class2_coul_long_proxy_omp.h
Dsrc/USER-OMP/pair_lj_class2_coul_pppm_omp.cpp
Dsrc/USER-OMP/pair_lj_class2_coul_pppm_omp.h
Dsrc/USER-OMP/pair_lj_coul_omp.cpp
Dsrc/USER-OMP/pair_lj_coul_omp.h
Asrc/USER-OMP/pair_lj_cut_coul_long_proxy_omp.cpp
Asrc/USER-OMP/pair_lj_cut_coul_long_proxy_omp.h
Dsrc/USER-OMP/pair_lj_cut_coul_long_tip4p_omp.cpp
Dsrc/USER-OMP/pair_lj_cut_coul_long_tip4p_omp.h
Dsrc/USER-OMP/pair_lj_cut_coul_pppm_omp.cpp
Dsrc/USER-OMP/pair_lj_cut_coul_pppm_omp.h
Dsrc/USER-OMP/pair_lj_cut_coul_pppm_tip4p_omp.cpp
Dsrc/USER-OMP/pair_lj_cut_coul_pppm_tip4p_omp.h
Asrc/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp
Asrc/USER-OMP/pair_lj_cut_tip4p_long_omp.h
Asrc/USER-OMP/pair_lj_cut_tip4p_long_proxy_omp.cpp
Asrc/USER-OMP/pair_lj_cut_tip4p_long_proxy_omp.h
Asrc/USER-OMP/pair_lj_long_coul_long_omp.cpp
Asrc/USER-OMP/pair_lj_long_coul_long_omp.h
Msrc/USER-OMP/pppm_proxy.cpp
Msrc/USER-OMP/pppm_tip4p_proxy.cpp
Msrc/atom.cpp
Msrc/change_box.cpp
Msrc/comm.cpp
Msrc/domain.cpp
Msrc/fix_adapt.cpp
Msrc/fix_ave_atom.cpp
Msrc/fix_ave_spatial.cpp
Msrc/fix_efield.cpp
Msrc/fix_efield.h
Msrc/fix_wall.cpp
Msrc/kspace.cpp
Msrc/kspace.h
Msrc/neighbor.cpp
Msrc/pair.cpp
Msrc/pair.h
Msrc/pair_born.cpp
Msrc/pair_buck.cpp
Msrc/pair_buck_coul_cut.cpp
Msrc/pair_coul_cut.cpp
Asrc/pair_coul_dsf.cpp
Asrc/pair_coul_dsf.h
Msrc/pair_gauss.cpp
Msrc/pair_hybrid.cpp
Msrc/pair_lj96_cut.cpp
Msrc/pair_lj_cut.cpp
Msrc/pair_lj_cut_coul_cut.cpp
Asrc/pair_lj_cut_coul_dsf.cpp
Asrc/pair_lj_cut_coul_dsf.h
Msrc/pair_lj_expand.cpp
Msrc/read_dump.cpp
Msrc/region_plane.cpp
Msrc/set.cpp
Msrc/version.h
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Atools/moltemplate/README.TXT
A(dir)tools/moltemplate/common/
A(dir)tools/moltemplate/common/same_files_with_comments/
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Atools/moltemplate/common/spce.lt
Atools/moltemplate/common/trappe1998.lt
Atools/moltemplate/common/watmw.lt
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A(dir)tools/moltemplate/examples/
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A(dir)tools/moltemplate/examples/CG_membrane_examples/membrane+protein/
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Atools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_run.sh
Atools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_setup.sh
Atools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_visualise.txt
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Atools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/README.sh
Atools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/peptide.lt
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Atools/moltemplate/examples/CG_misc/2bead_heteropolymer/run.in.min
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Atools/moltemplate/examples/CG_misc/translocation/README_setup.sh
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Atools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py
Atools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_dihedral_table.py
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Atools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.min
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Atools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README.TXT
Atools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh
Atools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_setup.sh
Atools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_visualise.txt
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Atools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Masses.template
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Atools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/In Init.template
Atools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/In Settings
Atools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/In Settings.template
Atools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/tmp_atom_coords.dat
Atools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/ttree_assignments.txt
Atools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/solvate.pdb
Atools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt
Atools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/system.data
Atools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/system.in
Atools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/system.in.coords
Atools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/system.in.init
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Atools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/README.TXT
Atools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/README_run.sh
Atools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/README_setup.sh
Atools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/README_visualise.txt
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A(dir)tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/
Atools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_run.sh
Atools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_setup.sh
Atools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_visualise.txt
A(dir)tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/
Atools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Cl.jpg
Atools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Na.jpg
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A(dir)tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/for_visualization/psf_file_created_by_topotools/
Atools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/for_visualization/psf_file_created_by_topotools/system.psf
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Atools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=0.jpg
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Atools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/spce.lt
Atools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/system.lt
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Atools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt
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Atools/moltemplate/src/ltemplify.py
Atools/moltemplate/src/lttree.py
Atools/moltemplate/src/lttree_check.py
Atools/moltemplate/src/lttree_missing_coeffs.py
Atools/moltemplate/src/lttree_styles.py
Atools/moltemplate/src/moltemplate.sh
Atools/moltemplate/src/nbody_Angles.py
Atools/moltemplate/src/nbody_Dihedrals.py
Atools/moltemplate/src/nbody_Impropers.py
Atools/moltemplate/src/nbody_by_type.py
Atools/moltemplate/src/nbody_by_type_lib.py
Atools/moltemplate/src/nbody_fix_ttree_assignments.py
Atools/moltemplate/src/nbody_graph_search.py
Atools/moltemplate/src/pdbsort.py
Atools/moltemplate/src/postprocess_input_script.py
Atools/moltemplate/src/remove_duplicate_atoms.py
Atools/moltemplate/src/remove_duplicates_nbody.py
Atools/moltemplate/src/renumber_DATA_first_column.py
Atools/moltemplate/src/ttree.py
Atools/moltemplate/src/ttree_lex.py
Atools/moltemplate/src/ttree_matrix_stack.py
Atools/moltemplate/src/ttree_render.py
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tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/system.lt

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tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.min

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tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.npt

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tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt

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tools/moltemplate/src/extract_lammps_data.py

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tools/moltemplate/src/ltemplify.py

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tools/moltemplate/src/lttree.py

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tools/moltemplate/src/lttree_check.py

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tools/moltemplate/src/lttree_missing_coeffs.py

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tools/moltemplate/src/lttree_styles.py

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tools/moltemplate/src/moltemplate.sh

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tools/moltemplate/src/nbody_Angles.py

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tools/moltemplate/src/nbody_Dihedrals.py

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tools/moltemplate/src/nbody_Impropers.py

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tools/moltemplate/src/nbody_by_type.py

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tools/moltemplate/src/nbody_by_type_lib.py

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tools/moltemplate/src/nbody_fix_ttree_assignments.py

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tools/moltemplate/src/nbody_graph_search.py

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tools/moltemplate/src/pdbsort.py

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tools/moltemplate/src/postprocess_input_script.py

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tools/moltemplate/src/remove_duplicate_atoms.py

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tools/moltemplate/src/remove_duplicates_nbody.py

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tools/moltemplate/src/renumber_DATA_first_column.py

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tools/moltemplate/src/ttree.py

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tools/moltemplate/src/ttree_lex.py

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tools/moltemplate/src/ttree_matrix_stack.py

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tools/moltemplate/src/ttree_render.py

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tools/restart2data.cpp

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