From 852f18525d8a6a93fe041036c96e1a2da7b1972d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 23 Jul 2021 18:00:28 -0400 Subject: [PATCH] complete moving packages and styles around --- cmake/CMakeLists.txt | 7 +- cmake/presets/all_off.cmake | 7 +- cmake/presets/all_on.cmake | 7 +- cmake/presets/mingw-cross.cmake | 8 +- cmake/presets/most.cmake | 7 +- src/.gitignore | 63 ++++++++++++++-- .../pair_lj_sf_dipole_sf.cpp | 0 .../pair_lj_sf_dipole_sf.h | 0 src/Depend.sh | 24 +++--- .../compute_ackland_atom.cpp | 0 .../compute_ackland_atom.h | 0 src/{ => EXTRA-COMPUTE}/compute_adf.cpp | 0 src/{ => EXTRA-COMPUTE}/compute_adf.h | 0 .../compute_aggregate_atom.cpp | 0 .../compute_aggregate_atom.h | 0 .../compute_basal_atom.cpp | 0 .../compute_basal_atom.h | 0 .../compute_cluster_atom.cpp | 0 .../compute_cluster_atom.h | 0 .../compute_cnp_atom.cpp | 0 .../compute_cnp_atom.h | 0 .../compute_entropy_atom.cpp | 0 .../compute_entropy_atom.h | 0 .../compute_fragment_atom.cpp | 0 .../compute_fragment_atom.h | 0 .../compute_gyration_shape.cpp | 0 .../compute_gyration_shape.h | 0 .../compute_gyration_shape_chunk.cpp | 0 .../compute_gyration_shape_chunk.h | 0 .../compute_hexorder_atom.cpp | 0 .../compute_hexorder_atom.h | 0 .../compute_hma.cpp | 0 .../compute_hma.h | 0 .../compute_momentum.cpp | 0 .../compute_momentum.h | 0 .../compute_msd_nongauss.cpp | 0 .../compute_msd_nongauss.h | 0 .../compute_orientorder_atom.cpp | 0 .../compute_orientorder_atom.h | 0 .../compute_pressure_cylinder.cpp | 0 .../compute_pressure_cylinder.h | 0 .../compute_stress_mop.cpp | 0 .../compute_stress_mop.h | 0 .../compute_stress_mop_profile.cpp | 0 .../compute_stress_mop_profile.h | 0 .../compute_temp_rotate.cpp | 0 .../compute_temp_rotate.h | 0 src/{MISC => EXTRA-COMPUTE}/compute_ti.cpp | 0 src/{MISC => EXTRA-COMPUTE}/compute_ti.h | 0 src/{ => EXTRA-DUMP}/dump_dcd.cpp | 0 src/{ => EXTRA-DUMP}/dump_dcd.h | 0 src/{MISC => EXTRA-DUMP}/dump_xtc.cpp | 0 src/{MISC => EXTRA-DUMP}/dump_xtc.h | 0 src/{MISC => EXTRA-DUMP}/xdr_compat.cpp | 0 src/{MISC => EXTRA-DUMP}/xdr_compat.h | 0 src/{MISC => EXTRA-FIX}/fix_addtorque.cpp | 0 src/{MISC => EXTRA-FIX}/fix_addtorque.h | 0 .../fix_ave_correlate_long.cpp | 0 .../fix_ave_correlate_long.h | 0 src/{ => EXTRA-FIX}/fix_controller.cpp | 0 src/{ => EXTRA-FIX}/fix_controller.h | 0 src/{ => EXTRA-FIX}/fix_drag.cpp | 0 src/{ => EXTRA-FIX}/fix_drag.h | 0 .../fix_electron_stopping.cpp | 0 .../fix_electron_stopping.h | 0 .../fix_electron_stopping_fit.cpp | 0 .../fix_electron_stopping_fit.h | 0 src/{USER-MISC => EXTRA-FIX}/fix_ffl.cpp | 0 src/{USER-MISC => EXTRA-FIX}/fix_ffl.h | 0 .../fix_filter_corotate.cpp | 0 .../fix_filter_corotate.h | 0 .../fix_flow_gauss.cpp | 0 src/{USER-MISC => EXTRA-FIX}/fix_flow_gauss.h | 0 src/{MISC => EXTRA-FIX}/fix_gld.cpp | 0 src/{MISC => EXTRA-FIX}/fix_gld.h | 0 src/{USER-MISC => EXTRA-FIX}/fix_gle.cpp | 0 src/{USER-MISC => EXTRA-FIX}/fix_gle.h | 0 .../fix_momentum_chunk.cpp | 0 .../fix_momentum_chunk.h | 0 .../fix_npt_cauchy.cpp | 0 src/{USER-MISC => EXTRA-FIX}/fix_npt_cauchy.h | 0 src/{ => EXTRA-FIX}/fix_numdiff.cpp | 0 src/{ => EXTRA-FIX}/fix_numdiff.h | 0 src/{ => EXTRA-FIX}/fix_nve_noforce.cpp | 0 src/{ => EXTRA-FIX}/fix_nve_noforce.h | 0 src/{USER-MISC => EXTRA-FIX}/fix_nvk.cpp | 0 src/{USER-MISC => EXTRA-FIX}/fix_nvk.h | 0 src/{MISC => EXTRA-FIX}/fix_oneway.cpp | 0 src/{MISC => EXTRA-FIX}/fix_oneway.h | 0 src/{USER-MISC => EXTRA-FIX}/fix_pafi.cpp | 0 src/{USER-MISC => EXTRA-FIX}/fix_pafi.h | 0 src/{USER-MISC => EXTRA-FIX}/fix_pimd.cpp | 0 src/{USER-MISC => EXTRA-FIX}/fix_pimd.h | 0 src/{USER-MISC => EXTRA-FIX}/fix_rhok.cpp | 0 src/{USER-MISC => EXTRA-FIX}/fix_rhok.h | 0 src/{MISC => EXTRA-FIX}/fix_smd.cpp | 0 src/{MISC => EXTRA-FIX}/fix_smd.h | 0 src/{ => EXTRA-FIX}/fix_spring_rg.cpp | 0 src/{ => EXTRA-FIX}/fix_spring_rg.h | 0 src/{ => EXTRA-FIX}/fix_temp_csld.cpp | 0 src/{ => EXTRA-FIX}/fix_temp_csld.h | 0 src/{ => EXTRA-FIX}/fix_temp_csvr.cpp | 0 src/{ => EXTRA-FIX}/fix_temp_csvr.h | 0 .../fix_ti_spring.cpp | 0 src/{USER-MISC => EXTRA-FIX}/fix_ti_spring.h | 0 src/{ => EXTRA-FIX}/fix_tmd.cpp | 0 src/{ => EXTRA-FIX}/fix_tmd.h | 0 src/{MISC => EXTRA-FIX}/fix_ttm.cpp | 0 src/{MISC => EXTRA-FIX}/fix_ttm.h | 0 src/{USER-MISC => EXTRA-FIX}/fix_ttm_mod.cpp | 0 src/{USER-MISC => EXTRA-FIX}/fix_ttm_mod.h | 0 src/{MISC => EXTRA-FIX}/fix_viscosity.cpp | 0 src/{MISC => EXTRA-FIX}/fix_viscosity.h | 0 src/{USER-MISC => EXTRA-FIX}/fix_wall_ees.cpp | 0 src/{USER-MISC => EXTRA-FIX}/fix_wall_ees.h | 0 .../fix_wall_reflect_stochastic.cpp | 0 .../fix_wall_reflect_stochastic.h | 0 .../fix_wall_region_ees.cpp | 0 .../fix_wall_region_ees.h | 0 .../angle_cosine_delta.cpp | 0 .../angle_cosine_delta.h | 0 .../angle_cosine_periodic.cpp | 0 .../angle_cosine_periodic.h | 0 .../angle_cosine_shift.cpp | 0 .../angle_cosine_shift.h | 0 .../angle_cosine_shift_exp.cpp | 0 .../angle_cosine_shift_exp.h | 0 .../angle_fourier.cpp | 0 .../angle_fourier.h | 0 .../angle_fourier_simple.cpp | 0 .../angle_fourier_simple.h | 0 .../angle_gaussian.cpp | 0 .../angle_gaussian.h | 0 .../angle_quartic.cpp | 0 .../angle_quartic.h | 0 .../bond_gaussian.cpp | 0 .../bond_gaussian.h | 0 .../bond_harmonic_shift.cpp | 0 .../bond_harmonic_shift.h | 0 .../bond_harmonic_shift_cut.cpp | 0 .../bond_harmonic_shift_cut.h | 0 .../bond_nonlinear.cpp | 0 .../bond_nonlinear.h | 0 .../dihedral_cosine_shift_exp.cpp | 0 .../dihedral_cosine_shift_exp.h | 0 .../dihedral_fourier.cpp | 0 .../dihedral_fourier.h | 0 .../dihedral_helix.cpp | 0 .../dihedral_helix.h | 0 .../dihedral_nharmonic.cpp | 0 .../dihedral_nharmonic.h | 0 .../dihedral_quadratic.cpp | 0 .../dihedral_quadratic.h | 0 .../dihedral_spherical.cpp | 0 .../dihedral_spherical.h | 0 .../dihedral_table_cut.cpp | 0 .../dihedral_table_cut.h | 0 .../improper_cossq.cpp | 0 .../improper_cossq.h | 0 .../improper_distance.cpp | 0 .../improper_distance.h | 0 .../improper_fourier.cpp | 0 .../improper_fourier.h | 0 .../improper_ring.cpp | 0 .../improper_ring.h | 0 src/{ => EXTRA-PAIR}/pair_born_coul_dsf.cpp | 0 src/{ => EXTRA-PAIR}/pair_born_coul_dsf.h | 0 src/{ => EXTRA-PAIR}/pair_born_coul_wolf.cpp | 0 src/{ => EXTRA-PAIR}/pair_born_coul_wolf.h | 0 .../pair_buck_mdf.cpp | 0 src/{USER-MISC => EXTRA-PAIR}/pair_buck_mdf.h | 0 .../pair_cosine_squared.cpp | 0 .../pair_cosine_squared.h | 0 src/{ => EXTRA-PAIR}/pair_coul_cut_global.cpp | 0 src/{ => EXTRA-PAIR}/pair_coul_cut_global.h | 0 .../pair_coul_diel.cpp | 0 .../pair_coul_diel.h | 0 .../pair_coul_slater_cut.cpp | 0 .../pair_coul_slater_cut.h | 0 .../pair_coul_slater_long.cpp | 0 .../pair_coul_slater_long.h | 0 src/{ => EXTRA-PAIR}/pair_coul_streitz.cpp | 0 src/{ => EXTRA-PAIR}/pair_coul_streitz.h | 0 src/{USER-MISC => EXTRA-PAIR}/pair_e3b.cpp | 0 src/{USER-MISC => EXTRA-PAIR}/pair_e3b.h | 0 src/{ => EXTRA-PAIR}/pair_gauss.cpp | 0 src/{ => EXTRA-PAIR}/pair_gauss.h | 0 .../pair_gauss_cut.cpp | 0 .../pair_gauss_cut.h | 0 .../pair_lennard_mdf.cpp | 0 .../pair_lennard_mdf.h | 0 src/{ => EXTRA-PAIR}/pair_lj96_cut.cpp | 0 src/{ => EXTRA-PAIR}/pair_lj96_cut.h | 0 src/{ => EXTRA-PAIR}/pair_lj_cubic.cpp | 0 src/{ => EXTRA-PAIR}/pair_lj_cubic.h | 0 src/{ => EXTRA-PAIR}/pair_lj_cubic_const.h | 0 .../pair_lj_cut_coul_debye.cpp | 0 src/{ => EXTRA-PAIR}/pair_lj_cut_coul_debye.h | 0 src/{ => EXTRA-PAIR}/pair_lj_cut_coul_dsf.cpp | 0 src/{ => EXTRA-PAIR}/pair_lj_cut_coul_dsf.h | 0 .../pair_lj_cut_coul_wolf.cpp | 0 src/{ => EXTRA-PAIR}/pair_lj_cut_coul_wolf.h | 0 .../pair_lj_expand_coul_long.cpp | 0 .../pair_lj_expand_coul_long.h | 0 src/{ => EXTRA-PAIR}/pair_lj_gromacs.cpp | 0 src/{ => EXTRA-PAIR}/pair_lj_gromacs.h | 0 .../pair_lj_gromacs_coul_gromacs.cpp | 0 .../pair_lj_gromacs_coul_gromacs.h | 0 src/{USER-MISC => EXTRA-PAIR}/pair_lj_mdf.cpp | 0 src/{USER-MISC => EXTRA-PAIR}/pair_lj_mdf.h | 0 src/{ => EXTRA-PAIR}/pair_lj_relres.cpp | 0 src/{ => EXTRA-PAIR}/pair_lj_relres.h | 0 src/{ => EXTRA-PAIR}/pair_lj_smooth.cpp | 0 src/{ => EXTRA-PAIR}/pair_lj_smooth.h | 0 .../pair_lj_smooth_linear.cpp | 0 src/{ => EXTRA-PAIR}/pair_lj_smooth_linear.h | 0 src/{ => EXTRA-PAIR}/pair_mie_cut.cpp | 0 src/{ => EXTRA-PAIR}/pair_mie_cut.h | 0 src/{USER-MISC => EXTRA-PAIR}/pair_momb.cpp | 0 src/{USER-MISC => EXTRA-PAIR}/pair_momb.h | 0 .../pair_morse_smooth_linear.cpp | 0 .../pair_morse_smooth_linear.h | 0 src/{MISC => EXTRA-PAIR}/pair_nm_cut.cpp | 0 src/{MISC => EXTRA-PAIR}/pair_nm_cut.h | 0 .../pair_nm_cut_coul_cut.cpp | 0 .../pair_nm_cut_coul_cut.h | 0 .../pair_nm_cut_coul_long.cpp | 0 .../pair_nm_cut_coul_long.h | 0 src/{ => EXTRA-PAIR}/pair_ufm.cpp | 0 src/{ => EXTRA-PAIR}/pair_ufm.h | 0 src/{USER-MISC => EXTRA-PAIR}/pair_wf_cut.cpp | 0 src/{USER-MISC => EXTRA-PAIR}/pair_wf_cut.h | 0 src/{ => GRANULAR}/compute_contact_atom.cpp | 0 src/{ => GRANULAR}/compute_contact_atom.h | 0 src/KOKKOS/Install.sh | 16 ++-- src/{USER-MISC => MANYBODY}/pair_edip.cpp | 0 src/{USER-MISC => MANYBODY}/pair_edip.h | 0 .../pair_edip_multi.cpp | 0 src/{USER-MISC => MANYBODY}/pair_edip_multi.h | 0 src/{USER-MISC => MANYBODY}/pair_extep.cpp | 0 src/{USER-MISC => MANYBODY}/pair_extep.h | 0 .../pair_local_density.cpp | 0 .../pair_local_density.h | 0 .../pair_meam_spline.cpp | 0 .../pair_meam_spline.h | 0 .../pair_meam_sw_spline.cpp | 0 .../pair_meam_sw_spline.h | 0 .../pair_tersoff_table.cpp | 0 .../pair_tersoff_table.h | 0 .../compute_viscosity_cos.cpp | 0 .../compute_viscosity_cos.h | 0 .../fix_accelerate_cos.cpp | 0 src/{USER-MISC => MISC}/fix_accelerate_cos.h | 0 src/{USER-MISC => MISC}/fix_ipi.cpp | 0 src/{USER-MISC => MISC}/fix_ipi.h | 0 src/{USER-MISC => MISC}/fix_srp.cpp | 0 src/{USER-MISC => MISC}/fix_srp.h | 0 src/{USER-MISC => MISC}/pair_agni.cpp | 0 src/{USER-MISC => MISC}/pair_agni.h | 0 src/Makefile | 16 +++- src/{MISC => ORIENT}/fix_orient_bcc.cpp | 0 src/{MISC => ORIENT}/fix_orient_bcc.h | 0 src/{USER-MISC => ORIENT}/fix_orient_eco.cpp | 0 src/{USER-MISC => ORIENT}/fix_orient_eco.h | 0 src/{MISC => ORIENT}/fix_orient_fcc.cpp | 0 src/{MISC => ORIENT}/fix_orient_fcc.h | 0 src/Purge.list | 7 -- src/USER-MISC/README | 73 ------------------- src/{MISC => }/fix_deposit.cpp | 0 src/{MISC => }/fix_deposit.h | 0 src/{MISC => }/fix_efield.cpp | 0 src/{MISC => }/fix_efield.h | 0 src/{MISC => }/fix_evaporate.cpp | 0 src/{MISC => }/fix_evaporate.h | 0 src/{MISC => }/fix_thermal_conductivity.cpp | 0 src/{MISC => }/fix_thermal_conductivity.h | 0 276 files changed, 122 insertions(+), 113 deletions(-) rename src/{USER-MISC => DIPOLE}/pair_lj_sf_dipole_sf.cpp (100%) rename src/{USER-MISC => DIPOLE}/pair_lj_sf_dipole_sf.h (100%) rename src/{USER-MISC => EXTRA-COMPUTE}/compute_ackland_atom.cpp (100%) rename src/{USER-MISC => EXTRA-COMPUTE}/compute_ackland_atom.h (100%) rename src/{ => EXTRA-COMPUTE}/compute_adf.cpp (100%) rename src/{ => EXTRA-COMPUTE}/compute_adf.h (100%) rename src/{ => EXTRA-COMPUTE}/compute_aggregate_atom.cpp (100%) rename src/{ => EXTRA-COMPUTE}/compute_aggregate_atom.h (100%) rename src/{USER-MISC => EXTRA-COMPUTE}/compute_basal_atom.cpp (100%) rename src/{USER-MISC => EXTRA-COMPUTE}/compute_basal_atom.h (100%) rename src/{ => EXTRA-COMPUTE}/compute_cluster_atom.cpp (100%) rename src/{ => EXTRA-COMPUTE}/compute_cluster_atom.h (100%) rename src/{USER-MISC => EXTRA-COMPUTE}/compute_cnp_atom.cpp (100%) rename src/{USER-MISC => EXTRA-COMPUTE}/compute_cnp_atom.h (100%) rename src/{USER-MISC => EXTRA-COMPUTE}/compute_entropy_atom.cpp (100%) rename src/{USER-MISC => EXTRA-COMPUTE}/compute_entropy_atom.h (100%) rename src/{ => EXTRA-COMPUTE}/compute_fragment_atom.cpp (100%) rename src/{ => EXTRA-COMPUTE}/compute_fragment_atom.h (100%) rename src/{USER-MISC => EXTRA-COMPUTE}/compute_gyration_shape.cpp (100%) rename src/{USER-MISC => EXTRA-COMPUTE}/compute_gyration_shape.h (100%) rename src/{USER-MISC => EXTRA-COMPUTE}/compute_gyration_shape_chunk.cpp (100%) rename src/{USER-MISC => EXTRA-COMPUTE}/compute_gyration_shape_chunk.h (100%) rename src/{ => EXTRA-COMPUTE}/compute_hexorder_atom.cpp (100%) rename src/{ => EXTRA-COMPUTE}/compute_hexorder_atom.h (100%) rename src/{USER-MISC => EXTRA-COMPUTE}/compute_hma.cpp (100%) rename src/{USER-MISC => EXTRA-COMPUTE}/compute_hma.h (100%) rename src/{USER-MISC => EXTRA-COMPUTE}/compute_momentum.cpp (100%) rename src/{USER-MISC => EXTRA-COMPUTE}/compute_momentum.h (100%) rename src/{MISC => EXTRA-COMPUTE}/compute_msd_nongauss.cpp (100%) rename src/{MISC => EXTRA-COMPUTE}/compute_msd_nongauss.h (100%) rename src/{ => EXTRA-COMPUTE}/compute_orientorder_atom.cpp (100%) rename src/{ => EXTRA-COMPUTE}/compute_orientorder_atom.h (100%) rename src/{USER-MISC => EXTRA-COMPUTE}/compute_pressure_cylinder.cpp (100%) rename src/{USER-MISC => EXTRA-COMPUTE}/compute_pressure_cylinder.h (100%) rename src/{USER-MISC => EXTRA-COMPUTE}/compute_stress_mop.cpp (100%) rename src/{USER-MISC => EXTRA-COMPUTE}/compute_stress_mop.h (100%) rename src/{USER-MISC => EXTRA-COMPUTE}/compute_stress_mop_profile.cpp (100%) rename src/{USER-MISC => EXTRA-COMPUTE}/compute_stress_mop_profile.h (100%) rename src/{USER-MISC => EXTRA-COMPUTE}/compute_temp_rotate.cpp (100%) rename src/{USER-MISC => EXTRA-COMPUTE}/compute_temp_rotate.h (100%) rename src/{MISC => EXTRA-COMPUTE}/compute_ti.cpp (100%) rename src/{MISC => EXTRA-COMPUTE}/compute_ti.h (100%) rename src/{ => EXTRA-DUMP}/dump_dcd.cpp (100%) rename src/{ => EXTRA-DUMP}/dump_dcd.h (100%) rename src/{MISC => EXTRA-DUMP}/dump_xtc.cpp (100%) rename src/{MISC => EXTRA-DUMP}/dump_xtc.h (100%) rename src/{MISC => EXTRA-DUMP}/xdr_compat.cpp (100%) rename src/{MISC => EXTRA-DUMP}/xdr_compat.h (100%) rename src/{MISC => EXTRA-FIX}/fix_addtorque.cpp (100%) rename src/{MISC => EXTRA-FIX}/fix_addtorque.h (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_ave_correlate_long.cpp (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_ave_correlate_long.h (100%) rename src/{ => EXTRA-FIX}/fix_controller.cpp (100%) rename src/{ => EXTRA-FIX}/fix_controller.h (100%) rename src/{ => EXTRA-FIX}/fix_drag.cpp (100%) rename src/{ => EXTRA-FIX}/fix_drag.h (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_electron_stopping.cpp (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_electron_stopping.h (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_electron_stopping_fit.cpp (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_electron_stopping_fit.h (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_ffl.cpp (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_ffl.h (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_filter_corotate.cpp (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_filter_corotate.h (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_flow_gauss.cpp (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_flow_gauss.h (100%) rename src/{MISC => EXTRA-FIX}/fix_gld.cpp (100%) rename src/{MISC => EXTRA-FIX}/fix_gld.h (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_gle.cpp (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_gle.h (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_momentum_chunk.cpp (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_momentum_chunk.h (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_npt_cauchy.cpp (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_npt_cauchy.h (100%) rename src/{ => EXTRA-FIX}/fix_numdiff.cpp (100%) rename src/{ => EXTRA-FIX}/fix_numdiff.h (100%) rename src/{ => EXTRA-FIX}/fix_nve_noforce.cpp (100%) rename src/{ => EXTRA-FIX}/fix_nve_noforce.h (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_nvk.cpp (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_nvk.h (100%) rename src/{MISC => EXTRA-FIX}/fix_oneway.cpp (100%) rename src/{MISC => EXTRA-FIX}/fix_oneway.h (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_pafi.cpp (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_pafi.h (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_pimd.cpp (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_pimd.h (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_rhok.cpp (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_rhok.h (100%) rename src/{MISC => EXTRA-FIX}/fix_smd.cpp (100%) rename src/{MISC => EXTRA-FIX}/fix_smd.h (100%) rename src/{ => EXTRA-FIX}/fix_spring_rg.cpp (100%) rename src/{ => EXTRA-FIX}/fix_spring_rg.h (100%) rename src/{ => EXTRA-FIX}/fix_temp_csld.cpp (100%) rename src/{ => EXTRA-FIX}/fix_temp_csld.h (100%) rename src/{ => EXTRA-FIX}/fix_temp_csvr.cpp (100%) rename src/{ => EXTRA-FIX}/fix_temp_csvr.h (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_ti_spring.cpp (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_ti_spring.h (100%) rename src/{ => EXTRA-FIX}/fix_tmd.cpp (100%) rename src/{ => EXTRA-FIX}/fix_tmd.h (100%) rename src/{MISC => EXTRA-FIX}/fix_ttm.cpp (100%) rename src/{MISC => EXTRA-FIX}/fix_ttm.h (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_ttm_mod.cpp (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_ttm_mod.h (100%) rename src/{MISC => EXTRA-FIX}/fix_viscosity.cpp (100%) rename src/{MISC => EXTRA-FIX}/fix_viscosity.h (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_wall_ees.cpp (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_wall_ees.h (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_wall_reflect_stochastic.cpp (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_wall_reflect_stochastic.h (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_wall_region_ees.cpp (100%) rename src/{USER-MISC => EXTRA-FIX}/fix_wall_region_ees.h (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/angle_cosine_delta.cpp (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/angle_cosine_delta.h (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/angle_cosine_periodic.cpp (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/angle_cosine_periodic.h (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/angle_cosine_shift.cpp (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/angle_cosine_shift.h (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/angle_cosine_shift_exp.cpp (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/angle_cosine_shift_exp.h (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/angle_fourier.cpp (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/angle_fourier.h (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/angle_fourier_simple.cpp (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/angle_fourier_simple.h (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/angle_gaussian.cpp (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/angle_gaussian.h (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/angle_quartic.cpp (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/angle_quartic.h (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/bond_gaussian.cpp (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/bond_gaussian.h (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/bond_harmonic_shift.cpp (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/bond_harmonic_shift.h (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/bond_harmonic_shift_cut.cpp (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/bond_harmonic_shift_cut.h (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/bond_nonlinear.cpp (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/bond_nonlinear.h (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/dihedral_cosine_shift_exp.cpp (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/dihedral_cosine_shift_exp.h (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/dihedral_fourier.cpp (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/dihedral_fourier.h (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/dihedral_helix.cpp (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/dihedral_helix.h (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/dihedral_nharmonic.cpp (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/dihedral_nharmonic.h (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/dihedral_quadratic.cpp (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/dihedral_quadratic.h (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/dihedral_spherical.cpp (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/dihedral_spherical.h (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/dihedral_table_cut.cpp (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/dihedral_table_cut.h (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/improper_cossq.cpp (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/improper_cossq.h (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/improper_distance.cpp (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/improper_distance.h (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/improper_fourier.cpp (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/improper_fourier.h (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/improper_ring.cpp (100%) rename src/{MOLECULE => EXTRA-MOLECULE}/improper_ring.h (100%) rename src/{ => EXTRA-PAIR}/pair_born_coul_dsf.cpp (100%) rename src/{ => EXTRA-PAIR}/pair_born_coul_dsf.h (100%) rename src/{ => EXTRA-PAIR}/pair_born_coul_wolf.cpp (100%) rename src/{ => EXTRA-PAIR}/pair_born_coul_wolf.h (100%) rename src/{USER-MISC => EXTRA-PAIR}/pair_buck_mdf.cpp (100%) rename src/{USER-MISC => EXTRA-PAIR}/pair_buck_mdf.h (100%) rename src/{USER-MISC => EXTRA-PAIR}/pair_cosine_squared.cpp (100%) rename src/{USER-MISC => EXTRA-PAIR}/pair_cosine_squared.h (100%) rename src/{ => EXTRA-PAIR}/pair_coul_cut_global.cpp (100%) rename src/{ => EXTRA-PAIR}/pair_coul_cut_global.h (100%) rename src/{USER-MISC => EXTRA-PAIR}/pair_coul_diel.cpp (100%) rename src/{USER-MISC => EXTRA-PAIR}/pair_coul_diel.h (100%) rename src/{USER-MISC => EXTRA-PAIR}/pair_coul_slater_cut.cpp (100%) rename src/{USER-MISC => EXTRA-PAIR}/pair_coul_slater_cut.h (100%) rename src/{USER-MISC => EXTRA-PAIR}/pair_coul_slater_long.cpp (100%) rename src/{USER-MISC => EXTRA-PAIR}/pair_coul_slater_long.h (100%) rename src/{ => EXTRA-PAIR}/pair_coul_streitz.cpp (100%) rename src/{ => EXTRA-PAIR}/pair_coul_streitz.h (100%) rename src/{USER-MISC => EXTRA-PAIR}/pair_e3b.cpp (100%) rename src/{USER-MISC => EXTRA-PAIR}/pair_e3b.h (100%) rename src/{ => EXTRA-PAIR}/pair_gauss.cpp (100%) rename src/{ => EXTRA-PAIR}/pair_gauss.h (100%) rename src/{USER-MISC => EXTRA-PAIR}/pair_gauss_cut.cpp (100%) rename src/{USER-MISC => EXTRA-PAIR}/pair_gauss_cut.h (100%) rename src/{USER-MISC => EXTRA-PAIR}/pair_lennard_mdf.cpp (100%) rename src/{USER-MISC => EXTRA-PAIR}/pair_lennard_mdf.h (100%) rename src/{ => EXTRA-PAIR}/pair_lj96_cut.cpp (100%) rename src/{ => EXTRA-PAIR}/pair_lj96_cut.h (100%) rename src/{ => EXTRA-PAIR}/pair_lj_cubic.cpp (100%) rename src/{ => EXTRA-PAIR}/pair_lj_cubic.h (100%) rename src/{ => EXTRA-PAIR}/pair_lj_cubic_const.h (100%) rename src/{ => EXTRA-PAIR}/pair_lj_cut_coul_debye.cpp (100%) rename src/{ => EXTRA-PAIR}/pair_lj_cut_coul_debye.h (100%) rename src/{ => EXTRA-PAIR}/pair_lj_cut_coul_dsf.cpp (100%) rename src/{ => EXTRA-PAIR}/pair_lj_cut_coul_dsf.h (100%) rename src/{ => EXTRA-PAIR}/pair_lj_cut_coul_wolf.cpp (100%) rename src/{ => EXTRA-PAIR}/pair_lj_cut_coul_wolf.h (100%) rename src/{USER-MISC => EXTRA-PAIR}/pair_lj_expand_coul_long.cpp (100%) rename src/{USER-MISC => EXTRA-PAIR}/pair_lj_expand_coul_long.h (100%) rename src/{ => EXTRA-PAIR}/pair_lj_gromacs.cpp (100%) rename src/{ => EXTRA-PAIR}/pair_lj_gromacs.h (100%) rename src/{ => EXTRA-PAIR}/pair_lj_gromacs_coul_gromacs.cpp (100%) rename src/{ => EXTRA-PAIR}/pair_lj_gromacs_coul_gromacs.h (100%) rename src/{USER-MISC => EXTRA-PAIR}/pair_lj_mdf.cpp (100%) rename src/{USER-MISC => EXTRA-PAIR}/pair_lj_mdf.h (100%) rename src/{ => EXTRA-PAIR}/pair_lj_relres.cpp (100%) rename src/{ => EXTRA-PAIR}/pair_lj_relres.h (100%) rename src/{ => EXTRA-PAIR}/pair_lj_smooth.cpp (100%) rename src/{ => EXTRA-PAIR}/pair_lj_smooth.h (100%) rename src/{ => EXTRA-PAIR}/pair_lj_smooth_linear.cpp (100%) rename src/{ => EXTRA-PAIR}/pair_lj_smooth_linear.h (100%) rename src/{ => EXTRA-PAIR}/pair_mie_cut.cpp (100%) rename src/{ => EXTRA-PAIR}/pair_mie_cut.h (100%) rename src/{USER-MISC => EXTRA-PAIR}/pair_momb.cpp (100%) rename src/{USER-MISC => EXTRA-PAIR}/pair_momb.h (100%) rename src/{USER-MISC => EXTRA-PAIR}/pair_morse_smooth_linear.cpp (100%) rename src/{USER-MISC => EXTRA-PAIR}/pair_morse_smooth_linear.h (100%) rename src/{MISC => EXTRA-PAIR}/pair_nm_cut.cpp (100%) rename src/{MISC => EXTRA-PAIR}/pair_nm_cut.h (100%) rename src/{MISC => EXTRA-PAIR}/pair_nm_cut_coul_cut.cpp (100%) rename src/{MISC => EXTRA-PAIR}/pair_nm_cut_coul_cut.h (100%) rename src/{MISC => EXTRA-PAIR}/pair_nm_cut_coul_long.cpp (100%) rename src/{MISC => EXTRA-PAIR}/pair_nm_cut_coul_long.h (100%) rename src/{ => EXTRA-PAIR}/pair_ufm.cpp (100%) rename src/{ => EXTRA-PAIR}/pair_ufm.h (100%) rename src/{USER-MISC => EXTRA-PAIR}/pair_wf_cut.cpp (100%) rename src/{USER-MISC => EXTRA-PAIR}/pair_wf_cut.h (100%) rename src/{ => GRANULAR}/compute_contact_atom.cpp (100%) rename src/{ => GRANULAR}/compute_contact_atom.h (100%) rename src/{USER-MISC => MANYBODY}/pair_edip.cpp (100%) rename src/{USER-MISC => MANYBODY}/pair_edip.h (100%) rename src/{USER-MISC => MANYBODY}/pair_edip_multi.cpp (100%) rename src/{USER-MISC => MANYBODY}/pair_edip_multi.h (100%) rename src/{USER-MISC => MANYBODY}/pair_extep.cpp (100%) rename src/{USER-MISC => MANYBODY}/pair_extep.h (100%) rename src/{USER-MISC => MANYBODY}/pair_local_density.cpp (100%) rename src/{USER-MISC => MANYBODY}/pair_local_density.h (100%) rename src/{USER-MISC => MANYBODY}/pair_meam_spline.cpp (100%) rename src/{USER-MISC => MANYBODY}/pair_meam_spline.h (100%) rename src/{USER-MISC => MANYBODY}/pair_meam_sw_spline.cpp (100%) rename src/{USER-MISC => MANYBODY}/pair_meam_sw_spline.h (100%) rename src/{USER-MISC => MANYBODY}/pair_tersoff_table.cpp (100%) rename src/{USER-MISC => MANYBODY}/pair_tersoff_table.h (100%) rename src/{USER-MISC => MISC}/compute_viscosity_cos.cpp (100%) rename src/{USER-MISC => MISC}/compute_viscosity_cos.h (100%) rename src/{USER-MISC => MISC}/fix_accelerate_cos.cpp (100%) rename src/{USER-MISC => MISC}/fix_accelerate_cos.h (100%) rename src/{USER-MISC => MISC}/fix_ipi.cpp (100%) rename src/{USER-MISC => MISC}/fix_ipi.h (100%) rename src/{USER-MISC => MISC}/fix_srp.cpp (100%) rename src/{USER-MISC => MISC}/fix_srp.h (100%) rename src/{USER-MISC => MISC}/pair_agni.cpp (100%) rename src/{USER-MISC => MISC}/pair_agni.h (100%) rename src/{MISC => ORIENT}/fix_orient_bcc.cpp (100%) rename src/{MISC => ORIENT}/fix_orient_bcc.h (100%) rename src/{USER-MISC => ORIENT}/fix_orient_eco.cpp (100%) rename src/{USER-MISC => ORIENT}/fix_orient_eco.h (100%) rename src/{MISC => ORIENT}/fix_orient_fcc.cpp (100%) rename src/{MISC => ORIENT}/fix_orient_fcc.h (100%) delete mode 100644 src/USER-MISC/README rename src/{MISC => }/fix_deposit.cpp (100%) rename src/{MISC => }/fix_deposit.h (100%) rename src/{MISC => }/fix_efield.cpp (100%) rename src/{MISC => }/fix_efield.h (100%) rename src/{MISC => }/fix_evaporate.cpp (100%) rename src/{MISC => }/fix_evaporate.h (100%) rename src/{MISC => }/fix_thermal_conductivity.cpp (100%) rename src/{MISC => }/fix_thermal_conductivity.h (100%) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index e340a8bdb3..b2f5360020 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -161,6 +161,11 @@ set(STANDARD_PACKAGES DPD-SMOOTH DRUDE EFF + EXTRA-COMPUTE + EXTRA-DUMP + EXTRA-FIX + EXTRA-MOLECULE + EXTRA-PAIR FEP GRANULAR H5MD @@ -191,6 +196,7 @@ set(STANDARD_PACKAGES MPIIO MSCG NETCDF + ORIENT PERI PHONON PLUGIN @@ -213,7 +219,6 @@ set(STANDARD_PACKAGES SRD TALLY UEF - USER-MISC VORONOI VTK YAFF) diff --git a/cmake/presets/all_off.cmake b/cmake/presets/all_off.cmake index b873965fe4..2893bbab6b 100644 --- a/cmake/presets/all_off.cmake +++ b/cmake/presets/all_off.cmake @@ -25,6 +25,11 @@ set(ALL_PACKAGES DPD-SMOOTH DRUDE EFF + EXTRA-COMPUTE + EXTRA-DUMP + EXTRA-FIX + EXTRA-MOLECULE + EXTRA-PAIR FEP GPU GRANULAR @@ -60,6 +65,7 @@ set(ALL_PACKAGES NETCDF OPENMP OPT + ORIENT PERI PHONON PLUGIN @@ -82,7 +88,6 @@ set(ALL_PACKAGES SRD TALLY UEF - USER-MISC VORONOI VTK YAFF) diff --git a/cmake/presets/all_on.cmake b/cmake/presets/all_on.cmake index b4fe8e5303..9f38f1e1e4 100644 --- a/cmake/presets/all_on.cmake +++ b/cmake/presets/all_on.cmake @@ -27,6 +27,11 @@ set(ALL_PACKAGES DPD-SMOOTH DRUDE EFF + EXTRA-COMPUTE + EXTRA-DUMP + EXTRA-FIX + EXTRA-MOLECULE + EXTRA-PAIR FEP GPU GRANULAR @@ -62,6 +67,7 @@ set(ALL_PACKAGES NETCDF OPENMP OPT + ORIENT PERI PHONON PLUGIN @@ -84,7 +90,6 @@ set(ALL_PACKAGES SRD TALLY UEF - USER-MISC VORONOI VTK YAFF) diff --git a/cmake/presets/mingw-cross.cmake b/cmake/presets/mingw-cross.cmake index 71675ba9d7..fe828a6d9a 100644 --- a/cmake/presets/mingw-cross.cmake +++ b/cmake/presets/mingw-cross.cmake @@ -21,6 +21,11 @@ set(WIN_PACKAGES DPD-SMOOTH DRUDE EFF + EXTRA-COMPUTE + EXTRA-DUMP + EXTRA-FIX + EXTRA-MOLECULE + EXTRA-PAIR FEP GPU GRANULAR @@ -40,11 +45,13 @@ set(WIN_PACKAGES ML-HDNNP ML-IAP ML-SNAP + ML-RANN MOFFF MOLECULE MOLFILE OPENMP OPT + ORIENT PERI PHONON POEMS @@ -62,7 +69,6 @@ set(WIN_PACKAGES SRD TALLY UEF - USER-MISC VORONOI YAFF) diff --git a/cmake/presets/most.cmake b/cmake/presets/most.cmake index 8ad6ff31dc..9546f1f9a3 100644 --- a/cmake/presets/most.cmake +++ b/cmake/presets/most.cmake @@ -23,6 +23,10 @@ set(ALL_PACKAGES DPD-SMOOTH DRUDE EFF + EXTRA-COMPUTE + EXTRA-FIX + EXTRA-MOLECULE + EXTRA-PAIR FEP GRANULAR INTERLAYER @@ -38,6 +42,7 @@ set(ALL_PACKAGES MOLECULE OPENMP OPT + ORIENT PERI PHONON PLUGIN @@ -52,8 +57,8 @@ set(ALL_PACKAGES SPH SPIN SRD + TALLY UEF - USER-MISC VORONOI YAFF) diff --git a/src/.gitignore b/src/.gitignore index 42e1548c43..961901e322 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -250,6 +250,61 @@ /pair_mesont_tpm.cpp /pair_mesont_tpm.h +/compute_contact_atom.cpp +/compute_contact_atom.h +/dump_dcd.cpp +/dump_dcd.h +/fix_controller.cpp +/fix_controller.h +/fix_drag.cpp +/fix_drag.h +/fix_numdiff.cpp +/fix_numdiff.h +/fix_nve_noforce.cpp +/fix_nve_noforce.h +/fix_spring_rg.cpp +/fix_spring_rg.h +/fix_temp_csld.cpp +/fix_temp_csld.h +/fix_temp_csvr.cpp +/fix_temp_csvr.h +/fix_tmd.cpp +/fix_tmd.h +/pair_born_coul_dsf.cpp +/pair_born_coul_dsf.h +/pair_born_coul_wolf.cpp +/pair_born_coul_wolf.h +/pair_coul_cut_global.cpp +/pair_coul_cut_global.h +/pair_coul_streitz.cpp +/pair_coul_streitz.h +/pair_gauss.cpp +/pair_gauss.h +/pair_lj96_cut.cpp +/pair_lj96_cut.h +/pair_lj_cubic.cpp +/pair_lj_cubic.h +/pair_lj_cut_coul_debye.cpp +/pair_lj_cut_coul_debye.h +/pair_lj_cut_coul_dsf.cpp +/pair_lj_cut_coul_dsf.h +/pair_lj_cut_coul_wolf.cpp +/pair_lj_cut_coul_wolf.h +/pair_lj_gromacs.cpp +/pair_lj_gromacs.h +/pair_lj_gromacs_could_gromacs.cpp +/pair_lj_gromacs_could_gromacs.h +/pair_lj_relres.cpp +/pair_lj_relres.h +/pair_lj_smooth.cpp +/pair_lj_smooth.h +/pair_lj_smooth_linear.cpp +/pair_lj_smooth_linear.h +/pair_mie_cut.cpp +/pair_mie_cut.h +/pair_ufm.cpp +/pair_ufm.h + /angle_cg_cmm.cpp /angle_cg_cmm.h /angle_charmm.cpp @@ -578,12 +633,8 @@ /fix_client_md.h /fix_cmap.cpp /fix_cmap.h -/fix_deposit.cpp -/fix_deposit.h /fix_dpd_energy.cpp /fix_dpd_energy.h -/fix_efield.cpp -/fix_efield.h /fix_electron_stopping.cpp /fix_electron_stopping.h /fix_electron_stopping_fit.cpp @@ -592,8 +643,6 @@ /fix_eos_cv.h /fix_eos_table.cpp /fix_eos_table.h -/fix_evaporate.cpp -/fix_evaporate.h /fix_ffl.cpp /fix_ffl.h /fix_filter_corotate.cpp @@ -797,8 +846,6 @@ /fix_tgnpt_drude.h /fix_tgnvt_drude.cpp /fix_tgnvt_drude.h -/fix_thermal_conductivity.cpp -/fix_thermal_conductivity.h /fix_ti_rs.cpp /fix_ti_rs.h /fix_ti_spring.cpp diff --git a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp b/src/DIPOLE/pair_lj_sf_dipole_sf.cpp similarity index 100% rename from src/USER-MISC/pair_lj_sf_dipole_sf.cpp rename to src/DIPOLE/pair_lj_sf_dipole_sf.cpp diff --git a/src/USER-MISC/pair_lj_sf_dipole_sf.h b/src/DIPOLE/pair_lj_sf_dipole_sf.h similarity index 100% rename from src/USER-MISC/pair_lj_sf_dipole_sf.h rename to src/DIPOLE/pair_lj_sf_dipole_sf.h diff --git a/src/Depend.sh b/src/Depend.sh index 4700b6f5f0..4bbbeb9a51 100755 --- a/src/Depend.sh +++ b/src/Depend.sh @@ -63,8 +63,11 @@ if (test $1 = "COLLOID") then depend OPENMP fi +if (test $1 = "DIELECTRIC") then + depend OPENMP +fi + if (test $1 = "DIPOLE") then - depend USER-MISC depend OPENMP fi @@ -72,6 +75,16 @@ if (test $1 = "DPD-BASIC") then depend GPU fi +if (test $1 = "EXTRA-MOLECULE") then + depend GPU + depend OPENMP +fi + +if (test $1 = "EXTRA-PAIR") then + depend GPU + depend OPENMP +fi + if (test $1 = "GRANULAR") then depend KOKKOS depend OPENMP @@ -96,14 +109,13 @@ if (test $1 = "MANYBODY") then depend KOKKOS depend OPT depend QEQ - depend USER-MISC depend OPENMP fi if (test $1 = "MOLECULE") then + depend EXTRA-MOLECULE depend GPU depend KOKKOS - depend USER-MISC depend FEP depend OPENMP depend INTEL @@ -146,12 +158,6 @@ if (test $1 = "FEP") then depend OPENMP fi -if (test $1 = "USER-MISC") then - depend GPU - depend OPENMP - depend INTEL -fi - if (test $1 = "REAXFF") then depend KOKKOS depend OPENMP diff --git a/src/USER-MISC/compute_ackland_atom.cpp b/src/EXTRA-COMPUTE/compute_ackland_atom.cpp similarity index 100% rename from src/USER-MISC/compute_ackland_atom.cpp rename to src/EXTRA-COMPUTE/compute_ackland_atom.cpp diff --git a/src/USER-MISC/compute_ackland_atom.h b/src/EXTRA-COMPUTE/compute_ackland_atom.h similarity index 100% rename from src/USER-MISC/compute_ackland_atom.h rename to src/EXTRA-COMPUTE/compute_ackland_atom.h diff --git a/src/compute_adf.cpp b/src/EXTRA-COMPUTE/compute_adf.cpp similarity index 100% rename from src/compute_adf.cpp rename to src/EXTRA-COMPUTE/compute_adf.cpp diff --git a/src/compute_adf.h b/src/EXTRA-COMPUTE/compute_adf.h similarity index 100% rename from src/compute_adf.h rename to src/EXTRA-COMPUTE/compute_adf.h diff --git a/src/compute_aggregate_atom.cpp b/src/EXTRA-COMPUTE/compute_aggregate_atom.cpp similarity index 100% rename from src/compute_aggregate_atom.cpp rename to src/EXTRA-COMPUTE/compute_aggregate_atom.cpp diff --git a/src/compute_aggregate_atom.h b/src/EXTRA-COMPUTE/compute_aggregate_atom.h similarity index 100% rename from src/compute_aggregate_atom.h rename to src/EXTRA-COMPUTE/compute_aggregate_atom.h diff --git a/src/USER-MISC/compute_basal_atom.cpp b/src/EXTRA-COMPUTE/compute_basal_atom.cpp similarity index 100% rename from src/USER-MISC/compute_basal_atom.cpp rename to src/EXTRA-COMPUTE/compute_basal_atom.cpp diff --git a/src/USER-MISC/compute_basal_atom.h b/src/EXTRA-COMPUTE/compute_basal_atom.h similarity index 100% rename from src/USER-MISC/compute_basal_atom.h rename to src/EXTRA-COMPUTE/compute_basal_atom.h diff --git a/src/compute_cluster_atom.cpp b/src/EXTRA-COMPUTE/compute_cluster_atom.cpp similarity index 100% rename from src/compute_cluster_atom.cpp rename to src/EXTRA-COMPUTE/compute_cluster_atom.cpp diff --git a/src/compute_cluster_atom.h b/src/EXTRA-COMPUTE/compute_cluster_atom.h similarity index 100% rename from src/compute_cluster_atom.h rename to src/EXTRA-COMPUTE/compute_cluster_atom.h diff --git a/src/USER-MISC/compute_cnp_atom.cpp b/src/EXTRA-COMPUTE/compute_cnp_atom.cpp similarity index 100% rename from src/USER-MISC/compute_cnp_atom.cpp rename to src/EXTRA-COMPUTE/compute_cnp_atom.cpp diff --git a/src/USER-MISC/compute_cnp_atom.h b/src/EXTRA-COMPUTE/compute_cnp_atom.h similarity index 100% rename from src/USER-MISC/compute_cnp_atom.h rename to src/EXTRA-COMPUTE/compute_cnp_atom.h diff --git a/src/USER-MISC/compute_entropy_atom.cpp b/src/EXTRA-COMPUTE/compute_entropy_atom.cpp similarity index 100% rename from src/USER-MISC/compute_entropy_atom.cpp rename to src/EXTRA-COMPUTE/compute_entropy_atom.cpp diff --git a/src/USER-MISC/compute_entropy_atom.h b/src/EXTRA-COMPUTE/compute_entropy_atom.h similarity index 100% rename from src/USER-MISC/compute_entropy_atom.h rename to src/EXTRA-COMPUTE/compute_entropy_atom.h diff --git a/src/compute_fragment_atom.cpp b/src/EXTRA-COMPUTE/compute_fragment_atom.cpp similarity index 100% rename from src/compute_fragment_atom.cpp rename to src/EXTRA-COMPUTE/compute_fragment_atom.cpp diff --git a/src/compute_fragment_atom.h b/src/EXTRA-COMPUTE/compute_fragment_atom.h similarity index 100% rename from src/compute_fragment_atom.h rename to src/EXTRA-COMPUTE/compute_fragment_atom.h diff --git a/src/USER-MISC/compute_gyration_shape.cpp b/src/EXTRA-COMPUTE/compute_gyration_shape.cpp similarity index 100% rename from src/USER-MISC/compute_gyration_shape.cpp rename to src/EXTRA-COMPUTE/compute_gyration_shape.cpp diff --git a/src/USER-MISC/compute_gyration_shape.h b/src/EXTRA-COMPUTE/compute_gyration_shape.h similarity index 100% rename from src/USER-MISC/compute_gyration_shape.h rename to src/EXTRA-COMPUTE/compute_gyration_shape.h diff --git a/src/USER-MISC/compute_gyration_shape_chunk.cpp b/src/EXTRA-COMPUTE/compute_gyration_shape_chunk.cpp similarity index 100% rename from src/USER-MISC/compute_gyration_shape_chunk.cpp rename to src/EXTRA-COMPUTE/compute_gyration_shape_chunk.cpp diff --git a/src/USER-MISC/compute_gyration_shape_chunk.h b/src/EXTRA-COMPUTE/compute_gyration_shape_chunk.h similarity index 100% rename from src/USER-MISC/compute_gyration_shape_chunk.h rename to src/EXTRA-COMPUTE/compute_gyration_shape_chunk.h diff --git a/src/compute_hexorder_atom.cpp b/src/EXTRA-COMPUTE/compute_hexorder_atom.cpp similarity index 100% rename from src/compute_hexorder_atom.cpp rename to src/EXTRA-COMPUTE/compute_hexorder_atom.cpp diff --git a/src/compute_hexorder_atom.h b/src/EXTRA-COMPUTE/compute_hexorder_atom.h similarity index 100% rename from src/compute_hexorder_atom.h rename to src/EXTRA-COMPUTE/compute_hexorder_atom.h diff --git a/src/USER-MISC/compute_hma.cpp b/src/EXTRA-COMPUTE/compute_hma.cpp similarity index 100% rename from src/USER-MISC/compute_hma.cpp rename to src/EXTRA-COMPUTE/compute_hma.cpp diff --git a/src/USER-MISC/compute_hma.h b/src/EXTRA-COMPUTE/compute_hma.h similarity index 100% rename from src/USER-MISC/compute_hma.h rename to src/EXTRA-COMPUTE/compute_hma.h diff --git a/src/USER-MISC/compute_momentum.cpp b/src/EXTRA-COMPUTE/compute_momentum.cpp similarity index 100% rename from src/USER-MISC/compute_momentum.cpp rename to src/EXTRA-COMPUTE/compute_momentum.cpp diff --git a/src/USER-MISC/compute_momentum.h b/src/EXTRA-COMPUTE/compute_momentum.h similarity index 100% rename from src/USER-MISC/compute_momentum.h rename to src/EXTRA-COMPUTE/compute_momentum.h diff --git a/src/MISC/compute_msd_nongauss.cpp b/src/EXTRA-COMPUTE/compute_msd_nongauss.cpp similarity index 100% rename from src/MISC/compute_msd_nongauss.cpp rename to src/EXTRA-COMPUTE/compute_msd_nongauss.cpp diff --git a/src/MISC/compute_msd_nongauss.h b/src/EXTRA-COMPUTE/compute_msd_nongauss.h similarity index 100% rename from src/MISC/compute_msd_nongauss.h rename to src/EXTRA-COMPUTE/compute_msd_nongauss.h diff --git a/src/compute_orientorder_atom.cpp b/src/EXTRA-COMPUTE/compute_orientorder_atom.cpp similarity index 100% rename from src/compute_orientorder_atom.cpp rename to src/EXTRA-COMPUTE/compute_orientorder_atom.cpp diff --git a/src/compute_orientorder_atom.h b/src/EXTRA-COMPUTE/compute_orientorder_atom.h similarity index 100% rename from src/compute_orientorder_atom.h rename to src/EXTRA-COMPUTE/compute_orientorder_atom.h diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/EXTRA-COMPUTE/compute_pressure_cylinder.cpp similarity index 100% rename from src/USER-MISC/compute_pressure_cylinder.cpp rename to src/EXTRA-COMPUTE/compute_pressure_cylinder.cpp diff --git a/src/USER-MISC/compute_pressure_cylinder.h b/src/EXTRA-COMPUTE/compute_pressure_cylinder.h similarity index 100% rename from src/USER-MISC/compute_pressure_cylinder.h rename to src/EXTRA-COMPUTE/compute_pressure_cylinder.h diff --git a/src/USER-MISC/compute_stress_mop.cpp b/src/EXTRA-COMPUTE/compute_stress_mop.cpp similarity index 100% rename from src/USER-MISC/compute_stress_mop.cpp rename to src/EXTRA-COMPUTE/compute_stress_mop.cpp diff --git a/src/USER-MISC/compute_stress_mop.h b/src/EXTRA-COMPUTE/compute_stress_mop.h similarity index 100% rename from src/USER-MISC/compute_stress_mop.h rename to src/EXTRA-COMPUTE/compute_stress_mop.h diff --git a/src/USER-MISC/compute_stress_mop_profile.cpp b/src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp similarity index 100% rename from src/USER-MISC/compute_stress_mop_profile.cpp rename to src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp diff --git a/src/USER-MISC/compute_stress_mop_profile.h b/src/EXTRA-COMPUTE/compute_stress_mop_profile.h similarity index 100% rename from src/USER-MISC/compute_stress_mop_profile.h rename to src/EXTRA-COMPUTE/compute_stress_mop_profile.h diff --git a/src/USER-MISC/compute_temp_rotate.cpp b/src/EXTRA-COMPUTE/compute_temp_rotate.cpp similarity index 100% rename from src/USER-MISC/compute_temp_rotate.cpp rename to src/EXTRA-COMPUTE/compute_temp_rotate.cpp diff --git a/src/USER-MISC/compute_temp_rotate.h b/src/EXTRA-COMPUTE/compute_temp_rotate.h similarity index 100% rename from src/USER-MISC/compute_temp_rotate.h rename to src/EXTRA-COMPUTE/compute_temp_rotate.h diff --git a/src/MISC/compute_ti.cpp b/src/EXTRA-COMPUTE/compute_ti.cpp similarity index 100% rename from src/MISC/compute_ti.cpp rename to src/EXTRA-COMPUTE/compute_ti.cpp diff --git a/src/MISC/compute_ti.h b/src/EXTRA-COMPUTE/compute_ti.h similarity index 100% rename from src/MISC/compute_ti.h rename to src/EXTRA-COMPUTE/compute_ti.h diff --git a/src/dump_dcd.cpp b/src/EXTRA-DUMP/dump_dcd.cpp similarity index 100% rename from src/dump_dcd.cpp rename to src/EXTRA-DUMP/dump_dcd.cpp diff --git a/src/dump_dcd.h b/src/EXTRA-DUMP/dump_dcd.h similarity index 100% rename from src/dump_dcd.h rename to src/EXTRA-DUMP/dump_dcd.h diff --git a/src/MISC/dump_xtc.cpp b/src/EXTRA-DUMP/dump_xtc.cpp similarity index 100% rename from src/MISC/dump_xtc.cpp rename to src/EXTRA-DUMP/dump_xtc.cpp diff --git a/src/MISC/dump_xtc.h b/src/EXTRA-DUMP/dump_xtc.h similarity index 100% rename from src/MISC/dump_xtc.h rename to src/EXTRA-DUMP/dump_xtc.h diff --git a/src/MISC/xdr_compat.cpp b/src/EXTRA-DUMP/xdr_compat.cpp similarity index 100% rename from src/MISC/xdr_compat.cpp rename to src/EXTRA-DUMP/xdr_compat.cpp diff --git a/src/MISC/xdr_compat.h b/src/EXTRA-DUMP/xdr_compat.h similarity index 100% rename from src/MISC/xdr_compat.h rename to src/EXTRA-DUMP/xdr_compat.h diff --git a/src/MISC/fix_addtorque.cpp b/src/EXTRA-FIX/fix_addtorque.cpp similarity index 100% rename from src/MISC/fix_addtorque.cpp rename to src/EXTRA-FIX/fix_addtorque.cpp diff --git a/src/MISC/fix_addtorque.h b/src/EXTRA-FIX/fix_addtorque.h similarity index 100% rename from src/MISC/fix_addtorque.h rename to src/EXTRA-FIX/fix_addtorque.h diff --git a/src/USER-MISC/fix_ave_correlate_long.cpp b/src/EXTRA-FIX/fix_ave_correlate_long.cpp similarity index 100% rename from src/USER-MISC/fix_ave_correlate_long.cpp rename to src/EXTRA-FIX/fix_ave_correlate_long.cpp diff --git a/src/USER-MISC/fix_ave_correlate_long.h b/src/EXTRA-FIX/fix_ave_correlate_long.h similarity index 100% rename from src/USER-MISC/fix_ave_correlate_long.h rename to src/EXTRA-FIX/fix_ave_correlate_long.h diff --git a/src/fix_controller.cpp b/src/EXTRA-FIX/fix_controller.cpp similarity index 100% rename from src/fix_controller.cpp rename to src/EXTRA-FIX/fix_controller.cpp diff --git a/src/fix_controller.h b/src/EXTRA-FIX/fix_controller.h similarity index 100% rename from src/fix_controller.h rename to src/EXTRA-FIX/fix_controller.h diff --git a/src/fix_drag.cpp b/src/EXTRA-FIX/fix_drag.cpp similarity index 100% rename from src/fix_drag.cpp rename to src/EXTRA-FIX/fix_drag.cpp diff --git a/src/fix_drag.h b/src/EXTRA-FIX/fix_drag.h similarity index 100% rename from src/fix_drag.h rename to src/EXTRA-FIX/fix_drag.h diff --git a/src/USER-MISC/fix_electron_stopping.cpp b/src/EXTRA-FIX/fix_electron_stopping.cpp similarity index 100% rename from src/USER-MISC/fix_electron_stopping.cpp rename to src/EXTRA-FIX/fix_electron_stopping.cpp diff --git a/src/USER-MISC/fix_electron_stopping.h b/src/EXTRA-FIX/fix_electron_stopping.h similarity index 100% rename from src/USER-MISC/fix_electron_stopping.h rename to src/EXTRA-FIX/fix_electron_stopping.h diff --git a/src/USER-MISC/fix_electron_stopping_fit.cpp b/src/EXTRA-FIX/fix_electron_stopping_fit.cpp similarity index 100% rename from src/USER-MISC/fix_electron_stopping_fit.cpp rename to src/EXTRA-FIX/fix_electron_stopping_fit.cpp diff --git a/src/USER-MISC/fix_electron_stopping_fit.h b/src/EXTRA-FIX/fix_electron_stopping_fit.h similarity index 100% rename from src/USER-MISC/fix_electron_stopping_fit.h rename to src/EXTRA-FIX/fix_electron_stopping_fit.h diff --git a/src/USER-MISC/fix_ffl.cpp b/src/EXTRA-FIX/fix_ffl.cpp similarity index 100% rename from src/USER-MISC/fix_ffl.cpp rename to src/EXTRA-FIX/fix_ffl.cpp diff --git a/src/USER-MISC/fix_ffl.h b/src/EXTRA-FIX/fix_ffl.h similarity index 100% rename from src/USER-MISC/fix_ffl.h rename to src/EXTRA-FIX/fix_ffl.h diff --git a/src/USER-MISC/fix_filter_corotate.cpp b/src/EXTRA-FIX/fix_filter_corotate.cpp similarity index 100% rename from src/USER-MISC/fix_filter_corotate.cpp rename to src/EXTRA-FIX/fix_filter_corotate.cpp diff --git a/src/USER-MISC/fix_filter_corotate.h b/src/EXTRA-FIX/fix_filter_corotate.h similarity index 100% rename from src/USER-MISC/fix_filter_corotate.h rename to src/EXTRA-FIX/fix_filter_corotate.h diff --git a/src/USER-MISC/fix_flow_gauss.cpp b/src/EXTRA-FIX/fix_flow_gauss.cpp similarity index 100% rename from src/USER-MISC/fix_flow_gauss.cpp rename to src/EXTRA-FIX/fix_flow_gauss.cpp diff --git a/src/USER-MISC/fix_flow_gauss.h b/src/EXTRA-FIX/fix_flow_gauss.h similarity index 100% rename from src/USER-MISC/fix_flow_gauss.h rename to src/EXTRA-FIX/fix_flow_gauss.h diff --git a/src/MISC/fix_gld.cpp b/src/EXTRA-FIX/fix_gld.cpp similarity index 100% rename from src/MISC/fix_gld.cpp rename to src/EXTRA-FIX/fix_gld.cpp diff --git a/src/MISC/fix_gld.h b/src/EXTRA-FIX/fix_gld.h similarity index 100% rename from src/MISC/fix_gld.h rename to src/EXTRA-FIX/fix_gld.h diff --git a/src/USER-MISC/fix_gle.cpp b/src/EXTRA-FIX/fix_gle.cpp similarity index 100% rename from src/USER-MISC/fix_gle.cpp rename to src/EXTRA-FIX/fix_gle.cpp diff --git a/src/USER-MISC/fix_gle.h b/src/EXTRA-FIX/fix_gle.h similarity index 100% rename from src/USER-MISC/fix_gle.h rename to src/EXTRA-FIX/fix_gle.h diff --git a/src/USER-MISC/fix_momentum_chunk.cpp b/src/EXTRA-FIX/fix_momentum_chunk.cpp similarity index 100% rename from src/USER-MISC/fix_momentum_chunk.cpp rename to src/EXTRA-FIX/fix_momentum_chunk.cpp diff --git a/src/USER-MISC/fix_momentum_chunk.h b/src/EXTRA-FIX/fix_momentum_chunk.h similarity index 100% rename from src/USER-MISC/fix_momentum_chunk.h rename to src/EXTRA-FIX/fix_momentum_chunk.h diff --git a/src/USER-MISC/fix_npt_cauchy.cpp b/src/EXTRA-FIX/fix_npt_cauchy.cpp similarity index 100% rename from src/USER-MISC/fix_npt_cauchy.cpp rename to src/EXTRA-FIX/fix_npt_cauchy.cpp diff --git a/src/USER-MISC/fix_npt_cauchy.h b/src/EXTRA-FIX/fix_npt_cauchy.h similarity index 100% rename from src/USER-MISC/fix_npt_cauchy.h rename to src/EXTRA-FIX/fix_npt_cauchy.h diff --git a/src/fix_numdiff.cpp b/src/EXTRA-FIX/fix_numdiff.cpp similarity index 100% rename from src/fix_numdiff.cpp rename to src/EXTRA-FIX/fix_numdiff.cpp diff --git a/src/fix_numdiff.h b/src/EXTRA-FIX/fix_numdiff.h similarity index 100% rename from src/fix_numdiff.h rename to src/EXTRA-FIX/fix_numdiff.h diff --git a/src/fix_nve_noforce.cpp b/src/EXTRA-FIX/fix_nve_noforce.cpp similarity index 100% rename from src/fix_nve_noforce.cpp rename to src/EXTRA-FIX/fix_nve_noforce.cpp diff --git a/src/fix_nve_noforce.h b/src/EXTRA-FIX/fix_nve_noforce.h similarity index 100% rename from src/fix_nve_noforce.h rename to src/EXTRA-FIX/fix_nve_noforce.h diff --git a/src/USER-MISC/fix_nvk.cpp b/src/EXTRA-FIX/fix_nvk.cpp similarity index 100% rename from src/USER-MISC/fix_nvk.cpp rename to src/EXTRA-FIX/fix_nvk.cpp diff --git a/src/USER-MISC/fix_nvk.h b/src/EXTRA-FIX/fix_nvk.h similarity index 100% rename from src/USER-MISC/fix_nvk.h rename to src/EXTRA-FIX/fix_nvk.h diff --git a/src/MISC/fix_oneway.cpp b/src/EXTRA-FIX/fix_oneway.cpp similarity index 100% rename from src/MISC/fix_oneway.cpp rename to src/EXTRA-FIX/fix_oneway.cpp diff --git a/src/MISC/fix_oneway.h b/src/EXTRA-FIX/fix_oneway.h similarity index 100% rename from src/MISC/fix_oneway.h rename to src/EXTRA-FIX/fix_oneway.h diff --git a/src/USER-MISC/fix_pafi.cpp b/src/EXTRA-FIX/fix_pafi.cpp similarity index 100% rename from src/USER-MISC/fix_pafi.cpp rename to src/EXTRA-FIX/fix_pafi.cpp diff --git a/src/USER-MISC/fix_pafi.h b/src/EXTRA-FIX/fix_pafi.h similarity index 100% rename from src/USER-MISC/fix_pafi.h rename to src/EXTRA-FIX/fix_pafi.h diff --git a/src/USER-MISC/fix_pimd.cpp b/src/EXTRA-FIX/fix_pimd.cpp similarity index 100% rename from src/USER-MISC/fix_pimd.cpp rename to src/EXTRA-FIX/fix_pimd.cpp diff --git a/src/USER-MISC/fix_pimd.h b/src/EXTRA-FIX/fix_pimd.h similarity index 100% rename from src/USER-MISC/fix_pimd.h rename to src/EXTRA-FIX/fix_pimd.h diff --git a/src/USER-MISC/fix_rhok.cpp b/src/EXTRA-FIX/fix_rhok.cpp similarity index 100% rename from src/USER-MISC/fix_rhok.cpp rename to src/EXTRA-FIX/fix_rhok.cpp diff --git a/src/USER-MISC/fix_rhok.h b/src/EXTRA-FIX/fix_rhok.h similarity index 100% rename from src/USER-MISC/fix_rhok.h rename to src/EXTRA-FIX/fix_rhok.h diff --git a/src/MISC/fix_smd.cpp b/src/EXTRA-FIX/fix_smd.cpp similarity index 100% rename from src/MISC/fix_smd.cpp rename to src/EXTRA-FIX/fix_smd.cpp diff --git a/src/MISC/fix_smd.h b/src/EXTRA-FIX/fix_smd.h similarity index 100% rename from src/MISC/fix_smd.h rename to src/EXTRA-FIX/fix_smd.h diff --git a/src/fix_spring_rg.cpp b/src/EXTRA-FIX/fix_spring_rg.cpp similarity index 100% rename from src/fix_spring_rg.cpp rename to src/EXTRA-FIX/fix_spring_rg.cpp diff --git a/src/fix_spring_rg.h b/src/EXTRA-FIX/fix_spring_rg.h similarity index 100% rename from src/fix_spring_rg.h rename to src/EXTRA-FIX/fix_spring_rg.h diff --git a/src/fix_temp_csld.cpp b/src/EXTRA-FIX/fix_temp_csld.cpp similarity index 100% rename from src/fix_temp_csld.cpp rename to src/EXTRA-FIX/fix_temp_csld.cpp diff --git a/src/fix_temp_csld.h b/src/EXTRA-FIX/fix_temp_csld.h similarity index 100% rename from src/fix_temp_csld.h rename to src/EXTRA-FIX/fix_temp_csld.h diff --git a/src/fix_temp_csvr.cpp b/src/EXTRA-FIX/fix_temp_csvr.cpp similarity index 100% rename from src/fix_temp_csvr.cpp rename to src/EXTRA-FIX/fix_temp_csvr.cpp diff --git a/src/fix_temp_csvr.h b/src/EXTRA-FIX/fix_temp_csvr.h similarity index 100% rename from src/fix_temp_csvr.h rename to src/EXTRA-FIX/fix_temp_csvr.h diff --git a/src/USER-MISC/fix_ti_spring.cpp b/src/EXTRA-FIX/fix_ti_spring.cpp similarity index 100% rename from src/USER-MISC/fix_ti_spring.cpp rename to src/EXTRA-FIX/fix_ti_spring.cpp diff --git a/src/USER-MISC/fix_ti_spring.h b/src/EXTRA-FIX/fix_ti_spring.h similarity index 100% rename from src/USER-MISC/fix_ti_spring.h rename to src/EXTRA-FIX/fix_ti_spring.h diff --git a/src/fix_tmd.cpp b/src/EXTRA-FIX/fix_tmd.cpp similarity index 100% rename from src/fix_tmd.cpp rename to src/EXTRA-FIX/fix_tmd.cpp diff --git a/src/fix_tmd.h b/src/EXTRA-FIX/fix_tmd.h similarity index 100% rename from src/fix_tmd.h rename to src/EXTRA-FIX/fix_tmd.h diff --git a/src/MISC/fix_ttm.cpp b/src/EXTRA-FIX/fix_ttm.cpp similarity index 100% rename from src/MISC/fix_ttm.cpp rename to src/EXTRA-FIX/fix_ttm.cpp diff --git a/src/MISC/fix_ttm.h b/src/EXTRA-FIX/fix_ttm.h similarity index 100% rename from src/MISC/fix_ttm.h rename to src/EXTRA-FIX/fix_ttm.h diff --git a/src/USER-MISC/fix_ttm_mod.cpp b/src/EXTRA-FIX/fix_ttm_mod.cpp similarity index 100% rename from src/USER-MISC/fix_ttm_mod.cpp rename to src/EXTRA-FIX/fix_ttm_mod.cpp diff --git a/src/USER-MISC/fix_ttm_mod.h b/src/EXTRA-FIX/fix_ttm_mod.h similarity index 100% rename from src/USER-MISC/fix_ttm_mod.h rename to src/EXTRA-FIX/fix_ttm_mod.h diff --git a/src/MISC/fix_viscosity.cpp b/src/EXTRA-FIX/fix_viscosity.cpp similarity index 100% rename from src/MISC/fix_viscosity.cpp rename to src/EXTRA-FIX/fix_viscosity.cpp diff --git a/src/MISC/fix_viscosity.h b/src/EXTRA-FIX/fix_viscosity.h similarity index 100% rename from src/MISC/fix_viscosity.h rename to src/EXTRA-FIX/fix_viscosity.h diff --git a/src/USER-MISC/fix_wall_ees.cpp b/src/EXTRA-FIX/fix_wall_ees.cpp similarity index 100% rename from src/USER-MISC/fix_wall_ees.cpp rename to src/EXTRA-FIX/fix_wall_ees.cpp diff --git a/src/USER-MISC/fix_wall_ees.h b/src/EXTRA-FIX/fix_wall_ees.h similarity index 100% rename from src/USER-MISC/fix_wall_ees.h rename to src/EXTRA-FIX/fix_wall_ees.h diff --git a/src/USER-MISC/fix_wall_reflect_stochastic.cpp b/src/EXTRA-FIX/fix_wall_reflect_stochastic.cpp similarity index 100% rename from src/USER-MISC/fix_wall_reflect_stochastic.cpp rename to src/EXTRA-FIX/fix_wall_reflect_stochastic.cpp diff --git a/src/USER-MISC/fix_wall_reflect_stochastic.h b/src/EXTRA-FIX/fix_wall_reflect_stochastic.h similarity index 100% rename from src/USER-MISC/fix_wall_reflect_stochastic.h rename to src/EXTRA-FIX/fix_wall_reflect_stochastic.h diff --git a/src/USER-MISC/fix_wall_region_ees.cpp b/src/EXTRA-FIX/fix_wall_region_ees.cpp similarity index 100% rename from src/USER-MISC/fix_wall_region_ees.cpp rename to src/EXTRA-FIX/fix_wall_region_ees.cpp diff --git a/src/USER-MISC/fix_wall_region_ees.h b/src/EXTRA-FIX/fix_wall_region_ees.h similarity index 100% rename from src/USER-MISC/fix_wall_region_ees.h rename to src/EXTRA-FIX/fix_wall_region_ees.h diff --git a/src/MOLECULE/angle_cosine_delta.cpp b/src/EXTRA-MOLECULE/angle_cosine_delta.cpp similarity index 100% rename from src/MOLECULE/angle_cosine_delta.cpp rename to src/EXTRA-MOLECULE/angle_cosine_delta.cpp diff --git a/src/MOLECULE/angle_cosine_delta.h b/src/EXTRA-MOLECULE/angle_cosine_delta.h similarity index 100% rename from src/MOLECULE/angle_cosine_delta.h rename to src/EXTRA-MOLECULE/angle_cosine_delta.h diff --git a/src/MOLECULE/angle_cosine_periodic.cpp b/src/EXTRA-MOLECULE/angle_cosine_periodic.cpp similarity index 100% rename from src/MOLECULE/angle_cosine_periodic.cpp rename to src/EXTRA-MOLECULE/angle_cosine_periodic.cpp diff --git a/src/MOLECULE/angle_cosine_periodic.h b/src/EXTRA-MOLECULE/angle_cosine_periodic.h similarity index 100% rename from src/MOLECULE/angle_cosine_periodic.h rename to src/EXTRA-MOLECULE/angle_cosine_periodic.h diff --git a/src/MOLECULE/angle_cosine_shift.cpp b/src/EXTRA-MOLECULE/angle_cosine_shift.cpp similarity index 100% rename from src/MOLECULE/angle_cosine_shift.cpp rename to src/EXTRA-MOLECULE/angle_cosine_shift.cpp diff --git a/src/MOLECULE/angle_cosine_shift.h b/src/EXTRA-MOLECULE/angle_cosine_shift.h similarity index 100% rename from src/MOLECULE/angle_cosine_shift.h rename to src/EXTRA-MOLECULE/angle_cosine_shift.h diff --git a/src/MOLECULE/angle_cosine_shift_exp.cpp b/src/EXTRA-MOLECULE/angle_cosine_shift_exp.cpp similarity index 100% rename from src/MOLECULE/angle_cosine_shift_exp.cpp rename to src/EXTRA-MOLECULE/angle_cosine_shift_exp.cpp diff --git a/src/MOLECULE/angle_cosine_shift_exp.h b/src/EXTRA-MOLECULE/angle_cosine_shift_exp.h similarity index 100% rename from src/MOLECULE/angle_cosine_shift_exp.h rename to src/EXTRA-MOLECULE/angle_cosine_shift_exp.h diff --git a/src/MOLECULE/angle_fourier.cpp b/src/EXTRA-MOLECULE/angle_fourier.cpp similarity index 100% rename from src/MOLECULE/angle_fourier.cpp rename to src/EXTRA-MOLECULE/angle_fourier.cpp diff --git a/src/MOLECULE/angle_fourier.h b/src/EXTRA-MOLECULE/angle_fourier.h similarity index 100% rename from src/MOLECULE/angle_fourier.h rename to src/EXTRA-MOLECULE/angle_fourier.h diff --git a/src/MOLECULE/angle_fourier_simple.cpp b/src/EXTRA-MOLECULE/angle_fourier_simple.cpp similarity index 100% rename from src/MOLECULE/angle_fourier_simple.cpp rename to src/EXTRA-MOLECULE/angle_fourier_simple.cpp diff --git a/src/MOLECULE/angle_fourier_simple.h b/src/EXTRA-MOLECULE/angle_fourier_simple.h similarity index 100% rename from src/MOLECULE/angle_fourier_simple.h rename to src/EXTRA-MOLECULE/angle_fourier_simple.h diff --git a/src/MOLECULE/angle_gaussian.cpp b/src/EXTRA-MOLECULE/angle_gaussian.cpp similarity index 100% rename from src/MOLECULE/angle_gaussian.cpp rename to src/EXTRA-MOLECULE/angle_gaussian.cpp diff --git a/src/MOLECULE/angle_gaussian.h b/src/EXTRA-MOLECULE/angle_gaussian.h similarity index 100% rename from src/MOLECULE/angle_gaussian.h rename to src/EXTRA-MOLECULE/angle_gaussian.h diff --git a/src/MOLECULE/angle_quartic.cpp b/src/EXTRA-MOLECULE/angle_quartic.cpp similarity index 100% rename from src/MOLECULE/angle_quartic.cpp rename to src/EXTRA-MOLECULE/angle_quartic.cpp diff --git a/src/MOLECULE/angle_quartic.h b/src/EXTRA-MOLECULE/angle_quartic.h similarity index 100% rename from src/MOLECULE/angle_quartic.h rename to src/EXTRA-MOLECULE/angle_quartic.h diff --git a/src/MOLECULE/bond_gaussian.cpp b/src/EXTRA-MOLECULE/bond_gaussian.cpp similarity index 100% rename from src/MOLECULE/bond_gaussian.cpp rename to src/EXTRA-MOLECULE/bond_gaussian.cpp diff --git a/src/MOLECULE/bond_gaussian.h b/src/EXTRA-MOLECULE/bond_gaussian.h similarity index 100% rename from src/MOLECULE/bond_gaussian.h rename to src/EXTRA-MOLECULE/bond_gaussian.h diff --git a/src/MOLECULE/bond_harmonic_shift.cpp b/src/EXTRA-MOLECULE/bond_harmonic_shift.cpp similarity index 100% rename from src/MOLECULE/bond_harmonic_shift.cpp rename to src/EXTRA-MOLECULE/bond_harmonic_shift.cpp diff --git a/src/MOLECULE/bond_harmonic_shift.h b/src/EXTRA-MOLECULE/bond_harmonic_shift.h similarity index 100% rename from src/MOLECULE/bond_harmonic_shift.h rename to src/EXTRA-MOLECULE/bond_harmonic_shift.h diff --git a/src/MOLECULE/bond_harmonic_shift_cut.cpp b/src/EXTRA-MOLECULE/bond_harmonic_shift_cut.cpp similarity index 100% rename from src/MOLECULE/bond_harmonic_shift_cut.cpp rename to src/EXTRA-MOLECULE/bond_harmonic_shift_cut.cpp diff --git a/src/MOLECULE/bond_harmonic_shift_cut.h b/src/EXTRA-MOLECULE/bond_harmonic_shift_cut.h similarity index 100% rename from src/MOLECULE/bond_harmonic_shift_cut.h rename to src/EXTRA-MOLECULE/bond_harmonic_shift_cut.h diff --git a/src/MOLECULE/bond_nonlinear.cpp b/src/EXTRA-MOLECULE/bond_nonlinear.cpp similarity index 100% rename from src/MOLECULE/bond_nonlinear.cpp rename to src/EXTRA-MOLECULE/bond_nonlinear.cpp diff --git a/src/MOLECULE/bond_nonlinear.h b/src/EXTRA-MOLECULE/bond_nonlinear.h similarity index 100% rename from src/MOLECULE/bond_nonlinear.h rename to src/EXTRA-MOLECULE/bond_nonlinear.h diff --git a/src/MOLECULE/dihedral_cosine_shift_exp.cpp b/src/EXTRA-MOLECULE/dihedral_cosine_shift_exp.cpp similarity index 100% rename from src/MOLECULE/dihedral_cosine_shift_exp.cpp rename to src/EXTRA-MOLECULE/dihedral_cosine_shift_exp.cpp diff --git a/src/MOLECULE/dihedral_cosine_shift_exp.h b/src/EXTRA-MOLECULE/dihedral_cosine_shift_exp.h similarity index 100% rename from src/MOLECULE/dihedral_cosine_shift_exp.h rename to src/EXTRA-MOLECULE/dihedral_cosine_shift_exp.h diff --git a/src/MOLECULE/dihedral_fourier.cpp b/src/EXTRA-MOLECULE/dihedral_fourier.cpp similarity index 100% rename from src/MOLECULE/dihedral_fourier.cpp rename to src/EXTRA-MOLECULE/dihedral_fourier.cpp diff --git a/src/MOLECULE/dihedral_fourier.h b/src/EXTRA-MOLECULE/dihedral_fourier.h similarity index 100% rename from src/MOLECULE/dihedral_fourier.h rename to src/EXTRA-MOLECULE/dihedral_fourier.h diff --git a/src/MOLECULE/dihedral_helix.cpp b/src/EXTRA-MOLECULE/dihedral_helix.cpp similarity index 100% rename from src/MOLECULE/dihedral_helix.cpp rename to src/EXTRA-MOLECULE/dihedral_helix.cpp diff --git a/src/MOLECULE/dihedral_helix.h b/src/EXTRA-MOLECULE/dihedral_helix.h similarity index 100% rename from src/MOLECULE/dihedral_helix.h rename to src/EXTRA-MOLECULE/dihedral_helix.h diff --git a/src/MOLECULE/dihedral_nharmonic.cpp b/src/EXTRA-MOLECULE/dihedral_nharmonic.cpp similarity index 100% rename from src/MOLECULE/dihedral_nharmonic.cpp rename to src/EXTRA-MOLECULE/dihedral_nharmonic.cpp diff --git a/src/MOLECULE/dihedral_nharmonic.h b/src/EXTRA-MOLECULE/dihedral_nharmonic.h similarity index 100% rename from src/MOLECULE/dihedral_nharmonic.h rename to src/EXTRA-MOLECULE/dihedral_nharmonic.h diff --git a/src/MOLECULE/dihedral_quadratic.cpp b/src/EXTRA-MOLECULE/dihedral_quadratic.cpp similarity index 100% rename from src/MOLECULE/dihedral_quadratic.cpp rename to src/EXTRA-MOLECULE/dihedral_quadratic.cpp diff --git a/src/MOLECULE/dihedral_quadratic.h b/src/EXTRA-MOLECULE/dihedral_quadratic.h similarity index 100% rename from src/MOLECULE/dihedral_quadratic.h rename to src/EXTRA-MOLECULE/dihedral_quadratic.h diff --git a/src/MOLECULE/dihedral_spherical.cpp b/src/EXTRA-MOLECULE/dihedral_spherical.cpp similarity index 100% rename from src/MOLECULE/dihedral_spherical.cpp rename to src/EXTRA-MOLECULE/dihedral_spherical.cpp diff --git a/src/MOLECULE/dihedral_spherical.h b/src/EXTRA-MOLECULE/dihedral_spherical.h similarity index 100% rename from src/MOLECULE/dihedral_spherical.h rename to src/EXTRA-MOLECULE/dihedral_spherical.h diff --git a/src/MOLECULE/dihedral_table_cut.cpp b/src/EXTRA-MOLECULE/dihedral_table_cut.cpp similarity index 100% rename from src/MOLECULE/dihedral_table_cut.cpp rename to src/EXTRA-MOLECULE/dihedral_table_cut.cpp diff --git a/src/MOLECULE/dihedral_table_cut.h b/src/EXTRA-MOLECULE/dihedral_table_cut.h similarity index 100% rename from src/MOLECULE/dihedral_table_cut.h rename to src/EXTRA-MOLECULE/dihedral_table_cut.h diff --git a/src/MOLECULE/improper_cossq.cpp b/src/EXTRA-MOLECULE/improper_cossq.cpp similarity index 100% rename from src/MOLECULE/improper_cossq.cpp rename to src/EXTRA-MOLECULE/improper_cossq.cpp diff --git a/src/MOLECULE/improper_cossq.h b/src/EXTRA-MOLECULE/improper_cossq.h similarity index 100% rename from src/MOLECULE/improper_cossq.h rename to src/EXTRA-MOLECULE/improper_cossq.h diff --git a/src/MOLECULE/improper_distance.cpp b/src/EXTRA-MOLECULE/improper_distance.cpp similarity index 100% rename from src/MOLECULE/improper_distance.cpp rename to src/EXTRA-MOLECULE/improper_distance.cpp diff --git a/src/MOLECULE/improper_distance.h b/src/EXTRA-MOLECULE/improper_distance.h similarity index 100% rename from src/MOLECULE/improper_distance.h rename to src/EXTRA-MOLECULE/improper_distance.h diff --git a/src/MOLECULE/improper_fourier.cpp b/src/EXTRA-MOLECULE/improper_fourier.cpp similarity index 100% rename from src/MOLECULE/improper_fourier.cpp rename to src/EXTRA-MOLECULE/improper_fourier.cpp diff --git a/src/MOLECULE/improper_fourier.h b/src/EXTRA-MOLECULE/improper_fourier.h similarity index 100% rename from src/MOLECULE/improper_fourier.h rename to src/EXTRA-MOLECULE/improper_fourier.h diff --git a/src/MOLECULE/improper_ring.cpp b/src/EXTRA-MOLECULE/improper_ring.cpp similarity index 100% rename from src/MOLECULE/improper_ring.cpp rename to src/EXTRA-MOLECULE/improper_ring.cpp diff --git a/src/MOLECULE/improper_ring.h b/src/EXTRA-MOLECULE/improper_ring.h similarity index 100% rename from src/MOLECULE/improper_ring.h rename to src/EXTRA-MOLECULE/improper_ring.h diff --git a/src/pair_born_coul_dsf.cpp b/src/EXTRA-PAIR/pair_born_coul_dsf.cpp similarity index 100% rename from src/pair_born_coul_dsf.cpp rename to src/EXTRA-PAIR/pair_born_coul_dsf.cpp diff --git a/src/pair_born_coul_dsf.h b/src/EXTRA-PAIR/pair_born_coul_dsf.h similarity index 100% rename from src/pair_born_coul_dsf.h rename to src/EXTRA-PAIR/pair_born_coul_dsf.h diff --git a/src/pair_born_coul_wolf.cpp b/src/EXTRA-PAIR/pair_born_coul_wolf.cpp similarity index 100% rename from src/pair_born_coul_wolf.cpp rename to src/EXTRA-PAIR/pair_born_coul_wolf.cpp diff --git a/src/pair_born_coul_wolf.h b/src/EXTRA-PAIR/pair_born_coul_wolf.h similarity index 100% rename from src/pair_born_coul_wolf.h rename to src/EXTRA-PAIR/pair_born_coul_wolf.h diff --git a/src/USER-MISC/pair_buck_mdf.cpp b/src/EXTRA-PAIR/pair_buck_mdf.cpp similarity index 100% rename from src/USER-MISC/pair_buck_mdf.cpp rename to src/EXTRA-PAIR/pair_buck_mdf.cpp diff --git a/src/USER-MISC/pair_buck_mdf.h b/src/EXTRA-PAIR/pair_buck_mdf.h similarity index 100% rename from src/USER-MISC/pair_buck_mdf.h rename to src/EXTRA-PAIR/pair_buck_mdf.h diff --git a/src/USER-MISC/pair_cosine_squared.cpp b/src/EXTRA-PAIR/pair_cosine_squared.cpp similarity index 100% rename from src/USER-MISC/pair_cosine_squared.cpp rename to src/EXTRA-PAIR/pair_cosine_squared.cpp diff --git a/src/USER-MISC/pair_cosine_squared.h b/src/EXTRA-PAIR/pair_cosine_squared.h similarity index 100% rename from src/USER-MISC/pair_cosine_squared.h rename to src/EXTRA-PAIR/pair_cosine_squared.h diff --git a/src/pair_coul_cut_global.cpp b/src/EXTRA-PAIR/pair_coul_cut_global.cpp similarity index 100% rename from src/pair_coul_cut_global.cpp rename to src/EXTRA-PAIR/pair_coul_cut_global.cpp diff --git a/src/pair_coul_cut_global.h b/src/EXTRA-PAIR/pair_coul_cut_global.h similarity index 100% rename from src/pair_coul_cut_global.h rename to src/EXTRA-PAIR/pair_coul_cut_global.h diff --git a/src/USER-MISC/pair_coul_diel.cpp b/src/EXTRA-PAIR/pair_coul_diel.cpp similarity index 100% rename from src/USER-MISC/pair_coul_diel.cpp rename to src/EXTRA-PAIR/pair_coul_diel.cpp diff --git a/src/USER-MISC/pair_coul_diel.h b/src/EXTRA-PAIR/pair_coul_diel.h similarity index 100% rename from src/USER-MISC/pair_coul_diel.h rename to src/EXTRA-PAIR/pair_coul_diel.h diff --git a/src/USER-MISC/pair_coul_slater_cut.cpp b/src/EXTRA-PAIR/pair_coul_slater_cut.cpp similarity index 100% rename from src/USER-MISC/pair_coul_slater_cut.cpp rename to src/EXTRA-PAIR/pair_coul_slater_cut.cpp diff --git a/src/USER-MISC/pair_coul_slater_cut.h b/src/EXTRA-PAIR/pair_coul_slater_cut.h similarity index 100% rename from src/USER-MISC/pair_coul_slater_cut.h rename to src/EXTRA-PAIR/pair_coul_slater_cut.h diff --git a/src/USER-MISC/pair_coul_slater_long.cpp b/src/EXTRA-PAIR/pair_coul_slater_long.cpp similarity index 100% rename from src/USER-MISC/pair_coul_slater_long.cpp rename to src/EXTRA-PAIR/pair_coul_slater_long.cpp diff --git a/src/USER-MISC/pair_coul_slater_long.h b/src/EXTRA-PAIR/pair_coul_slater_long.h similarity index 100% rename from src/USER-MISC/pair_coul_slater_long.h rename to src/EXTRA-PAIR/pair_coul_slater_long.h diff --git a/src/pair_coul_streitz.cpp b/src/EXTRA-PAIR/pair_coul_streitz.cpp similarity index 100% rename from src/pair_coul_streitz.cpp rename to src/EXTRA-PAIR/pair_coul_streitz.cpp diff --git a/src/pair_coul_streitz.h b/src/EXTRA-PAIR/pair_coul_streitz.h similarity index 100% rename from src/pair_coul_streitz.h rename to src/EXTRA-PAIR/pair_coul_streitz.h diff --git a/src/USER-MISC/pair_e3b.cpp b/src/EXTRA-PAIR/pair_e3b.cpp similarity index 100% rename from src/USER-MISC/pair_e3b.cpp rename to src/EXTRA-PAIR/pair_e3b.cpp diff --git a/src/USER-MISC/pair_e3b.h b/src/EXTRA-PAIR/pair_e3b.h similarity index 100% rename from src/USER-MISC/pair_e3b.h rename to src/EXTRA-PAIR/pair_e3b.h diff --git a/src/pair_gauss.cpp b/src/EXTRA-PAIR/pair_gauss.cpp similarity index 100% rename from src/pair_gauss.cpp rename to src/EXTRA-PAIR/pair_gauss.cpp diff --git a/src/pair_gauss.h b/src/EXTRA-PAIR/pair_gauss.h similarity index 100% rename from src/pair_gauss.h rename to src/EXTRA-PAIR/pair_gauss.h diff --git a/src/USER-MISC/pair_gauss_cut.cpp b/src/EXTRA-PAIR/pair_gauss_cut.cpp similarity index 100% rename from src/USER-MISC/pair_gauss_cut.cpp rename to src/EXTRA-PAIR/pair_gauss_cut.cpp diff --git a/src/USER-MISC/pair_gauss_cut.h b/src/EXTRA-PAIR/pair_gauss_cut.h similarity index 100% rename from src/USER-MISC/pair_gauss_cut.h rename to src/EXTRA-PAIR/pair_gauss_cut.h diff --git a/src/USER-MISC/pair_lennard_mdf.cpp b/src/EXTRA-PAIR/pair_lennard_mdf.cpp similarity index 100% rename from src/USER-MISC/pair_lennard_mdf.cpp rename to src/EXTRA-PAIR/pair_lennard_mdf.cpp diff --git a/src/USER-MISC/pair_lennard_mdf.h b/src/EXTRA-PAIR/pair_lennard_mdf.h similarity index 100% rename from src/USER-MISC/pair_lennard_mdf.h rename to src/EXTRA-PAIR/pair_lennard_mdf.h diff --git a/src/pair_lj96_cut.cpp b/src/EXTRA-PAIR/pair_lj96_cut.cpp similarity index 100% rename from src/pair_lj96_cut.cpp rename to src/EXTRA-PAIR/pair_lj96_cut.cpp diff --git a/src/pair_lj96_cut.h b/src/EXTRA-PAIR/pair_lj96_cut.h similarity index 100% rename from src/pair_lj96_cut.h rename to src/EXTRA-PAIR/pair_lj96_cut.h diff --git a/src/pair_lj_cubic.cpp b/src/EXTRA-PAIR/pair_lj_cubic.cpp similarity index 100% rename from src/pair_lj_cubic.cpp rename to src/EXTRA-PAIR/pair_lj_cubic.cpp diff --git a/src/pair_lj_cubic.h b/src/EXTRA-PAIR/pair_lj_cubic.h similarity index 100% rename from src/pair_lj_cubic.h rename to src/EXTRA-PAIR/pair_lj_cubic.h diff --git a/src/pair_lj_cubic_const.h b/src/EXTRA-PAIR/pair_lj_cubic_const.h similarity index 100% rename from src/pair_lj_cubic_const.h rename to src/EXTRA-PAIR/pair_lj_cubic_const.h diff --git a/src/pair_lj_cut_coul_debye.cpp b/src/EXTRA-PAIR/pair_lj_cut_coul_debye.cpp similarity index 100% rename from src/pair_lj_cut_coul_debye.cpp rename to src/EXTRA-PAIR/pair_lj_cut_coul_debye.cpp diff --git a/src/pair_lj_cut_coul_debye.h b/src/EXTRA-PAIR/pair_lj_cut_coul_debye.h similarity index 100% rename from src/pair_lj_cut_coul_debye.h rename to src/EXTRA-PAIR/pair_lj_cut_coul_debye.h diff --git a/src/pair_lj_cut_coul_dsf.cpp b/src/EXTRA-PAIR/pair_lj_cut_coul_dsf.cpp similarity index 100% rename from src/pair_lj_cut_coul_dsf.cpp rename to src/EXTRA-PAIR/pair_lj_cut_coul_dsf.cpp diff --git a/src/pair_lj_cut_coul_dsf.h b/src/EXTRA-PAIR/pair_lj_cut_coul_dsf.h similarity index 100% rename from src/pair_lj_cut_coul_dsf.h rename to src/EXTRA-PAIR/pair_lj_cut_coul_dsf.h diff --git a/src/pair_lj_cut_coul_wolf.cpp b/src/EXTRA-PAIR/pair_lj_cut_coul_wolf.cpp similarity index 100% rename from src/pair_lj_cut_coul_wolf.cpp rename to src/EXTRA-PAIR/pair_lj_cut_coul_wolf.cpp diff --git a/src/pair_lj_cut_coul_wolf.h b/src/EXTRA-PAIR/pair_lj_cut_coul_wolf.h similarity index 100% rename from src/pair_lj_cut_coul_wolf.h rename to src/EXTRA-PAIR/pair_lj_cut_coul_wolf.h diff --git a/src/USER-MISC/pair_lj_expand_coul_long.cpp b/src/EXTRA-PAIR/pair_lj_expand_coul_long.cpp similarity index 100% rename from src/USER-MISC/pair_lj_expand_coul_long.cpp rename to src/EXTRA-PAIR/pair_lj_expand_coul_long.cpp diff --git a/src/USER-MISC/pair_lj_expand_coul_long.h b/src/EXTRA-PAIR/pair_lj_expand_coul_long.h similarity index 100% rename from src/USER-MISC/pair_lj_expand_coul_long.h rename to src/EXTRA-PAIR/pair_lj_expand_coul_long.h diff --git a/src/pair_lj_gromacs.cpp b/src/EXTRA-PAIR/pair_lj_gromacs.cpp similarity index 100% rename from src/pair_lj_gromacs.cpp rename to src/EXTRA-PAIR/pair_lj_gromacs.cpp diff --git a/src/pair_lj_gromacs.h b/src/EXTRA-PAIR/pair_lj_gromacs.h similarity index 100% rename from src/pair_lj_gromacs.h rename to src/EXTRA-PAIR/pair_lj_gromacs.h diff --git a/src/pair_lj_gromacs_coul_gromacs.cpp b/src/EXTRA-PAIR/pair_lj_gromacs_coul_gromacs.cpp similarity index 100% rename from src/pair_lj_gromacs_coul_gromacs.cpp rename to src/EXTRA-PAIR/pair_lj_gromacs_coul_gromacs.cpp diff --git a/src/pair_lj_gromacs_coul_gromacs.h b/src/EXTRA-PAIR/pair_lj_gromacs_coul_gromacs.h similarity index 100% rename from src/pair_lj_gromacs_coul_gromacs.h rename to src/EXTRA-PAIR/pair_lj_gromacs_coul_gromacs.h diff --git a/src/USER-MISC/pair_lj_mdf.cpp b/src/EXTRA-PAIR/pair_lj_mdf.cpp similarity index 100% rename from src/USER-MISC/pair_lj_mdf.cpp rename to src/EXTRA-PAIR/pair_lj_mdf.cpp diff --git a/src/USER-MISC/pair_lj_mdf.h b/src/EXTRA-PAIR/pair_lj_mdf.h similarity index 100% rename from src/USER-MISC/pair_lj_mdf.h rename to src/EXTRA-PAIR/pair_lj_mdf.h diff --git a/src/pair_lj_relres.cpp b/src/EXTRA-PAIR/pair_lj_relres.cpp similarity index 100% rename from src/pair_lj_relres.cpp rename to src/EXTRA-PAIR/pair_lj_relres.cpp diff --git a/src/pair_lj_relres.h b/src/EXTRA-PAIR/pair_lj_relres.h similarity index 100% rename from src/pair_lj_relres.h rename to src/EXTRA-PAIR/pair_lj_relres.h diff --git a/src/pair_lj_smooth.cpp b/src/EXTRA-PAIR/pair_lj_smooth.cpp similarity index 100% rename from src/pair_lj_smooth.cpp rename to src/EXTRA-PAIR/pair_lj_smooth.cpp diff --git a/src/pair_lj_smooth.h b/src/EXTRA-PAIR/pair_lj_smooth.h similarity index 100% rename from src/pair_lj_smooth.h rename to src/EXTRA-PAIR/pair_lj_smooth.h diff --git a/src/pair_lj_smooth_linear.cpp b/src/EXTRA-PAIR/pair_lj_smooth_linear.cpp similarity index 100% rename from src/pair_lj_smooth_linear.cpp rename to src/EXTRA-PAIR/pair_lj_smooth_linear.cpp diff --git a/src/pair_lj_smooth_linear.h b/src/EXTRA-PAIR/pair_lj_smooth_linear.h similarity index 100% rename from src/pair_lj_smooth_linear.h rename to src/EXTRA-PAIR/pair_lj_smooth_linear.h diff --git a/src/pair_mie_cut.cpp b/src/EXTRA-PAIR/pair_mie_cut.cpp similarity index 100% rename from src/pair_mie_cut.cpp rename to src/EXTRA-PAIR/pair_mie_cut.cpp diff --git a/src/pair_mie_cut.h b/src/EXTRA-PAIR/pair_mie_cut.h similarity index 100% rename from src/pair_mie_cut.h rename to src/EXTRA-PAIR/pair_mie_cut.h diff --git a/src/USER-MISC/pair_momb.cpp b/src/EXTRA-PAIR/pair_momb.cpp similarity index 100% rename from src/USER-MISC/pair_momb.cpp rename to src/EXTRA-PAIR/pair_momb.cpp diff --git a/src/USER-MISC/pair_momb.h b/src/EXTRA-PAIR/pair_momb.h similarity index 100% rename from src/USER-MISC/pair_momb.h rename to src/EXTRA-PAIR/pair_momb.h diff --git a/src/USER-MISC/pair_morse_smooth_linear.cpp b/src/EXTRA-PAIR/pair_morse_smooth_linear.cpp similarity index 100% rename from src/USER-MISC/pair_morse_smooth_linear.cpp rename to src/EXTRA-PAIR/pair_morse_smooth_linear.cpp diff --git a/src/USER-MISC/pair_morse_smooth_linear.h b/src/EXTRA-PAIR/pair_morse_smooth_linear.h similarity index 100% rename from src/USER-MISC/pair_morse_smooth_linear.h rename to src/EXTRA-PAIR/pair_morse_smooth_linear.h diff --git a/src/MISC/pair_nm_cut.cpp b/src/EXTRA-PAIR/pair_nm_cut.cpp similarity index 100% rename from src/MISC/pair_nm_cut.cpp rename to src/EXTRA-PAIR/pair_nm_cut.cpp diff --git a/src/MISC/pair_nm_cut.h b/src/EXTRA-PAIR/pair_nm_cut.h similarity index 100% rename from src/MISC/pair_nm_cut.h rename to src/EXTRA-PAIR/pair_nm_cut.h diff --git a/src/MISC/pair_nm_cut_coul_cut.cpp b/src/EXTRA-PAIR/pair_nm_cut_coul_cut.cpp similarity index 100% rename from src/MISC/pair_nm_cut_coul_cut.cpp rename to src/EXTRA-PAIR/pair_nm_cut_coul_cut.cpp diff --git a/src/MISC/pair_nm_cut_coul_cut.h b/src/EXTRA-PAIR/pair_nm_cut_coul_cut.h similarity index 100% rename from src/MISC/pair_nm_cut_coul_cut.h rename to src/EXTRA-PAIR/pair_nm_cut_coul_cut.h diff --git a/src/MISC/pair_nm_cut_coul_long.cpp b/src/EXTRA-PAIR/pair_nm_cut_coul_long.cpp similarity index 100% rename from src/MISC/pair_nm_cut_coul_long.cpp rename to src/EXTRA-PAIR/pair_nm_cut_coul_long.cpp diff --git a/src/MISC/pair_nm_cut_coul_long.h b/src/EXTRA-PAIR/pair_nm_cut_coul_long.h similarity index 100% rename from src/MISC/pair_nm_cut_coul_long.h rename to src/EXTRA-PAIR/pair_nm_cut_coul_long.h diff --git a/src/pair_ufm.cpp b/src/EXTRA-PAIR/pair_ufm.cpp similarity index 100% rename from src/pair_ufm.cpp rename to src/EXTRA-PAIR/pair_ufm.cpp diff --git a/src/pair_ufm.h b/src/EXTRA-PAIR/pair_ufm.h similarity index 100% rename from src/pair_ufm.h rename to src/EXTRA-PAIR/pair_ufm.h diff --git a/src/USER-MISC/pair_wf_cut.cpp b/src/EXTRA-PAIR/pair_wf_cut.cpp similarity index 100% rename from src/USER-MISC/pair_wf_cut.cpp rename to src/EXTRA-PAIR/pair_wf_cut.cpp diff --git a/src/USER-MISC/pair_wf_cut.h b/src/EXTRA-PAIR/pair_wf_cut.h similarity index 100% rename from src/USER-MISC/pair_wf_cut.h rename to src/EXTRA-PAIR/pair_wf_cut.h diff --git a/src/compute_contact_atom.cpp b/src/GRANULAR/compute_contact_atom.cpp similarity index 100% rename from src/compute_contact_atom.cpp rename to src/GRANULAR/compute_contact_atom.cpp diff --git a/src/compute_contact_atom.h b/src/GRANULAR/compute_contact_atom.h similarity index 100% rename from src/compute_contact_atom.h rename to src/GRANULAR/compute_contact_atom.h diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh index a28b17270a..073f094836 100755 --- a/src/KOKKOS/Install.sh +++ b/src/KOKKOS/Install.sh @@ -137,12 +137,12 @@ action fix_nvt_kokkos.cpp action fix_nvt_kokkos.h action fix_property_atom_kokkos.cpp action fix_property_atom_kokkos.h -action fix_qeq_reax_kokkos.cpp fix_qeq_reax.cpp -action fix_qeq_reax_kokkos.h fix_qeq_reax.h -action fix_reaxc_bonds_kokkos.cpp fix_reaxc_bonds.cpp -action fix_reaxc_bonds_kokkos.h fix_reaxc_bonds.h -action fix_reaxc_species_kokkos.cpp fix_reaxc_species.cpp -action fix_reaxc_species_kokkos.h fix_reaxc_species.h +action fix_qeq_reaxff_kokkos.cpp fix_qeq_reaxff.cpp +action fix_qeq_reaxff_kokkos.h fix_qeq_reaxff.h +action fix_reaxff_bonds_kokkos.cpp fix_reaxff_bonds.cpp +action fix_reaxff_bonds_kokkos.h fix_reaxff_bonds.h +action fix_reaxff_species_kokkos.cpp fix_reaxff_species.cpp +action fix_reaxff_species_kokkos.h fix_reaxff_species.h action fix_setforce_kokkos.cpp action fix_setforce_kokkos.h action fix_shake_kokkos.cpp fix_shake.cpp @@ -271,8 +271,8 @@ action pair_morse_kokkos.cpp action pair_morse_kokkos.h action pair_multi_lucy_rx_kokkos.cpp pair_multi_lucy_rx.cpp action pair_multi_lucy_rx_kokkos.h pair_multi_lucy_rx.h -action pair_reaxc_kokkos.cpp pair_reaxc.cpp -action pair_reaxc_kokkos.h pair_reaxc.h +action pair_reaxff_kokkos.cpp pair_reaxff.cpp +action pair_reaxff_kokkos.h pair_reaxff.h action pair_snap_kokkos.cpp pair_snap.cpp action pair_snap_kokkos.h pair_snap.h action pair_snap_kokkos_impl.h pair_snap.cpp diff --git a/src/USER-MISC/pair_edip.cpp b/src/MANYBODY/pair_edip.cpp similarity index 100% rename from src/USER-MISC/pair_edip.cpp rename to src/MANYBODY/pair_edip.cpp diff --git a/src/USER-MISC/pair_edip.h b/src/MANYBODY/pair_edip.h similarity index 100% rename from src/USER-MISC/pair_edip.h rename to src/MANYBODY/pair_edip.h diff --git a/src/USER-MISC/pair_edip_multi.cpp b/src/MANYBODY/pair_edip_multi.cpp similarity index 100% rename from src/USER-MISC/pair_edip_multi.cpp rename to src/MANYBODY/pair_edip_multi.cpp diff --git a/src/USER-MISC/pair_edip_multi.h b/src/MANYBODY/pair_edip_multi.h similarity index 100% rename from src/USER-MISC/pair_edip_multi.h rename to src/MANYBODY/pair_edip_multi.h diff --git a/src/USER-MISC/pair_extep.cpp b/src/MANYBODY/pair_extep.cpp similarity index 100% rename from src/USER-MISC/pair_extep.cpp rename to src/MANYBODY/pair_extep.cpp diff --git a/src/USER-MISC/pair_extep.h b/src/MANYBODY/pair_extep.h similarity index 100% rename from src/USER-MISC/pair_extep.h rename to src/MANYBODY/pair_extep.h diff --git a/src/USER-MISC/pair_local_density.cpp b/src/MANYBODY/pair_local_density.cpp similarity index 100% rename from src/USER-MISC/pair_local_density.cpp rename to src/MANYBODY/pair_local_density.cpp diff --git a/src/USER-MISC/pair_local_density.h b/src/MANYBODY/pair_local_density.h similarity index 100% rename from src/USER-MISC/pair_local_density.h rename to src/MANYBODY/pair_local_density.h diff --git a/src/USER-MISC/pair_meam_spline.cpp b/src/MANYBODY/pair_meam_spline.cpp similarity index 100% rename from src/USER-MISC/pair_meam_spline.cpp rename to src/MANYBODY/pair_meam_spline.cpp diff --git a/src/USER-MISC/pair_meam_spline.h b/src/MANYBODY/pair_meam_spline.h similarity index 100% rename from src/USER-MISC/pair_meam_spline.h rename to src/MANYBODY/pair_meam_spline.h diff --git a/src/USER-MISC/pair_meam_sw_spline.cpp b/src/MANYBODY/pair_meam_sw_spline.cpp similarity index 100% rename from src/USER-MISC/pair_meam_sw_spline.cpp rename to src/MANYBODY/pair_meam_sw_spline.cpp diff --git a/src/USER-MISC/pair_meam_sw_spline.h b/src/MANYBODY/pair_meam_sw_spline.h similarity index 100% rename from src/USER-MISC/pair_meam_sw_spline.h rename to src/MANYBODY/pair_meam_sw_spline.h diff --git a/src/USER-MISC/pair_tersoff_table.cpp b/src/MANYBODY/pair_tersoff_table.cpp similarity index 100% rename from src/USER-MISC/pair_tersoff_table.cpp rename to src/MANYBODY/pair_tersoff_table.cpp diff --git a/src/USER-MISC/pair_tersoff_table.h b/src/MANYBODY/pair_tersoff_table.h similarity index 100% rename from src/USER-MISC/pair_tersoff_table.h rename to src/MANYBODY/pair_tersoff_table.h diff --git a/src/USER-MISC/compute_viscosity_cos.cpp b/src/MISC/compute_viscosity_cos.cpp similarity index 100% rename from src/USER-MISC/compute_viscosity_cos.cpp rename to src/MISC/compute_viscosity_cos.cpp diff --git a/src/USER-MISC/compute_viscosity_cos.h b/src/MISC/compute_viscosity_cos.h similarity index 100% rename from src/USER-MISC/compute_viscosity_cos.h rename to src/MISC/compute_viscosity_cos.h diff --git a/src/USER-MISC/fix_accelerate_cos.cpp b/src/MISC/fix_accelerate_cos.cpp similarity index 100% rename from src/USER-MISC/fix_accelerate_cos.cpp rename to src/MISC/fix_accelerate_cos.cpp diff --git a/src/USER-MISC/fix_accelerate_cos.h b/src/MISC/fix_accelerate_cos.h similarity index 100% rename from src/USER-MISC/fix_accelerate_cos.h rename to src/MISC/fix_accelerate_cos.h diff --git a/src/USER-MISC/fix_ipi.cpp b/src/MISC/fix_ipi.cpp similarity index 100% rename from src/USER-MISC/fix_ipi.cpp rename to src/MISC/fix_ipi.cpp diff --git a/src/USER-MISC/fix_ipi.h b/src/MISC/fix_ipi.h similarity index 100% rename from src/USER-MISC/fix_ipi.h rename to src/MISC/fix_ipi.h diff --git a/src/USER-MISC/fix_srp.cpp b/src/MISC/fix_srp.cpp similarity index 100% rename from src/USER-MISC/fix_srp.cpp rename to src/MISC/fix_srp.cpp diff --git a/src/USER-MISC/fix_srp.h b/src/MISC/fix_srp.h similarity index 100% rename from src/USER-MISC/fix_srp.h rename to src/MISC/fix_srp.h diff --git a/src/USER-MISC/pair_agni.cpp b/src/MISC/pair_agni.cpp similarity index 100% rename from src/USER-MISC/pair_agni.cpp rename to src/MISC/pair_agni.cpp diff --git a/src/USER-MISC/pair_agni.h b/src/MISC/pair_agni.h similarity index 100% rename from src/USER-MISC/pair_agni.h rename to src/MISC/pair_agni.h diff --git a/src/Makefile b/src/Makefile index 5e26de47ce..f7ec0a06f4 100644 --- a/src/Makefile +++ b/src/Makefile @@ -55,7 +55,7 @@ PACKAGE = \ body \ brownian \ cg-dna \ - cg-sdk\ + cg-sdk \ class2 \ colloid \ colvars \ @@ -69,6 +69,11 @@ PACKAGE = \ dpd-smooth \ drude \ eff \ + extra-compute \ + extra-dump \ + extra-fix \ + extra-molecule \ + extra-pair \ fep \ gpu \ granular \ @@ -103,6 +108,7 @@ PACKAGE = \ netcdf \ openmp \ opt \ + orient \ peri \ plugin \ plumed \ @@ -124,7 +130,6 @@ PACKAGE = \ srd \ tally \ uef \ - user-misc \ voronoi \ vtk \ yaff \ @@ -156,6 +161,11 @@ PACKMOST = \ dpd-smooth \ drude \ eff \ + extra-compute \ + extra-dump \ + extra-fix \ + extra-molecule \ + extra-pair \ fep \ granular \ interlayer \ @@ -169,6 +179,7 @@ PACKMOST = \ molecule \ openmp \ opt \ + orient \ peri \ plugin \ poems \ @@ -182,7 +193,6 @@ PACKMOST = \ spin \ srd \ uef \ - user-misc \ yaff \ dielectric \ ml-iap \ diff --git a/src/MISC/fix_orient_bcc.cpp b/src/ORIENT/fix_orient_bcc.cpp similarity index 100% rename from src/MISC/fix_orient_bcc.cpp rename to src/ORIENT/fix_orient_bcc.cpp diff --git a/src/MISC/fix_orient_bcc.h b/src/ORIENT/fix_orient_bcc.h similarity index 100% rename from src/MISC/fix_orient_bcc.h rename to src/ORIENT/fix_orient_bcc.h diff --git a/src/USER-MISC/fix_orient_eco.cpp b/src/ORIENT/fix_orient_eco.cpp similarity index 100% rename from src/USER-MISC/fix_orient_eco.cpp rename to src/ORIENT/fix_orient_eco.cpp diff --git a/src/USER-MISC/fix_orient_eco.h b/src/ORIENT/fix_orient_eco.h similarity index 100% rename from src/USER-MISC/fix_orient_eco.h rename to src/ORIENT/fix_orient_eco.h diff --git a/src/MISC/fix_orient_fcc.cpp b/src/ORIENT/fix_orient_fcc.cpp similarity index 100% rename from src/MISC/fix_orient_fcc.cpp rename to src/ORIENT/fix_orient_fcc.cpp diff --git a/src/MISC/fix_orient_fcc.h b/src/ORIENT/fix_orient_fcc.h similarity index 100% rename from src/MISC/fix_orient_fcc.h rename to src/ORIENT/fix_orient_fcc.h diff --git a/src/Purge.list b/src/Purge.list index 40bdc50d0d..feb30a9ad7 100644 --- a/src/Purge.list +++ b/src/Purge.list @@ -97,11 +97,6 @@ reaxc_reset_tools.cpp reaxc_tool_box.cpp reaxc_torsion_angles.cpp reaxc_valence_angles.cpp -# moved to DPD-BASIC package on 1 July 2021 -pair_dpd.cpp -pair_dpd.h -pair_dpd_tstat.cpp -pair_dpd_tstat.h # removed on 14 May 2021 nstencil_half_bin_2d_newton_ssa.cpp nstencil_half_bin_2d_newton_ssa.h @@ -170,8 +165,6 @@ pair_reax.h pair_reax_fortran.h fix_reax_bonds.cpp fix_reax_bonds.h -pair_meam.cpp -pair_meam.h # removed on 27 September 2018 pair_nb3b_harmonic_omp.h pair_nb3b_harmonic_omp.cpp diff --git a/src/USER-MISC/README b/src/USER-MISC/README deleted file mode 100644 index a5416c6804..0000000000 --- a/src/USER-MISC/README +++ /dev/null @@ -1,73 +0,0 @@ -The files in this package are a potpourri of (mostly) unrelated -features contributed to LAMMPS by users. Each feature is a single -pair of files (*.cpp and *.h). - -More information about each feature can be found by reading its doc -page in the LAMMPS doc directory. The doc page which lists all LAMMPS -input script commands is as follows: - -doc/Commands_all.html - -User-contributed features are listed at the bottom of the fix, -compute, pair, etc sections. - -The list of features and author of each is given below. - -You should contact the author directly if you have specific questions -about the feature or its coding. - ------------------------------------------------------------- - -compute ackland/atom, Gerolf Ziegenhain, gerolf at ziegenhain.com, 4 Oct 2007 -compute basal/atom, Christopher Barrett, cdb333 at cavs.msstate.edu, 3 Mar 2013 -compute cnp/atom, Paulo Branicio (USC), branicio at usc.edu, 31 May 2017 -compute entropy/atom, Pablo Piaggi (EPFL), pablo.piaggi at epfl.ch, 15 June 2018 -compute gyration/shape, Evangelos Voyiatzis, evoyiatzis at gmail.com, 25 July 2019 -compute gyration/shape/chunk, Evangelos Voyiatzis, evoyiatzis at gmail.com, 22 October 2019 -compute hma, Andrew Schultz & David Kofke (UB), ajs42 at buffalo.edu & kofke at buffalo.edu, 1 Jul 2019 -compute pressure/cylinder, Cody K. Addington (NCSU), , 2 Oct 2018 -compute momentum, Rupert Nash (University of Edinburgh), r.nash at epcc.ed.ac.uk, 28 June 2019 -compute stress/mop, Romain Vermorel (U Pau) & Laurent Joly (U Lyon), romain.vermorel at univ-pau.fr & ljoly.ulyon at gmail.com, 5 Sep 18 -compute stress/mop/profile, Romain Vermorel (U Pau) & Laurent Joly (U Lyon), romain.vermorel at univ-pau.fr & ljoly.ulyon at gmail.com, 5 Sep 18 -compute temp/rotate, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11 -compute viscosity/cos, Zheng Gong (ENS de Lyon), z.gong@outlook.com, 24 Apr 20 -fix accelerate/cos, Zheng Gong (ENS de Lyon), z.gong@outlook.com, 24 Apr 20 -fix ave/correlate/long, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 21 Oct 2015 -fix electron/stopping/fit, James Stewart (SNL), jstewa .at. sandia.gov, 23 Sep 2020 -fix electron/stopping, Konstantin Avchaciov, k.avchachov at gmail.com, 26 Feb 2019 -fix ffl, David Wilkins (EPFL Lausanne), david.wilkins @ epfl.ch, 28 Sep 2018 -fix filter/corotate, Lukas Fath (KIT), lukas.fath at kit.edu, 15 Mar 2017 -fix flow/gauss, Joel Eaves (CU Boulder), Joel.Eaves@Colorado.edu, 23 Aug 2016 -fix ipi, Michele Ceriotti (EPFL Lausanne), michele.ceriotti at gmail.com, 24 Nov 2014 -fix momentum/chunk, Jiang Xiao (Hong Kong Polytechnic University), polyu-xiao.jiang at connect.polyu.hk, 19 Aug 2020 -fix npt/cauchy, R. E. Miller (Carleton University), F. Pavia and S. Pattamatta, 12 Jan 2020 -fix nvk, Efrem Braun (UC Berkeley), efrem.braun at gmail.com, https://github.com/lammps/lammps/pull/310 -fix orient/eco Adrian A. Schratt and Volker Mohles (Ruhr-Uni Bochum), volker.mohles at rub.de, 6 Jun 2020 -fix pafi, Thomas Swinburne (CNRS), swinburne at cinam.univ-mrs.fr, 1st Sep 2020 -fix pimd, Yuxing Peng (U Chicago), yuxing at uchicago.edu, 24 Nov 2014 -fix rhok, Ulf Pedersen (Roskilde U), ulf at urp.dk, 25 Sep 2017 -fix ti/spring, Rodrigo Freitas (Unicamp/Brazil), rodrigohb at gmail.com, 7 Nov 2013 -fix ttm/mod, Sergey Starikov and Vasily Pisarev (JIHT), pisarevvv at gmail.com, 2 Feb 2015 -fix wall/ees, Abdoreza Ershadinia, a.ershadinia at gmail.com, Jul 2017 -fix wall/reflect/stochastic, Quy-Dong To (U Gustave Eiffel), toquydong at gmail.com, Jan 2020 -fix wall/region/ees, Abdoreza Ershadinia, a.ershadinia at gmail.com, Jul 2017 -pair_style agni, Axel Kohlmeyer, akohlmey at gmail.com, 9 Nov 16 -pair_style buck/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 -pair_style cosine/squared, Eugen Rozic, eugen.rozic.17 at ucl.ac.uk, 9 Aug 19 -pair_style coul/diel, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11 -pair_style coul/slater/cut, Evangelos Voyiatzis, evoyiatzis at gmail.com, 26 February 2020 -pair_style coul/slater/long, Evangelos Voyiatzis, evoyiatzis at gmail.com, 26 February 2020 -pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11 -pair_style e3b, Steven Strong (U Chicago), stevene.strong at gmail dot com, 16 Apr 19 -pair_style edip, Luca Ferraro, luca.ferraro at caspur.it, 15 Sep 11 -pair_style extep, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Nov 17 -pair_style gauss/cut, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11 -pair_style lennard/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 -pair_style lj/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 -pair_style local/density, Tanmoy Sanyal (tanmoy dot 7989 at gmail.com) and M. Scott Shell (UCSB), and David Rosenberger (TU Darmstadt), 9 Sept 19 -pair_style meam/spline, Alexander Stukowski (LLNL), alex at stukowski.com, 1 Feb 12 -pair_style meam/sw/spline, Robert Rudd (LLNL), robert.rudd at llnl.gov, 1 Oct 12 -pair_style morse/smooth/linear, Stefan Paquay (TU Eindhoven), stefanpaquay at gmail.com, 29 Feb 16 -pair_style tersoff/table, Luca Ferraro, luca.ferraro@caspur.it, 1 Dec 11 -pair_style momb, Kristen Fichthorn, Tonnam Balankura, Ya Zhou, fichthorn@psu.edu, 18 Mar 17 -pair_style wf_cut, Simon Ramirez-Hinestrosa, Xipeng Wang, sr802 at cam.ac.uk, 4 Nov 20 diff --git a/src/MISC/fix_deposit.cpp b/src/fix_deposit.cpp similarity index 100% rename from src/MISC/fix_deposit.cpp rename to src/fix_deposit.cpp diff --git a/src/MISC/fix_deposit.h b/src/fix_deposit.h similarity index 100% rename from src/MISC/fix_deposit.h rename to src/fix_deposit.h diff --git a/src/MISC/fix_efield.cpp b/src/fix_efield.cpp similarity index 100% rename from src/MISC/fix_efield.cpp rename to src/fix_efield.cpp diff --git a/src/MISC/fix_efield.h b/src/fix_efield.h similarity index 100% rename from src/MISC/fix_efield.h rename to src/fix_efield.h diff --git a/src/MISC/fix_evaporate.cpp b/src/fix_evaporate.cpp similarity index 100% rename from src/MISC/fix_evaporate.cpp rename to src/fix_evaporate.cpp diff --git a/src/MISC/fix_evaporate.h b/src/fix_evaporate.h similarity index 100% rename from src/MISC/fix_evaporate.h rename to src/fix_evaporate.h diff --git a/src/MISC/fix_thermal_conductivity.cpp b/src/fix_thermal_conductivity.cpp similarity index 100% rename from src/MISC/fix_thermal_conductivity.cpp rename to src/fix_thermal_conductivity.cpp diff --git a/src/MISC/fix_thermal_conductivity.h b/src/fix_thermal_conductivity.h similarity index 100% rename from src/MISC/fix_thermal_conductivity.h rename to src/fix_thermal_conductivity.h