[lammps] 02/06: Merge tag 'upstream/0_20161109.git9806da6'
Anton Gladky
gladk at moszumanska.debian.org
Sat Nov 12 07:01:19 UTC 2016
This is an automated email from the git hooks/post-receive script.
gladk pushed a commit to branch master
in repository lammps.
commit 2c045a166b17da6a3469bce9c3a98c51157493bf
Merge: 7c868a1 7328d32
Author: Anton Gladky <gladk at debian.org>
Date: Sat Nov 12 07:35:35 2016 +0100
Merge tag 'upstream/0_20161109.git9806da6'
Upstream version 0~20161109.git9806da6
bench/POTENTIALS/ffield.comb | 196 +-
bench/log.15May15.chain.fixed.icc.1 | 67 -
bench/log.15May15.chain.fixed.icc.4 | 67 -
bench/log.15May15.chain.scaled.icc.4 | 83 -
bench/log.15May15.chute.fixed.icc.1 | 69 -
bench/log.15May15.chute.fixed.icc.4 | 69 -
bench/log.15May15.chute.scaled.icc.4 | 79 -
bench/log.15May15.eam.fixed.icc.1 | 71 -
bench/log.15May15.eam.fixed.icc.4 | 71 -
bench/log.15May15.eam.scaled.icc.4 | 71 -
bench/log.15May15.lj.fixed.icc.1 | 68 -
bench/log.15May15.lj.fixed.icc.4 | 68 -
bench/log.15May15.lj.scaled.icc.4 | 68 -
bench/log.15May15.rhodo.fixed.icc.1 | 110 -
bench/log.15May15.rhodo.fixed.icc.4 | 110 -
bench/log.15May15.rhodo.scaled.icc.4 | 131 -
bench/log.6Oct16.chain.fixed.icc.1 | 78 +
bench/log.6Oct16.chain.fixed.icc.4 | 78 +
bench/log.6Oct16.chain.scaled.icc.4 | 94 +
bench/log.6Oct16.chute.fixed.icc.1 | 80 +
bench/log.6Oct16.chute.fixed.icc.4 | 80 +
bench/log.6Oct16.chute.scaled.icc.4 | 90 +
bench/log.6Oct16.eam.fixed.icc.1 | 83 +
bench/log.6Oct16.eam.fixed.icc.4 | 83 +
bench/log.6Oct16.eam.scaled.icc.4 | 83 +
bench/log.6Oct16.lj.fixed.icc.1 | 79 +
bench/log.6Oct16.lj.fixed.icc.4 | 79 +
bench/log.6Oct16.lj.scaled.icc.4 | 79 +
bench/log.6Oct16.rhodo.fixed.icc.1 | 122 +
bench/log.6Oct16.rhodo.fixed.icc.4 | 122 +
bench/log.6Oct16.rhodo.scaled.icc.4 | 143 +
doc/Developer.pdf | Bin 85778 -> 0 bytes
doc/Eqs/cna_cutoff1.tex | 14 -
doc/Eqs/cna_cutoff2.tex | 12 -
doc/Eqs/dihedral_sign.jpg | Bin 19297 -> 0 bytes
doc/Eqs/eff_ECP1.tex | 9 -
doc/Eqs/eff_ECP2.tex | 8 -
doc/Eqs/fix_nh1.jpg | Bin 31088 -> 0 bytes
doc/Eqs/fix_nh1.tex | 35 -
doc/Eqs/fix_ti_rs_force.jpg | Bin 1777 -> 0 bytes
doc/Eqs/fix_ti_rs_force.tex | 11 -
doc/Eqs/fix_ti_rs_function_1.jpg | Bin 2534 -> 0 bytes
doc/Eqs/fix_ti_rs_function_1.tex | 9 -
doc/Eqs/fix_ti_rs_function_2.jpg | Bin 3233 -> 0 bytes
doc/Eqs/fix_ti_rs_function_2.tex | 9 -
doc/Eqs/fix_ti_rs_function_3.jpg | Bin 4801 -> 0 bytes
doc/Eqs/fix_ti_rs_function_3.tex | 9 -
doc/Eqs/fix_ti_spring_force.jpg | Bin 3627 -> 0 bytes
doc/Eqs/fix_ti_spring_force.tex | 11 -
doc/Eqs/fix_ti_spring_function_1.jpg | Bin 1040 -> 0 bytes
doc/Eqs/fix_ti_spring_function_2.jpg | Bin 5753 -> 0 bytes
doc/Eqs/fix_wall_lj1043.tex | 12 -
doc/Eqs/heat_flux_k.tex | 11 -
doc/Eqs/improper_umbrella.tex | 13 -
doc/Eqs/pair_comb1.tex | 7 -
doc/Eqs/pair_comb2.tex | 23 -
doc/Makefile | 145 +
doc/Manual.html | 456 -
doc/Manual.html.html | 318 -
doc/Manual.pdf | Bin 10368659 -> 0 bytes
doc/Manual.txt | 304 -
doc/PDF/colvars-refman-lammps.pdf | 8124 --
doc/README | 115 +
doc/Scripts/correlate.py | 89 -
doc/Section_accelerate.html | 642 -
doc/Section_accelerate.txt | 415 -
doc/Section_commands.html | 1529 -
doc/Section_commands.txt | 1085 -
doc/Section_errors.html | 6378 -
doc/Section_errors.txt | 11163 --
doc/Section_example.html | 401 -
doc/Section_example.txt | 124 -
doc/Section_history.html | 313 -
doc/Section_history.txt | 123 -
doc/Section_howto.html | 2891 -
doc/Section_howto.txt | 2809 -
doc/Section_intro.html | 695 -
doc/Section_intro.txt | 540 -
doc/Section_modify.html | 1254 -
doc/Section_modify.txt | 768 -
doc/Section_packages.html | 1591 -
doc/Section_packages.txt | 858 -
doc/Section_perf.html | 304 -
doc/Section_perf.txt | 77 -
doc/Section_python.html | 978 -
doc/Section_python.txt | 779 -
doc/Section_start.html | 1990 -
doc/Section_start.txt | 1930 -
doc/Section_tools.html | 707 -
doc/Section_tools.txt | 566 -
doc/_images/angle_charmm.jpg | Bin 3932 -> 0 bytes
doc/_images/angle_class2.jpg | Bin 16202 -> 0 bytes
doc/_images/angle_cosine.jpg | Bin 2380 -> 0 bytes
doc/_images/angle_cosine_delta.jpg | Bin 2576 -> 0 bytes
doc/_images/angle_cosine_periodic.jpg | Bin 3362 -> 0 bytes
doc/_images/angle_cosine_shift.jpg | Bin 3933 -> 0 bytes
doc/_images/angle_cosine_shift_exp.jpg | Bin 7884 -> 0 bytes
doc/_images/angle_cosine_squared.jpg | Bin 3265 -> 0 bytes
doc/_images/angle_dipole_gamma.jpg | Bin 2709 -> 0 bytes
doc/_images/angle_dipole_potential.jpg | Bin 2616 -> 0 bytes
doc/_images/angle_dipole_torque.jpg | Bin 5110 -> 0 bytes
doc/_images/angle_fourier.jpg | Bin 4618 -> 0 bytes
doc/_images/angle_fourier_simple.jpg | Bin 2761 -> 0 bytes
doc/_images/angle_harmonic.jpg | Bin 2005 -> 0 bytes
doc/_images/angle_quartic.jpg | Bin 5273 -> 0 bytes
doc/_images/atc_nanotube.jpg | Bin 13402 -> 0 bytes
doc/_images/balance_nonuniform.jpg | Bin 78857 -> 0 bytes
doc/_images/balance_rcb.jpg | Bin 72941 -> 0 bytes
doc/_images/balance_uniform.jpg | Bin 79281 -> 0 bytes
doc/_images/bond_class2.jpg | Bin 5142 -> 0 bytes
doc/_images/bond_fene.jpg | Bin 8322 -> 0 bytes
doc/_images/bond_fene_expand.jpg | Bin 11506 -> 0 bytes
doc/_images/bond_harmonic.jpg | Bin 1861 -> 0 bytes
doc/_images/bond_harmonic_shift.jpg | Bin 5078 -> 0 bytes
doc/_images/bond_harmonic_shift_cut.jpg | Bin 5184 -> 0 bytes
doc/_images/bond_morse.jpg | Bin 2509 -> 0 bytes
doc/_images/bond_nonlinear.jpg | Bin 3593 -> 0 bytes
doc/_images/bond_quartic.jpg | Bin 9554 -> 0 bytes
doc/_images/bondswap.jpg | Bin 10548 -> 0 bytes
doc/_images/box.jpg | Bin 11093 -> 0 bytes
doc/_images/box_inverse.jpg | Bin 10250 -> 0 bytes
doc/_images/centro_symmetry.jpg | Bin 4111 -> 0 bytes
doc/_images/cna_cutoff1.jpg | Bin 13431 -> 0 bytes
doc/_images/cna_cutoff2.jpg | Bin 2518 -> 0 bytes
doc/_images/compute_fep_bar.jpg | Bin 18106 -> 0 bytes
doc/_images/compute_fep_fdti.jpg | Bin 15544 -> 0 bytes
doc/_images/compute_fep_fep.jpg | Bin 18055 -> 0 bytes
doc/_images/compute_fep_lambda.jpg | Bin 10511 -> 0 bytes
doc/_images/compute_fep_ti.jpg | Bin 18149 -> 0 bytes
doc/_images/compute_fep_u.jpg | Bin 9337 -> 0 bytes
doc/_images/compute_fep_vol.jpg | Bin 15209 -> 0 bytes
doc/_images/compute_gyration.jpg | Bin 3658 -> 0 bytes
doc/_images/compute_msd_nongauss.jpg | Bin 7277 -> 0 bytes
doc/_images/compute_saed1.jpg | Bin 1471 -> 0 bytes
doc/_images/compute_saed2.jpg | Bin 4911 -> 0 bytes
doc/_images/compute_saed3.jpg | Bin 7048 -> 0 bytes
doc/_images/compute_sna_atom1.jpg | Bin 19001 -> 0 bytes
doc/_images/compute_sna_atom2.jpg | Bin 17114 -> 0 bytes
doc/_images/compute_sna_atom3.jpg | Bin 19644 -> 0 bytes
doc/_images/compute_sna_atom4.jpg | Bin 35933 -> 0 bytes
doc/_images/compute_sna_atom5.jpg | Bin 14734 -> 0 bytes
doc/_images/compute_sna_atom6.jpg | Bin 17274 -> 0 bytes
doc/_images/compute_xrd1.jpg | Bin 2363 -> 0 bytes
doc/_images/compute_xrd2.jpg | Bin 4778 -> 0 bytes
doc/_images/compute_xrd3.jpg | Bin 4745 -> 0 bytes
doc/_images/compute_xrd4.jpg | Bin 2278 -> 0 bytes
doc/_images/compute_xrd5.jpg | Bin 7603 -> 0 bytes
doc/_images/coul_soft.jpg | Bin 12676 -> 0 bytes
doc/_images/dihedral_charmm.jpg | Bin 3118 -> 0 bytes
doc/_images/dihedral_class2.jpg | Bin 47795 -> 0 bytes
doc/_images/dihedral_cosine_shift_exp.jpg | Bin 8004 -> 0 bytes
doc/_images/dihedral_fourier.jpg | Bin 4544 -> 0 bytes
doc/_images/dihedral_harmonic.jpg | Bin 2937 -> 0 bytes
doc/_images/dihedral_helix.jpg | Bin 6810 -> 0 bytes
doc/_images/dihedral_multi_harmonic.jpg | Bin 3103 -> 0 bytes
doc/_images/dihedral_nharmonic.jpg | Bin 3231 -> 0 bytes
doc/_images/dihedral_opls.jpg | Bin 10755 -> 0 bytes
doc/_images/dihedral_quadratic.jpg | Bin 2067 -> 0 bytes
doc/_images/dihedral_sign.jpg | Bin 19297 -> 0 bytes
doc/_images/dreiding_hbond.jpg | Bin 21369 -> 0 bytes
doc/_images/dump1.jpg | Bin 608016 -> 0 bytes
doc/_images/dump2.jpg | Bin 172441 -> 0 bytes
doc/_images/eff_ECP1.jpg | Bin 5146 -> 0 bytes
doc/_images/eff_ECP2.jpg | Bin 9744 -> 0 bytes
doc/_images/eff_KE.jpg | Bin 3385 -> 0 bytes
doc/_images/eff_NN.jpg | Bin 4153 -> 0 bytes
doc/_images/eff_Ne.jpg | Bin 6425 -> 0 bytes
doc/_images/eff_Pauli.jpg | Bin 5676 -> 0 bytes
doc/_images/eff_ee.jpg | Bin 6829 -> 0 bytes
doc/_images/eff_energy_expression.jpg | Bin 9538 -> 0 bytes
doc/_images/fix_box_relax1.jpg | Bin 3375 -> 0 bytes
doc/_images/fix_box_relax2.jpg | Bin 3029 -> 0 bytes
doc/_images/fix_gld1.jpg | Bin 14274 -> 0 bytes
doc/_images/fix_lb_fluid_boltzmann.jpg | Bin 4643 -> 0 bytes
doc/_images/fix_lb_fluid_fluidforce.jpg | Bin 2358 -> 0 bytes
doc/_images/fix_lb_fluid_gammadefault.jpg | Bin 4793 -> 0 bytes
doc/_images/fix_lb_fluid_navierstokes.jpg | Bin 9311 -> 0 bytes
doc/_images/fix_lb_fluid_properties.jpg | Bin 3471 -> 0 bytes
doc/_images/fix_lb_fluid_stress.jpg | Bin 2530 -> 0 bytes
doc/_images/fix_lb_fluid_viscosity.jpg | Bin 6522 -> 0 bytes
doc/_images/fix_nh1.jpg | Bin 31088 -> 0 bytes
doc/_images/fix_nphug.jpg | Bin 7506 -> 0 bytes
doc/_images/fix_orient_fcc.jpg | Bin 26005 -> 0 bytes
doc/_images/fix_pimd.jpg | Bin 14569 -> 0 bytes
doc/_images/fix_rattle_constraints.jpg | Bin 4556 -> 0 bytes
doc/_images/fix_rattle_rij.jpg | Bin 1812 -> 0 bytes
doc/_images/fix_spring_rg.jpg | Bin 16204 -> 0 bytes
doc/_images/fix_ti_rs_force.jpg | Bin 1777 -> 0 bytes
doc/_images/fix_ti_rs_function_1.jpg | Bin 2534 -> 0 bytes
doc/_images/fix_ti_rs_function_2.jpg | Bin 3233 -> 0 bytes
doc/_images/fix_ti_rs_function_3.jpg | Bin 4801 -> 0 bytes
doc/_images/fix_ti_spring_force.jpg | Bin 3627 -> 0 bytes
doc/_images/fix_ti_spring_function_1.jpg | Bin 1040 -> 0 bytes
doc/_images/fix_ti_spring_function_2.jpg | Bin 5753 -> 0 bytes
doc/_images/fix_ttm.jpg | Bin 5869 -> 0 bytes
doc/_images/fix_ttm_blast.jpg | Bin 4449 -> 0 bytes
doc/_images/fix_ttm_blast1.jpg | Bin 8657 -> 0 bytes
doc/_images/fix_ttm_ce.jpg | Bin 7446 -> 0 bytes
doc/_images/fix_ttm_mod.jpg | Bin 10179 -> 0 bytes
doc/_images/fix_wall_colloid.jpg | Bin 17879 -> 0 bytes
doc/_images/fix_wall_harmonic.jpg | Bin 2413 -> 0 bytes
doc/_images/fix_wall_lj1043.jpg | Bin 10996 -> 0 bytes
doc/_images/fix_wall_lj93.jpg | Bin 4883 -> 0 bytes
doc/_images/fld.jpg | Bin 3640 -> 0 bytes
doc/_images/fld2.jpg | Bin 4161 -> 0 bytes
doc/_images/heat_flux_J.jpg | Bin 15205 -> 0 bytes
doc/_images/heat_flux_k.jpg | Bin 8760 -> 0 bytes
doc/_images/hop1.jpg | Bin 52996 -> 0 bytes
doc/_images/hop2.jpg | Bin 53149 -> 0 bytes
doc/_images/improper_class2.jpg | Bin 15728 -> 0 bytes
doc/_images/improper_cossq.jpg | Bin 2995 -> 0 bytes
doc/_images/improper_cvff.jpg | Bin 2826 -> 0 bytes
doc/_images/improper_fourier.jpg | Bin 4746 -> 0 bytes
doc/_images/improper_harmonic.jpg | Bin 2005 -> 0 bytes
doc/_images/improper_ring.jpg | Bin 11101 -> 0 bytes
doc/_images/improper_umbrella.jpg | Bin 9598 -> 0 bytes
doc/_images/lj_soft.jpg | Bin 12313 -> 0 bytes
doc/_images/min_energy.jpg | Bin 19599 -> 0 bytes
doc/_images/pair_adp.jpg | Bin 20391 -> 0 bytes
doc/_images/pair_airebo.jpg | Bin 9380 -> 0 bytes
doc/_images/pair_beck.jpg | Bin 9451 -> 0 bytes
doc/_images/pair_bop.jpg | Bin 13202 -> 0 bytes
doc/_images/pair_born.jpg | Bin 5099 -> 0 bytes
doc/_images/pair_buck.jpg | Bin 2861 -> 0 bytes
doc/_images/pair_charmm.jpg | Bin 25138 -> 0 bytes
doc/_images/pair_class2.jpg | Bin 5093 -> 0 bytes
doc/_images/pair_cmm.jpg | Bin 11921 -> 0 bytes
doc/_images/pair_colloid_cc.jpg | Bin 43501 -> 0 bytes
doc/_images/pair_colloid_cs.jpg | Bin 11599 -> 0 bytes
doc/_images/pair_colloid_ss.jpg | Bin 5573 -> 0 bytes
doc/_images/pair_comb1.jpg | Bin 18596 -> 0 bytes
doc/_images/pair_comb2.jpg | Bin 39601 -> 0 bytes
doc/_images/pair_coul_diel.jpg | Bin 10587 -> 0 bytes
doc/_images/pair_coul_dsf.jpg | Bin 12261 -> 0 bytes
doc/_images/pair_coul_soft.jpg | Bin 11309 -> 0 bytes
doc/_images/pair_coul_wolf.jpg | Bin 8758 -> 0 bytes
doc/_images/pair_coulomb.jpg | Bin 2505 -> 0 bytes
doc/_images/pair_cs.jpg | Bin 3500 -> 0 bytes
doc/_images/pair_debye.jpg | Bin 3641 -> 0 bytes
doc/_images/pair_dipole.jpg | Bin 47516 -> 0 bytes
doc/_images/pair_dipole_sf.jpg | Bin 93270 -> 0 bytes
doc/_images/pair_dipole_sf2.jpg | Bin 40855 -> 0 bytes
doc/_images/pair_dpd.jpg | Bin 12376 -> 0 bytes
doc/_images/pair_eam.jpg | Bin 6693 -> 0 bytes
doc/_images/pair_eam_fs.jpg | Bin 6547 -> 0 bytes
doc/_images/pair_edip.jpg | Bin 42939 -> 0 bytes
doc/_images/pair_eim1.jpg | Bin 6824 -> 0 bytes
doc/_images/pair_eim2.jpg | Bin 8494 -> 0 bytes
doc/_images/pair_eim3.jpg | Bin 40993 -> 0 bytes
doc/_images/pair_gauss.jpg | Bin 2835 -> 0 bytes
doc/_images/pair_gauss_cut.jpg | Bin 3855 -> 0 bytes
doc/_images/pair_gayberne.jpg | Bin 13814 -> 0 bytes
doc/_images/pair_gayberne2.jpg | Bin 4203 -> 0 bytes
doc/_images/pair_gran_hertz.jpg | Bin 12512 -> 0 bytes
doc/_images/pair_gran_hooke.jpg | Bin 5737 -> 0 bytes
doc/_images/pair_gromacs.jpg | Bin 50447 -> 0 bytes
doc/_images/pair_hbond_dreiding.jpg | Bin 32047 -> 0 bytes
doc/_images/pair_lj.jpg | Bin 4547 -> 0 bytes
doc/_images/pair_lj96.jpg | Bin 4851 -> 0 bytes
doc/_images/pair_lj_cubic.jpg | Bin 9352 -> 0 bytes
doc/_images/pair_lj_expand.jpg | Bin 5905 -> 0 bytes
doc/_images/pair_lj_sf.jpg | Bin 15535 -> 0 bytes
doc/_images/pair_lj_smooth.jpg | Bin 11580 -> 0 bytes
doc/_images/pair_lj_smooth_linear.jpg | Bin 10372 -> 0 bytes
doc/_images/pair_lj_soft.jpg | Bin 17984 -> 0 bytes
doc/_images/pair_lubricate.jpg | Bin 14321 -> 0 bytes
doc/_images/pair_meam.jpg | Bin 6110 -> 0 bytes
doc/_images/pair_meam_spline.jpg | Bin 10530 -> 0 bytes
doc/_images/pair_meam_sw_spline.jpg | Bin 17215 -> 0 bytes
doc/_images/pair_mgpt.jpg | Bin 12874 -> 0 bytes
doc/_images/pair_mie.jpg | Bin 4686 -> 0 bytes
doc/_images/pair_mie2.jpg | Bin 6502 -> 0 bytes
doc/_images/pair_morse.jpg | Bin 4042 -> 0 bytes
doc/_images/pair_nb3b_harmonic.jpg | Bin 1918 -> 0 bytes
doc/_images/pair_nm.jpg | Bin 6304 -> 0 bytes
doc/_images/pair_resquared.jpg | Bin 2683 -> 0 bytes
doc/_images/pair_resquared2.jpg | Bin 2303 -> 0 bytes
doc/_images/pair_resquared3.jpg | Bin 1156 -> 0 bytes
doc/_images/pair_resquared4.jpg | Bin 4779 -> 0 bytes
doc/_images/pair_smtbq1.jpg | Bin 27807 -> 0 bytes
doc/_images/pair_smtbq2.jpg | Bin 15544 -> 0 bytes
doc/_images/pair_smtbq3.jpg | Bin 6832 -> 0 bytes
doc/_images/pair_snap.jpg | Bin 32505 -> 0 bytes
doc/_images/pair_soft.jpg | Bin 4085 -> 0 bytes
doc/_images/pair_sph_ideal.jpg | Bin 1540 -> 0 bytes
doc/_images/pair_sph_tait.jpg | Bin 2303 -> 0 bytes
doc/_images/pair_srp1.jpg | Bin 3537 -> 0 bytes
doc/_images/pair_srp2.jpg | Bin 5648 -> 0 bytes
doc/_images/pair_sw.jpg | Bin 28707 -> 0 bytes
doc/_images/pair_tersoff_1.jpg | Bin 36584 -> 0 bytes
doc/_images/pair_tersoff_2.jpg | Bin 13756 -> 0 bytes
doc/_images/pair_tersoff_mod.jpg | Bin 91727 -> 0 bytes
doc/_images/pair_tersoff_zbl.jpg | Bin 392677 -> 0 bytes
doc/_images/pair_vashishta.jpg | Bin 73306 -> 0 bytes
doc/_images/pair_yukawa.jpg | Bin 2189 -> 0 bytes
doc/_images/pair_yukawa_colloid.jpg | Bin 3067 -> 0 bytes
doc/_images/pair_zbl.jpg | Bin 32209 -> 0 bytes
doc/_images/pimd.jpg | Bin 29560 -> 0 bytes
doc/_images/polymorphic1.jpg | Bin 9186 -> 0 bytes
doc/_images/polymorphic2.jpg | Bin 7156 -> 0 bytes
doc/_images/polymorphic3.jpg | Bin 2425 -> 0 bytes
doc/_images/polymorphic4.jpg | Bin 27028 -> 0 bytes
doc/_images/polymorphic5.jpg | Bin 30052 -> 0 bytes
doc/_images/polymorphic6.jpg | Bin 9063 -> 0 bytes
doc/_images/polymorphic7.jpg | Bin 58111 -> 0 bytes
doc/_images/polymorphic8.jpg | Bin 10249 -> 0 bytes
doc/_images/polymorphic9.jpg | Bin 13704 -> 0 bytes
doc/_images/pressure.jpg | Bin 4097 -> 0 bytes
doc/_images/pressure_tensor.jpg | Bin 5038 -> 0 bytes
doc/_images/qbmsst_init.jpg | Bin 38407 -> 0 bytes
doc/_images/qbmsst_shock.jpg | Bin 79334 -> 0 bytes
doc/_images/rhodo_staggered.jpg | Bin 42303 -> 0 bytes
doc/_images/rotate.jpg | Bin 17991 -> 0 bytes
doc/_images/saed_ewald_intersect.jpg | Bin 112619 -> 0 bytes
doc/_images/saed_mesh.jpg | Bin 110946 -> 0 bytes
doc/_images/screenshot_atomeye.jpg | Bin 426608 -> 0 bytes
doc/_images/screenshot_gl.jpg | Bin 306252 -> 0 bytes
doc/_images/screenshot_pymol.jpg | Bin 417093 -> 0 bytes
doc/_images/screenshot_vmd.jpg | Bin 327211 -> 0 bytes
doc/_images/sinusoid.jpg | Bin 128596 -> 0 bytes
doc/_images/stress_tensor.jpg | Bin 22403 -> 0 bytes
doc/_images/transform.jpg | Bin 60790 -> 0 bytes
doc/_images/umbrella.jpg | Bin 20442 -> 0 bytes
doc/_images/xrd_mesh.jpg | Bin 121055 -> 0 bytes
doc/_static/ajax-loader.gif | Bin 673 -> 0 bytes
doc/_static/basic.css | 599 -
doc/_static/comment-bright.png | Bin 3500 -> 0 bytes
doc/_static/comment-close.png | Bin 3578 -> 0 bytes
doc/_static/comment.png | Bin 3445 -> 0 bytes
doc/_static/css/badge_only.css | 226 -
doc/_static/css/badge_only.css.map | 7 -
doc/_static/css/theme.css | 5096 -
doc/_static/css/theme.css.map | 7 -
doc/_static/down-pressed.png | Bin 347 -> 0 bytes
doc/_static/down.png | Bin 347 -> 0 bytes
doc/_static/file.png | Bin 358 -> 0 bytes
doc/_static/fonts/FontAwesome.otf | Bin 62856 -> 0 bytes
doc/_static/fonts/Inconsolata-Bold.ttf | Bin 47064 -> 0 bytes
doc/_static/fonts/Inconsolata.ttf | Bin 63184 -> 0 bytes
doc/_static/fonts/Lato-Bold.ttf | Bin 82368 -> 0 bytes
doc/_static/fonts/Lato-Regular.ttf | Bin 81980 -> 0 bytes
doc/_static/fonts/RobotoSlab-Bold.ttf | Bin 36596 -> 0 bytes
doc/_static/fonts/RobotoSlab-Regular.ttf | Bin 36276 -> 0 bytes
doc/_static/fonts/fontawesome-webfont.eot | Bin 38205 -> 0 bytes
doc/_static/fonts/fontawesome-webfont.svg | 414 -
doc/_static/fonts/fontawesome-webfont.ttf | Bin 80652 -> 0 bytes
doc/_static/fonts/fontawesome-webfont.woff | Bin 44432 -> 0 bytes
doc/_static/minus.png | Bin 173 -> 0 bytes
doc/_static/plus.png | Bin 173 -> 0 bytes
doc/_static/pygments.css | 63 -
.../LightBox2/lightbox2/css/lightbox.css | 210 -
.../LightBox2/lightbox2/img/close.png | Bin 280 -> 0 bytes
.../LightBox2/lightbox2/img/loading.gif | Bin 8476 -> 0 bytes
.../LightBox2/lightbox2/img/next.png | Bin 1350 -> 0 bytes
.../LightBox2/lightbox2/img/prev.png | Bin 1360 -> 0 bytes
.../LightBox2/lightbox2/js/lightbox.min.map | 1 -
doc/_static/up-pressed.png | Bin 345 -> 0 bytes
doc/_static/up.png | Bin 345 -> 0 bytes
doc/accelerate_cuda.html | 372 -
doc/accelerate_cuda.txt | 223 -
doc/accelerate_gpu.html | 401 -
doc/accelerate_gpu.txt | 252 -
doc/accelerate_intel.html | 461 -
doc/accelerate_intel.txt | 321 -
doc/accelerate_kokkos.html | 622 -
doc/accelerate_kokkos.txt | 516 -
doc/accelerate_omp.html | 338 -
doc/accelerate_omp.txt | 186 -
doc/accelerate_opt.html | 239 -
doc/accelerate_opt.txt | 71 -
doc/angle_charmm.html | 264 -
doc/angle_charmm.txt | 89 -
doc/angle_class2.html | 291 -
doc/angle_class2.txt | 119 -
doc/angle_coeff.html | 279 -
doc/angle_cosine.html | 249 -
doc/angle_cosine.txt | 71 -
doc/angle_cosine_delta.html | 253 -
doc/angle_cosine_delta.txt | 77 -
doc/angle_cosine_periodic.html | 263 -
doc/angle_cosine_periodic.txt | 90 -
doc/angle_cosine_shift.html | 254 -
doc/angle_cosine_shift.txt | 75 -
doc/angle_cosine_shift_exp.html | 265 -
doc/angle_cosine_shift_exp.txt | 88 -
doc/angle_cosine_squared.html | 253 -
doc/angle_cosine_squared.txt | 76 -
doc/angle_dipole.html | 290 -
doc/angle_dipole.txt | 122 -
doc/angle_fourier.html | 250 -
doc/angle_fourier.txt | 72 -
doc/angle_fourier_simple.html | 249 -
doc/angle_fourier_simple.txt | 71 -
doc/angle_harmonic.html | 258 -
doc/angle_harmonic.txt | 77 -
doc/angle_hybrid.html | 274 -
doc/angle_hybrid.txt | 91 -
doc/angle_none.html | 218 -
doc/angle_none.txt | 29 -
doc/angle_quartic.html | 256 -
doc/angle_quartic.txt | 78 -
doc/angle_sdk.html | 242 -
doc/angle_sdk.txt | 58 -
doc/angle_style.html | 277 -
doc/angle_style.txt | 96 -
doc/angle_table.html | 327 -
doc/angle_table.txt | 157 -
doc/atom_modify.html | 343 -
doc/atom_modify.txt | 170 -
doc/atom_style.html | 482 -
doc/atom_style.txt | 269 -
doc/balance.html | 543 -
doc/balance.txt | 348 -
doc/body.html | 337 -
doc/body.txt | 154 -
doc/bond_class2.html | 256 -
doc/bond_class2.txt | 81 -
doc/bond_coeff.html | 276 -
doc/bond_fene.html | 264 -
doc/bond_fene.txt | 88 -
doc/bond_fene_expand.html | 265 -
doc/bond_fene_expand.txt | 92 -
doc/bond_harmonic.html | 254 -
doc/bond_harmonic.txt | 74 -
doc/bond_harmonic_shift.html | 256 -
doc/bond_harmonic_shift.txt | 77 -
doc/bond_harmonic_shift_cut.html | 257 -
doc/bond_harmonic_shift_cut.txt | 78 -
doc/bond_hybrid.html | 257 -
doc/bond_hybrid.txt | 74 -
doc/bond_morse.html | 252 -
doc/bond_morse.txt | 74 -
doc/bond_none.html | 218 -
doc/bond_none.txt | 29 -
doc/bond_nonlinear.html | 254 -
doc/bond_nonlinear.txt | 79 -
doc/bond_quartic.html | 286 -
doc/bond_quartic.txt | 113 -
doc/bond_style.html | 285 -
doc/bond_style.txt | 104 -
doc/bond_table.html | 324 -
doc/bond_table.txt | 154 -
doc/boundary.html | 282 -
doc/boundary.txt | 99 -
doc/box.html | 246 -
doc/change_box.html | 498 -
doc/change_box.txt | 332 -
doc/clear.html | 226 -
doc/comm_modify.html | 341 -
doc/comm_modify.txt | 159 -
doc/comm_style.html | 251 -
doc/comm_style.txt | 63 -
doc/compute.html | 429 -
doc/compute.txt | 258 -
doc/compute_ackland_atom.html | 252 -
doc/compute_ackland_atom.txt | 74 -
doc/compute_angle_local.html | 260 -
doc/compute_angle_local.txt | 77 -
doc/compute_angmom_chunk.html | 270 -
doc/compute_angmom_chunk.txt | 89 -
doc/compute_basal_atom.html | 250 -
doc/compute_basal_atom.txt | 76 -
doc/compute_body_local.html | 272 -
doc/compute_body_local.txt | 89 -
doc/compute_bond_local.html | 268 -
doc/compute_bond_local.txt | 84 -
doc/compute_centro_atom.html | 297 -
doc/compute_centro_atom.txt | 119 -
doc/compute_chunk_atom.html | 664 -
doc/compute_chunk_atom.txt | 554 -
doc/compute_cluster_atom.html | 260 -
doc/compute_cluster_atom.txt | 73 -
doc/compute_cna_atom.html | 272 -
doc/compute_cna_atom.txt | 97 -
doc/compute_com.html | 244 -
doc/compute_com.txt | 57 -
doc/compute_com_chunk.html | 268 -
doc/compute_com_chunk.txt | 87 -
doc/compute_contact_atom.html | 237 -
doc/compute_contact_atom.txt | 54 -
doc/compute_coord_atom.html | 276 -
doc/compute_coord_atom.txt | 92 -
doc/compute_damage_atom.html | 240 -
doc/compute_damage_atom.txt | 63 -
doc/compute_dihedral_local.html | 253 -
doc/compute_dihedral_local.txt | 69 -
doc/compute_dilatation_atom.html | 242 -
doc/compute_dilatation_atom.txt | 66 -
doc/compute_displace_atom.html | 256 -
doc/compute_displace_atom.txt | 69 -
doc/compute_erotate_asphere.html | 250 -
doc/compute_erotate_asphere.txt | 70 -
doc/compute_erotate_rigid.html | 242 -
doc/compute_erotate_rigid.txt | 61 -
doc/compute_erotate_sphere.html | 242 -
doc/compute_erotate_sphere.txt | 57 -
doc/compute_erotate_sphere_atom.html | 241 -
doc/compute_erotate_sphere_atom.txt | 53 -
doc/compute_event_displace.html | 248 -
doc/compute_event_displace.txt | 62 -
doc/compute_fep.html | 447 -
doc/compute_fep.txt | 263 -
doc/compute_group_group.html | 295 -
doc/compute_group_group.txt | 123 -
doc/compute_gyration.html | 257 -
doc/compute_gyration.txt | 73 -
doc/compute_gyration_chunk.html | 288 -
doc/compute_gyration_chunk.txt | 111 -
doc/compute_heat_flux.html | 371 -
doc/compute_heat_flux.txt | 187 -
doc/compute_hexorder_atom.html | 296 -
doc/compute_hexorder_atom.txt | 116 -
doc/compute_improper_local.html | 253 -
doc/compute_improper_local.txt | 69 -
doc/compute_inertia_chunk.html | 269 -
doc/compute_inertia_chunk.txt | 88 -
doc/compute_ke.html | 245 -
doc/compute_ke.txt | 59 -
doc/compute_ke_atom.html | 234 -
doc/compute_ke_atom.txt | 48 -
doc/compute_ke_atom_eff.html | 261 -
doc/compute_ke_atom_eff.txt | 77 -
doc/compute_ke_eff.html | 257 -
doc/compute_ke_eff.txt | 78 -
doc/compute_ke_rigid.html | 240 -
doc/compute_ke_rigid.txt | 60 -
doc/compute_meso_e_atom.html | 237 -
doc/compute_meso_e_atom.txt | 56 -
doc/compute_meso_rho_atom.html | 237 -
doc/compute_meso_rho_atom.txt | 56 -
doc/compute_meso_t_atom.html | 238 -
doc/compute_meso_t_atom.txt | 58 -
doc/compute_modify.html | 258 -
doc/compute_modify.txt | 71 -
doc/compute_msd.html | 273 -
doc/compute_msd.txt | 89 -
doc/compute_msd_chunk.html | 304 -
doc/compute_msd_chunk.txt | 120 -
doc/compute_msd_nongauss.html | 260 -
doc/compute_msd_nongauss.txt | 80 -
doc/compute_omega_chunk.html | 270 -
doc/compute_omega_chunk.txt | 89 -
doc/compute_orientorder_atom.html | 298 -
doc/compute_orientorder_atom.txt | 119 -
doc/compute_pair.html | 264 -
doc/compute_pair.txt | 81 -
doc/compute_pair_local.html | 298 -
doc/compute_pair_local.txt | 117 -
doc/compute_pe.html | 279 -
doc/compute_pe.txt | 103 -
doc/compute_pe_atom.html | 270 -
doc/compute_pe_atom.txt | 91 -
doc/compute_plasticity_atom.html | 242 -
doc/compute_plasticity_atom.txt | 67 -
doc/compute_pressure.html | 311 -
doc/compute_pressure.txt | 148 -
doc/compute_property_atom.html | 344 -
doc/compute_property_atom.txt | 163 -
doc/compute_property_chunk.html | 291 -
doc/compute_property_chunk.txt | 118 -
doc/compute_property_local.html | 321 -
doc/compute_property_local.txt | 142 -
doc/compute_rdf.html | 335 -
doc/compute_rdf.txt | 155 -
doc/compute_reduce.html | 361 -
doc/compute_reduce.txt | 185 -
doc/compute_saed.html | 364 -
doc/compute_saed.txt | 177 -
doc/compute_slice.html | 290 -
doc/compute_slice.txt | 112 -
doc/compute_smd_contact_radius.html | 235 -
doc/compute_smd_contact_radius.txt | 53 -
doc/compute_smd_damage.html | 232 -
doc/compute_smd_damage.txt | 48 -
doc/compute_smd_hourglass_error.html | 239 -
doc/compute_smd_hourglass_error.txt | 57 -
doc/compute_smd_internal_energy.html | 231 -
doc/compute_smd_internal_energy.txt | 49 -
doc/compute_smd_plastic_strain.html | 234 -
doc/compute_smd_plastic_strain.txt | 51 -
doc/compute_smd_plastic_strain_rate.html | 234 -
doc/compute_smd_plastic_strain_rate.txt | 50 -
doc/compute_smd_rho.html | 233 -
doc/compute_smd_rho.txt | 49 -
doc/compute_smd_tlsph_defgrad.html | 236 -
doc/compute_smd_tlsph_defgrad.txt | 53 -
doc/compute_smd_tlsph_dt.html | 237 -
doc/compute_smd_tlsph_dt.txt | 54 -
doc/compute_smd_tlsph_num_neighs.html | 233 -
doc/compute_smd_tlsph_num_neighs.txt | 50 -
doc/compute_smd_tlsph_shape.html | 235 -
doc/compute_smd_tlsph_shape.txt | 52 -
doc/compute_smd_tlsph_strain.html | 236 -
doc/compute_smd_tlsph_strain.txt | 53 -
doc/compute_smd_tlsph_strain_rate.html | 234 -
doc/compute_smd_tlsph_strain_rate.txt | 53 -
doc/compute_smd_tlsph_stress.html | 235 -
doc/compute_smd_tlsph_stress.txt | 53 -
doc/compute_smd_triangle_mesh_vertices.html | 238 -
doc/compute_smd_triangle_mesh_vertices.txt | 59 -
doc/compute_smd_ulsph_num_neighs.html | 232 -
doc/compute_smd_ulsph_num_neighs.txt | 48 -
doc/compute_smd_ulsph_strain.html | 234 -
doc/compute_smd_ulsph_strain.txt | 51 -
doc/compute_smd_ulsph_strain_rate.html | 234 -
doc/compute_smd_ulsph_strain_rate.txt | 52 -
doc/compute_smd_ulsph_stress.html | 237 -
doc/compute_smd_ulsph_stress.txt | 53 -
doc/compute_smd_vol.html | 236 -
doc/compute_smd_vol.txt | 52 -
doc/compute_sna_atom.html | 396 -
doc/compute_sna_atom.txt | 241 -
doc/compute_stress_atom.html | 329 -
doc/compute_stress_atom.txt | 164 -
doc/compute_tally.html | 269 -
doc/compute_tally.txt | 85 -
doc/compute_temp.html | 287 -
doc/compute_temp.txt | 114 -
doc/compute_temp_asphere.html | 324 -
doc/compute_temp_asphere.txt | 153 -
doc/compute_temp_chunk.html | 397 -
doc/compute_temp_chunk.txt | 237 -
doc/compute_temp_com.html | 269 -
doc/compute_temp_cs.html | 288 -
doc/compute_temp_cs.txt | 119 -
doc/compute_temp_deform.html | 311 -
doc/compute_temp_deform.txt | 134 -
doc/compute_temp_deform_eff.html | 250 -
doc/compute_temp_deform_eff.txt | 73 -
doc/compute_temp_drude.html | 259 -
doc/compute_temp_drude.txt | 82 -
doc/compute_temp_eff.html | 275 -
doc/compute_temp_eff.txt | 95 -
doc/compute_temp_partial.html | 289 -
doc/compute_temp_partial.txt | 121 -
doc/compute_temp_profile.html | 352 -
doc/compute_temp_profile.txt | 182 -
doc/compute_temp_ramp.html | 290 -
doc/compute_temp_region.html | 282 -
doc/compute_temp_region.txt | 110 -
doc/compute_temp_region_eff.html | 242 -
doc/compute_temp_rotate.html | 268 -
doc/compute_temp_sphere.html | 312 -
doc/compute_temp_sphere.txt | 137 -
doc/compute_ti.html | 307 -
doc/compute_ti.txt | 137 -
doc/compute_torque_chunk.html | 269 -
doc/compute_torque_chunk.txt | 87 -
doc/compute_vacf.html | 259 -
doc/compute_vacf.txt | 71 -
doc/compute_vcm_chunk.html | 256 -
doc/compute_vcm_chunk.txt | 77 -
doc/compute_voronoi_atom.html | 348 -
doc/compute_voronoi_atom.txt | 172 -
doc/compute_xrd.html | 390 -
doc/compute_xrd.txt | 200 -
doc/create_atoms.html | 495 -
doc/create_atoms.txt | 318 -
doc/create_bonds.html | 293 -
doc/create_bonds.txt | 109 -
doc/create_box.html | 327 -
doc/create_box.txt | 152 -
doc/delete_atoms.html | 329 -
doc/delete_atoms.txt | 144 -
doc/delete_bonds.html | 328 -
doc/delete_bonds.txt | 149 -
doc/dielectric.html | 233 -
doc/dielectric.txt | 39 -
doc/dihedral_charmm.html | 286 -
doc/dihedral_charmm.txt | 114 -
doc/dihedral_class2.html | 349 -
doc/dihedral_class2.txt | 178 -
doc/dihedral_coeff.html | 290 -
doc/dihedral_coeff.txt | 108 -
doc/dihedral_cosine_shift_exp.html | 263 -
doc/dihedral_cosine_shift_exp.txt | 86 -
doc/dihedral_fourier.html | 256 -
doc/dihedral_fourier.txt | 77 -
doc/dihedral_harmonic.html | 264 -
doc/dihedral_harmonic.txt | 84 -
doc/dihedral_helix.html | 259 -
doc/dihedral_helix.txt | 84 -
doc/dihedral_hybrid.html | 275 -
doc/dihedral_hybrid.txt | 92 -
doc/dihedral_multi_harmonic.html | 252 -
doc/dihedral_multi_harmonic.txt | 73 -
doc/dihedral_nharmonic.html | 253 -
doc/dihedral_nharmonic.txt | 73 -
doc/dihedral_none.html | 218 -
doc/dihedral_none.txt | 29 -
doc/dihedral_opls.html | 261 -
doc/dihedral_opls.txt | 85 -
doc/dihedral_quadratic.html | 253 -
doc/dihedral_quadratic.txt | 75 -
doc/dihedral_style.html | 296 -
doc/dihedral_style.txt | 117 -
doc/dihedral_table.html | 376 -
doc/dihedral_table.txt | 205 -
doc/dimension.html | 240 -
doc/dimension.txt | 48 -
doc/displace_atoms.html | 323 -
doc/displace_atoms.txt | 134 -
doc/doc2/Eqs/.log | 30 -
doc/doc2/Eqs/angle_charmm.jpg | Bin 3932 -> 0 bytes
doc/doc2/Eqs/angle_charmm.tex | 9 -
doc/doc2/Eqs/angle_class2.jpg | Bin 16202 -> 0 bytes
doc/doc2/Eqs/angle_class2.tex | 12 -
doc/doc2/Eqs/angle_cosine.jpg | Bin 2380 -> 0 bytes
doc/doc2/Eqs/angle_cosine.tex | 9 -
doc/doc2/Eqs/angle_cosine_delta.jpg | Bin 2576 -> 0 bytes
doc/doc2/Eqs/angle_cosine_delta.tex | 9 -
doc/doc2/Eqs/angle_cosine_periodic.jpg | Bin 3362 -> 0 bytes
doc/doc2/Eqs/angle_cosine_periodic.tex | 9 -
doc/doc2/Eqs/angle_cosine_shift.jpg | Bin 3933 -> 0 bytes
doc/doc2/Eqs/angle_cosine_shift.tex | 9 -
doc/doc2/Eqs/angle_cosine_shift_exp.jpg | Bin 7884 -> 0 bytes
doc/doc2/Eqs/angle_cosine_shift_exp.tex | 13 -
doc/doc2/Eqs/angle_cosine_squared.jpg | Bin 3265 -> 0 bytes
doc/doc2/Eqs/angle_cosine_squared.tex | 9 -
doc/doc2/Eqs/angle_dipole_gamma.jpg | Bin 2709 -> 0 bytes
doc/doc2/Eqs/angle_dipole_gamma.tex | 9 -
doc/doc2/Eqs/angle_dipole_potential.jpg | Bin 2616 -> 0 bytes
doc/doc2/Eqs/angle_dipole_potential.tex | 9 -
doc/doc2/Eqs/angle_dipole_torque.jpg | Bin 5110 -> 0 bytes
doc/doc2/Eqs/angle_dipole_torque.tex | 9 -
doc/doc2/Eqs/angle_fourier.jpg | Bin 4618 -> 0 bytes
doc/doc2/Eqs/angle_fourier.tex | 9 -
doc/doc2/Eqs/angle_fourier_simple.jpg | Bin 2761 -> 0 bytes
doc/doc2/Eqs/angle_fourier_simple.tex | 9 -
doc/doc2/Eqs/angle_harmonic.jpg | Bin 2005 -> 0 bytes
doc/doc2/Eqs/angle_harmonic.tex | 9 -
doc/doc2/Eqs/angle_quartic.jpg | Bin 5273 -> 0 bytes
doc/doc2/Eqs/angle_quartic.tex | 9 -
doc/doc2/Eqs/bond_class2.jpg | Bin 5142 -> 0 bytes
doc/doc2/Eqs/bond_class2.tex | 9 -
doc/doc2/Eqs/bond_fene.jpg | Bin 8322 -> 0 bytes
doc/doc2/Eqs/bond_fene.tex | 11 -
doc/doc2/Eqs/bond_fene_expand.jpg | Bin 11506 -> 0 bytes
doc/doc2/Eqs/bond_fene_expand.tex | 13 -
doc/doc2/Eqs/bond_harmonic.jpg | Bin 1861 -> 0 bytes
doc/doc2/Eqs/bond_harmonic.tex | 9 -
doc/doc2/Eqs/bond_harmonic_shift.jpg | Bin 5078 -> 0 bytes
doc/doc2/Eqs/bond_harmonic_shift.tex | 9 -
doc/doc2/Eqs/bond_harmonic_shift_cut.jpg | Bin 5184 -> 0 bytes
doc/doc2/Eqs/bond_harmonic_shift_cut.tex | 9 -
doc/doc2/Eqs/bond_morse.jpg | Bin 2509 -> 0 bytes
doc/doc2/Eqs/bond_morse.tex | 10 -
doc/doc2/Eqs/bond_nonlinear.jpg | Bin 3593 -> 0 bytes
doc/doc2/Eqs/bond_nonlinear.tex | 9 -
doc/doc2/Eqs/bond_quartic.jpg | Bin 9554 -> 0 bytes
doc/doc2/Eqs/bond_quartic.tex | 11 -
doc/doc2/Eqs/box.jpg | Bin 11093 -> 0 bytes
doc/doc2/Eqs/box.tex | 14 -
doc/doc2/Eqs/box_inverse.jpg | Bin 10250 -> 0 bytes
doc/doc2/Eqs/box_inverse.tex | 14 -
doc/doc2/Eqs/centro_symmetry.jpg | Bin 4111 -> 0 bytes
doc/doc2/Eqs/centro_symmetry.tex | 9 -
doc/doc2/Eqs/cna_cutoff1.jpg | Bin 13431 -> 0 bytes
doc/doc2/Eqs/cna_cutoff1.tex | 14 -
doc/doc2/Eqs/cna_cutoff2.jpg | Bin 2518 -> 0 bytes
doc/doc2/Eqs/cna_cutoff2.tex | 12 -
doc/doc2/Eqs/compute_fep_bar.jpg | Bin 18106 -> 0 bytes
doc/doc2/Eqs/compute_fep_bar.tex | 7 -
doc/doc2/Eqs/compute_fep_fdti.jpg | Bin 15544 -> 0 bytes
doc/doc2/Eqs/compute_fep_fdti.tex | 10 -
doc/doc2/Eqs/compute_fep_fep.jpg | Bin 18055 -> 0 bytes
doc/doc2/Eqs/compute_fep_fep.tex | 9 -
doc/doc2/Eqs/compute_fep_lambda.jpg | Bin 10511 -> 0 bytes
doc/doc2/Eqs/compute_fep_lambda.tex | 10 -
doc/doc2/Eqs/compute_fep_ti.jpg | Bin 18149 -> 0 bytes
doc/doc2/Eqs/compute_fep_ti.tex | 10 -
doc/doc2/Eqs/compute_fep_u.jpg | Bin 9337 -> 0 bytes
doc/doc2/Eqs/compute_fep_u.tex | 7 -
doc/doc2/Eqs/compute_fep_vol.jpg | Bin 15209 -> 0 bytes
doc/doc2/Eqs/compute_fep_vol.tex | 9 -
doc/doc2/Eqs/compute_gyration.jpg | Bin 3658 -> 0 bytes
doc/doc2/Eqs/compute_gyration.tex | 9 -
doc/doc2/Eqs/compute_msd_nongauss.jpg | Bin 7277 -> 0 bytes
doc/doc2/Eqs/compute_msd_nongauss.tex | 9 -
doc/doc2/Eqs/compute_saed1.jpg | Bin 1471 -> 0 bytes
doc/doc2/Eqs/compute_saed1.tex | 10 -
doc/doc2/Eqs/compute_saed2.jpg | Bin 4911 -> 0 bytes
doc/doc2/Eqs/compute_saed2.tex | 9 -
doc/doc2/Eqs/compute_saed3.jpg | Bin 7048 -> 0 bytes
doc/doc2/Eqs/compute_saed3.tex | 10 -
doc/doc2/Eqs/compute_sna_atom1.jpg | Bin 19001 -> 0 bytes
doc/doc2/Eqs/compute_sna_atom1.tex | 11 -
doc/doc2/Eqs/compute_sna_atom2.jpg | Bin 17114 -> 0 bytes
doc/doc2/Eqs/compute_sna_atom2.tex | 11 -
doc/doc2/Eqs/compute_sna_atom3.jpg | Bin 19644 -> 0 bytes
doc/doc2/Eqs/compute_sna_atom3.tex | 16 -
doc/doc2/Eqs/compute_sna_atom4.jpg | Bin 35933 -> 0 bytes
doc/doc2/Eqs/compute_sna_atom4.tex | 14 -
doc/doc2/Eqs/compute_sna_atom5.jpg | Bin 14734 -> 0 bytes
doc/doc2/Eqs/compute_sna_atom5.tex | 12 -
doc/doc2/Eqs/compute_sna_atom6.jpg | Bin 17274 -> 0 bytes
doc/doc2/Eqs/compute_sna_atom6.tex | 12 -
doc/doc2/Eqs/compute_xrd1.jpg | Bin 2363 -> 0 bytes
doc/doc2/Eqs/compute_xrd1.tex | 10 -
doc/doc2/Eqs/compute_xrd2.jpg | Bin 4778 -> 0 bytes
doc/doc2/Eqs/compute_xrd2.tex | 9 -
doc/doc2/Eqs/compute_xrd3.jpg | Bin 4745 -> 0 bytes
doc/doc2/Eqs/compute_xrd3.tex | 9 -
doc/doc2/Eqs/compute_xrd4.jpg | Bin 2278 -> 0 bytes
doc/doc2/Eqs/compute_xrd4.tex | 9 -
doc/doc2/Eqs/compute_xrd5.jpg | Bin 7603 -> 0 bytes
doc/doc2/Eqs/compute_xrd5.tex | 10 -
doc/doc2/Eqs/dihedral_charmm.jpg | Bin 3118 -> 0 bytes
doc/doc2/Eqs/dihedral_charmm.tex | 9 -
doc/doc2/Eqs/dihedral_class2.jpg | Bin 47795 -> 0 bytes
doc/doc2/Eqs/dihedral_class2.tex | 17 -
doc/doc2/Eqs/dihedral_cosine_shift_exp.jpg | Bin 8004 -> 0 bytes
doc/doc2/Eqs/dihedral_cosine_shift_exp.tex | 13 -
doc/doc2/Eqs/dihedral_fourier.jpg | Bin 4544 -> 0 bytes
doc/doc2/Eqs/dihedral_fourier.tex | 9 -
doc/doc2/Eqs/dihedral_harmonic.jpg | Bin 2937 -> 0 bytes
doc/doc2/Eqs/dihedral_harmonic.tex | 9 -
doc/doc2/Eqs/dihedral_helix.jpg | Bin 6810 -> 0 bytes
doc/doc2/Eqs/dihedral_helix.tex | 10 -
doc/doc2/Eqs/dihedral_multi_harmonic.jpg | Bin 3103 -> 0 bytes
doc/doc2/Eqs/dihedral_multi_harmonic.tex | 9 -
doc/doc2/Eqs/dihedral_nharmonic.jpg | Bin 3231 -> 0 bytes
doc/doc2/Eqs/dihedral_nharmonic.tex | 9 -
doc/doc2/Eqs/dihedral_opls.jpg | Bin 10755 -> 0 bytes
doc/doc2/Eqs/dihedral_opls.tex | 10 -
doc/doc2/Eqs/dihedral_quadratic.jpg | Bin 2067 -> 0 bytes
doc/doc2/Eqs/dihedral_quadratic.tex | 9 -
doc/doc2/Eqs/dihedral_sign.jpg | Bin 19297 -> 0 bytes
doc/doc2/Eqs/dreiding_hbond.jpg | Bin 21369 -> 0 bytes
doc/doc2/Eqs/eff_ECP1.jpg | Bin 5146 -> 0 bytes
doc/doc2/Eqs/eff_ECP1.tex | 9 -
doc/doc2/Eqs/eff_ECP2.jpg | Bin 9744 -> 0 bytes
doc/doc2/Eqs/eff_ECP2.tex | 8 -
doc/doc2/Eqs/eff_KE.jpg | Bin 3385 -> 0 bytes
doc/doc2/Eqs/eff_KE.tex | 9 -
doc/doc2/Eqs/eff_NN.jpg | Bin 4153 -> 0 bytes
doc/doc2/Eqs/eff_NN.tex | 9 -
doc/doc2/Eqs/eff_Ne.jpg | Bin 6425 -> 0 bytes
doc/doc2/Eqs/eff_Ne.tex | 9 -
doc/doc2/Eqs/eff_Pauli.jpg | Bin 5676 -> 0 bytes
doc/doc2/Eqs/eff_Pauli.tex | 9 -
doc/doc2/Eqs/eff_ee.jpg | Bin 6829 -> 0 bytes
doc/doc2/Eqs/eff_ee.tex | 9 -
doc/doc2/Eqs/eff_energy_expression.gif | Bin 2471 -> 0 bytes
doc/doc2/Eqs/eff_energy_expression.jpg | Bin 9538 -> 0 bytes
doc/doc2/Eqs/eff_energy_expression.tex | 9 -
doc/doc2/Eqs/fix_box_relax1.jpg | Bin 3375 -> 0 bytes
doc/doc2/Eqs/fix_box_relax1.tex | 9 -
doc/doc2/Eqs/fix_box_relax2.jpg | Bin 3029 -> 0 bytes
doc/doc2/Eqs/fix_box_relax2.tex | 9 -
doc/doc2/Eqs/fix_gld1.jpg | Bin 14274 -> 0 bytes
doc/doc2/Eqs/fix_gld1.tex | 13 -
doc/doc2/Eqs/fix_lb_fluid_boltzmann.jpg | Bin 4643 -> 0 bytes
doc/doc2/Eqs/fix_lb_fluid_boltzmann.tex | 14 -
doc/doc2/Eqs/fix_lb_fluid_fluidforce.jpg | Bin 2358 -> 0 bytes
doc/doc2/Eqs/fix_lb_fluid_fluidforce.tex | 14 -
doc/doc2/Eqs/fix_lb_fluid_gammadefault.jpg | Bin 4793 -> 0 bytes
doc/doc2/Eqs/fix_lb_fluid_gammadefault.tex | 14 -
doc/doc2/Eqs/fix_lb_fluid_navierstokes.jpg | Bin 9311 -> 0 bytes
doc/doc2/Eqs/fix_lb_fluid_navierstokes.tex | 16 -
doc/doc2/Eqs/fix_lb_fluid_properties.jpg | Bin 3471 -> 0 bytes
doc/doc2/Eqs/fix_lb_fluid_properties.tex | 17 -
doc/doc2/Eqs/fix_lb_fluid_stress.jpg | Bin 2530 -> 0 bytes
doc/doc2/Eqs/fix_lb_fluid_stress.tex | 14 -
doc/doc2/Eqs/fix_lb_fluid_viscosity.jpg | Bin 6522 -> 0 bytes
doc/doc2/Eqs/fix_lb_fluid_viscosity.tex | 14 -
doc/doc2/Eqs/fix_nh1.jpg | Bin 31088 -> 0 bytes
doc/doc2/Eqs/fix_nh1.tex | 35 -
doc/doc2/Eqs/fix_nphug.jpg | Bin 7506 -> 0 bytes
doc/doc2/Eqs/fix_nphug.tex | 9 -
doc/doc2/Eqs/fix_orient_fcc.jpg | Bin 26005 -> 0 bytes
doc/doc2/Eqs/fix_orient_fcc.tex | 30 -
doc/doc2/Eqs/fix_pimd.jpg | Bin 14569 -> 0 bytes
doc/doc2/Eqs/fix_pimd.tex | 17 -
doc/doc2/Eqs/fix_rattle_constraints.jpg | Bin 4556 -> 0 bytes
doc/doc2/Eqs/fix_rattle_constraints.tex | 9 -
doc/doc2/Eqs/fix_rattle_rij.jpg | Bin 1812 -> 0 bytes
doc/doc2/Eqs/fix_rattle_rij.tex | 8 -
doc/doc2/Eqs/fix_spring_rg.jpg | Bin 16204 -> 0 bytes
doc/doc2/Eqs/fix_spring_rg.tex | 19 -
doc/doc2/Eqs/fix_ti_rs_force.jpg | Bin 1777 -> 0 bytes
doc/doc2/Eqs/fix_ti_rs_force.tex | 11 -
doc/doc2/Eqs/fix_ti_rs_function_1.jpg | Bin 2534 -> 0 bytes
doc/doc2/Eqs/fix_ti_rs_function_1.tex | 9 -
doc/doc2/Eqs/fix_ti_rs_function_2.jpg | Bin 3233 -> 0 bytes
doc/doc2/Eqs/fix_ti_rs_function_2.tex | 9 -
doc/doc2/Eqs/fix_ti_rs_function_3.jpg | Bin 4801 -> 0 bytes
doc/doc2/Eqs/fix_ti_rs_function_3.tex | 9 -
doc/doc2/Eqs/fix_ti_spring_force.jpg | Bin 3627 -> 0 bytes
doc/doc2/Eqs/fix_ti_spring_force.tex | 11 -
doc/doc2/Eqs/fix_ti_spring_function_1.jpg | Bin 1040 -> 0 bytes
doc/doc2/Eqs/fix_ti_spring_function_1.tex | 9 -
doc/doc2/Eqs/fix_ti_spring_function_2.jpg | Bin 5753 -> 0 bytes
doc/doc2/Eqs/fix_ti_spring_function_2.tex | 9 -
doc/doc2/Eqs/fix_ttm.jpg | Bin 5869 -> 0 bytes
doc/doc2/Eqs/fix_ttm.tex | 15 -
doc/doc2/Eqs/fix_ttm_blast.jpg | Bin 4449 -> 0 bytes
doc/doc2/Eqs/fix_ttm_blast.tex | 13 -
doc/doc2/Eqs/fix_ttm_blast1.jpg | Bin 8657 -> 0 bytes
doc/doc2/Eqs/fix_ttm_blast1.tex | 13 -
doc/doc2/Eqs/fix_ttm_ce.jpg | Bin 7446 -> 0 bytes
doc/doc2/Eqs/fix_ttm_ce.tex | 13 -
doc/doc2/Eqs/fix_ttm_mod.jpg | Bin 10179 -> 0 bytes
doc/doc2/Eqs/fix_ttm_mod.tex | 15 -
doc/doc2/Eqs/fix_wall_colloid.jpg | Bin 17879 -> 0 bytes
doc/doc2/Eqs/fix_wall_colloid.tex | 14 -
doc/doc2/Eqs/fix_wall_harmonic.jpg | Bin 2413 -> 0 bytes
doc/doc2/Eqs/fix_wall_harmonic.tex | 9 -
doc/doc2/Eqs/fix_wall_lj1043.jpg | Bin 10996 -> 0 bytes
doc/doc2/Eqs/fix_wall_lj1043.tex | 12 -
doc/doc2/Eqs/fix_wall_lj93.jpg | Bin 4883 -> 0 bytes
doc/doc2/Eqs/fix_wall_lj93.tex | 11 -
doc/doc2/Eqs/fld.jpg | Bin 3640 -> 0 bytes
doc/doc2/Eqs/fld.tex | 9 -
doc/doc2/Eqs/fld2.jpg | Bin 4161 -> 0 bytes
doc/doc2/Eqs/fld2.tex | 9 -
doc/doc2/Eqs/heat_flux_J.jpg | Bin 15205 -> 0 bytes
doc/doc2/Eqs/heat_flux_J.tex | 11 -
doc/doc2/Eqs/heat_flux_k.jpg | Bin 8760 -> 0 bytes
doc/doc2/Eqs/heat_flux_k.tex | 11 -
doc/doc2/Eqs/improper_class2.jpg | Bin 15728 -> 0 bytes
doc/doc2/Eqs/improper_class2.tex | 13 -
doc/doc2/Eqs/improper_cossq.jpg | Bin 2995 -> 0 bytes
doc/doc2/Eqs/improper_cossq.tex | 9 -
doc/doc2/Eqs/improper_cvff.jpg | Bin 2826 -> 0 bytes
doc/doc2/Eqs/improper_cvff.tex | 9 -
doc/doc2/Eqs/improper_fourier.jpg | Bin 4746 -> 0 bytes
doc/doc2/Eqs/improper_fourier.tex | 9 -
doc/doc2/Eqs/improper_harmonic.jpg | Bin 2005 -> 0 bytes
doc/doc2/Eqs/improper_harmonic.tex | 9 -
doc/doc2/Eqs/improper_ring.jpg | Bin 11101 -> 0 bytes
doc/doc2/Eqs/improper_ring.tex | 12 -
doc/doc2/Eqs/improper_umbrella.jpg | Bin 9598 -> 0 bytes
doc/doc2/Eqs/improper_umbrella.tex | 13 -
doc/doc2/Eqs/min_energy.jpg | Bin 19599 -> 0 bytes
doc/doc2/Eqs/min_energy.tex | 15 -
doc/doc2/Eqs/pair_adp.jpg | Bin 20391 -> 0 bytes
doc/doc2/Eqs/pair_adp.tex | 16 -
doc/doc2/Eqs/pair_airebo.jpg | Bin 9380 -> 0 bytes
doc/doc2/Eqs/pair_airebo.tex | 11 -
doc/doc2/Eqs/pair_beck.jpg | Bin 9451 -> 0 bytes
doc/doc2/Eqs/pair_beck.tex | 11 -
doc/doc2/Eqs/pair_bop.jpg | Bin 13202 -> 0 bytes
doc/doc2/Eqs/pair_bop.tex | 9 -
doc/doc2/Eqs/pair_born.jpg | Bin 5099 -> 0 bytes
doc/doc2/Eqs/pair_born.tex | 10 -
doc/doc2/Eqs/pair_buck.jpg | Bin 2861 -> 0 bytes
doc/doc2/Eqs/pair_buck.tex | 9 -
doc/doc2/Eqs/pair_charmm.jpg | Bin 25138 -> 0 bytes
doc/doc2/Eqs/pair_charmm.tex | 22 -
doc/doc2/Eqs/pair_class2.jpg | Bin 5093 -> 0 bytes
doc/doc2/Eqs/pair_class2.tex | 11 -
doc/doc2/Eqs/pair_cmm.jpg | Bin 11921 -> 0 bytes
doc/doc2/Eqs/pair_cmm.tex | 16 -
doc/doc2/Eqs/pair_colloid_cc.jpg | Bin 43501 -> 0 bytes
doc/doc2/Eqs/pair_colloid_cc.tex | 31 -
doc/doc2/Eqs/pair_colloid_cs.jpg | Bin 11599 -> 0 bytes
doc/doc2/Eqs/pair_colloid_cs.tex | 12 -
doc/doc2/Eqs/pair_colloid_ss.jpg | Bin 5573 -> 0 bytes
doc/doc2/Eqs/pair_colloid_ss.tex | 12 -
doc/doc2/Eqs/pair_comb1.jpg | Bin 18596 -> 0 bytes
doc/doc2/Eqs/pair_comb1.tex | 7 -
doc/doc2/Eqs/pair_comb2.jpg | Bin 39601 -> 0 bytes
doc/doc2/Eqs/pair_comb2.tex | 23 -
doc/doc2/Eqs/pair_coul_diel.jpg | Bin 10587 -> 0 bytes
doc/doc2/Eqs/pair_coul_diel.tex | 9 -
doc/doc2/Eqs/pair_coul_dsf.jpg | Bin 12261 -> 0 bytes
doc/doc2/Eqs/pair_coul_dsf.tex | 10 -
doc/doc2/Eqs/pair_coul_soft.jpg | Bin 11309 -> 0 bytes
doc/doc2/Eqs/pair_coul_soft.tex | 10 -
doc/doc2/Eqs/pair_coul_wolf.jpg | Bin 8758 -> 0 bytes
doc/doc2/Eqs/pair_coul_wolf.tex | 11 -
doc/doc2/Eqs/pair_coulomb.jpg | Bin 2505 -> 0 bytes
doc/doc2/Eqs/pair_coulomb.tex | 9 -
doc/doc2/Eqs/pair_cs.jpg | Bin 3500 -> 0 bytes
doc/doc2/Eqs/pair_cs.tex | 9 -
doc/doc2/Eqs/pair_debye.jpg | Bin 3641 -> 0 bytes
doc/doc2/Eqs/pair_debye.tex | 8 -
doc/doc2/Eqs/pair_dipole.jpg | Bin 47516 -> 0 bytes
doc/doc2/Eqs/pair_dipole.tex | 38 -
doc/doc2/Eqs/pair_dipole_sf.jpg | Bin 93270 -> 0 bytes
doc/doc2/Eqs/pair_dipole_sf.tex | 51 -
doc/doc2/Eqs/pair_dipole_sf2.jpg | Bin 40855 -> 0 bytes
doc/doc2/Eqs/pair_dipole_sf2.tex | 24 -
doc/doc2/Eqs/pair_dpd.jpg | Bin 12376 -> 0 bytes
doc/doc2/Eqs/pair_dpd.tex | 13 -
doc/doc2/Eqs/pair_eam.jpg | Bin 6693 -> 0 bytes
doc/doc2/Eqs/pair_eam.tex | 10 -
doc/doc2/Eqs/pair_eam_fs.jpg | Bin 6547 -> 0 bytes
doc/doc2/Eqs/pair_eam_fs.tex | 11 -
doc/doc2/Eqs/pair_edip.jpg | Bin 42939 -> 0 bytes
doc/doc2/Eqs/pair_edip.tex | 22 -
doc/doc2/Eqs/pair_eim1.jpg | Bin 6824 -> 0 bytes
doc/doc2/Eqs/pair_eim1.tex | 9 -
doc/doc2/Eqs/pair_eim2.jpg | Bin 8494 -> 0 bytes
doc/doc2/Eqs/pair_eim2.tex | 11 -
doc/doc2/Eqs/pair_eim3.jpg | Bin 40993 -> 0 bytes
doc/doc2/Eqs/pair_eim3.tex | 25 -
doc/doc2/Eqs/pair_gauss.jpg | Bin 2835 -> 0 bytes
doc/doc2/Eqs/pair_gauss.tex | 9 -
doc/doc2/Eqs/pair_gauss_cut.jpg | Bin 3855 -> 0 bytes
doc/doc2/Eqs/pair_gauss_cut.tex | 8 -
doc/doc2/Eqs/pair_gayberne.jpg | Bin 13814 -> 0 bytes
doc/doc2/Eqs/pair_gayberne.tex | 14 -
doc/doc2/Eqs/pair_gayberne2.jpg | Bin 4203 -> 0 bytes
doc/doc2/Eqs/pair_gayberne2.tex | 9 -
doc/doc2/Eqs/pair_gran_hertz.jpg | Bin 12512 -> 0 bytes
doc/doc2/Eqs/pair_gran_hertz.tex | 14 -
doc/doc2/Eqs/pair_gran_hooke.jpg | Bin 5737 -> 0 bytes
doc/doc2/Eqs/pair_gran_hooke.tex | 12 -
doc/doc2/Eqs/pair_gromacs.jpg | Bin 50447 -> 0 bytes
doc/doc2/Eqs/pair_gromacs.tex | 17 -
doc/doc2/Eqs/pair_hbond_dreiding.jpg | Bin 32047 -> 0 bytes
doc/doc2/Eqs/pair_hbond_dreiding.tex | 18 -
doc/doc2/Eqs/pair_lj.jpg | Bin 4547 -> 0 bytes
doc/doc2/Eqs/pair_lj.tex | 11 -
doc/doc2/Eqs/pair_lj96.jpg | Bin 4851 -> 0 bytes
doc/doc2/Eqs/pair_lj96.tex | 11 -
doc/doc2/Eqs/pair_lj_cubic.jpg | Bin 9352 -> 0 bytes
doc/doc2/Eqs/pair_lj_cubic.tex | 12 -
doc/doc2/Eqs/pair_lj_expand.jpg | Bin 5905 -> 0 bytes
doc/doc2/Eqs/pair_lj_expand.tex | 11 -
doc/doc2/Eqs/pair_lj_sf.jpg | Bin 15535 -> 0 bytes
doc/doc2/Eqs/pair_lj_sf.tex | 11 -
doc/doc2/Eqs/pair_lj_smooth.jpg | Bin 11580 -> 0 bytes
doc/doc2/Eqs/pair_lj_smooth.tex | 15 -
doc/doc2/Eqs/pair_lj_smooth_linear.jpg | Bin 10372 -> 0 bytes
doc/doc2/Eqs/pair_lj_smooth_linear.tex | 13 -
doc/doc2/Eqs/pair_lj_soft.jpg | Bin 17984 -> 0 bytes
doc/doc2/Eqs/pair_lj_soft.tex | 15 -
doc/doc2/Eqs/pair_lubricate.jpg | Bin 14321 -> 0 bytes
doc/doc2/Eqs/pair_lubricate.tex | 17 -
doc/doc2/Eqs/pair_meam.jpg | Bin 6110 -> 0 bytes
doc/doc2/Eqs/pair_meam.tex | 10 -
doc/doc2/Eqs/pair_meam_spline.jpg | Bin 10530 -> 0 bytes
doc/doc2/Eqs/pair_meam_spline.tex | 13 -
doc/doc2/Eqs/pair_meam_sw_spline.jpg | Bin 17215 -> 0 bytes
doc/doc2/Eqs/pair_meam_sw_spline.tex | 23 -
doc/doc2/Eqs/pair_mgpt.jpg | Bin 12874 -> 0 bytes
doc/doc2/Eqs/pair_mgpt.tex | 12 -
doc/doc2/Eqs/pair_mie.jpg | Bin 4686 -> 0 bytes
doc/doc2/Eqs/pair_mie.tex | 10 -
doc/doc2/Eqs/pair_mie2.jpg | Bin 6502 -> 0 bytes
doc/doc2/Eqs/pair_mie2.tex | 9 -
doc/doc2/Eqs/pair_morse.jpg | Bin 4042 -> 0 bytes
doc/doc2/Eqs/pair_morse.tex | 10 -
doc/doc2/Eqs/pair_nb3b_harmonic.jpg | Bin 1918 -> 0 bytes
doc/doc2/Eqs/pair_nb3b_harmonic.tex | 9 -
doc/doc2/Eqs/pair_nm.jpg | Bin 6304 -> 0 bytes
doc/doc2/Eqs/pair_nm.tex | 10 -
doc/doc2/Eqs/pair_resquared.jpg | Bin 2683 -> 0 bytes
doc/doc2/Eqs/pair_resquared.tex | 7 -
doc/doc2/Eqs/pair_resquared2.jpg | Bin 2303 -> 0 bytes
doc/doc2/Eqs/pair_resquared2.tex | 7 -
doc/doc2/Eqs/pair_resquared3.jpg | Bin 1156 -> 0 bytes
doc/doc2/Eqs/pair_resquared3.tex | 7 -
doc/doc2/Eqs/pair_resquared4.jpg | Bin 4779 -> 0 bytes
doc/doc2/Eqs/pair_resquared4.tex | 9 -
doc/doc2/Eqs/pair_smtbq1.jpg | Bin 27807 -> 0 bytes
doc/doc2/Eqs/pair_smtbq1.tex | 13 -
doc/doc2/Eqs/pair_smtbq2.jpg | Bin 15544 -> 0 bytes
doc/doc2/Eqs/pair_smtbq2.tex | 12 -
doc/doc2/Eqs/pair_smtbq3.jpg | Bin 6832 -> 0 bytes
doc/doc2/Eqs/pair_smtbq3.tex | 10 -
doc/doc2/Eqs/pair_snap.jpg | Bin 32505 -> 0 bytes
doc/doc2/Eqs/pair_snap.tex | 9 -
doc/doc2/Eqs/pair_soft.jpg | Bin 4085 -> 0 bytes
doc/doc2/Eqs/pair_soft.tex | 10 -
doc/doc2/Eqs/pair_sph_ideal.jpg | Bin 1540 -> 0 bytes
doc/doc2/Eqs/pair_sph_ideal.tex | 9 -
doc/doc2/Eqs/pair_sph_tait.jpg | Bin 2303 -> 0 bytes
doc/doc2/Eqs/pair_sph_tait.tex | 9 -
doc/doc2/Eqs/pair_srp1.jpg | Bin 3537 -> 0 bytes
doc/doc2/Eqs/pair_srp1.tex | 9 -
doc/doc2/Eqs/pair_srp2.jpg | Bin 5648 -> 0 bytes
doc/doc2/Eqs/pair_srp2.tex | 10 -
doc/doc2/Eqs/pair_sw.jpg | Bin 28707 -> 0 bytes
doc/doc2/Eqs/pair_sw.tex | 18 -
doc/doc2/Eqs/pair_tersoff.jpg | Bin 36139 -> 0 bytes
doc/doc2/Eqs/pair_tersoff_1.jpg | Bin 36584 -> 0 bytes
doc/doc2/Eqs/pair_tersoff_1.tex | 24 -
doc/doc2/Eqs/pair_tersoff_2.jpg | Bin 13756 -> 0 bytes
doc/doc2/Eqs/pair_tersoff_2.tex | 14 -
doc/doc2/Eqs/pair_tersoff_mod.jpg | Bin 91727 -> 0 bytes
doc/doc2/Eqs/pair_tersoff_mod.tex | 24 -
doc/doc2/Eqs/pair_tersoff_zbl.jpg | Bin 392677 -> 0 bytes
doc/doc2/Eqs/pair_tersoff_zbl.tex | 33 -
doc/doc2/Eqs/pair_vashishta.jpg | Bin 73306 -> 0 bytes
doc/doc2/Eqs/pair_vashishta.tex | 22 -
doc/doc2/Eqs/pair_yukawa.jpg | Bin 2189 -> 0 bytes
doc/doc2/Eqs/pair_yukawa.tex | 9 -
doc/doc2/Eqs/pair_yukawa_colloid.jpg | Bin 3067 -> 0 bytes
doc/doc2/Eqs/pair_yukawa_colloid.tex | 9 -
doc/doc2/Eqs/pair_zbl.jpg | Bin 32209 -> 0 bytes
doc/doc2/Eqs/pair_zbl.tex | 11 -
doc/doc2/Eqs/polymorphic1.jpg | Bin 9186 -> 0 bytes
doc/doc2/Eqs/polymorphic1.tex | 9 -
doc/doc2/Eqs/polymorphic2.jpg | Bin 7156 -> 0 bytes
doc/doc2/Eqs/polymorphic2.tex | 10 -
doc/doc2/Eqs/polymorphic3.jpg | Bin 2425 -> 0 bytes
doc/doc2/Eqs/polymorphic3.tex | 10 -
doc/doc2/Eqs/polymorphic4.jpg | Bin 27028 -> 0 bytes
doc/doc2/Eqs/polymorphic4.tex | 17 -
doc/doc2/Eqs/polymorphic5.jpg | Bin 30052 -> 0 bytes
doc/doc2/Eqs/polymorphic5.tex | 17 -
doc/doc2/Eqs/polymorphic6.jpg | Bin 9063 -> 0 bytes
doc/doc2/Eqs/polymorphic6.tex | 13 -
doc/doc2/Eqs/polymorphic7.jpg | Bin 58111 -> 0 bytes
doc/doc2/Eqs/polymorphic7.tex | 25 -
doc/doc2/Eqs/polymorphic8.jpg | Bin 10249 -> 0 bytes
doc/doc2/Eqs/polymorphic8.tex | 13 -
doc/doc2/Eqs/polymorphic9.jpg | Bin 13704 -> 0 bytes
doc/doc2/Eqs/polymorphic9.tex | 17 -
doc/doc2/Eqs/pressure.jpg | Bin 4097 -> 0 bytes
doc/doc2/Eqs/pressure.tex | 9 -
doc/doc2/Eqs/pressure_tensor.jpg | Bin 5038 -> 0 bytes
doc/doc2/Eqs/pressure_tensor.tex | 10 -
doc/doc2/Eqs/rotate.jpg | Bin 17991 -> 0 bytes
doc/doc2/Eqs/rotate.tex | 26 -
doc/doc2/Eqs/stress_tensor.jpg | Bin 22403 -> 0 bytes
doc/doc2/Eqs/stress_tensor.tex | 20 -
doc/doc2/Eqs/transform.jpg | Bin 60790 -> 0 bytes
doc/doc2/Eqs/transform.tex | 27 -
doc/doc2/Eqs/umbrella.jpg | Bin 20442 -> 0 bytes
doc/doc2/JPG/atc_nanotube.jpg | Bin 13402 -> 0 bytes
doc/doc2/JPG/balance_nonuniform.jpg | Bin 78857 -> 0 bytes
doc/doc2/JPG/balance_nonuniform_small.jpg | Bin 16588 -> 0 bytes
doc/doc2/JPG/balance_rcb.jpg | Bin 72941 -> 0 bytes
doc/doc2/JPG/balance_rcb_small.jpg | Bin 15571 -> 0 bytes
doc/doc2/JPG/balance_uniform.jpg | Bin 79281 -> 0 bytes
doc/doc2/JPG/balance_uniform_small.jpg | Bin 17279 -> 0 bytes
doc/doc2/JPG/bondswap.jpg | Bin 10548 -> 0 bytes
doc/doc2/JPG/coul_soft.jpg | Bin 12676 -> 0 bytes
doc/doc2/JPG/dump1.jpg | Bin 608016 -> 0 bytes
doc/doc2/JPG/dump1_small.jpg | Bin 16529 -> 0 bytes
doc/doc2/JPG/dump2.jpg | Bin 172441 -> 0 bytes
doc/doc2/JPG/dump2_small.jpg | Bin 6506 -> 0 bytes
doc/doc2/JPG/hop1.jpg | Bin 52996 -> 0 bytes
doc/doc2/JPG/hop1_small.jpg | Bin 4302 -> 0 bytes
doc/doc2/JPG/hop2.jpg | Bin 53149 -> 0 bytes
doc/doc2/JPG/hop2_small.jpg | Bin 4214 -> 0 bytes
doc/doc2/JPG/lj_soft.jpg | Bin 12313 -> 0 bytes
doc/doc2/JPG/pimd.jpg | Bin 29560 -> 0 bytes
doc/doc2/JPG/qbmsst_init.jpg | Bin 38407 -> 0 bytes
doc/doc2/JPG/qbmsst_shock.jpg | Bin 79334 -> 0 bytes
doc/doc2/JPG/rhodo_staggered.jpg | Bin 42303 -> 0 bytes
doc/doc2/JPG/saed_ewald_intersect.jpg | Bin 112619 -> 0 bytes
doc/doc2/JPG/saed_ewald_intersect_small.jpg | Bin 41372 -> 0 bytes
doc/doc2/JPG/saed_mesh.jpg | Bin 110946 -> 0 bytes
doc/doc2/JPG/saed_mesh_small.jpg | Bin 43053 -> 0 bytes
doc/doc2/JPG/screenshot_atomeye.jpg | Bin 426608 -> 0 bytes
doc/doc2/JPG/screenshot_atomeye_small.jpg | Bin 7498 -> 0 bytes
doc/doc2/JPG/screenshot_gl.jpg | Bin 306252 -> 0 bytes
doc/doc2/JPG/screenshot_gl_small.jpg | Bin 5875 -> 0 bytes
doc/doc2/JPG/screenshot_pymol.jpg | Bin 417093 -> 0 bytes
doc/doc2/JPG/screenshot_pymol_small.jpg | Bin 7660 -> 0 bytes
doc/doc2/JPG/screenshot_vmd.jpg | Bin 327211 -> 0 bytes
doc/doc2/JPG/screenshot_vmd_small.jpg | Bin 6787 -> 0 bytes
doc/doc2/JPG/sinusoid.jpg | Bin 128596 -> 0 bytes
doc/doc2/JPG/sinusoid_small.jpg | Bin 29397 -> 0 bytes
doc/doc2/JPG/xrd_mesh.jpg | Bin 121055 -> 0 bytes
doc/doc2/JPG/xrd_mesh_small.jpg | Bin 46491 -> 0 bytes
doc/doc2/Manual.html | 478 -
doc/doc2/Manual.html.html | 318 -
doc/doc2/PDF/PDLammps_EPS.pdf | Bin 79021 -> 0 bytes
doc/doc2/PDF/PDLammps_VES.pdf | Bin 74846 -> 0 bytes
doc/doc2/PDF/PDLammps_overview.pdf | Bin 254253 -> 0 bytes
doc/doc2/PDF/colvars-refman-lammps.pdf | 8124 --
doc/doc2/PDF/kspace.pdf | Bin 158427 -> 0 bytes
doc/doc2/PDF/pair_gayberne_extra.aux | 1 -
doc/doc2/PDF/pair_gayberne_extra.dvi | Bin 8508 -> 0 bytes
doc/doc2/PDF/pair_gayberne_extra.log | 148 -
doc/doc2/PDF/pair_gayberne_extra.pdf | Bin 55448 -> 0 bytes
doc/doc2/PDF/pair_gayberne_extra.tex | 167 -
doc/doc2/PDF/pair_resquared_extra.aux | 1 -
doc/doc2/PDF/pair_resquared_extra.dvi | Bin 6264 -> 0 bytes
doc/doc2/PDF/pair_resquared_extra.log | 154 -
doc/doc2/PDF/pair_resquared_extra.pdf | Bin 55733 -> 0 bytes
doc/doc2/PDF/pair_resquared_extra.tex | 113 -
doc/doc2/Scripts/correlate.py | 89 -
doc/doc2/Section_accelerate.html | 420 -
doc/doc2/Section_commands.html | 669 -
doc/doc2/Section_errors.html | 11168 --
doc/doc2/Section_example.html | 132 -
doc/doc2/Section_history.html | 129 -
doc/doc2/Section_howto.html | 2840 -
doc/doc2/Section_intro.html | 551 -
doc/doc2/Section_modify.html | 798 -
doc/doc2/Section_packages.html | 875 -
doc/doc2/Section_perf.html | 84 -
doc/doc2/Section_python.html | 794 -
doc/doc2/Section_start.html | 1940 -
doc/doc2/Section_tools.html | 572 -
doc/doc2/USER/atc/man_add_molecule.html | 59 -
doc/doc2/USER/atc/man_add_species.html | 59 -
doc/doc2/USER/atc/man_atom_element_map.html | 52 -
doc/doc2/USER/atc/man_atom_weight.html | 61 -
doc/doc2/USER/atc/man_atomic_charge.html | 51 -
doc/doc2/USER/atc/man_boundary.html | 48 -
doc/doc2/USER/atc/man_boundary_dynamics.html | 46 -
doc/doc2/USER/atc/man_boundary_faceset.html | 47 -
doc/doc2/USER/atc/man_boundary_integral.html | 53 -
.../USER/atc/man_consistent_fe_initialization.html | 51 -
doc/doc2/USER/atc/man_contour_integral.html | 54 -
doc/doc2/USER/atc/man_control.html | 72 -
doc/doc2/USER/atc/man_control_momentum.html | 68 -
doc/doc2/USER/atc/man_control_thermal.html | 76 -
..._control_thermal_correction_max_iterations.html | 53 -
doc/doc2/USER/atc/man_decomposition.html | 55 -
doc/doc2/USER/atc/man_electron_integration.html | 56 -
doc/doc2/USER/atc/man_equilibrium_start.html | 50 -
doc/doc2/USER/atc/man_extrinsic_exchange.html | 50 -
doc/doc2/USER/atc/man_fe_md_boundary.html | 50 -
doc/doc2/USER/atc/man_fem_mesh.html | 25 -
doc/doc2/USER/atc/man_filter_scale.html | 55 -
doc/doc2/USER/atc/man_filter_type.html | 51 -
doc/doc2/USER/atc/man_fix_atc.html | 254 -
doc/doc2/USER/atc/man_fix_flux.html | 53 -
doc/doc2/USER/atc/man_fix_nodes.html | 56 -
doc/doc2/USER/atc/man_hardy_computes.html | 67 -
doc/doc2/USER/atc/man_hardy_fields.html | 83 -
doc/doc2/USER/atc/man_hardy_gradients.html | 57 -
doc/doc2/USER/atc/man_hardy_kernel.html | 65 -
doc/doc2/USER/atc/man_hardy_on_the_fly.html | 60 -
doc/doc2/USER/atc/man_hardy_rates.html | 58 -
doc/doc2/USER/atc/man_initial.html | 51 -
doc/doc2/USER/atc/man_internal_atom_integrate.html | 40 -
doc/doc2/USER/atc/man_internal_element_set.html | 52 -
doc/doc2/USER/atc/man_internal_quadrature.html | 50 -
doc/doc2/USER/atc/man_kernel_function.html | 64 -
doc/doc2/USER/atc/man_localized_lambda.html | 48 -
doc/doc2/USER/atc/man_lumped_lambda_solve.html | 47 -
doc/doc2/USER/atc/man_mask_direction.html | 47 -
doc/doc2/USER/atc/man_mass_matrix.html | 51 -
doc/doc2/USER/atc/man_material.html | 49 -
doc/doc2/USER/atc/man_mesh_add_to_nodeset.html | 51 -
doc/doc2/USER/atc/man_mesh_create.html | 56 -
doc/doc2/USER/atc/man_mesh_create_elementset.html | 52 -
doc/doc2/USER/atc/man_mesh_create_faceset_box.html | 54 -
.../USER/atc/man_mesh_create_faceset_plane.html | 54 -
doc/doc2/USER/atc/man_mesh_create_nodeset.html | 51 -
doc/doc2/USER/atc/man_mesh_delete_elements.html | 50 -
.../USER/atc/man_mesh_nodeset_to_elementset.html | 53 -
doc/doc2/USER/atc/man_mesh_output.html | 49 -
doc/doc2/USER/atc/man_mesh_quadrature.html | 51 -
doc/doc2/USER/atc/man_mesh_read.html | 52 -
doc/doc2/USER/atc/man_mesh_write.html | 50 -
.../USER/atc/man_momentum_time_integration.html | 60 -
doc/doc2/USER/atc/man_output.html | 63 -
doc/doc2/USER/atc/man_output_elementset.html | 54 -
doc/doc2/USER/atc/man_output_nodeset.html | 55 -
doc/doc2/USER/atc/man_pair_interactions.html | 50 -
doc/doc2/USER/atc/man_poisson_solver.html | 53 -
doc/doc2/USER/atc/man_read_restart.html | 51 -
doc/doc2/USER/atc/man_remove_molecule.html | 54 -
doc/doc2/USER/atc/man_remove_source.html | 52 -
doc/doc2/USER/atc/man_remove_species.html | 54 -
.../atc/man_reset_atomic_reference_positions.html | 49 -
doc/doc2/USER/atc/man_reset_time.html | 65 -
doc/doc2/USER/atc/man_sample_frequency.html | 52 -
doc/doc2/USER/atc/man_set.html | 56 -
doc/doc2/USER/atc/man_source.html | 53 -
doc/doc2/USER/atc/man_source_integration.html | 46 -
doc/doc2/USER/atc/man_temperature_definition.html | 47 -
.../USER/atc/man_thermal_time_integration.html | 59 -
doc/doc2/USER/atc/man_time_filter.html | 57 -
doc/doc2/USER/atc/man_track_displacement.html | 48 -
doc/doc2/USER/atc/man_unfix_flux.html | 52 -
doc/doc2/USER/atc/man_unfix_nodes.html | 53 -
doc/doc2/USER/atc/man_write_atom_weights.html | 53 -
doc/doc2/USER/atc/man_write_restart.html | 51 -
doc/doc2/accelerate_cuda.html | 228 -
doc/doc2/accelerate_gpu.html | 257 -
doc/doc2/accelerate_intel.html | 326 -
doc/doc2/accelerate_kokkos.html | 514 -
doc/doc2/accelerate_omp.html | 191 -
doc/doc2/accelerate_opt.html | 76 -
doc/doc2/angle_charmm.html | 97 -
doc/doc2/angle_class2.html | 126 -
doc/doc2/angle_coeff.html | 104 -
doc/doc2/angle_cosine.html | 77 -
doc/doc2/angle_cosine_delta.html | 83 -
doc/doc2/angle_cosine_periodic.html | 97 -
doc/doc2/angle_cosine_shift.html | 81 -
doc/doc2/angle_cosine_shift_exp.html | 94 -
doc/doc2/angle_cosine_squared.html | 82 -
doc/doc2/angle_dipole.html | 130 -
doc/doc2/angle_fourier.html | 78 -
doc/doc2/angle_fourier_simple.html | 77 -
doc/doc2/angle_harmonic.html | 84 -
doc/doc2/angle_hybrid.html | 96 -
doc/doc2/angle_none.html | 34 -
doc/doc2/angle_quartic.html | 84 -
doc/doc2/angle_sdk.html | 64 -
doc/doc2/angle_style.html | 100 -
doc/doc2/angle_table.html | 163 -
doc/doc2/atom_modify.html | 179 -
doc/doc2/atom_style.html | 276 -
doc/doc2/balance.html | 360 -
doc/doc2/body.html | 163 -
doc/doc2/bond_class2.html | 88 -
doc/doc2/bond_coeff.html | 100 -
doc/doc2/bond_fene.html | 96 -
doc/doc2/bond_fene_expand.html | 99 -
doc/doc2/bond_harmonic.html | 81 -
doc/doc2/bond_harmonic_shift.html | 85 -
doc/doc2/bond_harmonic_shift_cut.html | 84 -
doc/doc2/bond_hybrid.html | 79 -
doc/doc2/bond_morse.html | 80 -
doc/doc2/bond_none.html | 34 -
doc/doc2/bond_nonlinear.html | 86 -
doc/doc2/bond_quartic.html | 119 -
doc/doc2/bond_style.html | 109 -
doc/doc2/bond_table.html | 160 -
doc/doc2/boundary.html | 106 -
doc/doc2/box.html | 69 -
doc/doc2/change_box.html | 342 -
doc/doc2/clear.html | 43 -
doc/doc2/comm_modify.html | 167 -
doc/doc2/comm_style.html | 68 -
doc/doc2/compute.html | 265 -
doc/doc2/compute_ackland_atom.html | 80 -
doc/doc2/compute_angle_local.html | 87 -
doc/doc2/compute_angmom_chunk.html | 94 -
doc/doc2/compute_basal_atom.html | 82 -
doc/doc2/compute_body_local.html | 99 -
doc/doc2/compute_bond_local.html | 94 -
doc/doc2/compute_centro_atom.html | 126 -
doc/doc2/compute_chunk_atom.html | 568 -
doc/doc2/compute_cluster_atom.html | 78 -
doc/doc2/compute_cna_atom.html | 104 -
doc/doc2/compute_com.html | 62 -
doc/doc2/compute_com_chunk.html | 92 -
doc/doc2/compute_contact_atom.html | 59 -
doc/doc2/compute_coord_atom.html | 97 -
doc/doc2/compute_damage_atom.html | 68 -
doc/doc2/compute_dihedral_local.html | 79 -
doc/doc2/compute_dilatation_atom.html | 71 -
doc/doc2/compute_displace_atom.html | 74 -
doc/doc2/compute_erotate_asphere.html | 75 -
doc/doc2/compute_erotate_rigid.html | 66 -
doc/doc2/compute_erotate_sphere.html | 62 -
doc/doc2/compute_erotate_sphere_atom.html | 58 -
doc/doc2/compute_event_displace.html | 67 -
doc/doc2/compute_fep.html | 279 -
doc/doc2/compute_group_group.html | 135 -
doc/doc2/compute_gyration.html | 78 -
doc/doc2/compute_gyration_chunk.html | 122 -
doc/doc2/compute_heat_flux.html | 192 -
doc/doc2/compute_hexorder_atom.html | 125 -
doc/doc2/compute_improper_local.html | 79 -
doc/doc2/compute_inertia_chunk.html | 93 -
doc/doc2/compute_ke.html | 64 -
doc/doc2/compute_ke_atom.html | 53 -
doc/doc2/compute_ke_atom_eff.html | 82 -
doc/doc2/compute_ke_eff.html | 83 -
doc/doc2/compute_ke_rigid.html | 65 -
doc/doc2/compute_meso_e_atom.html | 61 -
doc/doc2/compute_meso_rho_atom.html | 61 -
doc/doc2/compute_meso_t_atom.html | 63 -
doc/doc2/compute_modify.html | 80 -
doc/doc2/compute_msd.html | 99 -
doc/doc2/compute_msd_chunk.html | 125 -
doc/doc2/compute_msd_nongauss.html | 90 -
doc/doc2/compute_omega_chunk.html | 94 -
doc/doc2/compute_orientorder_atom.html | 129 -
doc/doc2/compute_pair.html | 86 -
doc/doc2/compute_pair_local.html | 127 -
doc/doc2/compute_pe.html | 109 -
doc/doc2/compute_pe_atom.html | 97 -
doc/doc2/compute_plasticity_atom.html | 73 -
doc/doc2/compute_pressure.html | 155 -
doc/doc2/compute_property_atom.html | 173 -
doc/doc2/compute_property_chunk.html | 127 -
doc/doc2/compute_property_local.html | 151 -
doc/doc2/compute_rdf.html | 160 -
doc/doc2/compute_reduce.html | 200 -
doc/doc2/compute_saed.html | 191 -
doc/doc2/compute_slice.html | 124 -
doc/doc2/compute_smd_contact_radius.html | 58 -
doc/doc2/compute_smd_damage.html | 53 -
doc/doc2/compute_smd_hourglass_error.html | 61 -
doc/doc2/compute_smd_internal_energy.html | 51 -
doc/doc2/compute_smd_plastic_strain.html | 54 -
doc/doc2/compute_smd_plastic_strain_rate.html | 54 -
doc/doc2/compute_smd_rho.html | 54 -
doc/doc2/compute_smd_tlsph_defgrad.html | 57 -
doc/doc2/compute_smd_tlsph_dt.html | 59 -
doc/doc2/compute_smd_tlsph_num_neighs.html | 55 -
doc/doc2/compute_smd_tlsph_shape.html | 57 -
doc/doc2/compute_smd_tlsph_strain.html | 58 -
doc/doc2/compute_smd_tlsph_strain_rate.html | 57 -
doc/doc2/compute_smd_tlsph_stress.html | 58 -
doc/doc2/compute_smd_triangle_mesh_vertices.html | 64 -
doc/doc2/compute_smd_ulsph_num_neighs.html | 53 -
doc/doc2/compute_smd_ulsph_strain.html | 56 -
doc/doc2/compute_smd_ulsph_strain_rate.html | 56 -
doc/doc2/compute_smd_ulsph_stress.html | 57 -
doc/doc2/compute_smd_vol.html | 57 -
doc/doc2/compute_sna_atom.html | 262 -
doc/doc2/compute_stress_atom.html | 172 -
doc/doc2/compute_tally.html | 92 -
doc/doc2/compute_temp.html | 121 -
doc/doc2/compute_temp_asphere.html | 163 -
doc/doc2/compute_temp_chunk.html | 251 -
doc/doc2/compute_temp_com.html | 98 -
doc/doc2/compute_temp_cs.html | 125 -
doc/doc2/compute_temp_deform.html | 139 -
doc/doc2/compute_temp_deform_eff.html | 78 -
doc/doc2/compute_temp_drude.html | 87 -
doc/doc2/compute_temp_eff.html | 100 -
doc/doc2/compute_temp_partial.html | 127 -
doc/doc2/compute_temp_profile.html | 195 -
doc/doc2/compute_temp_ramp.html | 122 -
doc/doc2/compute_temp_region.html | 115 -
doc/doc2/compute_temp_region_eff.html | 69 -
doc/doc2/compute_temp_rotate.html | 101 -
doc/doc2/compute_temp_sphere.html | 147 -
doc/doc2/compute_ti.html | 148 -
doc/doc2/compute_torque_chunk.html | 92 -
doc/doc2/compute_vacf.html | 76 -
doc/doc2/compute_vcm_chunk.html | 82 -
doc/doc2/compute_voronoi_atom.html | 183 -
doc/doc2/compute_xrd.html | 214 -
doc/doc2/create_atoms.html | 329 -
doc/doc2/create_bonds.html | 114 -
doc/doc2/create_box.html | 162 -
doc/doc2/delete_atoms.html | 154 -
doc/doc2/delete_bonds.html | 159 -
doc/doc2/dielectric.html | 44 -
doc/doc2/dihedral_charmm.html | 123 -
doc/doc2/dihedral_class2.html | 185 -
doc/doc2/dihedral_coeff.html | 113 -
doc/doc2/dihedral_cosine_shift_exp.html | 92 -
doc/doc2/dihedral_fourier.html | 82 -
doc/doc2/dihedral_harmonic.html | 90 -
doc/doc2/dihedral_helix.html | 91 -
doc/doc2/dihedral_hybrid.html | 97 -
doc/doc2/dihedral_multi_harmonic.html | 79 -
doc/doc2/dihedral_nharmonic.html | 79 -
doc/doc2/dihedral_none.html | 34 -
doc/doc2/dihedral_opls.html | 93 -
doc/doc2/dihedral_quadratic.html | 80 -
doc/doc2/dihedral_style.html | 121 -
doc/doc2/dihedral_table.html | 211 -
doc/doc2/dimension.html | 53 -
doc/doc2/displace_atoms.html | 143 -
doc/doc2/dump.html | 649 -
doc/doc2/dump_h5md.html | 136 -
doc/doc2/dump_image.html | 566 -
doc/doc2/dump_modify.html | 817 -
doc/doc2/dump_molfile.html | 138 -
doc/doc2/echo.html | 43 -
doc/doc2/fix.html | 280 -
doc/doc2/fix_adapt.html | 267 -
doc/doc2/fix_adapt_fep.html | 275 -
doc/doc2/fix_addforce.html | 184 -
doc/doc2/fix_addtorque.html | 102 -
doc/doc2/fix_append_atoms.html | 123 -
doc/doc2/fix_atc.html | 258 -
doc/doc2/fix_atom_swap.html | 201 -
doc/doc2/fix_ave_atom.html | 165 -
doc/doc2/fix_ave_chunk.html | 464 -
doc/doc2/fix_ave_correlate.html | 353 -
doc/doc2/fix_ave_correlate_long.html | 159 -
doc/doc2/fix_ave_histo.html | 351 -
doc/doc2/fix_ave_spatial.html | 435 -
doc/doc2/fix_ave_spatial_sphere.html | 342 -
doc/doc2/fix_ave_time.html | 341 -
doc/doc2/fix_aveforce.html | 128 -
doc/doc2/fix_balance.html | 361 -
doc/doc2/fix_bond_break.html | 158 -
doc/doc2/fix_bond_create.html | 256 -
doc/doc2/fix_bond_swap.html | 199 -
doc/doc2/fix_box_relax.html | 369 -
doc/doc2/fix_colvars.html | 147 -
doc/doc2/fix_deform.html | 607 -
doc/doc2/fix_deposit.html | 292 -
doc/doc2/fix_drag.html | 66 -
doc/doc2/fix_drude.html | 60 -
doc/doc2/fix_drude_transform.html | 171 -
doc/doc2/fix_dt_reset.html | 96 -
doc/doc2/fix_efield.html | 170 -
doc/doc2/fix_enforce2d.html | 74 -
doc/doc2/fix_evaporate.html | 109 -
doc/doc2/fix_external.html | 163 -
doc/doc2/fix_freeze.html | 93 -
doc/doc2/fix_gcmc.html | 369 -
doc/doc2/fix_gld.html | 171 -
doc/doc2/fix_gle.html | 170 -
doc/doc2/fix_gravity.html | 154 -
doc/doc2/fix_heat.html | 137 -
doc/doc2/fix_imd.html | 172 -
doc/doc2/fix_indent.html | 211 -
doc/doc2/fix_ipi.html | 98 -
doc/doc2/fix_langevin.html | 362 -
doc/doc2/fix_langevin_drude.html | 280 -
doc/doc2/fix_langevin_eff.html | 128 -
doc/doc2/fix_lb_fluid.html | 388 -
doc/doc2/fix_lb_momentum.html | 84 -
doc/doc2/fix_lb_pc.html | 68 -
doc/doc2/fix_lb_rigid_pc_sphere.html | 158 -
doc/doc2/fix_lb_viscous.html | 100 -
doc/doc2/fix_lineforce.html | 56 -
doc/doc2/fix_meso.html | 57 -
doc/doc2/fix_meso_stationary.html | 58 -
doc/doc2/fix_modify.html | 81 -
doc/doc2/fix_momentum.html | 85 -
doc/doc2/fix_move.html | 234 -
doc/doc2/fix_msst.html | 171 -
doc/doc2/fix_neb.html | 113 -
doc/doc2/fix_nh.html | 633 -
doc/doc2/fix_nh_eff.html | 158 -
doc/doc2/fix_nph_asphere.html | 159 -
doc/doc2/fix_nph_sphere.html | 154 -
doc/doc2/fix_nphug.html | 239 -
doc/doc2/fix_npt_asphere.html | 183 -
doc/doc2/fix_npt_sphere.html | 178 -
doc/doc2/fix_nve.html | 81 -
doc/doc2/fix_nve_asphere.html | 65 -
doc/doc2/fix_nve_asphere_noforce.html | 70 -
doc/doc2/fix_nve_body.html | 67 -
doc/doc2/fix_nve_eff.html | 59 -
doc/doc2/fix_nve_limit.html | 91 -
doc/doc2/fix_nve_line.html | 62 -
doc/doc2/fix_nve_noforce.html | 59 -
doc/doc2/fix_nve_sphere.html | 106 -
doc/doc2/fix_nve_tri.html | 62 -
doc/doc2/fix_nvt_asphere.html | 159 -
doc/doc2/fix_nvt_sllod.html | 187 -
doc/doc2/fix_nvt_sllod_eff.html | 100 -
doc/doc2/fix_nvt_sphere.html | 155 -
doc/doc2/fix_oneway.html | 69 -
doc/doc2/fix_orient_fcc.html | 188 -
doc/doc2/fix_phonon.html | 221 -
doc/doc2/fix_pimd.html | 195 -
doc/doc2/fix_planeforce.html | 56 -
doc/doc2/fix_poems.html | 146 -
doc/doc2/fix_pour.html | 242 -
doc/doc2/fix_press_berendsen.html | 227 -
doc/doc2/fix_print.html | 102 -
doc/doc2/fix_property_atom.html | 226 -
doc/doc2/fix_qbmsst.html | 232 -
doc/doc2/fix_qeq.html | 209 -
doc/doc2/fix_qeq_comb.html | 145 -
doc/doc2/fix_qeq_reax.html | 106 -
doc/doc2/fix_qmmm.html | 71 -
doc/doc2/fix_qtb.html | 194 -
doc/doc2/fix_reax_bonds.html | 73 -
doc/doc2/fix_reaxc_species.html | 165 -
doc/doc2/fix_recenter.html | 136 -
doc/doc2/fix_restrain.html | 193 -
doc/doc2/fix_rigid.html | 814 -
doc/doc2/fix_saed_vtk.html | 199 -
doc/doc2/fix_setforce.html | 129 -
doc/doc2/fix_shake.html | 247 -
doc/doc2/fix_smd.html | 162 -
doc/doc2/fix_smd_adjust_dt.html | 63 -
doc/doc2/fix_smd_integrate_tlsph.html | 59 -
doc/doc2/fix_smd_integrate_ulsph.html | 63 -
doc/doc2/fix_smd_move_triangulated_surface.html | 81 -
doc/doc2/fix_smd_setvel.html | 96 -
.../fix_smd_tlsph_reference_configuration.html | 2 -
doc/doc2/fix_smd_wall_surface.html | 68 -
doc/doc2/fix_spring.html | 151 -
doc/doc2/fix_spring_rg.html | 72 -
doc/doc2/fix_spring_self.html | 84 -
doc/doc2/fix_srd.html | 410 -
doc/doc2/fix_store_force.html | 77 -
doc/doc2/fix_store_state.html | 143 -
doc/doc2/fix_temp_berendsen.html | 190 -
doc/doc2/fix_temp_csvr.html | 182 -
doc/doc2/fix_temp_rescale.html | 184 -
doc/doc2/fix_temp_rescale_eff.html | 81 -
doc/doc2/fix_tfmc.html | 168 -
doc/doc2/fix_thermal_conductivity.html | 177 -
doc/doc2/fix_ti_rs.html | 156 -
doc/doc2/fix_ti_spring.html | 175 -
doc/doc2/fix_tmd.html | 138 -
doc/doc2/fix_ttm.html | 350 -
doc/doc2/fix_tune_kspace.html | 109 -
doc/doc2/fix_vector.html | 171 -
doc/doc2/fix_viscosity.html | 184 -
doc/doc2/fix_viscous.html | 134 -
doc/doc2/fix_wall.html | 310 -
doc/doc2/fix_wall_gran.html | 176 -
doc/doc2/fix_wall_piston.html | 131 -
doc/doc2/fix_wall_reflect.html | 199 -
doc/doc2/fix_wall_region.html | 210 -
doc/doc2/fix_wall_srd.html | 203 -
doc/doc2/genindex.html | 2244 -
doc/doc2/group.html | 289 -
doc/doc2/group2ndx.html | 58 -
doc/doc2/if.html | 194 -
doc/doc2/improper_class2.html | 131 -
doc/doc2/improper_coeff.html | 102 -
doc/doc2/improper_cossq.html | 95 -
doc/doc2/improper_cvff.html | 92 -
doc/doc2/improper_fourier.html | 87 -
doc/doc2/improper_harmonic.html | 97 -
doc/doc2/improper_hybrid.html | 75 -
doc/doc2/improper_none.html | 34 -
doc/doc2/improper_ring.html | 102 -
doc/doc2/improper_style.html | 99 -
doc/doc2/improper_umbrella.html | 97 -
doc/doc2/include.html | 45 -
doc/doc2/info.html | 91 -
doc/doc2/jump.html | 136 -
doc/doc2/kspace_modify.html | 350 -
doc/doc2/kspace_style.html | 394 -
doc/doc2/label.html | 41 -
doc/doc2/lattice.html | 300 -
doc/doc2/log.html | 51 -
doc/doc2/mass.html | 89 -
doc/doc2/min_modify.html | 83 -
doc/doc2/min_style.html | 104 -
doc/doc2/minimize.html | 279 -
doc/doc2/molecule.html | 473 -
doc/doc2/neb.html | 442 -
doc/doc2/neigh_modify.html | 219 -
doc/doc2/neighbor.html | 88 -
doc/doc2/newton.html | 67 -
doc/doc2/next.html | 148 -
doc/doc2/package.html | 675 -
doc/doc2/pair_adp.html | 194 -
doc/doc2/pair_airebo.html | 203 -
doc/doc2/pair_awpmd.html | 130 -
doc/doc2/pair_beck.html | 117 -
doc/doc2/pair_body.html | 124 -
doc/doc2/pair_bop.html | 460 -
doc/doc2/pair_born.html | 210 -
doc/doc2/pair_brownian.html | 150 -
doc/doc2/pair_buck.html | 220 -
doc/doc2/pair_buck_long.html | 182 -
doc/doc2/pair_charmm.html | 219 -
doc/doc2/pair_class2.html | 193 -
doc/doc2/pair_coeff.html | 150 -
doc/doc2/pair_colloid.html | 213 -
doc/doc2/pair_comb.html | 204 -
doc/doc2/pair_coul.html | 373 -
doc/doc2/pair_coul_diel.html | 120 -
doc/doc2/pair_cs.html | 91 -
doc/doc2/pair_dipole.html | 286 -
doc/doc2/pair_dpd.html | 221 -
doc/doc2/pair_dsmc.html | 154 -
doc/doc2/pair_eam.html | 480 -
doc/doc2/pair_edip.html | 174 -
doc/doc2/pair_eff.html | 325 -
doc/doc2/pair_eim.html | 181 -
doc/doc2/pair_gauss.html | 172 -
doc/doc2/pair_gayberne.html | 243 -
doc/doc2/pair_gran.html | 279 -
doc/doc2/pair_gromacs.html | 170 -
doc/doc2/pair_hbond_dreiding.html | 255 -
doc/doc2/pair_hybrid.html | 390 -
doc/doc2/pair_kim.html | 123 -
doc/doc2/pair_lcbop.html | 103 -
doc/doc2/pair_line_lj.html | 142 -
doc/doc2/pair_list.html | 154 -
doc/doc2/pair_lj.html | 366 -
doc/doc2/pair_lj96.html | 116 -
doc/doc2/pair_lj_cubic.html | 138 -
doc/doc2/pair_lj_cut_smooth.html | 111 -
doc/doc2/pair_lj_expand.html | 120 -
doc/doc2/pair_lj_long.html | 235 -
doc/doc2/pair_lj_sf.html | 121 -
doc/doc2/pair_lj_smooth.html | 130 -
doc/doc2/pair_lj_smooth_linear.html | 111 -
doc/doc2/pair_lj_soft.html | 299 -
doc/doc2/pair_lubricate.html | 239 -
doc/doc2/pair_lubricateU.html | 225 -
doc/doc2/pair_meam.html | 383 -
doc/doc2/pair_meam_spline.html | 152 -
doc/doc2/pair_meam_sw_spline.html | 146 -
doc/doc2/pair_mgpt.html | 229 -
doc/doc2/pair_mie.html | 107 -
doc/doc2/pair_modify.html | 271 -
doc/doc2/pair_morse.html | 114 -
doc/doc2/pair_nb3b_harmonic.html | 129 -
doc/doc2/pair_nm.html | 183 -
doc/doc2/pair_none.html | 45 -
doc/doc2/pair_peri.html | 231 -
doc/doc2/pair_polymorphic.html | 245 -
doc/doc2/pair_quip.html | 102 -
doc/doc2/pair_reax.html | 218 -
doc/doc2/pair_reax_c.html | 323 -
doc/doc2/pair_resquared.html | 244 -
doc/doc2/pair_sdk.html | 169 -
doc/doc2/pair_smd_hertz.html | 60 -
doc/doc2/pair_smd_tlsph.html | 70 -
doc/doc2/pair_smd_triangulated_surface.html | 61 -
doc/doc2/pair_smd_ulsph.html | 76 -
doc/doc2/pair_smtbq.html | 272 -
doc/doc2/pair_snap.html | 201 -
doc/doc2/pair_soft.html | 143 -
doc/doc2/pair_sph_heatconduction.html | 68 -
doc/doc2/pair_sph_idealgas.html | 82 -
doc/doc2/pair_sph_lj.html | 86 -
doc/doc2/pair_sph_rhosum.html | 69 -
doc/doc2/pair_sph_taitwater.html | 85 -
doc/doc2/pair_sph_taitwater_morris.html | 83 -
doc/doc2/pair_srp.html | 176 -
doc/doc2/pair_style.html | 235 -
doc/doc2/pair_sw.html | 228 -
doc/doc2/pair_table.html | 263 -
doc/doc2/pair_tersoff.html | 267 -
doc/doc2/pair_tersoff_mod.html | 204 -
doc/doc2/pair_tersoff_zbl.html | 278 -
doc/doc2/pair_thole.html | 133 -
doc/doc2/pair_tri_lj.html | 145 -
doc/doc2/pair_vashishta.html | 236 -
doc/doc2/pair_write.html | 83 -
doc/doc2/pair_yukawa.html | 111 -
doc/doc2/pair_yukawa_colloid.html | 163 -
doc/doc2/pair_zbl.html | 148 -
doc/doc2/partition.html | 78 -
doc/doc2/prd.html | 339 -
doc/doc2/print.html | 86 -
doc/doc2/processors.html | 351 -
doc/doc2/python.html | 490 -
doc/doc2/quit.html | 51 -
doc/doc2/read_data.html | 1234 -
doc/doc2/read_dump.html | 336 -
doc/doc2/read_restart.html | 223 -
doc/doc2/region.html | 327 -
doc/doc2/replicate.html | 100 -
doc/doc2/rerun.html | 210 -
doc/doc2/reset_timestep.html | 66 -
doc/doc2/restart.html | 187 -
doc/doc2/run.html | 215 -
doc/doc2/run_style.html | 298 -
doc/doc2/search.html | 206 -
doc/doc2/set.html | 415 -
doc/doc2/shell.html | 114 -
doc/doc2/special_bonds.html | 276 -
doc/doc2/suffix.html | 111 -
doc/doc2/tad.html | 327 -
doc/doc2/temper.html | 137 -
doc/doc2/thermo.html | 64 -
doc/doc2/thermo_modify.html | 173 -
doc/doc2/thermo_style.html | 371 -
doc/doc2/timer.html | 79 -
doc/doc2/timestep.html | 58 -
doc/doc2/tutorial_drude.html | 467 -
doc/doc2/uncompute.html | 39 -
doc/doc2/undump.html | 38 -
doc/doc2/unfix.html | 39 -
doc/doc2/units.html | 223 -
doc/doc2/variable.html | 1218 -
doc/doc2/velocity.html | 270 -
doc/doc2/write_data.html | 131 -
doc/doc2/write_dump.html | 101 -
doc/doc2/write_restart.html | 130 -
doc/dump.html | 771 -
doc/dump.txt | 631 -
doc/dump_h5md.html | 299 -
doc/dump_h5md.txt | 124 -
doc/dump_image.html | 711 -
doc/dump_image.txt | 551 -
doc/dump_modify.html | 1045 -
doc/dump_modify.txt | 911 -
doc/dump_molfile.html | 305 -
doc/dump_molfile.txt | 127 -
doc/echo.html | 230 -
doc/fix.html | 449 -
doc/fix.txt | 293 -
doc/fix_adapt.html | 466 -
doc/fix_adapt.txt | 251 -
doc/fix_adapt_fep.html | 465 -
doc/fix_adapt_fep.txt | 259 -
doc/fix_addforce.html | 346 -
doc/fix_addforce.txt | 171 -
doc/fix_addtorque.html | 269 -
doc/fix_addtorque.txt | 93 -
doc/fix_append_atoms.html | 291 -
doc/fix_atc.html | 434 -
doc/fix_atc.txt | 243 -
doc/fix_atom_swap.html | 357 -
doc/fix_atom_swap.txt | 187 -
doc/fix_ave_atom.html | 320 -
doc/fix_ave_atom.txt | 153 -
doc/fix_ave_chunk.html | 582 -
doc/fix_ave_chunk.txt | 448 -
doc/fix_ave_correlate.html | 483 -
doc/fix_ave_correlate.txt | 338 -
doc/fix_ave_correlate_long.html | 317 -
doc/fix_ave_correlate_long.txt | 144 -
doc/fix_ave_histo.html | 486 -
doc/fix_ave_histo.txt | 333 -
doc/fix_ave_spatial.html | 567 -
doc/fix_ave_spatial.txt | 418 -
doc/fix_ave_spatial_sphere.html | 477 -
doc/fix_ave_spatial_sphere.txt | 323 -
doc/fix_ave_time.html | 479 -
doc/fix_ave_time.txt | 326 -
doc/fix_aveforce.html | 296 -
doc/fix_aveforce.txt | 115 -
doc/fix_balance.html | 535 -
doc/fix_balance.txt | 347 -
doc/fix_bond_break.html | 328 -
doc/fix_bond_break.txt | 145 -
doc/fix_bond_create.html | 425 -
doc/fix_bond_create.txt | 242 -
doc/fix_bond_swap.html | 359 -
doc/fix_bond_swap.txt | 193 -
doc/fix_box_relax.html | 518 -
doc/fix_box_relax.txt | 359 -
doc/fix_colvars.html | 304 -
doc/fix_colvars.txt | 136 -
doc/fix_deform.html | 726 -
doc/fix_deform.txt | 594 -
doc/fix_deposit.html | 449 -
doc/fix_deposit.txt | 278 -
doc/fix_drag.html | 246 -
doc/fix_drag.txt | 62 -
doc/fix_drude.html | 235 -
doc/fix_drude.txt | 56 -
doc/fix_drude_transform.html | 335 -
doc/fix_drude_transform.txt | 165 -
doc/fix_dt_reset.html | 274 -
doc/fix_efield.html | 328 -
doc/fix_efield.txt | 158 -
doc/fix_enforce2d.html | 249 -
doc/fix_enforce2d.txt | 68 -
doc/fix_evaporate.html | 279 -
doc/fix_evaporate.txt | 96 -
doc/fix_external.html | 322 -
doc/fix_external.txt | 154 -
doc/fix_freeze.html | 263 -
doc/fix_freeze.txt | 87 -
doc/fix_gcmc.html | 505 -
doc/fix_gcmc.txt | 351 -
doc/fix_gld.html | 323 -
doc/fix_gld.txt | 155 -
doc/fix_gle.html | 321 -
doc/fix_gle.txt | 155 -
doc/fix_gravity.html | 317 -
doc/fix_gravity.txt | 141 -
doc/fix_heat.html | 304 -
doc/fix_heat.txt | 124 -
doc/fix_imd.html | 327 -
doc/fix_imd.txt | 160 -
doc/fix_indent.html | 377 -
doc/fix_indent.txt | 200 -
doc/fix_ipi.html | 267 -
doc/fix_ipi.txt | 91 -
doc/fix_langevin.html | 490 -
doc/fix_langevin.txt | 344 -
doc/fix_langevin_drude.html | 434 -
doc/fix_langevin_drude.txt | 261 -
doc/fix_langevin_eff.html | 290 -
doc/fix_langevin_eff.txt | 113 -
doc/fix_lb_fluid.html | 498 -
doc/fix_lb_fluid.txt | 371 -
doc/fix_lb_momentum.html | 259 -
doc/fix_lb_momentum.txt | 73 -
doc/fix_lb_pc.html | 240 -
doc/fix_lb_pc.txt | 62 -
doc/fix_lb_rigid_pc_sphere.html | 329 -
doc/fix_lb_rigid_pc_sphere.txt | 146 -
doc/fix_lb_viscous.html | 265 -
doc/fix_lb_viscous.txt | 94 -
doc/fix_lineforce.html | 238 -
doc/fix_lineforce.txt | 51 -
doc/fix_meso.html | 236 -
doc/fix_meso_stationary.html | 237 -
doc/fix_modify.html | 260 -
doc/fix_modify.txt | 72 -
doc/fix_momentum.html | 261 -
doc/fix_move.html | 404 -
doc/fix_move.txt | 223 -
doc/fix_msst.html | 329 -
doc/fix_msst.txt | 158 -
doc/fix_neb.html | 282 -
doc/fix_neb.txt | 106 -
doc/fix_nh.html | 753 -
doc/fix_nh.txt | 611 -
doc/fix_nh_eff.html | 330 -
doc/fix_nh_eff.txt | 144 -
doc/fix_nph_asphere.html | 315 -
doc/fix_nph_asphere.txt | 153 -
doc/fix_nph_sphere.html | 313 -
doc/fix_nph_sphere.txt | 148 -
doc/fix_nphug.html | 393 -
doc/fix_nphug.txt | 230 -
doc/fix_npt_asphere.html | 338 -
doc/fix_npt_asphere.txt | 177 -
doc/fix_npt_sphere.html | 334 -
doc/fix_npt_sphere.txt | 172 -
doc/fix_nve.html | 260 -
doc/fix_nve.txt | 73 -
doc/fix_nve_asphere.html | 242 -
doc/fix_nve_asphere.txt | 60 -
doc/fix_nve_asphere_noforce.html | 243 -
doc/fix_nve_asphere_noforce.txt | 65 -
doc/fix_nve_body.html | 242 -
doc/fix_nve_body.txt | 62 -
doc/fix_nve_eff.html | 235 -
doc/fix_nve_limit.html | 273 -
doc/fix_nve_limit.txt | 86 -
doc/fix_nve_line.html | 240 -
doc/fix_nve_line.txt | 57 -
doc/fix_nve_noforce.html | 241 -
doc/fix_nve_sphere.html | 273 -
doc/fix_nve_sphere.txt | 95 -
doc/fix_nve_tri.html | 240 -
doc/fix_nve_tri.txt | 57 -
doc/fix_nvt_asphere.html | 317 -
doc/fix_nvt_asphere.txt | 153 -
doc/fix_nvt_sllod.html | 341 -
doc/fix_nvt_sllod.txt | 179 -
doc/fix_nvt_sllod_eff.html | 264 -
doc/fix_nvt_sllod_eff.txt | 94 -
doc/fix_nvt_sphere.html | 314 -
doc/fix_nvt_sphere.txt | 149 -
doc/fix_oneway.html | 244 -
doc/fix_orient_fcc.html | 345 -
doc/fix_orient_fcc.txt | 182 -
doc/fix_phonon.html | 353 -
doc/fix_phonon.txt | 202 -
doc/fix_pimd.html | 346 -
doc/fix_pimd.txt | 179 -
doc/fix_planeforce.html | 238 -
doc/fix_poems.html | 300 -
doc/fix_pour.html | 396 -
doc/fix_pour.txt | 229 -
doc/fix_press_berendsen.html | 384 -
doc/fix_press_berendsen.txt | 219 -
doc/fix_print.html | 276 -
doc/fix_property_atom.html | 387 -
doc/fix_property_atom.txt | 214 -
doc/fix_qbmsst.html | 379 -
doc/fix_qbmsst.txt | 219 -
doc/fix_qeq.html | 370 -
doc/fix_qeq.txt | 196 -
doc/fix_qeq_comb.html | 296 -
doc/fix_qeq_comb.txt | 128 -
doc/fix_qeq_reax.html | 271 -
doc/fix_qeq_reax.txt | 98 -
doc/fix_qmmm.html | 243 -
doc/fix_qmmm.txt | 66 -
doc/fix_qtb.html | 342 -
doc/fix_qtb.txt | 182 -
doc/fix_reax_bonds.html | 249 -
doc/fix_reax_bonds.txt | 67 -
doc/fix_reaxc_species.html | 324 -
doc/fix_reaxc_species.txt | 153 -
doc/fix_recenter.html | 308 -
doc/fix_recenter.txt | 126 -
doc/fix_restrain.html | 355 -
doc/fix_restrain.txt | 183 -
doc/fix_rigid.html | 917 -
doc/fix_rigid.txt | 789 -
doc/fix_saed_vtk.html | 354 -
doc/fix_saed_vtk.txt | 189 -
doc/fix_setforce.html | 293 -
doc/fix_setforce.txt | 116 -
doc/fix_shake.html | 388 -
doc/fix_shake.txt | 227 -
doc/fix_smd.html | 324 -
doc/fix_smd.rst | 168 -
doc/fix_smd.txt | 150 -
doc/fix_smd_adjust_dt.html | 240 -
doc/fix_smd_adjust_dt.txt | 55 -
doc/fix_smd_integrate_tlsph.html | 238 -
doc/fix_smd_integrate_tlsph.txt | 54 -
doc/fix_smd_integrate_ulsph.html | 246 -
doc/fix_smd_integrate_ulsph.txt | 60 -
doc/fix_smd_move_triangulated_surface.html | 257 -
doc/fix_smd_move_triangulated_surface.txt | 75 -
doc/fix_smd_setvel.html | 263 -
doc/fix_smd_setvel.txt | 84 -
doc/fix_smd_tlsph_reference_configuration.html | 190 -
doc/fix_smd_wall_surface.html | 244 -
doc/fix_smd_wall_surface.txt | 58 -
doc/fix_spring.html | 326 -
doc/fix_spring.txt | 142 -
doc/fix_spring_rg.html | 253 -
doc/fix_spring_rg.txt | 66 -
doc/fix_spring_self.html | 266 -
doc/fix_spring_self.txt | 79 -
doc/fix_srd.html | 577 -
doc/fix_srd.txt | 399 -
doc/fix_store_force.html | 258 -
doc/fix_store_force.txt | 72 -
doc/fix_store_state.html | 316 -
doc/fix_store_state.txt | 131 -
doc/fix_temp_berendsen.html | 345 -
doc/fix_temp_berendsen.txt | 180 -
doc/fix_temp_csvr.html | 344 -
doc/fix_temp_csvr.txt | 167 -
doc/fix_temp_rescale.html | 345 -
doc/fix_temp_rescale.txt | 171 -
doc/fix_temp_rescale_eff.html | 253 -
doc/fix_temp_rescale_eff.txt | 76 -
doc/fix_tfmc.html | 324 -
doc/fix_tfmc.txt | 152 -
doc/fix_thermal_conductivity.html | 335 -
doc/fix_thermal_conductivity.txt | 163 -
doc/fix_ti_rs.html | 298 -
doc/fix_ti_rs.txt | 140 -
doc/fix_ti_spring.html | 322 -
doc/fix_ti_spring.txt | 160 -
doc/fix_tmd.html | 298 -
doc/fix_ttm.html | 481 -
doc/fix_ttm.txt | 332 -
doc/fix_tune_kspace.html | 275 -
doc/fix_tune_kspace.txt | 102 -
doc/fix_vector.html | 331 -
doc/fix_vector.txt | 160 -
doc/fix_viscosity.html | 339 -
doc/fix_viscosity.txt | 169 -
doc/fix_viscous.html | 302 -
doc/fix_viscous.txt | 123 -
doc/fix_wall.html | 468 -
doc/fix_wall.txt | 292 -
doc/fix_wall_gran.html | 340 -
doc/fix_wall_gran.txt | 157 -
doc/fix_wall_piston.html | 295 -
doc/fix_wall_piston.txt | 120 -
doc/fix_wall_reflect.html | 358 -
doc/fix_wall_reflect.txt | 184 -
doc/fix_wall_region.html | 383 -
doc/fix_wall_region.txt | 205 -
doc/fix_wall_srd.html | 376 -
doc/fix_wall_srd.txt | 191 -
doc/genindex.html | 2244 -
doc/group.html | 458 -
doc/group.txt | 284 -
doc/group2ndx.html | 234 -
doc/group2ndx.txt | 51 -
doc/if.html | 367 -
doc/if.txt | 189 -
doc/improper_class2.html | 293 -
doc/improper_class2.txt | 124 -
doc/improper_coeff.html | 278 -
doc/improper_cossq.html | 265 -
doc/improper_cossq.txt | 89 -
doc/improper_cvff.html | 262 -
doc/improper_cvff.txt | 86 -
doc/improper_fourier.html | 258 -
doc/improper_fourier.txt | 82 -
doc/improper_harmonic.html | 267 -
doc/improper_harmonic.txt | 90 -
doc/improper_hybrid.html | 251 -
doc/improper_hybrid.txt | 70 -
doc/improper_none.html | 218 -
doc/improper_none.txt | 29 -
doc/improper_ring.html | 270 -
doc/improper_ring.txt | 96 -
doc/improper_style.html | 278 -
doc/improper_style.txt | 94 -
doc/improper_umbrella.html | 262 -
doc/improper_umbrella.txt | 90 -
doc/include.html | 230 -
doc/info.html | 266 -
doc/info.txt | 86 -
doc/jump.html | 320 -
doc/jump.txt | 131 -
doc/kspace_modify.html | 491 -
doc/kspace_modify.txt | 335 -
doc/kspace_style.html | 512 -
doc/kspace_style.txt | 370 -
doc/label.html | 226 -
doc/lattice.html | 469 -
doc/lattice.txt | 290 -
doc/log.html | 235 -
doc/log.txt | 46 -
doc/mass.html | 262 -
doc/min_modify.html | 266 -
doc/min_modify.txt | 76 -
doc/min_style.html | 284 -
doc/min_style.txt | 97 -
doc/minimize.html | 430 -
doc/minimize.txt | 274 -
doc/molecule.html | 604 -
doc/molecule.txt | 463 -
doc/neb.html | 584 -
doc/neb.txt | 426 -
doc/neigh_modify.html | 389 -
doc/neigh_modify.txt | 212 -
doc/neighbor.html | 271 -
doc/neighbor.txt | 83 -
doc/newton.html | 250 -
doc/next.html | 325 -
doc/next.txt | 142 -
doc/package.html | 771 -
doc/package.txt | 667 -
doc/pair_adp.html | 343 -
doc/pair_adp.txt | 186 -
doc/pair_airebo.html | 357 -
doc/pair_airebo.txt | 193 -
doc/pair_awpmd.html | 297 -
doc/pair_beck.html | 282 -
doc/pair_beck.txt | 109 -
doc/pair_body.html | 289 -
doc/pair_body.txt | 119 -
doc/pair_bop.html | 562 -
doc/pair_bop.txt | 416 -
doc/pair_born.html | 377 -
doc/pair_born.txt | 192 -
doc/pair_brownian.html | 308 -
doc/pair_brownian.txt | 143 -
doc/pair_buck.html | 398 -
doc/pair_buck.txt | 197 -
doc/pair_buck_long.html | 338 -
doc/pair_buck_long.txt | 170 -
doc/pair_charmm.html | 391 -
doc/pair_charmm.txt | 199 -
doc/pair_class2.html | 362 -
doc/pair_class2.txt | 173 -
doc/pair_coeff.html | 323 -
doc/pair_coeff.txt | 145 -
doc/pair_colloid.html | 360 -
doc/pair_colloid.txt | 205 -
doc/pair_comb.html | 352 -
doc/pair_comb.txt | 192 -
doc/pair_coul.html | 533 -
doc/pair_coul.txt | 339 -
doc/pair_coul_diel.html | 280 -
doc/pair_coul_diel.txt | 112 -
doc/pair_cs.html | 266 -
doc/pair_cs.txt | 83 -
doc/pair_dipole.html | 425 -
doc/pair_dipole.txt | 263 -
doc/pair_dpd.html | 372 -
doc/pair_dpd.txt | 209 -
doc/pair_dsmc.html | 316 -
doc/pair_dsmc.txt | 148 -
doc/pair_eam.html | 621 -
doc/pair_eam.txt | 451 -
doc/pair_edip.html | 327 -
doc/pair_edip.txt | 167 -
doc/pair_eff.html | 466 -
doc/pair_eff.txt | 314 -
doc/pair_eim.html | 338 -
doc/pair_eim.txt | 174 -
doc/pair_gauss.html | 328 -
doc/pair_gauss.txt | 163 -
doc/pair_gayberne.html | 380 -
doc/pair_gayberne.txt | 231 -
doc/pair_gran.html | 425 -
doc/pair_gran.txt | 260 -
doc/pair_gromacs.html | 337 -
doc/pair_gromacs.txt | 157 -
doc/pair_hbond_dreiding.html | 415 -
doc/pair_hbond_dreiding.txt | 245 -
doc/pair_hybrid.html | 543 -
doc/pair_hybrid.txt | 382 -
doc/pair_kim.html | 289 -
doc/pair_lcbop.html | 269 -
doc/pair_lcbop.txt | 97 -
doc/pair_line_lj.html | 302 -
doc/pair_line_lj.txt | 136 -
doc/pair_list.html | 315 -
doc/pair_list.txt | 144 -
doc/pair_lj.html | 549 -
doc/pair_lj.txt | 324 -
doc/pair_lj96.html | 285 -
doc/pair_lj96.txt | 108 -
doc/pair_lj_cubic.html | 298 -
doc/pair_lj_cubic.txt | 129 -
doc/pair_lj_cut_smooth.html | 111 -
doc/pair_lj_expand.html | 289 -
doc/pair_lj_expand.txt | 112 -
doc/pair_lj_long.html | 391 -
doc/pair_lj_long.txt | 225 -
doc/pair_lj_sf.html | 281 -
doc/pair_lj_sf.txt | 114 -
doc/pair_lj_smooth.html | 298 -
doc/pair_lj_smooth.txt | 123 -
doc/pair_lj_smooth_linear.html | 278 -
doc/pair_lj_smooth_linear.txt | 105 -
doc/pair_lj_soft.html | 471 -
doc/pair_lj_soft.txt | 277 -
doc/pair_lubricate.html | 379 -
doc/pair_lubricate.txt | 229 -
doc/pair_lubricateU.html | 366 -
doc/pair_lubricateU.txt | 217 -
doc/pair_meam.html | 516 -
doc/pair_meam.txt | 371 -
doc/pair_meam_spline.html | 310 -
doc/pair_meam_spline.txt | 145 -
doc/pair_meam_sw_spline.html | 303 -
doc/pair_meam_sw_spline.txt | 139 -
doc/pair_mgpt.html | 378 -
doc/pair_mgpt.txt | 219 -
doc/pair_mie.html | 273 -
doc/pair_mie.txt | 101 -
doc/pair_modify.html | 433 -
doc/pair_modify.txt | 261 -
doc/pair_morse.html | 284 -
doc/pair_morse.txt | 105 -
doc/pair_nb3b_harmonic.html | 293 -
doc/pair_nb3b_harmonic.txt | 123 -
doc/pair_nm.html | 342 -
doc/pair_nm.txt | 169 -
doc/pair_none.html | 227 -
doc/pair_none.txt | 40 -
doc/pair_peri.html | 372 -
doc/pair_peri.txt | 216 -
doc/pair_polymorphic.html | 380 -
doc/pair_polymorphic.txt | 229 -
doc/pair_quip.html | 266 -
doc/pair_quip.txt | 96 -
doc/pair_reax.html | 384 -
doc/pair_reax.txt | 212 -
doc/pair_reax_c.html | 456 -
doc/pair_reax_c.txt | 312 -
doc/pair_resquared.html | 376 -
doc/pair_resquared.txt | 235 -
doc/pair_sdk.html | 329 -
doc/pair_sdk.txt | 156 -
doc/pair_smd_hertz.html | 233 -
doc/pair_smd_hertz.txt | 56 -
doc/pair_smd_tlsph.html | 243 -
doc/pair_smd_triangulated_surface.html | 234 -
doc/pair_smd_triangulated_surface.txt | 57 -
doc/pair_smd_ulsph.html | 248 -
doc/pair_smtbq.html | 428 -
doc/pair_smtbq.txt | 261 -
doc/pair_snap.html | 353 -
doc/pair_snap.txt | 193 -
doc/pair_soft.html | 312 -
doc/pair_soft.txt | 136 -
doc/pair_sph_heatconduction.html | 240 -
doc/pair_sph_idealgas.html | 248 -
doc/pair_sph_idealgas.txt | 77 -
doc/pair_sph_lj.html | 250 -
doc/pair_sph_rhosum.html | 242 -
doc/pair_sph_taitwater.html | 250 -
doc/pair_sph_taitwater.txt | 79 -
doc/pair_sph_taitwater_morris.html | 248 -
doc/pair_srp.html | 328 -
doc/pair_srp.txt | 164 -
doc/pair_style.html | 405 -
doc/pair_style.txt | 230 -
doc/pair_sw.html | 384 -
doc/pair_sw.txt | 217 -
doc/pair_table.html | 412 -
doc/pair_table.txt | 254 -
doc/pair_tersoff.html | 411 -
doc/pair_tersoff.txt | 253 -
doc/pair_tersoff_mod.html | 348 -
doc/pair_tersoff_mod.txt | 192 -
doc/pair_tersoff_zbl.html | 414 -
doc/pair_tersoff_zbl.txt | 267 -
doc/pair_thole.html | 285 -
doc/pair_thole.txt | 126 -
doc/pair_tri_lj.html | 305 -
doc/pair_tri_lj.txt | 139 -
doc/pair_vashishta.html | 384 -
doc/pair_vashishta.txt | 228 -
doc/pair_write.html | 259 -
doc/pair_write.txt | 78 -
doc/pair_yukawa.html | 279 -
doc/pair_yukawa.txt | 104 -
doc/pair_yukawa_colloid.html | 318 -
doc/pair_yukawa_colloid.txt | 155 -
doc/pair_zbl.html | 313 -
doc/pair_zbl.txt | 139 -
doc/partition.html | 257 -
doc/partition.txt | 73 -
doc/prd.html | 465 -
doc/prd.txt | 322 -
doc/print.html | 266 -
doc/print.txt | 77 -
doc/processors.html | 500 -
doc/processors.txt | 342 -
doc/python.html | 640 -
doc/python.txt | 482 -
doc/quit.html | 230 -
doc/read_data.html | 1339 -
doc/read_data.txt | 1121 -
doc/read_dump.html | 477 -
doc/read_dump.txt | 324 -
doc/read_restart.html | 381 -
doc/read_restart.txt | 218 -
doc/region.html | 485 -
doc/region.txt | 316 -
doc/replicate.html | 277 -
doc/replicate.txt | 95 -
doc/rerun.html | 367 -
doc/rerun.txt | 202 -
doc/reset_timestep.html | 247 -
doc/restart.html | 351 -
doc/restart.txt | 175 -
doc/run.html | 385 -
doc/run.txt | 206 -
doc/run_style.html | 455 -
doc/run_style.txt | 289 -
doc/search.html | 206 -
doc/searchindex.js | 1 -
doc/set.html | 557 -
doc/set.txt | 411 -
doc/shell.html | 286 -
doc/special_bonds.html | 432 -
doc/special_bonds.txt | 264 -
doc/{ => src}/2001/README.html | 0
doc/{ => src}/2001/basics.html | 0
doc/{ => src}/2001/data_format.html | 0
doc/{ => src}/2001/deficiencies.html | 0
doc/{ => src}/2001/force_fields.html | 0
doc/{ => src}/2001/history.html | 0
doc/{ => src}/2001/input_commands.html | 0
doc/{ => src}/2001/units.html | 0
doc/{ => src}/99/README.html | 0
doc/{ => src}/99/basics.html | 0
doc/{ => src}/99/crib.html | 0
doc/{ => src}/99/data_format.html | 0
doc/{ => src}/99/force_fields.html | 0
doc/{ => src}/99/history.html | 0
doc/{ => src}/99/input_commands.html | 0
doc/{ => src}/99/units.html | 0
doc/src/Developer/classes.fig | 198 +
doc/src/Developer/classes.pdf | Bin 0 -> 9215 bytes
doc/src/Developer/developer.tex | 698 +
doc/{ => src}/Eqs/angle_charmm.jpg | Bin
doc/{ => src}/Eqs/angle_charmm.tex | 0
doc/{ => src}/Eqs/angle_class2.jpg | Bin
doc/{ => src}/Eqs/angle_class2.tex | 0
doc/{ => src}/Eqs/angle_cosine.jpg | Bin
doc/{ => src}/Eqs/angle_cosine.tex | 0
doc/{ => src}/Eqs/angle_cosine_delta.jpg | Bin
doc/{ => src}/Eqs/angle_cosine_delta.tex | 0
doc/{ => src}/Eqs/angle_cosine_periodic.jpg | Bin
doc/{ => src}/Eqs/angle_cosine_periodic.tex | 0
doc/{ => src}/Eqs/angle_cosine_shift.jpg | Bin
doc/{ => src}/Eqs/angle_cosine_shift.tex | 0
doc/{ => src}/Eqs/angle_cosine_shift_exp.jpg | Bin
doc/{ => src}/Eqs/angle_cosine_shift_exp.tex | 0
doc/{ => src}/Eqs/angle_cosine_squared.jpg | Bin
doc/{ => src}/Eqs/angle_cosine_squared.tex | 0
doc/src/Eqs/angle_dipole_couple.jpg | Bin 0 -> 2930 bytes
doc/src/Eqs/angle_dipole_couple.tex | 10 +
doc/{ => src}/Eqs/angle_dipole_gamma.jpg | Bin
doc/{ => src}/Eqs/angle_dipole_gamma.tex | 0
doc/{ => src}/Eqs/angle_dipole_potential.jpg | Bin
doc/{ => src}/Eqs/angle_dipole_potential.tex | 0
doc/{ => src}/Eqs/angle_dipole_torque.jpg | Bin
doc/{ => src}/Eqs/angle_dipole_torque.tex | 0
doc/{ => src}/Eqs/angle_fourier.jpg | Bin
doc/{ => src}/Eqs/angle_fourier.tex | 0
doc/{ => src}/Eqs/angle_fourier_simple.jpg | Bin
doc/{ => src}/Eqs/angle_fourier_simple.tex | 0
doc/{ => src}/Eqs/angle_harmonic.jpg | Bin
doc/{ => src}/Eqs/angle_harmonic.tex | 0
doc/{ => src}/Eqs/angle_quartic.jpg | Bin
doc/{ => src}/Eqs/angle_quartic.tex | 0
doc/{ => src}/Eqs/bond_class2.jpg | Bin
doc/{ => src}/Eqs/bond_class2.tex | 0
doc/{ => src}/Eqs/bond_fene.jpg | Bin
doc/{ => src}/Eqs/bond_fene.tex | 0
doc/{ => src}/Eqs/bond_fene_expand.jpg | Bin
doc/{ => src}/Eqs/bond_fene_expand.tex | 0
doc/{ => src}/Eqs/bond_harmonic.jpg | Bin
doc/{ => src}/Eqs/bond_harmonic.tex | 0
doc/{ => src}/Eqs/bond_harmonic_shift.jpg | Bin
doc/{ => src}/Eqs/bond_harmonic_shift.tex | 0
doc/{ => src}/Eqs/bond_harmonic_shift_cut.jpg | Bin
doc/{ => src}/Eqs/bond_harmonic_shift_cut.tex | 0
doc/{ => src}/Eqs/bond_morse.jpg | Bin
doc/{ => src}/Eqs/bond_morse.tex | 0
doc/{ => src}/Eqs/bond_nonlinear.jpg | Bin
doc/{ => src}/Eqs/bond_nonlinear.tex | 0
doc/{ => src}/Eqs/bond_quartic.jpg | Bin
doc/{ => src}/Eqs/bond_quartic.tex | 0
doc/{ => src}/Eqs/box.jpg | Bin
doc/{ => src}/Eqs/box.tex | 0
doc/{ => src}/Eqs/box_inverse.jpg | Bin
doc/{ => src}/Eqs/box_inverse.tex | 0
doc/{ => src}/Eqs/centro_symmetry.jpg | Bin
doc/{ => src}/Eqs/centro_symmetry.tex | 0
doc/{ => src}/Eqs/cna_cutoff1.jpg | Bin
doc/src/Eqs/cna_cutoff1.tex | 14 +
doc/{ => src}/Eqs/cna_cutoff2.jpg | Bin
doc/src/Eqs/cna_cutoff2.tex | 12 +
doc/src/Eqs/compute_dpd.jpg | Bin 0 -> 21381 bytes
doc/src/Eqs/compute_dpd.tex | 13 +
doc/{ => src}/Eqs/compute_fep_bar.jpg | Bin
doc/{ => src}/Eqs/compute_fep_bar.tex | 0
doc/{ => src}/Eqs/compute_fep_fdti.jpg | Bin
doc/{ => src}/Eqs/compute_fep_fdti.tex | 0
doc/{ => src}/Eqs/compute_fep_fep.jpg | Bin
doc/{ => src}/Eqs/compute_fep_fep.tex | 0
doc/{ => src}/Eqs/compute_fep_lambda.jpg | Bin
doc/{ => src}/Eqs/compute_fep_lambda.tex | 0
doc/{ => src}/Eqs/compute_fep_ti.jpg | Bin
doc/{ => src}/Eqs/compute_fep_ti.tex | 0
doc/{ => src}/Eqs/compute_fep_u.jpg | Bin
doc/{ => src}/Eqs/compute_fep_u.tex | 0
doc/{ => src}/Eqs/compute_fep_vol.jpg | Bin
doc/{ => src}/Eqs/compute_fep_vol.tex | 0
doc/{ => src}/Eqs/compute_gyration.jpg | Bin
doc/{ => src}/Eqs/compute_gyration.tex | 0
doc/{ => src}/Eqs/compute_msd_nongauss.jpg | Bin
doc/{ => src}/Eqs/compute_msd_nongauss.tex | 0
doc/{ => src}/Eqs/compute_saed1.jpg | Bin
doc/{ => src}/Eqs/compute_saed1.tex | 0
doc/{ => src}/Eqs/compute_saed2.jpg | Bin
doc/{ => src}/Eqs/compute_saed2.tex | 0
doc/{ => src}/Eqs/compute_saed3.jpg | Bin
doc/{ => src}/Eqs/compute_saed3.tex | 0
doc/{ => src}/Eqs/compute_sna_atom1.jpg | Bin
doc/{ => src}/Eqs/compute_sna_atom1.tex | 0
doc/{ => src}/Eqs/compute_sna_atom2.jpg | Bin
doc/{ => src}/Eqs/compute_sna_atom2.tex | 0
doc/{ => src}/Eqs/compute_sna_atom3.jpg | Bin
doc/{ => src}/Eqs/compute_sna_atom3.tex | 0
doc/{ => src}/Eqs/compute_sna_atom4.jpg | Bin
doc/{ => src}/Eqs/compute_sna_atom4.tex | 0
doc/{ => src}/Eqs/compute_sna_atom5.jpg | Bin
doc/{ => src}/Eqs/compute_sna_atom5.tex | 0
doc/{ => src}/Eqs/compute_sna_atom6.jpg | Bin
doc/{ => src}/Eqs/compute_sna_atom6.tex | 0
doc/{ => src}/Eqs/compute_xrd1.jpg | Bin
doc/{ => src}/Eqs/compute_xrd1.tex | 0
doc/{ => src}/Eqs/compute_xrd2.jpg | Bin
doc/{ => src}/Eqs/compute_xrd2.tex | 0
doc/{ => src}/Eqs/compute_xrd3.jpg | Bin
doc/{ => src}/Eqs/compute_xrd3.tex | 0
doc/{ => src}/Eqs/compute_xrd4.jpg | Bin
doc/{ => src}/Eqs/compute_xrd4.tex | 0
doc/{ => src}/Eqs/compute_xrd5.jpg | Bin
doc/{ => src}/Eqs/compute_xrd5.tex | 0
doc/{ => src}/Eqs/dihedral_charmm.jpg | Bin
doc/{ => src}/Eqs/dihedral_charmm.tex | 0
doc/{ => src}/Eqs/dihedral_class2.jpg | Bin
doc/{ => src}/Eqs/dihedral_class2.tex | 0
doc/{ => src}/Eqs/dihedral_cosine_shift_exp.jpg | Bin
doc/{ => src}/Eqs/dihedral_cosine_shift_exp.tex | 0
doc/{ => src}/Eqs/dihedral_fourier.jpg | Bin
doc/{ => src}/Eqs/dihedral_fourier.tex | 0
doc/{ => src}/Eqs/dihedral_harmonic.jpg | Bin
doc/{ => src}/Eqs/dihedral_harmonic.tex | 0
doc/{ => src}/Eqs/dihedral_helix.jpg | Bin
doc/{ => src}/Eqs/dihedral_helix.tex | 0
doc/{ => src}/Eqs/dihedral_multi_harmonic.jpg | Bin
doc/{ => src}/Eqs/dihedral_multi_harmonic.tex | 0
doc/{ => src}/Eqs/dihedral_nharmonic.jpg | Bin
doc/{ => src}/Eqs/dihedral_nharmonic.tex | 0
doc/{ => src}/Eqs/dihedral_opls.jpg | Bin
doc/{ => src}/Eqs/dihedral_opls.tex | 0
doc/{ => src}/Eqs/dihedral_quadratic.jpg | Bin
doc/{ => src}/Eqs/dihedral_quadratic.tex | 0
doc/src/Eqs/dihedral_spherical.jpg | Bin 0 -> 14432 bytes
doc/src/Eqs/dihedral_spherical.tex | 15 +
doc/{ => src}/Eqs/dreiding_hbond.jpg | Bin
doc/{ => src}/Eqs/eff_ECP1.jpg | Bin
doc/src/Eqs/eff_ECP1.tex | 9 +
doc/{ => src}/Eqs/eff_ECP2.jpg | Bin
doc/src/Eqs/eff_ECP2.tex | 8 +
doc/{ => src}/Eqs/eff_KE.jpg | Bin
doc/{ => src}/Eqs/eff_KE.tex | 0
doc/{ => src}/Eqs/eff_NN.jpg | Bin
doc/{ => src}/Eqs/eff_NN.tex | 0
doc/{ => src}/Eqs/eff_Ne.jpg | Bin
doc/{ => src}/Eqs/eff_Ne.tex | 0
doc/{ => src}/Eqs/eff_Pauli.jpg | Bin
doc/{ => src}/Eqs/eff_Pauli.tex | 0
doc/{ => src}/Eqs/eff_ee.jpg | Bin
doc/{ => src}/Eqs/eff_ee.tex | 0
doc/{ => src}/Eqs/eff_energy_expression.jpg | Bin
doc/{ => src}/Eqs/eff_energy_expression.tex | 0
doc/{ => src}/Eqs/fix_box_relax1.jpg | Bin
doc/{ => src}/Eqs/fix_box_relax1.tex | 0
doc/{ => src}/Eqs/fix_box_relax2.jpg | Bin
doc/{ => src}/Eqs/fix_box_relax2.tex | 0
doc/src/Eqs/fix_controller1.jpg | Bin 0 -> 4832 bytes
doc/src/Eqs/fix_controller1.tex | 12 +
doc/src/Eqs/fix_controller2.jpg | Bin 0 -> 5571 bytes
doc/src/Eqs/fix_controller2.tex | 12 +
doc/src/Eqs/fix_ehex_eom.jpg | Bin 0 -> 3272 bytes
doc/src/Eqs/fix_ehex_eom.tex | 8 +
doc/src/Eqs/fix_ehex_f.jpg | Bin 0 -> 10352 bytes
doc/src/Eqs/fix_ehex_f.tex | 12 +
doc/src/Eqs/fix_eos-cv.jpg | Bin 0 -> 3016 bytes
doc/src/Eqs/fix_eos-cv.tex | 9 +
doc/src/Eqs/fix_eos_table_rx.jpg | Bin 0 -> 17367 bytes
doc/src/Eqs/fix_eos_table_rx.tex | 9 +
doc/{ => src}/Eqs/fix_gld1.jpg | Bin
doc/{ => src}/Eqs/fix_gld1.tex | 0
doc/{ => src}/Eqs/fix_lb_fluid_boltzmann.jpg | Bin
doc/{ => src}/Eqs/fix_lb_fluid_boltzmann.tex | 0
doc/{ => src}/Eqs/fix_lb_fluid_fluidforce.jpg | Bin
doc/{ => src}/Eqs/fix_lb_fluid_fluidforce.tex | 0
doc/{ => src}/Eqs/fix_lb_fluid_gammadefault.jpg | Bin
doc/{ => src}/Eqs/fix_lb_fluid_gammadefault.tex | 0
doc/{ => src}/Eqs/fix_lb_fluid_navierstokes.jpg | Bin
doc/{ => src}/Eqs/fix_lb_fluid_navierstokes.tex | 0
doc/{ => src}/Eqs/fix_lb_fluid_properties.jpg | Bin
doc/{ => src}/Eqs/fix_lb_fluid_properties.tex | 0
doc/{ => src}/Eqs/fix_lb_fluid_stress.jpg | Bin
doc/{ => src}/Eqs/fix_lb_fluid_stress.tex | 0
doc/{ => src}/Eqs/fix_lb_fluid_viscosity.jpg | Bin
doc/{ => src}/Eqs/fix_lb_fluid_viscosity.tex | 0
doc/src/Eqs/fix_nh1.jpg | Bin 0 -> 68243 bytes
doc/src/Eqs/fix_nh1.tex | 36 +
doc/{ => src}/Eqs/fix_nphug.jpg | Bin
doc/{ => src}/Eqs/fix_nphug.tex | 0
doc/{ => src}/Eqs/fix_orient_fcc.jpg | Bin
doc/{ => src}/Eqs/fix_orient_fcc.tex | 0
doc/{ => src}/Eqs/fix_pimd.jpg | Bin
doc/{ => src}/Eqs/fix_pimd.tex | 0
doc/{ => src}/Eqs/fix_rattle_constraints.jpg | Bin
doc/{ => src}/Eqs/fix_rattle_constraints.tex | 0
doc/{ => src}/Eqs/fix_rattle_rij.jpg | Bin
doc/{ => src}/Eqs/fix_rattle_rij.tex | 0
doc/src/Eqs/fix_rx.jpg | Bin 0 -> 2427 bytes
doc/src/Eqs/fix_rx.tex | 9 +
doc/src/Eqs/fix_rx_localTemp.jpg | Bin 0 -> 16562 bytes
doc/src/Eqs/fix_rx_localTemp.tex | 9 +
doc/src/Eqs/fix_rx_localTemp2.jpg | Bin 0 -> 16284 bytes
doc/src/Eqs/fix_rx_localTemp2.tex | 9 +
doc/src/Eqs/fix_rx_reaction.jpg | Bin 0 -> 2896 bytes
doc/src/Eqs/fix_rx_reaction.tex | 9 +
doc/src/Eqs/fix_rx_reactionRate.jpg | Bin 0 -> 2939 bytes
doc/src/Eqs/fix_rx_reactionRate.tex | 9 +
doc/{ => src}/Eqs/fix_spring_rg.jpg | Bin
doc/{ => src}/Eqs/fix_spring_rg.tex | 0
doc/src/Eqs/fix_ti_spring_force.jpg | Bin 0 -> 2673 bytes
doc/src/Eqs/fix_ti_spring_force.tex | 11 +
doc/src/Eqs/fix_ti_spring_function_1.jpg | Bin 0 -> 1173 bytes
doc/{ => src}/Eqs/fix_ti_spring_function_1.tex | 0
doc/src/Eqs/fix_ti_spring_function_2.jpg | Bin 0 -> 5662 bytes
doc/{ => src}/Eqs/fix_ti_spring_function_2.tex | 0
doc/{ => src}/Eqs/fix_ttm.jpg | Bin
doc/{ => src}/Eqs/fix_ttm.tex | 0
doc/{ => src}/Eqs/fix_ttm_blast.jpg | Bin
doc/{ => src}/Eqs/fix_ttm_blast.tex | 0
doc/{ => src}/Eqs/fix_ttm_blast1.jpg | Bin
doc/{ => src}/Eqs/fix_ttm_blast1.tex | 0
doc/{ => src}/Eqs/fix_ttm_ce.jpg | Bin
doc/{ => src}/Eqs/fix_ttm_ce.tex | 0
doc/{ => src}/Eqs/fix_ttm_mod.jpg | Bin
doc/{ => src}/Eqs/fix_ttm_mod.tex | 0
doc/{ => src}/Eqs/fix_wall_colloid.jpg | Bin
doc/{ => src}/Eqs/fix_wall_colloid.tex | 0
doc/{ => src}/Eqs/fix_wall_harmonic.jpg | Bin
doc/{ => src}/Eqs/fix_wall_harmonic.tex | 0
doc/{ => src}/Eqs/fix_wall_lj1043.jpg | Bin
doc/src/Eqs/fix_wall_lj1043.tex | 12 +
doc/{ => src}/Eqs/fix_wall_lj93.jpg | Bin
doc/{ => src}/Eqs/fix_wall_lj93.tex | 0
doc/{ => src}/Eqs/fld.jpg | Bin
doc/{ => src}/Eqs/fld.tex | 0
doc/{ => src}/Eqs/fld2.jpg | Bin
doc/{ => src}/Eqs/fld2.tex | 0
doc/{ => src}/Eqs/heat_flux_J.jpg | Bin
doc/{ => src}/Eqs/heat_flux_J.tex | 0
doc/{ => src}/Eqs/heat_flux_k.jpg | Bin
doc/src/Eqs/heat_flux_k.tex | 11 +
doc/{ => src}/Eqs/hexorder.jpg | Bin
doc/{ => src}/Eqs/hexorder.tex | 0
doc/{ => src}/Eqs/improper_class2.jpg | Bin
doc/{ => src}/Eqs/improper_class2.tex | 0
doc/{ => src}/Eqs/improper_cossq.jpg | Bin
doc/{ => src}/Eqs/improper_cossq.tex | 0
doc/{ => src}/Eqs/improper_cvff.jpg | Bin
doc/{ => src}/Eqs/improper_cvff.tex | 0
doc/src/Eqs/improper_dist-1.jpg | Bin 0 -> 2169 bytes
doc/src/Eqs/improper_dist-1.tex | 9 +
doc/{ => src}/Eqs/improper_fourier.jpg | Bin
doc/{ => src}/Eqs/improper_fourier.tex | 0
doc/{ => src}/Eqs/improper_harmonic.jpg | Bin
doc/{ => src}/Eqs/improper_harmonic.tex | 0
doc/{ => src}/Eqs/improper_ring.jpg | Bin
doc/{ => src}/Eqs/improper_ring.tex | 0
doc/{ => src}/Eqs/improper_umbrella.jpg | Bin
doc/src/Eqs/improper_umbrella.tex | 13 +
doc/{ => src}/Eqs/min_energy.jpg | Bin
doc/{ => src}/Eqs/min_energy.tex | 0
doc/{ => src}/Eqs/orientorder.jpg | Bin
doc/{ => src}/Eqs/orientorder.tex | 0
doc/{ => src}/Eqs/pair_adp.jpg | Bin
doc/{ => src}/Eqs/pair_adp.tex | 0
doc/{ => src}/Eqs/pair_airebo.jpg | Bin
doc/{ => src}/Eqs/pair_airebo.tex | 0
doc/{ => src}/Eqs/pair_beck.jpg | Bin
doc/{ => src}/Eqs/pair_beck.tex | 0
doc/{ => src}/Eqs/pair_bop.jpg | Bin
doc/{ => src}/Eqs/pair_bop.tex | 0
doc/{ => src}/Eqs/pair_born.jpg | Bin
doc/{ => src}/Eqs/pair_born.tex | 0
doc/{ => src}/Eqs/pair_buck.jpg | Bin
doc/{ => src}/Eqs/pair_buck.tex | 0
doc/{ => src}/Eqs/pair_charmm.jpg | Bin
doc/{ => src}/Eqs/pair_charmm.tex | 0
doc/{ => src}/Eqs/pair_class2.jpg | Bin
doc/{ => src}/Eqs/pair_class2.tex | 0
doc/{ => src}/Eqs/pair_cmm.jpg | Bin
doc/{ => src}/Eqs/pair_cmm.tex | 0
doc/{ => src}/Eqs/pair_colloid_cc.jpg | Bin
doc/{ => src}/Eqs/pair_colloid_cc.tex | 0
doc/{ => src}/Eqs/pair_colloid_cs.jpg | Bin
doc/{ => src}/Eqs/pair_colloid_cs.tex | 0
doc/{ => src}/Eqs/pair_colloid_ss.jpg | Bin
doc/{ => src}/Eqs/pair_colloid_ss.tex | 0
doc/{ => src}/Eqs/pair_comb1.jpg | Bin
doc/src/Eqs/pair_comb1.tex | 7 +
doc/{ => src}/Eqs/pair_comb2.jpg | Bin
doc/src/Eqs/pair_comb2.tex | 23 +
doc/{ => src}/Eqs/pair_coul_diel.jpg | Bin
doc/{ => src}/Eqs/pair_coul_diel.tex | 0
doc/{ => src}/Eqs/pair_coul_dsf.jpg | Bin
doc/{ => src}/Eqs/pair_coul_dsf.tex | 0
doc/{ => src}/Eqs/pair_coul_soft.jpg | Bin
doc/{ => src}/Eqs/pair_coul_soft.tex | 0
doc/{ => src}/Eqs/pair_coul_wolf.jpg | Bin
doc/{ => src}/Eqs/pair_coul_wolf.tex | 0
doc/{ => src}/Eqs/pair_coulomb.jpg | Bin
doc/{ => src}/Eqs/pair_coulomb.tex | 0
doc/{ => src}/Eqs/pair_cs.jpg | Bin
doc/{ => src}/Eqs/pair_cs.tex | 0
doc/{ => src}/Eqs/pair_debye.jpg | Bin
doc/{ => src}/Eqs/pair_debye.tex | 0
doc/{ => src}/Eqs/pair_dipole.jpg | Bin
doc/{ => src}/Eqs/pair_dipole.tex | 0
doc/{ => src}/Eqs/pair_dipole_sf.jpg | Bin
doc/{ => src}/Eqs/pair_dipole_sf.tex | 0
doc/{ => src}/Eqs/pair_dipole_sf2.jpg | Bin
doc/{ => src}/Eqs/pair_dipole_sf2.tex | 0
doc/{ => src}/Eqs/pair_dpd.jpg | Bin
doc/{ => src}/Eqs/pair_dpd.tex | 0
doc/src/Eqs/pair_dpd_energy.jpg | Bin 0 -> 25636 bytes
doc/src/Eqs/pair_dpd_energy.tex | 12 +
doc/src/Eqs/pair_dpd_energy_terms.jpg | Bin 0 -> 8883 bytes
doc/src/Eqs/pair_dpd_energy_terms.tex | 11 +
doc/src/Eqs/pair_dpd_omega.jpg | Bin 0 -> 1689 bytes
doc/src/Eqs/pair_dpd_omega.tex | 9 +
doc/{ => src}/Eqs/pair_eam.jpg | Bin
doc/{ => src}/Eqs/pair_eam.tex | 0
doc/{ => src}/Eqs/pair_eam_fs.jpg | Bin
doc/{ => src}/Eqs/pair_eam_fs.tex | 0
doc/{ => src}/Eqs/pair_edip.jpg | Bin
doc/{ => src}/Eqs/pair_edip.tex | 0
doc/{ => src}/Eqs/pair_eim1.jpg | Bin
doc/{ => src}/Eqs/pair_eim1.tex | 0
doc/{ => src}/Eqs/pair_eim2.jpg | Bin
doc/{ => src}/Eqs/pair_eim2.tex | 0
doc/{ => src}/Eqs/pair_eim3.jpg | Bin
doc/{ => src}/Eqs/pair_eim3.tex | 0
doc/src/Eqs/pair_exp6_rx.jpg | Bin 0 -> 9372 bytes
doc/src/Eqs/pair_exp6_rx.tex | 9 +
doc/src/Eqs/pair_exp6_rx_oneFluid.jpg | Bin 0 -> 16062 bytes
doc/src/Eqs/pair_exp6_rx_oneFluid.tex | 11 +
doc/src/Eqs/pair_exp6_rx_oneFluid2.jpg | Bin 0 -> 7629 bytes
doc/src/Eqs/pair_exp6_rx_oneFluid2.tex | 11 +
doc/{ => src}/Eqs/pair_gauss.jpg | Bin
doc/{ => src}/Eqs/pair_gauss.tex | 0
doc/{ => src}/Eqs/pair_gauss_cut.jpg | Bin
doc/{ => src}/Eqs/pair_gauss_cut.tex | 0
doc/{ => src}/Eqs/pair_gayberne.jpg | Bin
doc/{ => src}/Eqs/pair_gayberne.tex | 0
doc/{ => src}/Eqs/pair_gayberne2.jpg | Bin
doc/{ => src}/Eqs/pair_gayberne2.tex | 0
doc/{ => src}/Eqs/pair_gran_hertz.jpg | Bin
doc/{ => src}/Eqs/pair_gran_hertz.tex | 0
doc/{ => src}/Eqs/pair_gran_hooke.jpg | Bin
doc/{ => src}/Eqs/pair_gran_hooke.tex | 0
doc/{ => src}/Eqs/pair_gromacs.jpg | Bin
doc/{ => src}/Eqs/pair_gromacs.tex | 0
doc/{ => src}/Eqs/pair_hbond_dreiding.jpg | Bin
doc/{ => src}/Eqs/pair_hbond_dreiding.tex | 0
doc/{ => src}/Eqs/pair_lj.jpg | Bin
doc/{ => src}/Eqs/pair_lj.tex | 0
doc/{ => src}/Eqs/pair_lj96.jpg | Bin
doc/{ => src}/Eqs/pair_lj96.tex | 0
doc/{ => src}/Eqs/pair_lj_cubic.jpg | Bin
doc/{ => src}/Eqs/pair_lj_cubic.tex | 0
doc/{ => src}/Eqs/pair_lj_expand.jpg | Bin
doc/{ => src}/Eqs/pair_lj_expand.tex | 0
doc/{ => src}/Eqs/pair_lj_sf.jpg | Bin
doc/{ => src}/Eqs/pair_lj_sf.tex | 0
doc/{ => src}/Eqs/pair_lj_smooth.jpg | Bin
doc/{ => src}/Eqs/pair_lj_smooth.tex | 0
doc/{ => src}/Eqs/pair_lj_smooth_linear.jpg | Bin
doc/{ => src}/Eqs/pair_lj_smooth_linear.tex | 0
doc/{ => src}/Eqs/pair_lj_soft.jpg | Bin
doc/{ => src}/Eqs/pair_lj_soft.tex | 0
doc/{ => src}/Eqs/pair_lubricate.jpg | Bin
doc/{ => src}/Eqs/pair_lubricate.tex | 0
doc/src/Eqs/pair_mdf-1.jpg | Bin 0 -> 3128 bytes
doc/src/Eqs/pair_mdf-1.tex | 9 +
doc/src/Eqs/pair_mdf-2.jpg | Bin 0 -> 10104 bytes
doc/src/Eqs/pair_mdf-2.tex | 13 +
doc/src/Eqs/pair_mdf-3.jpg | Bin 0 -> 2847 bytes
doc/src/Eqs/pair_mdf-3.tex | 9 +
doc/src/Eqs/pair_mdf-4.jpg | Bin 0 -> 3909 bytes
doc/src/Eqs/pair_mdf-4.tex | 9 +
doc/src/Eqs/pair_mdf-5.jpg | Bin 0 -> 2685 bytes
doc/src/Eqs/pair_mdf-5.tex | 9 +
doc/src/Eqs/pair_mdf-6.jpg | Bin 0 -> 2407 bytes
doc/src/Eqs/pair_mdf-6.tex | 9 +
doc/{ => src}/Eqs/pair_meam.jpg | Bin
doc/{ => src}/Eqs/pair_meam.tex | 0
doc/{ => src}/Eqs/pair_meam_spline.jpg | Bin
doc/{ => src}/Eqs/pair_meam_spline.tex | 0
doc/{ => src}/Eqs/pair_meam_sw_spline.jpg | Bin
doc/{ => src}/Eqs/pair_meam_sw_spline.tex | 0
doc/{ => src}/Eqs/pair_mgpt.jpg | Bin
doc/{ => src}/Eqs/pair_mgpt.tex | 0
doc/{ => src}/Eqs/pair_mie.jpg | Bin
doc/{ => src}/Eqs/pair_mie.tex | 0
doc/{ => src}/Eqs/pair_mie2.jpg | Bin
doc/{ => src}/Eqs/pair_mie2.tex | 0
doc/{ => src}/Eqs/pair_morse.jpg | Bin
doc/{ => src}/Eqs/pair_morse.tex | 0
doc/src/Eqs/pair_morse_smooth_linear.jpg | Bin 0 -> 9935 bytes
doc/src/Eqs/pair_morse_smooth_linear.tex | 13 +
doc/src/Eqs/pair_morse_soft.jpg | Bin 0 -> 20988 bytes
doc/src/Eqs/pair_morse_soft.tex | 13 +
doc/src/Eqs/pair_multi_lucy.jpg | Bin 0 -> 18222 bytes
doc/src/Eqs/pair_multi_lucy.tex | 10 +
doc/src/Eqs/pair_multi_lucy2.jpg | Bin 0 -> 16516 bytes
doc/src/Eqs/pair_multi_lucy2.tex | 9 +
doc/src/Eqs/pair_multi_lucy_energy.jpg | Bin 0 -> 15425 bytes
doc/src/Eqs/pair_multi_lucy_energy.tex | 9 +
doc/{ => src}/Eqs/pair_nb3b_harmonic.jpg | Bin
doc/{ => src}/Eqs/pair_nb3b_harmonic.tex | 0
doc/{ => src}/Eqs/pair_nm.jpg | Bin
doc/{ => src}/Eqs/pair_nm.tex | 0
doc/{ => src}/Eqs/pair_resquared.jpg | Bin
doc/{ => src}/Eqs/pair_resquared.tex | 0
doc/{ => src}/Eqs/pair_resquared2.jpg | Bin
doc/{ => src}/Eqs/pair_resquared2.tex | 0
doc/{ => src}/Eqs/pair_resquared3.jpg | Bin
doc/{ => src}/Eqs/pair_resquared3.tex | 0
doc/{ => src}/Eqs/pair_resquared4.jpg | Bin
doc/{ => src}/Eqs/pair_resquared4.tex | 0
doc/{ => src}/Eqs/pair_smtbq1.jpg | Bin
doc/{ => src}/Eqs/pair_smtbq1.tex | 0
doc/{ => src}/Eqs/pair_smtbq2.jpg | Bin
doc/{ => src}/Eqs/pair_smtbq2.tex | 0
doc/{ => src}/Eqs/pair_smtbq3.jpg | Bin
doc/{ => src}/Eqs/pair_smtbq3.tex | 0
doc/{ => src}/Eqs/pair_snap.jpg | Bin
doc/{ => src}/Eqs/pair_snap.tex | 0
doc/{ => src}/Eqs/pair_soft.jpg | Bin
doc/{ => src}/Eqs/pair_soft.tex | 0
doc/{ => src}/Eqs/pair_sph_ideal.jpg | Bin
doc/{ => src}/Eqs/pair_sph_ideal.tex | 0
doc/{ => src}/Eqs/pair_sph_tait.jpg | Bin
doc/{ => src}/Eqs/pair_sph_tait.tex | 0
doc/{ => src}/Eqs/pair_srp1.jpg | Bin
doc/{ => src}/Eqs/pair_srp1.tex | 0
doc/{ => src}/Eqs/pair_srp2.jpg | Bin
doc/{ => src}/Eqs/pair_srp2.tex | 0
doc/{ => src}/Eqs/pair_sw.jpg | Bin
doc/{ => src}/Eqs/pair_sw.tex | 0
doc/{ => src}/Eqs/pair_tersoff.jpg | Bin
doc/{ => src}/Eqs/pair_tersoff_1.jpg | Bin
doc/{ => src}/Eqs/pair_tersoff_1.tex | 0
doc/{ => src}/Eqs/pair_tersoff_2.jpg | Bin
doc/{ => src}/Eqs/pair_tersoff_2.tex | 0
doc/{ => src}/Eqs/pair_tersoff_mod.jpg | Bin
doc/{ => src}/Eqs/pair_tersoff_mod.tex | 0
doc/{ => src}/Eqs/pair_tersoff_zbl.jpg | Bin
doc/{ => src}/Eqs/pair_tersoff_zbl.tex | 0
doc/{ => src}/Eqs/pair_vashishta.jpg | Bin
doc/{ => src}/Eqs/pair_vashishta.tex | 0
doc/{ => src}/Eqs/pair_yukawa.jpg | Bin
doc/{ => src}/Eqs/pair_yukawa.tex | 0
doc/{ => src}/Eqs/pair_yukawa_colloid.jpg | Bin
doc/{ => src}/Eqs/pair_yukawa_colloid.tex | 0
doc/{ => src}/Eqs/pair_zbl.jpg | Bin
doc/{ => src}/Eqs/pair_zbl.tex | 0
doc/{ => src}/Eqs/polymorphic1.jpg | Bin
doc/{ => src}/Eqs/polymorphic1.tex | 0
doc/{ => src}/Eqs/polymorphic2.jpg | Bin
doc/{ => src}/Eqs/polymorphic2.tex | 0
doc/{ => src}/Eqs/polymorphic3.jpg | Bin
doc/{ => src}/Eqs/polymorphic3.tex | 0
doc/{ => src}/Eqs/polymorphic4.jpg | Bin
doc/{ => src}/Eqs/polymorphic4.tex | 0
doc/{ => src}/Eqs/polymorphic5.jpg | Bin
doc/{ => src}/Eqs/polymorphic5.tex | 0
doc/{ => src}/Eqs/polymorphic6.jpg | Bin
doc/{ => src}/Eqs/polymorphic6.tex | 0
doc/{ => src}/Eqs/polymorphic7.jpg | Bin
doc/{ => src}/Eqs/polymorphic7.tex | 0
doc/{ => src}/Eqs/polymorphic8.jpg | Bin
doc/{ => src}/Eqs/polymorphic8.tex | 0
doc/{ => src}/Eqs/polymorphic9.jpg | Bin
doc/{ => src}/Eqs/polymorphic9.tex | 0
doc/{ => src}/Eqs/pressure.jpg | Bin
doc/{ => src}/Eqs/pressure.tex | 0
doc/{ => src}/Eqs/pressure_tensor.jpg | Bin
doc/{ => src}/Eqs/pressure_tensor.tex | 0
doc/{ => src}/Eqs/rotate.jpg | Bin
doc/{ => src}/Eqs/rotate.tex | 0
doc/{ => src}/Eqs/stress_tensor.jpg | Bin
doc/{ => src}/Eqs/stress_tensor.tex | 0
doc/{ => src}/Eqs/transform.jpg | Bin
doc/{ => src}/Eqs/transform.tex | 0
doc/{ => src}/Eqs/umbrella.jpg | Bin
doc/{ => src}/JPG/atc_nanotube.jpg | Bin
doc/{ => src}/JPG/balance_nonuniform.jpg | Bin
doc/{ => src}/JPG/balance_nonuniform_small.jpg | Bin
doc/{ => src}/JPG/balance_rcb.jpg | Bin
doc/{ => src}/JPG/balance_rcb_small.jpg | Bin
doc/{ => src}/JPG/balance_uniform.jpg | Bin
doc/{ => src}/JPG/balance_uniform_small.jpg | Bin
doc/{ => src}/JPG/bondswap.jpg | Bin
doc/{ => src}/JPG/coul_soft.jpg | Bin
doc/src/JPG/dihedral_sign.jpg | Bin 0 -> 23845 bytes
doc/src/JPG/dihedral_spherical_angles.jpg | Bin 0 -> 25519 bytes
doc/{ => src}/JPG/dump1.jpg | Bin
doc/{ => src}/JPG/dump1_small.jpg | Bin
doc/{ => src}/JPG/dump2.jpg | Bin
doc/{ => src}/JPG/dump2_small.jpg | Bin
doc/src/JPG/gran_funnel.png | Bin 0 -> 119645 bytes
doc/src/JPG/gran_funnel_small.jpg | Bin 0 -> 2266 bytes
doc/src/JPG/gran_mixer.png | Bin 0 -> 229532 bytes
doc/src/JPG/gran_mixer_small.jpg | Bin 0 -> 3053 bytes
doc/{ => src}/JPG/hop1.jpg | Bin
doc/{ => src}/JPG/hop1_small.jpg | Bin
doc/{ => src}/JPG/hop2.jpg | Bin
doc/{ => src}/JPG/hop2_small.jpg | Bin
doc/src/JPG/improper_distance.jpg | Bin 0 -> 9687 bytes
doc/src/JPG/lammps-logo.png | Bin 0 -> 4900 bytes
doc/{ => src}/JPG/lj_soft.jpg | Bin
doc/src/JPG/offload_knc.png | Bin 0 -> 12755 bytes
doc/{ => src}/JPG/pimd.jpg | Bin
doc/{ => src}/JPG/qbmsst_init.jpg | Bin
doc/{ => src}/JPG/qbmsst_shock.jpg | Bin
doc/{ => src}/JPG/rhodo_staggered.jpg | Bin
doc/{ => src}/JPG/saed_ewald_intersect.jpg | Bin
doc/{ => src}/JPG/saed_ewald_intersect_small.jpg | Bin
doc/{ => src}/JPG/saed_mesh.jpg | Bin
doc/{ => src}/JPG/saed_mesh_small.jpg | Bin
doc/{ => src}/JPG/screenshot_atomeye.jpg | Bin
doc/{ => src}/JPG/screenshot_atomeye_small.jpg | Bin
doc/{ => src}/JPG/screenshot_gl.jpg | Bin
doc/{ => src}/JPG/screenshot_gl_small.jpg | Bin
doc/{ => src}/JPG/screenshot_pymol.jpg | Bin
doc/{ => src}/JPG/screenshot_pymol_small.jpg | Bin
doc/{ => src}/JPG/screenshot_vmd.jpg | Bin
doc/{ => src}/JPG/screenshot_vmd_small.jpg | Bin
doc/{ => src}/JPG/sinusoid.jpg | Bin
doc/{ => src}/JPG/sinusoid_small.jpg | Bin
doc/src/JPG/tutorial_branch.png | Bin 0 -> 74432 bytes
doc/src/JPG/tutorial_fork.png | Bin 0 -> 33708 bytes
doc/src/JPG/tutorial_https_block.png | Bin 0 -> 17671 bytes
doc/src/JPG/tutorial_merged.png | Bin 0 -> 58444 bytes
doc/src/JPG/tutorial_pull_request2.png | Bin 0 -> 15019 bytes
doc/src/JPG/tutorial_pull_request3.png | Bin 0 -> 27736 bytes
doc/src/JPG/tutorial_pull_request4.png | Bin 0 -> 88565 bytes
.../JPG/tutorial_pull_request_feature_branch1.png | Bin 0 -> 21596 bytes
doc/src/JPG/user_intel.png | Bin 0 -> 14684 bytes
doc/{ => src}/JPG/xrd_mesh.jpg | Bin
doc/{ => src}/JPG/xrd_mesh_small.jpg | Bin
doc/src/Manual.txt | 340 +
doc/{ => src}/PDF/PDLammps_EPS.pdf | Bin
doc/{ => src}/PDF/PDLammps_VES.pdf | Bin
doc/{ => src}/PDF/PDLammps_overview.pdf | Bin
doc/{ => src}/PDF/SMD_LAMMPS_userguide.pdf | Bin
doc/{ => src}/PDF/SPH_LAMMPS_userguide.pdf | Bin
doc/src/PDF/colvars-refman-lammps.pdf | Bin 0 -> 564148 bytes
doc/{ => src}/PDF/kspace.pdf | Bin
doc/{ => src}/PDF/pair_gayberne_extra.pdf | Bin
doc/{ => src}/PDF/pair_gayberne_extra.tex | 0
doc/{ => src}/PDF/pair_resquared_extra.pdf | Bin
doc/{ => src}/PDF/pair_resquared_extra.tex | 0
doc/src/Section_accelerate.txt | 391 +
doc/src/Section_commands.txt | 1200 +
doc/src/Section_errors.txt | 11909 ++
doc/src/Section_example.txt | 140 +
doc/src/Section_history.txt | 135 +
doc/src/Section_howto.txt | 2885 +
doc/src/Section_intro.txt | 542 +
doc/src/Section_modify.txt | 827 +
doc/src/Section_packages.txt | 1873 +
doc/src/Section_perf.txt | 87 +
doc/src/Section_python.txt | 826 +
doc/src/Section_start.txt | 1907 +
doc/src/Section_tools.txt | 568 +
doc/{ => src}/USER/atc/man_add_molecule.html | 0
doc/{ => src}/USER/atc/man_add_species.html | 0
doc/{ => src}/USER/atc/man_atom_element_map.html | 0
doc/{ => src}/USER/atc/man_atom_weight.html | 0
doc/{ => src}/USER/atc/man_atomic_charge.html | 0
doc/{ => src}/USER/atc/man_boundary.html | 0
doc/{ => src}/USER/atc/man_boundary_dynamics.html | 0
doc/{ => src}/USER/atc/man_boundary_faceset.html | 0
doc/{ => src}/USER/atc/man_boundary_integral.html | 0
.../USER/atc/man_consistent_fe_initialization.html | 0
doc/{ => src}/USER/atc/man_contour_integral.html | 0
doc/{ => src}/USER/atc/man_control.html | 0
doc/{ => src}/USER/atc/man_control_momentum.html | 0
doc/{ => src}/USER/atc/man_control_thermal.html | 0
..._control_thermal_correction_max_iterations.html | 0
doc/{ => src}/USER/atc/man_decomposition.html | 0
.../USER/atc/man_electron_integration.html | 0
doc/{ => src}/USER/atc/man_equilibrium_start.html | 0
doc/{ => src}/USER/atc/man_extrinsic_exchange.html | 0
doc/{ => src}/USER/atc/man_fe_md_boundary.html | 0
doc/{ => src}/USER/atc/man_fem_mesh.html | 0
doc/{ => src}/USER/atc/man_filter_scale.html | 0
doc/{ => src}/USER/atc/man_filter_type.html | 0
doc/{ => src}/USER/atc/man_fix_atc.html | 0
doc/{ => src}/USER/atc/man_fix_flux.html | 0
doc/{ => src}/USER/atc/man_fix_nodes.html | 0
doc/{ => src}/USER/atc/man_hardy_computes.html | 0
doc/{ => src}/USER/atc/man_hardy_fields.html | 0
doc/{ => src}/USER/atc/man_hardy_gradients.html | 0
doc/{ => src}/USER/atc/man_hardy_kernel.html | 0
doc/{ => src}/USER/atc/man_hardy_on_the_fly.html | 0
doc/{ => src}/USER/atc/man_hardy_rates.html | 0
doc/{ => src}/USER/atc/man_initial.html | 0
.../USER/atc/man_internal_atom_integrate.html | 0
.../USER/atc/man_internal_element_set.html | 0
.../USER/atc/man_internal_quadrature.html | 0
doc/{ => src}/USER/atc/man_kernel_function.html | 0
doc/{ => src}/USER/atc/man_localized_lambda.html | 0
.../USER/atc/man_lumped_lambda_solve.html | 0
doc/{ => src}/USER/atc/man_mask_direction.html | 0
doc/{ => src}/USER/atc/man_mass_matrix.html | 0
doc/{ => src}/USER/atc/man_material.html | 0
.../USER/atc/man_mesh_add_to_nodeset.html | 0
doc/{ => src}/USER/atc/man_mesh_create.html | 0
.../USER/atc/man_mesh_create_elementset.html | 0
.../USER/atc/man_mesh_create_faceset_box.html | 0
.../USER/atc/man_mesh_create_faceset_plane.html | 0
.../USER/atc/man_mesh_create_nodeset.html | 0
.../USER/atc/man_mesh_delete_elements.html | 0
.../USER/atc/man_mesh_nodeset_to_elementset.html | 0
doc/{ => src}/USER/atc/man_mesh_output.html | 0
doc/{ => src}/USER/atc/man_mesh_quadrature.html | 0
doc/{ => src}/USER/atc/man_mesh_read.html | 0
doc/{ => src}/USER/atc/man_mesh_write.html | 0
.../USER/atc/man_momentum_time_integration.html | 0
doc/{ => src}/USER/atc/man_output.html | 0
doc/{ => src}/USER/atc/man_output_elementset.html | 0
doc/{ => src}/USER/atc/man_output_nodeset.html | 0
doc/{ => src}/USER/atc/man_pair_interactions.html | 0
doc/{ => src}/USER/atc/man_poisson_solver.html | 0
doc/{ => src}/USER/atc/man_read_restart.html | 0
doc/{ => src}/USER/atc/man_remove_molecule.html | 0
doc/{ => src}/USER/atc/man_remove_source.html | 0
doc/{ => src}/USER/atc/man_remove_species.html | 0
.../atc/man_reset_atomic_reference_positions.html | 0
doc/{ => src}/USER/atc/man_reset_time.html | 0
doc/{ => src}/USER/atc/man_sample_frequency.html | 0
doc/{ => src}/USER/atc/man_set.html | 0
doc/{ => src}/USER/atc/man_source.html | 0
doc/{ => src}/USER/atc/man_source_integration.html | 0
.../USER/atc/man_temperature_definition.html | 0
.../USER/atc/man_thermal_time_integration.html | 0
doc/{ => src}/USER/atc/man_time_filter.html | 0
doc/{ => src}/USER/atc/man_track_displacement.html | 0
doc/{ => src}/USER/atc/man_unfix_flux.html | 0
doc/{ => src}/USER/atc/man_unfix_nodes.html | 0
doc/{ => src}/USER/atc/man_write_atom_weights.html | 0
doc/{ => src}/USER/atc/man_write_restart.html | 0
doc/src/accelerate_gpu.txt | 254 +
doc/src/accelerate_intel.txt | 476 +
doc/src/accelerate_kokkos.txt | 496 +
doc/src/accelerate_omp.txt | 187 +
doc/src/accelerate_opt.txt | 71 +
doc/src/angle_charmm.txt | 90 +
doc/src/angle_class2.txt | 119 +
doc/{ => src}/angle_coeff.txt | 0
doc/src/angle_cosine.txt | 71 +
doc/src/angle_cosine_delta.txt | 77 +
doc/src/angle_cosine_periodic.txt | 90 +
doc/src/angle_cosine_shift.txt | 75 +
doc/src/angle_cosine_shift_exp.txt | 88 +
doc/src/angle_cosine_squared.txt | 76 +
doc/src/angle_dipole.txt | 126 +
doc/src/angle_fourier.txt | 72 +
doc/src/angle_fourier_simple.txt | 71 +
doc/src/angle_harmonic.txt | 78 +
doc/src/angle_hybrid.txt | 91 +
doc/src/angle_none.txt | 34 +
doc/src/angle_quartic.txt | 78 +
doc/src/angle_sdk.txt | 58 +
doc/src/angle_style.txt | 97 +
doc/src/angle_table.txt | 157 +
doc/src/angle_zero.txt | 49 +
doc/src/angles.txt | 27 +
doc/src/atom_modify.txt | 170 +
doc/src/atom_style.txt | 301 +
doc/src/balance.txt | 510 +
doc/src/body.txt | 274 +
doc/src/bond_class2.txt | 81 +
doc/{ => src}/bond_coeff.txt | 0
doc/src/bond_fene.txt | 89 +
doc/src/bond_fene_expand.txt | 92 +
doc/src/bond_harmonic.txt | 75 +
doc/src/bond_harmonic_shift.txt | 77 +
doc/src/bond_harmonic_shift_cut.txt | 78 +
doc/src/bond_hybrid.txt | 74 +
doc/src/bond_morse.txt | 74 +
doc/src/bond_none.txt | 34 +
doc/src/bond_nonlinear.txt | 79 +
doc/src/bond_quartic.txt | 113 +
doc/src/bond_style.txt | 105 +
doc/src/bond_table.txt | 154 +
doc/src/bond_write.txt | 64 +
doc/src/bond_zero.txt | 48 +
doc/src/bonds.txt | 22 +
doc/src/boundary.txt | 107 +
doc/{ => src}/box.txt | 0
doc/src/change_box.txt | 331 +
doc/{ => src}/clear.txt | 0
doc/src/comm_modify.txt | 159 +
doc/src/comm_style.txt | 63 +
doc/src/commands.txt | 110 +
doc/src/compute.txt | 262 +
doc/src/compute_ackland_atom.txt | 74 +
doc/src/compute_angle.txt | 53 +
doc/src/compute_angle_local.txt | 87 +
doc/src/compute_angmom_chunk.txt | 89 +
doc/src/compute_basal_atom.txt | 76 +
doc/src/compute_body_local.txt | 93 +
doc/src/compute_bond.txt | 53 +
doc/src/compute_bond_local.txt | 137 +
doc/src/compute_centro_atom.txt | 151 +
doc/src/compute_chunk_atom.txt | 665 +
doc/src/compute_cluster_atom.txt | 73 +
doc/src/compute_cna_atom.txt | 97 +
doc/src/compute_com.txt | 57 +
doc/src/compute_com_chunk.txt | 87 +
doc/src/compute_contact_atom.txt | 54 +
doc/src/compute_coord_atom.txt | 92 +
doc/src/compute_damage_atom.txt | 63 +
doc/src/compute_dihedral.txt | 53 +
doc/src/compute_dihedral_local.txt | 78 +
doc/src/compute_dilatation_atom.txt | 66 +
doc/src/compute_dipole_chunk.txt | 92 +
doc/src/compute_displace_atom.txt | 69 +
doc/src/compute_dpd.txt | 71 +
doc/src/compute_dpd_atom.txt | 66 +
doc/src/compute_erotate_asphere.txt | 70 +
doc/src/compute_erotate_rigid.txt | 61 +
doc/src/compute_erotate_sphere.txt | 57 +
doc/src/compute_erotate_sphere_atom.txt | 53 +
doc/src/compute_event_displace.txt | 62 +
doc/src/compute_fep.txt | 263 +
doc/src/compute_group_group.txt | 127 +
doc/src/compute_gyration.txt | 72 +
doc/src/compute_gyration_chunk.txt | 110 +
doc/src/compute_heat_flux.txt | 190 +
doc/src/compute_hexorder_atom.txt | 116 +
doc/src/compute_improper.txt | 53 +
doc/src/compute_improper_local.txt | 79 +
doc/src/compute_inertia_chunk.txt | 88 +
doc/src/compute_ke.txt | 59 +
doc/src/compute_ke_atom.txt | 48 +
doc/src/compute_ke_atom_eff.txt | 76 +
doc/src/compute_ke_eff.txt | 78 +
doc/src/compute_ke_rigid.txt | 60 +
doc/src/compute_meso_e_atom.txt | 56 +
doc/src/compute_meso_rho_atom.txt | 56 +
doc/src/compute_meso_t_atom.txt | 58 +
doc/src/compute_modify.txt | 64 +
doc/src/compute_msd.txt | 114 +
doc/src/compute_msd_chunk.txt | 121 +
doc/src/compute_msd_nongauss.txt | 80 +
doc/src/compute_omega_chunk.txt | 89 +
doc/src/compute_orientorder_atom.txt | 121 +
doc/src/compute_pair.txt | 84 +
doc/src/compute_pair_local.txt | 138 +
doc/src/compute_pe.txt | 80 +
doc/src/compute_pe_atom.txt | 101 +
doc/src/compute_plasticity_atom.txt | 67 +
doc/src/compute_pressure.txt | 147 +
doc/src/compute_property_atom.txt | 163 +
doc/src/compute_property_chunk.txt | 118 +
doc/src/compute_property_local.txt | 155 +
doc/src/compute_rdf.txt | 156 +
doc/src/compute_reduce.txt | 212 +
doc/src/compute_rigid_local.txt | 185 +
doc/src/compute_saed.txt | 182 +
doc/src/compute_slice.txt | 123 +
doc/src/compute_smd_contact_radius.txt | 55 +
doc/src/compute_smd_damage.txt | 48 +
doc/src/compute_smd_hourglass_error.txt | 62 +
doc/src/compute_smd_internal_energy.txt | 49 +
doc/src/compute_smd_plastic_strain.txt | 54 +
doc/src/compute_smd_plastic_strain_rate.txt | 54 +
doc/src/compute_smd_rho.txt | 51 +
doc/src/compute_smd_tlsph_defgrad.txt | 57 +
doc/src/compute_smd_tlsph_dt.txt | 58 +
doc/src/compute_smd_tlsph_num_neighs.txt | 53 +
doc/src/compute_smd_tlsph_shape.txt | 61 +
doc/src/compute_smd_tlsph_strain.txt | 58 +
doc/src/compute_smd_tlsph_strain_rate.txt | 57 +
doc/src/compute_smd_tlsph_stress.txt | 59 +
doc/src/compute_smd_triangle_mesh_vertices.txt | 62 +
doc/src/compute_smd_ulsph_num_neighs.txt | 52 +
doc/src/compute_smd_ulsph_strain.txt | 55 +
doc/src/compute_smd_ulsph_strain_rate.txt | 56 +
doc/src/compute_smd_ulsph_stress.txt | 58 +
doc/src/compute_smd_vol.txt | 53 +
doc/src/compute_sna_atom.txt | 241 +
doc/src/compute_stress_atom.txt | 169 +
doc/src/compute_tally.txt | 97 +
doc/src/compute_temp.txt | 113 +
doc/src/compute_temp_asphere.txt | 153 +
doc/src/compute_temp_body.txt | 131 +
doc/src/compute_temp_chunk.txt | 237 +
doc/{ => src}/compute_temp_com.txt | 0
doc/src/compute_temp_cs.txt | 119 +
doc/src/compute_temp_deform.txt | 134 +
doc/src/compute_temp_deform_eff.txt | 72 +
doc/src/compute_temp_drude.txt | 81 +
doc/src/compute_temp_eff.txt | 95 +
doc/src/compute_temp_partial.txt | 120 +
doc/src/compute_temp_profile.txt | 182 +
doc/{ => src}/compute_temp_ramp.txt | 0
doc/src/compute_temp_region.txt | 110 +
doc/{ => src}/compute_temp_region_eff.txt | 0
doc/{ => src}/compute_temp_rotate.txt | 0
doc/src/compute_temp_sphere.txt | 137 +
doc/src/compute_ti.txt | 137 +
doc/src/compute_torque_chunk.txt | 87 +
doc/src/compute_vacf.txt | 71 +
doc/src/compute_vcm_chunk.txt | 77 +
doc/src/compute_voronoi_atom.txt | 224 +
doc/src/compute_xrd.txt | 200 +
doc/src/computes.txt | 120 +
doc/src/create_atoms.txt | 318 +
doc/src/create_bonds.txt | 108 +
doc/src/create_box.txt | 152 +
doc/src/delete_atoms.txt | 144 +
doc/src/delete_bonds.txt | 154 +
doc/src/dielectric.txt | 39 +
doc/src/dihedral_charmm.txt | 129 +
doc/src/dihedral_class2.txt | 178 +
doc/src/dihedral_coeff.txt | 106 +
doc/src/dihedral_cosine_shift_exp.txt | 86 +
doc/src/dihedral_fourier.txt | 77 +
doc/src/dihedral_harmonic.txt | 86 +
doc/src/dihedral_helix.txt | 84 +
doc/src/dihedral_hybrid.txt | 92 +
doc/src/dihedral_multi_harmonic.txt | 73 +
doc/src/dihedral_nharmonic.txt | 73 +
doc/src/dihedral_none.txt | 34 +
doc/src/dihedral_opls.txt | 86 +
doc/src/dihedral_quadratic.txt | 75 +
doc/src/dihedral_spherical.txt | 87 +
doc/src/dihedral_style.txt | 118 +
doc/src/dihedral_table.txt | 205 +
doc/src/dihedral_zero.txt | 48 +
doc/src/dihedrals.txt | 39 +
doc/src/dimension.txt | 48 +
doc/src/displace_atoms.txt | 139 +
doc/src/dump.txt | 681 +
doc/src/dump_custom_vtk.txt | 339 +
doc/src/dump_h5md.txt | 123 +
doc/src/dump_image.txt | 679 +
doc/src/dump_modify.txt | 996 +
doc/src/dump_molfile.txt | 126 +
doc/src/dump_nc.txt | 66 +
doc/{ => src}/echo.txt | 0
doc/src/fix.txt | 315 +
doc/src/fix_adapt.txt | 260 +
doc/src/fix_adapt_fep.txt | 260 +
doc/src/fix_addforce.txt | 176 +
doc/src/fix_addtorque.txt | 98 +
doc/{ => src}/fix_append_atoms.txt | 0
doc/src/fix_atc.txt | 244 +
doc/src/fix_atom_swap.txt | 187 +
doc/src/fix_ave_atom.txt | 179 +
doc/src/fix_ave_chunk.txt | 478 +
doc/src/fix_ave_correlate.txt | 370 +
doc/src/fix_ave_correlate_long.txt | 144 +
doc/src/fix_ave_histo.txt | 359 +
doc/src/fix_ave_time.txt | 349 +
doc/src/fix_aveforce.txt | 118 +
doc/src/fix_balance.txt | 378 +
doc/src/fix_bond_break.txt | 145 +
doc/src/fix_bond_create.txt | 242 +
doc/src/fix_bond_swap.txt | 191 +
doc/src/fix_box_relax.txt | 372 +
doc/src/fix_cmap.txt | 132 +
doc/src/fix_colvars.txt | 136 +
doc/src/fix_controller.txt | 206 +
doc/src/fix_deform.txt | 594 +
doc/src/fix_deposit.txt | 285 +
doc/src/fix_dpd_energy.txt | 83 +
doc/src/fix_drag.txt | 65 +
doc/src/fix_drude.txt | 56 +
doc/src/fix_drude_transform.txt | 164 +
doc/{ => src}/fix_dt_reset.txt | 0
doc/src/fix_efield.txt | 162 +
doc/src/fix_ehex.txt | 178 +
doc/src/fix_enforce2d.txt | 68 +
doc/src/fix_eos_cv.txt | 60 +
doc/src/fix_eos_table.txt | 117 +
doc/src/fix_eos_table_rx.txt | 142 +
doc/src/fix_evaporate.txt | 96 +
doc/src/fix_external.txt | 154 +
doc/src/fix_flow_gauss.txt | 160 +
doc/src/fix_freeze.txt | 87 +
doc/src/fix_gcmc.txt | 355 +
doc/src/fix_gld.txt | 155 +
doc/src/fix_gle.txt | 155 +
doc/src/fix_gravity.txt | 144 +
doc/src/fix_halt.txt | 121 +
doc/src/fix_heat.txt | 129 +
doc/src/fix_imd.txt | 160 +
doc/src/fix_indent.txt | 205 +
doc/src/fix_ipi.txt | 91 +
doc/src/fix_langevin.txt | 344 +
doc/src/fix_langevin_drude.txt | 273 +
doc/src/fix_langevin_eff.txt | 113 +
doc/src/fix_lb_fluid.txt | 370 +
doc/src/fix_lb_momentum.txt | 73 +
doc/src/fix_lb_pc.txt | 62 +
doc/src/fix_lb_rigid_pc_sphere.txt | 146 +
doc/src/fix_lb_viscous.txt | 94 +
doc/src/fix_lineforce.txt | 51 +
doc/src/fix_manifoldforce.txt | 61 +
doc/{ => src}/fix_meso.txt | 0
doc/{ => src}/fix_meso_stationary.txt | 0
doc/src/fix_modify.txt | 91 +
doc/{ => src}/fix_momentum.txt | 0
doc/src/fix_move.txt | 226 +
doc/src/fix_msst.txt | 158 +
doc/src/fix_neb.txt | 106 +
doc/src/fix_nh.txt | 652 +
doc/src/fix_nh_eff.txt | 142 +
doc/src/fix_nph_asphere.txt | 153 +
doc/src/fix_nph_body.txt | 148 +
doc/src/fix_nph_sphere.txt | 148 +
doc/src/fix_nphug.txt | 229 +
doc/src/fix_npt_asphere.txt | 177 +
doc/src/fix_npt_body.txt | 172 +
doc/src/fix_npt_sphere.txt | 172 +
doc/src/fix_nve.txt | 73 +
doc/src/fix_nve_asphere.txt | 86 +
doc/src/fix_nve_asphere_noforce.txt | 65 +
doc/src/fix_nve_body.txt | 62 +
doc/{ => src}/fix_nve_eff.txt | 0
doc/src/fix_nve_limit.txt | 86 +
doc/src/fix_nve_line.txt | 57 +
doc/src/fix_nve_manifold_rattle.txt | 102 +
doc/{ => src}/fix_nve_noforce.txt | 0
doc/src/fix_nve_sphere.txt | 111 +
doc/src/fix_nve_tri.txt | 57 +
doc/src/fix_nvt_asphere.txt | 153 +
doc/src/fix_nvt_body.txt | 148 +
doc/src/fix_nvt_manifold_rattle.txt | 81 +
doc/src/fix_nvt_sllod.txt | 180 +
doc/src/fix_nvt_sllod_eff.txt | 94 +
doc/src/fix_nvt_sphere.txt | 149 +
doc/{ => src}/fix_oneway.txt | 0
doc/src/fix_orient.txt | 201 +
doc/src/fix_phonon.txt | 213 +
doc/src/fix_pimd.txt | 179 +
doc/{ => src}/fix_planeforce.txt | 0
doc/{ => src}/fix_poems.txt | 0
doc/src/fix_pour.txt | 264 +
doc/src/fix_press_berendsen.txt | 227 +
doc/{ => src}/fix_print.txt | 0
doc/src/fix_property_atom.txt | 262 +
doc/src/fix_qbmsst.txt | 219 +
doc/src/fix_qeq.txt | 217 +
doc/src/fix_qeq_comb.txt | 132 +
doc/src/fix_qeq_reax.txt | 124 +
doc/src/fix_qmmm.txt | 66 +
doc/src/fix_qtb.txt | 182 +
doc/src/fix_reax_bonds.txt | 93 +
doc/src/fix_reaxc_species.txt | 180 +
doc/src/fix_recenter.txt | 126 +
doc/src/fix_restrain.txt | 198 +
doc/src/fix_rigid.txt | 800 +
doc/src/fix_rx.txt | 203 +
doc/src/fix_saed_vtk.txt | 190 +
doc/src/fix_setforce.txt | 126 +
doc/src/fix_shake.txt | 227 +
doc/src/fix_shardlow.txt | 96 +
doc/src/fix_smd.txt | 151 +
doc/src/fix_smd_adjust_dt.txt | 55 +
doc/src/fix_smd_integrate_tlsph.txt | 54 +
doc/src/fix_smd_integrate_ulsph.txt | 60 +
doc/src/fix_smd_move_triangulated_surface.txt | 75 +
doc/src/fix_smd_setvel.txt | 84 +
doc/src/fix_smd_wall_surface.txt | 58 +
doc/src/fix_spring.txt | 146 +
doc/src/fix_spring_chunk.txt | 86 +
doc/src/fix_spring_rg.txt | 70 +
doc/src/fix_spring_self.txt | 83 +
doc/src/fix_srd.txt | 398 +
doc/src/fix_store_force.txt | 71 +
doc/src/fix_store_state.txt | 129 +
doc/src/fix_temp_berendsen.txt | 163 +
doc/src/fix_temp_csvr.txt | 168 +
doc/src/fix_temp_rescale.txt | 153 +
doc/src/fix_temp_rescale_eff.txt | 76 +
doc/src/fix_tfmc.txt | 152 +
doc/src/fix_thermal_conductivity.txt | 163 +
doc/src/fix_ti_spring.txt | 160 +
doc/{ => src}/fix_tmd.txt | 0
doc/src/fix_ttm.txt | 332 +
doc/src/fix_tune_kspace.txt | 100 +
doc/src/fix_vector.txt | 163 +
doc/src/fix_viscosity.txt | 169 +
doc/src/fix_viscous.txt | 105 +
doc/src/fix_wall.txt | 296 +
doc/src/fix_wall_gran.txt | 170 +
doc/src/fix_wall_gran_region.txt | 203 +
doc/src/fix_wall_piston.txt | 120 +
doc/src/fix_wall_reflect.txt | 184 +
doc/src/fix_wall_region.txt | 218 +
doc/src/fix_wall_srd.txt | 190 +
doc/src/fixes.txt | 159 +
doc/src/group.txt | 284 +
doc/src/group2ndx.txt | 64 +
doc/src/if.txt | 192 +
doc/src/improper_class2.txt | 124 +
doc/{ => src}/improper_coeff.txt | 0
doc/src/improper_cossq.txt | 89 +
doc/src/improper_cvff.txt | 87 +
doc/src/improper_distance.txt | 58 +
doc/src/improper_fourier.txt | 82 +
doc/src/improper_harmonic.txt | 91 +
doc/src/improper_hybrid.txt | 70 +
doc/src/improper_none.txt | 34 +
doc/src/improper_ring.txt | 96 +
doc/src/improper_style.txt | 95 +
doc/src/improper_umbrella.txt | 90 +
doc/src/improper_zero.txt | 48 +
doc/src/impropers.txt | 20 +
doc/{ => src}/include.txt | 0
doc/src/info.txt | 109 +
doc/src/jump.txt | 130 +
doc/src/kspace_modify.txt | 342 +
doc/src/kspace_style.txt | 377 +
doc/{ => src}/label.txt | 0
doc/src/lammps.book | 624 +
doc/src/lattice.txt | 293 +
doc/src/log.txt | 46 +
doc/src/manifolds.txt | 40 +
doc/{ => src}/mass.txt | 0
doc/src/min_modify.txt | 76 +
doc/src/min_style.txt | 96 +
doc/src/minimize.txt | 279 +
doc/src/molecule.txt | 467 +
doc/src/neb.txt | 416 +
doc/src/neigh_modify.txt | 213 +
doc/src/neighbor.txt | 83 +
doc/{ => src}/newton.txt | 0
doc/src/next.txt | 142 +
doc/src/package.txt | 597 +
doc/src/pair_adp.txt | 186 +
doc/src/pair_airebo.txt | 236 +
doc/{ => src}/pair_awpmd.txt | 0
doc/src/pair_beck.txt | 109 +
doc/src/pair_body.txt | 118 +
doc/src/pair_bop.txt | 429 +
doc/src/pair_born.txt | 205 +
doc/src/pair_brownian.txt | 143 +
doc/src/pair_buck.txt | 196 +
doc/src/pair_buck_long.txt | 171 +
doc/src/pair_charmm.txt | 196 +
doc/src/pair_class2.txt | 170 +
doc/src/pair_coeff.txt | 148 +
doc/src/pair_colloid.txt | 205 +
doc/src/pair_comb.txt | 192 +
doc/src/pair_coul.txt | 338 +
doc/src/pair_coul_diel.txt | 112 +
doc/src/pair_cs.txt | 100 +
doc/src/pair_dipole.txt | 267 +
doc/src/pair_dpd.txt | 209 +
doc/src/pair_dpd_fdt.txt | 154 +
doc/src/pair_dsmc.txt | 148 +
doc/src/pair_eam.txt | 447 +
doc/src/pair_edip.txt | 167 +
doc/src/pair_eff.txt | 313 +
doc/src/pair_eim.txt | 174 +
doc/src/pair_exp6_rx.txt | 120 +
doc/src/pair_gauss.txt | 188 +
doc/src/pair_gayberne.txt | 231 +
doc/src/pair_gran.txt | 271 +
doc/src/pair_gromacs.txt | 155 +
doc/src/pair_hbond_dreiding.txt | 243 +
doc/src/pair_hybrid.txt | 382 +
doc/{ => src}/pair_kim.txt | 0
doc/src/pair_lcbop.txt | 97 +
doc/src/pair_line_lj.txt | 144 +
doc/src/pair_list.txt | 144 +
doc/src/pair_lj.txt | 320 +
doc/src/pair_lj96.txt | 107 +
doc/src/pair_lj_cubic.txt | 129 +
doc/src/pair_lj_expand.txt | 111 +
doc/src/pair_lj_long.txt | 225 +
doc/src/pair_lj_sf.txt | 114 +
doc/src/pair_lj_smooth.txt | 122 +
doc/src/pair_lj_smooth_linear.txt | 105 +
doc/src/pair_lj_soft.txt | 278 +
doc/src/pair_lubricate.txt | 228 +
doc/src/pair_lubricateU.txt | 218 +
doc/src/pair_mdf.txt | 163 +
doc/src/pair_meam.txt | 371 +
doc/src/pair_meam_spline.txt | 144 +
doc/src/pair_meam_sw_spline.txt | 139 +
doc/src/pair_mgpt.txt | 219 +
doc/src/pair_mie.txt | 101 +
doc/src/pair_modify.txt | 260 +
doc/src/pair_morse.txt | 162 +
doc/src/pair_multi_lucy.txt | 199 +
doc/src/pair_multi_lucy_rx.txt | 220 +
doc/src/pair_nb3b_harmonic.txt | 123 +
doc/src/pair_nm.txt | 169 +
doc/src/pair_none.txt | 46 +
doc/src/pair_peri.txt | 216 +
doc/src/pair_polymorphic.txt | 229 +
doc/src/pair_quip.txt | 96 +
doc/src/pair_reax.txt | 216 +
doc/src/pair_reax_c.txt | 349 +
doc/src/pair_resquared.txt | 235 +
doc/src/pair_sdk.txt | 156 +
doc/src/pair_smd_hertz.txt | 56 +
doc/{ => src}/pair_smd_tlsph.txt | 0
doc/src/pair_smd_triangulated_surface.txt | 57 +
doc/{ => src}/pair_smd_ulsph.txt | 0
doc/src/pair_smtbq.txt | 261 +
doc/src/pair_snap.txt | 192 +
doc/src/pair_soft.txt | 136 +
doc/{ => src}/pair_sph_heatconduction.txt | 0
doc/src/pair_sph_idealgas.txt | 77 +
doc/{ => src}/pair_sph_lj.txt | 0
doc/{ => src}/pair_sph_rhosum.txt | 0
doc/src/pair_sph_taitwater.txt | 79 +
doc/{ => src}/pair_sph_taitwater_morris.txt | 0
doc/src/pair_srp.txt | 166 +
doc/src/pair_style.txt | 234 +
doc/src/pair_sw.txt | 216 +
doc/src/pair_table.txt | 272 +
doc/src/pair_table_rx.txt | 238 +
doc/src/pair_tersoff.txt | 253 +
doc/src/pair_tersoff_mod.txt | 193 +
doc/src/pair_tersoff_zbl.txt | 268 +
doc/src/pair_thole.txt | 193 +
doc/src/pair_tri_lj.txt | 115 +
doc/src/pair_vashishta.txt | 245 +
doc/src/pair_write.txt | 79 +
doc/src/pair_yukawa.txt | 104 +
doc/src/pair_yukawa_colloid.txt | 155 +
doc/src/pair_zbl.txt | 139 +
doc/src/pair_zero.txt | 87 +
doc/src/pairs.txt | 102 +
doc/src/partition.txt | 73 +
doc/src/prd.txt | 324 +
doc/src/print.txt | 77 +
doc/src/processors.txt | 340 +
doc/src/python.txt | 482 +
doc/{ => src}/quit.txt | 0
doc/src/read_data.txt | 1133 +
doc/src/read_dump.txt | 327 +
doc/src/read_restart.txt | 272 +
doc/src/region.txt | 400 +
doc/src/replicate.txt | 88 +
doc/src/rerun.txt | 203 +
doc/{ => src}/reset_timestep.txt | 0
doc/src/restart.txt | 174 +
doc/src/run.txt | 206 +
doc/src/run_style.txt | 294 +
doc/src/set.txt | 434 +
doc/{ => src}/shell.txt | 0
doc/src/special_bonds.txt | 263 +
doc/src/suffix.txt | 110 +
doc/src/tad.txt | 312 +
doc/src/temper.txt | 149 +
doc/src/thermo.txt | 59 +
doc/src/thermo_modify.txt | 179 +
doc/src/thermo_style.txt | 408 +
doc/src/timer.txt | 119 +
doc/src/timestep.txt | 51 +
doc/src/tutorial_drude.txt | 471 +
doc/src/tutorial_github.txt | 214 +
doc/src/tutorials.txt | 13 +
doc/{ => src}/uncompute.txt | 0
doc/{ => src}/undump.txt | 0
doc/{ => src}/unfix.txt | 0
doc/src/units.txt | 221 +
doc/src/variable.txt | 1325 +
doc/src/velocity.txt | 260 +
doc/src/write_coeff.txt | 46 +
doc/src/write_data.txt | 123 +
doc/src/write_dump.txt | 92 +
doc/src/write_restart.txt | 121 +
doc/suffix.html | 284 -
doc/suffix.txt | 106 -
doc/tad.html | 463 -
doc/tad.txt | 312 -
doc/temper.html | 311 -
doc/temper.txt | 132 -
doc/thermo.html | 249 -
doc/thermo.txt | 59 -
doc/thermo_modify.html | 355 -
doc/thermo_modify.txt | 166 -
doc/thermo_style.html | 518 -
doc/thermo_style.txt | 363 -
doc/timer.html | 265 -
doc/timer.txt | 73 -
doc/timestep.html | 277 -
doc/timestep.txt | 51 -
doc/tutorial_drude.html | 595 -
doc/tutorial_drude.txt | 463 -
doc/uncompute.html | 225 -
doc/undump.html | 224 -
doc/unfix.html | 225 -
doc/units.html | 403 -
doc/units.txt | 218 -
doc/utils/converters/.travis.yml | 14 +
doc/utils/converters/LICENSE | 674 +
doc/utils/converters/README.md | 104 +
.../converters/lammpsdoc/__init__.py} | 0
doc/utils/converters/lammpsdoc/lammps_filters.py | 113 +
doc/utils/converters/lammpsdoc/txt2html.py | 722 +
doc/utils/converters/lammpsdoc/txt2rst.py | 410 +
doc/utils/converters/setup.py | 17 +
doc/utils/converters/tests/test_lammps_filters.py | 56 +
doc/utils/converters/tests/test_txt2html.py | 674 +
doc/utils/converters/tests/test_txt2rst.py | 527 +
doc/utils/sha1sum.py | 7 +
doc/utils/txt2html/README.html | 237 +
doc/utils/txt2html/txt2html.cpp | 940 +
doc/variable.html | 1301 -
doc/variable.txt | 1210 -
doc/velocity.html | 419 -
doc/velocity.txt | 260 -
doc/write_data.html | 304 -
doc/write_data.txt | 123 -
doc/write_dump.html | 273 -
doc/write_dump.txt | 91 -
doc/write_restart.html | 301 -
doc/write_restart.txt | 121 -
.../box/{log.box.1Feb14 => log.1Feb14.box.g++.8} | 0
.../{log.box.mp.1Feb14 => log.1Feb14.box.mp.g++.8} | 0
.../{log.dimer.1Feb14 => log.1Feb14.dimer.g++.8} | 0
...g.dimer.mp.1Feb14 => log.1Feb14.dimer.mp.g++.8} | 0
...ellipsoid.1Feb14 => log.1Feb14.ellipsoid.g++.8} | 0
...oid.mp.1Feb14 => log.1Feb14.ellipsoid.mp.g++.8} | 0
examples/ASPHERE/line/in.line | 2 +-
examples/ASPHERE/line/in.line.srd | 6 +-
.../{log.line.1Feb14 => log.1Feb14.line.g++.8} | 0
...g.line.srd.1Feb14 => log.1Feb14.line.srd.g++.8} | 0
.../{log.poly.1Feb14 => log.1Feb14.poly.g++.8} | 0
...log.poly.mp.1Feb14 => log.1Feb14.poly.mp.g++.8} | 0
.../{log.star.1Feb14 => log.1Feb14.star.g++.8} | 0
...log.star.mp.1Feb14 => log.1Feb14.star.mp.g++.8} | 0
...log.tri.srd.1Feb14 => log.1Feb14.tri.srd.g++.8} | 0
examples/COUPLE/fortran2/LAMMPS.F90 | 1884 +-
examples/COUPLE/fortran2/README | 530 +-
examples/COUPLE/fortran2/makefile | 2 +-
examples/COUPLE/library/Makefile.g++ | 6 +-
examples/COUPLE/library/error.cpp | 6 +-
examples/COUPLE/library/error.h | 2 +-
examples/COUPLE/library/files.cpp | 4 +-
examples/COUPLE/library/files.h | 3 +
examples/COUPLE/library/irregular.h | 2 +-
examples/COUPLE/library/lammps_data_write.cpp | 5 +-
examples/COUPLE/library/lammps_data_write.h | 2 +-
examples/COUPLE/library/many2many.cpp | 4 +-
examples/COUPLE/library/many2many.h | 2 +-
examples/COUPLE/library/many2one.h | 2 +-
examples/COUPLE/library/memory.cpp | 6 +-
examples/COUPLE/library/memory.h | 2 +-
examples/COUPLE/library/one2many.cpp | 3 +-
examples/COUPLE/library/one2many.h | 2 +-
examples/COUPLE/library/send2one.h | 2 +-
examples/COUPLE/simple/in.lj | 2 +
examples/COUPLE/simple/simple.c | 71 +-
examples/COUPLE/simple/simple.cpp | 61 +-
examples/DIFFUSE/log.13Oct16.msd.2d.g++.8 | 245 +
examples/DIFFUSE/log.13Oct16.vacf.2d.g++.8 | 246 +
examples/DIFFUSE/log.msd.2d.1Feb14 | 223 -
examples/DIFFUSE/log.vacf.2d.1Feb14 | 224 -
examples/ELASTIC/compliance.py | 95 +
examples/HEAT/README | 40 +
examples/HEAT/data.lj | 4018 +
examples/HEAT/data.spce | 9245 ++
examples/HEAT/in.lj.ehex | 132 +
examples/HEAT/in.lj.hex | 132 +
examples/HEAT/in.spce.ehex | 160 +
examples/HEAT/in.spce.hex | 160 +
examples/HEAT/log.10May16.lj.ehex.g++.32 | 256 +
examples/HEAT/log.10May16.lj.hex.g++.32 | 256 +
examples/HEAT/log.10May16.spce.ehex.g++.32 | 574 +
examples/HEAT/log.10May16.spce.hex.g++.32 | 574 +
examples/HEAT/out.10May16.Elj.ehex.g++.32 | 73 +
examples/HEAT/out.10May16.Elj.hex.g++.32 | 73 +
examples/HEAT/out.10May16.Espce.ehex.g++.32 | 68 +
examples/HEAT/out.10May16.Espce.hex.g++.32 | 68 +
examples/HEAT/out.10May16.Tlj.ehex.g++.32 | 64 +
examples/HEAT/out.10May16.Tlj.hex.g++.32 | 64 +
examples/HEAT/out.10May16.Tspce.ehex.g++.32 | 64 +
examples/HEAT/out.10May16.Tspce.hex.g++.32 | 64 +
examples/KAPPA/README | 29 +-
examples/KAPPA/in.ehex | 76 +
examples/KAPPA/in.heat | 6 +-
examples/KAPPA/in.langevin | 4 +-
examples/KAPPA/in.mp | 6 +-
examples/KAPPA/log.13Oct16.ehex.g++.8 | 225 +
examples/KAPPA/log.13Oct16.heat.g++.8 | 225 +
examples/KAPPA/log.13Oct16.heatflux.g++.8 | 230 +
examples/KAPPA/log.13Oct16.langevin.g++.8 | 245 +
examples/KAPPA/log.13Oct16.mp.g++.8 | 232 +
examples/KAPPA/log.heat.1Feb14 | 208 -
examples/KAPPA/log.heatflux.1Feb14 | 208 -
examples/KAPPA/log.langevin.1Feb14 | 215 -
examples/KAPPA/log.mp.1Feb14 | 200 -
...e.heat.1Feb14 => profile.1Feb14.heatflux.g++.8} | 0
...ngevin.1Feb14 => profile.1Feb14.langevin.g++.8} | 0
.../{profile.mp.1Feb14 => profile.1Feb14.mp.g++.8} | 0
examples/KAPPA/profile.7Jun16.ehex.g++.8 | 423 +
examples/KAPPA/profile.7Jun16.heat.g++.8 | 423 +
examples/KAPPA/profile.heatflux.1Feb14 | 10254 --
examples/MC/log.13Oct16.mc.g++.1 | 112262 +++++++++++++++
examples/MC/log.mc.6Jun14 | 106235 --------------
examples/README | 9 +-
.../USER/atc/drift_diffusion/in.convective_pulse | 144 +-
.../USER/atc/drift_diffusion/in.ddm_schrodinger | 132 +-
examples/USER/atc/drift_diffusion/in.finite_well | 150 +-
examples/USER/atc/drift_diffusion/in.no_atoms_ddm | 130 +-
.../USER/atc/drift_diffusion/in.null_material_ddm | 158 +-
examples/USER/atc/elastic/in.bar1d | 182 +-
examples/USER/atc/elastic/in.bar1d_damped | 232 +-
examples/USER/atc/elastic/in.bar1d_flux | 196 +-
examples/USER/atc/elastic/in.bar1d_frac_step | 198 +-
examples/USER/atc/elastic/in.bar1d_ghost_flux | 202 +-
examples/USER/atc/elastic/in.bar1d_thermo_elastic | 278 +-
examples/USER/atc/elastic/in.eam_energy | 160 +-
examples/USER/atc/elastic/in.electron_density | 148 +-
examples/USER/atc/mesh/in.gaussianIC1d_hex | 112 +-
examples/USER/atc/mesh/in.gaussianIC2d_hex | 138 +-
.../USER/atc/mesh/in.gaussianIC2d_hex20_uniform | 74 +-
.../USER/atc/mesh/in.gaussianIC2d_hex27_uniform | 74 +-
examples/USER/atc/mesh/in.gaussianIC2d_tet | 80 +-
examples/USER/atc/mesh/in.kernel2d_hex | 64 +-
examples/USER/atc/mesh/in.kernel2d_tet | 56 +-
examples/USER/atc/mesh/in.mesh2d_tet | 58 +-
examples/USER/atc/mesh/in.semicircle | 202 +-
examples/USER/atc/thermal/in.no_atoms | 112 +-
examples/USER/atc/two_temperature/in.cutout | 174 +-
.../USER/atc/two_temperature/in.gaussianIC_ttm | 188 +-
examples/USER/atc/two_temperature/in.no_atoms | 122 +-
.../USER/atc/two_temperature/in.uniform_exchange | 132 +-
examples/USER/dpd/README | 12 +
examples/USER/dpd/dpd-shardlow/data.dpd | 2018 +
examples/USER/dpd/dpd-shardlow/in.dpd-shardlow | 27 +
.../dpd/dpd-shardlow/log.dpd-shardlow.reference | 171 +
examples/USER/dpd/dpd-vv/data.dpd | 20266 +++
examples/USER/dpd/dpd-vv/in.dpd-vv | 29 +
examples/USER/dpd/dpd-vv/log.dpd-vv.reference | 169 +
examples/USER/dpd/dpde-shardlow/data.dpde | 2018 +
examples/USER/dpd/dpde-shardlow/in.dpde-shardlow | 31 +
.../dpd/dpde-shardlow/log.dpde-shardlow.reference | 177 +
examples/USER/dpd/dpde-vv/data.dpd | 20266 +++
examples/USER/dpd/dpde-vv/in.dpde-vv | 33 +
examples/USER/dpd/dpde-vv/log.dpde-vv.reference | 173 +
examples/USER/dpd/dpdh-shardlow/data.dpdh | 20266 +++
examples/USER/dpd/dpdh-shardlow/in.dpdh-shardlow | 31 +
.../dpd/dpdh-shardlow/log.dpdh-shardlow.reference | 175 +
examples/USER/dpd/dpdp-shardlow/data.dpd | 2018 +
examples/USER/dpd/dpdp-shardlow/in.dpdp-shardlow | 27 +
.../dpd/dpdp-shardlow/log.dpdp-shardlow.reference | 171 +
examples/USER/dpd/dpdrx-shardlow/in.dpdrx-shardlow | 59 +
examples/USER/dpd/dpdrx-shardlow/kinetics.dpdrx | 12 +
.../dpdrx-shardlow/log.dpdrx-shardlow.reference | 120 +
examples/USER/dpd/dpdrx-shardlow/params.exp6 | 16 +
examples/USER/dpd/dpdrx-shardlow/table.eos | 4006 +
examples/USER/dpd/dpdrx-shardlow/thermo.dpdrx | 17 +
examples/USER/dpd/dpdrx-shardlow/thermo.dpdrx.new | 17 +
examples/USER/dpd/multi-lucy/in.multi-lucy | 40 +
.../USER/dpd/multi-lucy/log.multi-lucy.reference | 192 +
examples/USER/dpd/multi-lucy/table.multibody | 74928 ++++++++++
examples/USER/eff/Auger-Adamantane/data.adamantane | 238 +-
.../eff/Auger-Adamantane/data.adamantane_ionized | 236 +-
examples/USER/eff/Li-dendritic/data.Li-dendritic | 6944 +-
examples/USER/flow_gauss/README | 45 +
examples/USER/flow_gauss/in.GD | 258 +
examples/USER/lb/polymer/data.polymer | 2080 +-
examples/USER/lb/polymer/in.polymer_default_gamma | 214 +-
examples/USER/lb/polymer/in.polymer_setgamma | 210 +-
examples/USER/manifold/diffusion/README | 1 +
examples/USER/manifold/diffusion/msd.cyl.data | 4018 +
examples/USER/manifold/diffusion/msd.cyl.in | 30 +
examples/USER/manifold/diffusion/msd.pdf | Bin 0 -> 145018 bytes
examples/USER/manifold/diffusion/msd.plane.data | 2016 +
examples/USER/manifold/diffusion/msd.plane.in | 29 +
examples/USER/manifold/diffusion/msd.sphere.data | 2016 +
examples/USER/manifold/diffusion/msd.sphere.in | 27 +
examples/USER/manifold/diffusion/msd_plot2.pdf | Bin 0 -> 66627 bytes
examples/USER/manifold/diffusion/plot_msd.gpl | 63 +
examples/USER/manifold/energy/README | 3 +
examples/USER/manifold/energy/cylinder.data | 1018 +
examples/USER/manifold/energy/cylinder.setup | 3 +
examples/USER/manifold/energy/energy.in | 28 +
examples/USER/manifold/energy/energy.plane.in | 27 +
examples/USER/manifold/energy/energy.sh | 39 +
.../USER/manifold/energy/energy_conservation.pdf | Bin 0 -> 1023627 bytes
.../USER/manifold/energy/energy_conservation.png | Bin 0 -> 85635 bytes
examples/USER/manifold/energy/plane.anneal.data | 1022 +
examples/USER/manifold/energy/plane.data | 1018 +
examples/USER/manifold/energy/plot_energies.gpl | 78 +
examples/USER/manifold/energy/sphere.data | 1018 +
examples/USER/manifold/energy/sphere.setup | 3 +
examples/USER/manifold/energy/torus.data | 1018 +
examples/USER/manifold/energy/torus.setup | 3 +
examples/USER/manifold/thylakoid/README | 1 +
examples/USER/manifold/thylakoid/thylakoid.data | 8026 ++
examples/USER/manifold/thylakoid/thylakoid.in | 33 +
examples/USER/manifold/virus/README | 1 +
examples/USER/manifold/virus/init.data | 704 +
examples/USER/manifold/virus/vir.in | 75 +
examples/USER/misc/basal/in.basal | 326 +-
.../USER/{ => misc}/gauss-diel/data.gauss-diel | 0
examples/USER/{ => misc}/gauss-diel/in.gauss-diel | 0
.../USER/{ => misc}/gauss-diel/in.gauss-diel-cg | 0
.../USER/{ => misc}/gauss-diel/in.gauss-diel-split | 0
examples/USER/{ => misc}/gauss-diel/log.gauss-diel | 0
.../USER/{ => misc}/gauss-diel/log.gauss-diel-cg | 0
.../{ => misc}/gauss-diel/log.gauss-diel-split | 0
examples/USER/{ => misc}/gle/data.h2o-quantum | 0
examples/USER/{ => misc}/gle/data.h2o-smart | 0
examples/USER/{ => misc}/gle/in.h2o-quantum | 0
examples/USER/{ => misc}/gle/in.h2o-smart | 0
examples/USER/{ => misc}/gle/log.h2o-quantum | 0
examples/USER/{ => misc}/gle/log.h2o-smart | 0
examples/USER/{ => misc}/gle/qt-300k.A | 0
examples/USER/{ => misc}/gle/qt-300k.C | 0
examples/USER/{ => misc}/gle/smart.A | 0
examples/USER/{ => misc}/i-pi/C.opt.tersoff | 0
examples/USER/{ => misc}/i-pi/README | 0
examples/USER/{ => misc}/i-pi/data.graphene | 0
examples/USER/{ => misc}/i-pi/i-pi_input.xml | 0
examples/USER/{ => misc}/i-pi/i-pi_positions.xyz | 0
examples/USER/{ => misc}/i-pi/in.graphene | 0
examples/USER/{ => misc}/imd/README | 0
.../USER/{ => misc}/imd/bucky-plus-cnt-mol.psf | 0
examples/USER/{ => misc}/imd/bucky_cnt_imd.vmd | 0
examples/USER/{ => misc}/imd/data.bucky-plus-cnt | 0
examples/USER/{ => misc}/imd/data.deca-ala-solv | 0
examples/USER/{ => misc}/imd/deca-ala-solv.psf | 0
.../USER/{ => misc}/imd/deca-ala-solv_imd-demo.vmd | 0
examples/USER/{ => misc}/imd/deca-ala.psf | 0
examples/USER/{ => misc}/imd/deca-ala_imd-demo.vmd | 0
examples/USER/{ => misc}/imd/falcon.tcl | 0
examples/USER/{ => misc}/imd/in.bucky-plus-cnt | 0
examples/USER/{ => misc}/imd/in.bucky-plus-cnt-gpu | 0
.../{ => misc}/imd/in.deca-ala-solv-filter_imd | 0
examples/USER/{ => misc}/imd/in.deca-ala-solv_imd | 0
examples/USER/{ => misc}/imd/in.deca-ala_imd | 0
examples/USER/{ => misc}/imd/in.deca-ala_imd-gpu | 0
examples/USER/{ => misc}/imd/in.melt_imd | 0
examples/USER/{ => misc}/imd/in.melt_imd-gpu | 0
examples/USER/{ => misc}/imd/melt.psf | 0
examples/USER/{ => misc}/imd/melt_imd-demo.vmd | 0
examples/USER/{ => misc}/pimd/para-h2/H2.data | 0
examples/USER/{ => misc}/pimd/para-h2/H2.xyz | 0
examples/USER/{ => misc}/pimd/para-h2/NM.info | 0
examples/USER/{ => misc}/pimd/para-h2/in.scp | 0
examples/USER/{ => misc}/pimd/para-h2/pair.table | 0
examples/USER/{ => misc}/pimd/para-h2/run.sh | 0
examples/USER/{ => misc}/pimd/para-h2/vmd.src | 0
examples/USER/{ => misc}/pimd/prot-hairpin/in.scp | 0
examples/USER/{ => misc}/pimd/prot-hairpin/run.sh | 0
.../USER/{ => misc}/pimd/prot-hairpin/system.data | 0
examples/USER/{ => misc}/srp/data.chain | 0
examples/USER/misc/srp/in.srp | 41 +
examples/USER/misc/ti/in.ti_rs | 64 -
examples/USER/misc/ti/in.ti_spring | 85 +-
examples/USER/phonon/1-1D-mono/README | 7 +-
examples/USER/phonon/1-1D-mono/disp.dat | 34 +-
examples/USER/phonon/1-1D-mono/in.disp | 1 +
examples/USER/phonon/1-1D-mono/log.lammps | 20090 +++
examples/USER/phonon/1-1D-mono/log.lammps.example | 146 -
examples/USER/phonon/1-1D-mono/pdisp.eps | 99 +-
examples/USER/phonon/1-1D-mono/pdisp.gnuplot | 16 +
examples/USER/phonon/1-1D-mono/phonon.bin.2000000 | Bin 384 -> 384 bytes
examples/USER/phonon/1-1D-mono/phonon.log | 96 +-
examples/USER/phonon/2-1D-diatomic/README | 7 +-
examples/USER/phonon/2-1D-diatomic/disp.dat | 2 +-
examples/USER/phonon/2-1D-diatomic/in.Ana | 2 +-
examples/USER/phonon/2-1D-diatomic/in.disp | 1 +
examples/USER/phonon/2-1D-diatomic/log.lammps | 20088 +++
.../USER/phonon/2-1D-diatomic/log.lammps.example | 113 -
examples/USER/phonon/2-1D-diatomic/pdisp.eps | 4 +-
examples/USER/phonon/2-1D-diatomic/pdisp.gnuplot | 17 +
examples/USER/phonon/2-1D-diatomic/pdos.dat | 203 -
examples/USER/phonon/2-1D-diatomic/phonon.log | 2 +-
examples/USER/phonon/3-3D-FCC-Cu-EAM/CuPhonon.log | 6792 +
.../phonon/3-3D-FCC-Cu-EAM/CuPhonon.log.example | 1575 -
examples/USER/phonon/3-3D-FCC-Cu-EAM/README | 11 +-
examples/USER/phonon/3-3D-FCC-Cu-EAM/disp.dat | 266 +-
examples/USER/phonon/3-3D-FCC-Cu-EAM/in.disp | 1 +
examples/USER/phonon/3-3D-FCC-Cu-EAM/in.disp2 | 6 +
.../USER/phonon/3-3D-FCC-Cu-EAM/log.lammps.example | 107 -
examples/USER/phonon/3-3D-FCC-Cu-EAM/pdisp.eps | 1398 +-
examples/USER/phonon/3-3D-FCC-Cu-EAM/pdisp.gnuplot | 18 +
.../USER/phonon/4-Graphene/Graphene.bin.6000000 | Bin 0 -> 57780 bytes
examples/USER/phonon/4-Graphene/Graphene.log | 1316 +
examples/USER/phonon/4-Graphene/README | 35 +
examples/USER/phonon/4-Graphene/SiC.tersoff | 39 +
examples/USER/phonon/4-Graphene/data.pos | 211 +
examples/USER/phonon/4-Graphene/in.disp | 16 +
examples/USER/phonon/4-Graphene/in.graphene | 45 +
examples/USER/phonon/4-Graphene/map.in | 202 +
examples/USER/phonon/4-Graphene/pdisp.dat | 55 +
examples/USER/phonon/4-Graphene/pdisp.eps | 1350 +
examples/USER/phonon/4-Graphene/pdisp.gnuplot | 21 +
examples/USER/phonon/4-Graphene/plot.disp | 17 +
examples/USER/quip/in.gap | 1 -
examples/USER/quip/in.sw | 1 -
.../aluminum_strip_pull/aluminum_strip_pull.lmp | 2 +-
.../fluid_structure_interaction.lmp | 6 +-
examples/USER/smd/funnel_flow/boundary.stl | 132612 +++++++++---------
examples/USER/smd/funnel_flow/funnel_flow.lmp | 4 +-
.../USER/smd/rubber_rings_3d/rubber_rings_3d.lmp | 2 +-
examples/USER/smtbq/log.smtbq.Al | 279 -
examples/USER/smtbq/log.smtbq.Al.g++.1 | 280 +
examples/USER/smtbq/log.smtbq.Al.g++.4 | 278 +
.../{log.smtbq.Al2O3 => log.smtbq.Al2O3.g++.1} | 0
examples/USER/smtbq/log.smtbq.Al2O3.g++.4 | 210 +
.../smtbq/{log.smtbq.TiO2 => log.smtbq.TiO2.g++.1} | 0
examples/USER/smtbq/log.smtbq.TiO2.g++.4 | 256 +
examples/USER/sph/cavity_flow/cavity_flow.lmp | 6 +-
.../sph/heatconduction/sph_heat_conduction_2d.lmp | 8 +-
.../sph/heatconduction/sph_heat_conduction_3d.lmp | 8 +-
examples/USER/sph/shock_tube/shock2d.lmp | 12 +-
examples/USER/sph/shock_tube/shock3d.lmp | 12 +-
.../USER/sph/water_collapse/water_collapse.lmp | 4 +-
examples/USER/srp/in.srp | 37 -
examples/USER/tally/in.force | 3 +
examples/USER/tally/in.pe | 3 +
examples/USER/tally/in.stress | 3 +
examples/VISCOSITY/README | 23 +-
examples/VISCOSITY/in.einstein.2d | 84 +
examples/VISCOSITY/in.mp.2d | 5 +-
examples/VISCOSITY/in.nemd.2d | 13 +-
examples/VISCOSITY/in.wall.2d | 6 +-
examples/VISCOSITY/log.13Oct16.einstein.2d.g++.1 | 436 +
examples/VISCOSITY/log.13Oct16.gk.2d.g++.1 | 423 +
examples/VISCOSITY/log.13Oct16.mp.2d.g++.1 | 260 +
examples/VISCOSITY/log.13Oct16.nemd.2d.g++.1 | 304 +
examples/VISCOSITY/log.13Oct16.wall.2d.g++.1 | 246 +
examples/VISCOSITY/log.gk.2d.1Feb14 | 386 -
examples/VISCOSITY/log.mp.2d.1Feb14 | 230 -
examples/VISCOSITY/log.nemd.2d.1Feb14 | 271 -
examples/VISCOSITY/log.wall.2d.1Feb14 | 221 -
.../VISCOSITY/profile.13Oct16.einstein.2d.g++.1 | 252 +
examples/VISCOSITY/profile.13Oct16.gk.2d.g++.1 | 100654 +++++++++++++
examples/VISCOSITY/profile.13Oct16.mp.2d.g++.1 | 1473 +
examples/VISCOSITY/profile.13Oct16.nemd.2d.g++.1 | 423 +
examples/VISCOSITY/profile.13Oct16.wall.2d.g++.1 | 150 +
examples/VISCOSITY/profile.gk.2d.1Feb14 | 100654 -------------
examples/VISCOSITY/profile.mp.2d.1Feb14 | 1473 -
examples/VISCOSITY/profile.nemd.2d.1Feb14 | 423 -
examples/VISCOSITY/profile.wall.2d.1Feb14 | 150 -
examples/balance/in.balance.bond.fast | 2 +-
examples/balance/in.balance.clock.dynamic | 54 +
examples/balance/in.balance.clock.static | 48 +
examples/balance/in.balance.group.dynamic | 47 +
examples/balance/in.balance.group.static | 54 +
examples/balance/in.balance.kspace | 47 +
examples/balance/in.balance.neigh.dynamic | 53 +
examples/balance/in.balance.neigh.rcb | 53 +
examples/balance/in.balance.neigh.static | 51 +
examples/balance/in.balance.var.dynamic | 66 +
.../balance/log.15May15.balance.bond.fast.g++.1 | 211 -
.../balance/log.15May15.balance.bond.fast.g++.4 | 211 -
.../balance/log.15May15.balance.bond.slow.g++.1 | 510 -
.../balance/log.15May15.balance.bond.slow.g++.4 | 510 -
examples/balance/log.15May15.balance.g++.1 | 191 -
examples/balance/log.15May15.balance.g++.4 | 191 -
.../balance/log.5Oct16.balance.bond.fast.g++.4 | 225 +
.../balance/log.5Oct16.balance.bond.slow.g++.4 | 524 +
.../balance/log.5Oct16.balance.clock.dynamic.g++.4 | 220 +
.../balance/log.5Oct16.balance.clock.static.g++.4 | 188 +
examples/balance/log.5Oct16.balance.g++.4 | 202 +
.../balance/log.5Oct16.balance.group.dynamic.g++.4 | 103 +
.../balance/log.5Oct16.balance.group.static.g++.4 | 139 +
examples/balance/log.5Oct16.balance.kspace.g++.4 | 110 +
.../balance/log.5Oct16.balance.neigh.dynamic.g++.4 | 221 +
.../balance/log.5Oct16.balance.neigh.rcb.g++.4 | 134 +
.../balance/log.5Oct16.balance.neigh.static.g++.4 | 207 +
.../balance/log.5Oct16.balance.var.dynamic.g++.2 | 250 +
examples/body/in.body | 10 +-
examples/body/log.15May15.body.g++.1 | 75 -
examples/body/log.15May15.body.g++.4 | 75 -
examples/body/log.5Oct16.body.g++.1 | 171 +
examples/body/log.5Oct16.body.g++.4 | 171 +
examples/cmap/charmm22.cmap | 1023 +
examples/cmap/gagg.data | 380 +
examples/cmap/in.cmap | 36 +
examples/cmap/log.5Oct16.cmap.g++.1 | 201 +
examples/cmap/log.5Oct16.cmap.g++.4 | 201 +
examples/colloid/log.15May15.colloid.g++.1 | 135 -
examples/colloid/log.15May15.colloid.g++.4 | 135 -
examples/colloid/log.5Oct16.colloid.g++.1 | 146 +
examples/colloid/log.5Oct16.colloid.g++.4 | 146 +
examples/comb/ffield.comb | 196 +-
examples/comb/log.15May15.comb.Cu.g++.1 | 80 -
examples/comb/log.15May15.comb.Cu.g++.4 | 80 -
examples/comb/log.15May15.comb.Cu2O.elastic.g++.1 | 329 -
examples/comb/log.15May15.comb.Cu2O.elastic.g++.4 | 329 -
examples/comb/log.15May15.comb.HfO2.g++.1 | 197 -
examples/comb/log.15May15.comb.HfO2.g++.4 | 197 -
examples/comb/log.15May15.comb.Si.elastic.g++.1 | 284 -
examples/comb/log.15May15.comb.Si.elastic.g++.4 | 282 -
examples/comb/log.15May15.comb.Si.g++.1 | 80 -
examples/comb/log.15May15.comb.Si.g++.4 | 80 -
examples/comb/log.15May15.comb3.g++.1 | 77 -
examples/comb/log.15May15.comb3.g++.4 | 77 -
examples/comb/log.5Oct16.comb.Cu.g++.1 | 92 +
examples/comb/log.5Oct16.comb.Cu.g++.4 | 92 +
examples/comb/log.5Oct16.comb.Cu2O.elastic.g++.1 | 409 +
examples/comb/log.5Oct16.comb.Cu2O.elastic.g++.4 | 409 +
examples/comb/log.5Oct16.comb.HfO2.g++.1 | 235 +
examples/comb/log.5Oct16.comb.HfO2.g++.4 | 235 +
examples/comb/log.5Oct16.comb.Si.elastic.g++.1 | 333 +
examples/comb/log.5Oct16.comb.Si.elastic.g++.4 | 331 +
examples/comb/log.5Oct16.comb.Si.g++.1 | 92 +
examples/comb/log.5Oct16.comb.Si.g++.4 | 92 +
examples/comb/log.5Oct16.comb3.g++.1 | 90 +
examples/comb/log.5Oct16.comb3.g++.4 | 90 +
examples/controller/in.controller | 44 +
examples/controller/log.5Oct16.controller.g++.1 | 173 +
examples/controller/log.5Oct16.controller.g++.4 | 173 +
examples/coreshell/in.coreshell.dsf | 71 +
examples/coreshell/log.5Oct16.coreshell.g++.1 | 209 +
examples/coreshell/log.5Oct16.coreshell.g++.4 | 209 +
examples/coreshell/log.9Nov16.coreshell.dsf.1 | 185 +
examples/coreshell/log.coreshell.6Mar15.linux.1 | 188 -
examples/coreshell/log.coreshell.6Mar15.linux.4 | 188 -
examples/crack/log.15May15.crack.g++.1 | 142 -
examples/crack/log.15May15.crack.g++.4 | 142 -
examples/crack/log.5Oct16.crack.g++.1 | 153 +
examples/crack/log.5Oct16.crack.g++.4 | 153 +
examples/deposit/log.15May15.deposit.atom.g++.1 | 182 -
examples/deposit/log.15May15.deposit.atom.g++.4 | 182 -
.../deposit/log.15May15.deposit.molecule.g++.1 | 194 -
.../deposit/log.15May15.deposit.molecule.g++.4 | 194 -
.../log.15May15.deposit.molecule.shake.g++.1 | 220 -
.../log.15May15.deposit.molecule.shake.g++.4 | 220 -
examples/deposit/log.5Oct16.deposit.atom.g++.1 | 193 +
examples/deposit/log.5Oct16.deposit.atom.g++.4 | 193 +
examples/deposit/log.5Oct16.deposit.molecule.g++.1 | 205 +
examples/deposit/log.5Oct16.deposit.molecule.g++.4 | 205 +
.../log.5Oct16.deposit.molecule.shake.g++.1 | 231 +
.../log.5Oct16.deposit.molecule.shake.g++.4 | 231 +
examples/dipole/log.15May15.dipole.g++.1 | 93 -
examples/dipole/log.15May15.dipole.g++.4 | 93 -
examples/dipole/log.5Oct16.dipole.g++.1 | 104 +
examples/dipole/log.5Oct16.dipole.g++.4 | 104 +
examples/dreiding/log.15May15.dreiding.g++.1 | 107 -
examples/dreiding/log.15May15.dreiding.g++.4 | 107 -
examples/dreiding/log.5Oct16.dreiding.g++.1 | 118 +
examples/dreiding/log.5Oct16.dreiding.g++.4 | 118 +
examples/eim/log.15May15.eim.g++.1 | 76 -
examples/eim/log.15May15.eim.g++.4 | 76 -
examples/eim/log.5Oct16.eim.g++.1 | 88 +
examples/eim/log.5Oct16.eim.g++.4 | 88 +
.../ellipse/log.15May15.ellipse.gayberne.g++.1 | 167 -
.../ellipse/log.15May15.ellipse.gayberne.g++.4 | 167 -
.../ellipse/log.15May15.ellipse.resquared.g++.1 | 164 -
.../ellipse/log.15May15.ellipse.resquared.g++.4 | 164 -
examples/ellipse/log.5Oct16.ellipse.gayberne.g++.1 | 185 +
examples/ellipse/log.5Oct16.ellipse.gayberne.g++.4 | 185 +
.../ellipse/log.5Oct16.ellipse.resquared.g++.1 | 182 +
.../ellipse/log.5Oct16.ellipse.resquared.g++.4 | 182 +
examples/flow/log.15May15.flow.couette.g++.1 | 134 -
examples/flow/log.15May15.flow.couette.g++.4 | 134 -
examples/flow/log.15May15.flow.pois.g++.1 | 134 -
examples/flow/log.15May15.flow.pois.g++.4 | 134 -
examples/flow/log.5Oct16.flow.couette.g++.1 | 145 +
examples/flow/log.5Oct16.flow.couette.g++.4 | 145 +
examples/flow/log.5Oct16.flow.pois.g++.1 | 145 +
examples/flow/log.5Oct16.flow.pois.g++.4 | 145 +
examples/friction/log.15May15.friction.g++.1 | 153 -
examples/friction/log.15May15.friction.g++.4 | 153 -
examples/friction/log.5Oct16.friction.g++.1 | 164 +
examples/friction/log.5Oct16.friction.g++.4 | 164 +
examples/granregion/in.granregion.box | 66 +
examples/granregion/in.granregion.funnel | 157 +
examples/granregion/in.granregion.mixer | 96 +
.../granregion/log.6Oct16.granregion.box.g++.1 | 468 +
.../granregion/log.6Oct16.granregion.box.g++.4 | 468 +
.../granregion/log.6Oct16.granregion.funnel.g++.1 | 608 +
.../granregion/log.6Oct16.granregion.funnel.g++.4 | 608 +
.../granregion/log.6Oct16.granregion.mixer.g++.1 | 609 +
.../granregion/log.6Oct16.granregion.mixer.g++.4 | 609 +
examples/hugoniostat/log.15May15.hugoniostat.g++.1 | 98 -
examples/hugoniostat/log.15May15.hugoniostat.g++.4 | 98 -
examples/hugoniostat/log.5Oct16.hugoniostat.g++.1 | 110 +
examples/hugoniostat/log.5Oct16.hugoniostat.g++.4 | 110 +
examples/indent/log.15May15.indent.g++.1 | 183 -
examples/indent/log.15May15.indent.g++.4 | 183 -
examples/indent/log.15May15.indent.min.g++.1 | 406 -
examples/indent/log.15May15.indent.min.g++.4 | 399 -
examples/indent/log.5Oct16.indent.g++.1 | 201 +
examples/indent/log.5Oct16.indent.g++.4 | 201 +
examples/indent/log.5Oct16.indent.min.g++.1 | 452 +
examples/indent/log.5Oct16.indent.min.g++.4 | 445 +
...15.ubuntu.1 => log.28Jun15.kim.lj.lmp.ubuntu.1} | 0
...15.ubuntu.4 => log.28Jun15.kim.lj.lmp.ubuntu.4} | 0
...8jun15.ubuntu.1 => log.28Jun15.kim.lj.ubuntu.1} | 0
...8jun15.ubuntu.4 => log.28Jun15.kim.lj.ubuntu.4} | 0
examples/meam/log.15May15.meam.icc.1 | 71 -
examples/meam/log.15May15.meam.icc.4 | 71 -
examples/meam/log.15May15.meam.shear.icc.1 | 176 -
examples/meam/log.15May15.meam.shear.icc.4 | 176 -
examples/meam/log.5Oct16.meam.icc.1 | 84 +
examples/meam/log.5Oct16.meam.icc.4 | 84 +
examples/meam/log.5Oct16.meam.shear.icc.1 | 196 +
examples/meam/log.5Oct16.meam.shear.icc.4 | 196 +
examples/melt/log.15May15.melt.g++.1 | 67 -
examples/melt/log.15May15.melt.g++.4 | 67 -
examples/melt/log.5Oct16.melt.g++.1 | 78 +
examples/melt/log.5Oct16.melt.g++.4 | 78 +
examples/micelle/log.15May15.micelle.g++.1 | 223 -
examples/micelle/log.15May15.micelle.g++.4 | 223 -
examples/micelle/log.5Oct16.micelle.g++.1 | 244 +
examples/micelle/log.5Oct16.micelle.g++.4 | 244 +
examples/min/log.15May15.min.box.g++.1 | 500 -
examples/min/log.15May15.min.box.g++.4 | 489 -
examples/min/log.15May15.min.g++.1 | 124 -
examples/min/log.15May15.min.g++.4 | 120 -
examples/min/log.5Oct16.min.box.g++.1 | 553 +
examples/min/log.5Oct16.min.box.g++.4 | 542 +
examples/min/log.5Oct16.min.g++.1 | 141 +
examples/min/log.5Oct16.min.g++.4 | 137 +
examples/msst/log.15May15.msst.g++.1 | 142 -
examples/msst/log.15May15.msst.g++.4 | 142 -
examples/msst/log.5Oct16.msst.g++.1 | 160 +
examples/msst/log.5Oct16.msst.g++.4 | 160 +
examples/nb3b/MOH.nb3b.harmonic | 27 +-
examples/nb3b/log.15May15.nb3b.g++.1 | 152 -
examples/nb3b/log.15May15.nb3b.g++.4 | 152 -
examples/nb3b/log.5Oct16.nb3b.g++.1 | 173 +
examples/nb3b/log.5Oct16.nb3b.g++.4 | 173 +
examples/neb/README | 18 +-
examples/neb/in.neb.hop1 | 9 +-
examples/neb/in.neb.hop2 | 11 +-
examples/neb/in.neb.sivac | 18 +-
examples/neb/initial.hop1 | 860 +
examples/neb/initial.hop2 | 862 +
examples/neb/initial.sivac | 1042 +
examples/neb/log.5Oct16.neb.hop1.g++.4 | 10 +
examples/neb/log.5Oct16.neb.hop1.g++.8 | 10 +
examples/neb/log.5Oct16.neb.hop2.g++.4 | 18 +
examples/neb/log.5Oct16.neb.hop2.g++.8 | 18 +
examples/neb/log.5Oct16.neb.sivac.g++.3 | 14 +
examples/neb/log.5Oct16.neb.sivac.g++.6 | 14 +
examples/neb/log.5Oct16.neb.sivac.g++.9 | 14 +
examples/neb/log.neb.hop1.1Feb14.linux.4 | 10 -
examples/neb/log.neb.hop2.1Feb14.linux.4 | 17 -
examples/neb/log.neb.sivac.1Feb14.linux.3 | 13 -
examples/nemd/log.15May15.nemd.g++.1 | 119 -
examples/nemd/log.15May15.nemd.g++.4 | 119 -
examples/nemd/log.5Oct16.nemd.g++.1 | 130 +
examples/nemd/log.5Oct16.nemd.g++.4 | 130 +
examples/obstacle/log.15May15.obstacle.g++.1 | 144 -
examples/obstacle/log.15May15.obstacle.g++.4 | 144 -
examples/obstacle/log.5Oct16.obstacle.g++.1 | 155 +
examples/obstacle/log.5Oct16.obstacle.g++.4 | 155 +
examples/peptide/log.15May15.peptide.g++.1 | 178 -
examples/peptide/log.15May15.peptide.g++.4 | 178 -
examples/peptide/log.5Oct16.peptide.g++.1 | 190 +
examples/peptide/log.5Oct16.peptide.g++.4 | 190 +
examples/peri/log.15May15.peri.g++.1 | 94 -
examples/peri/log.15May15.peri.g++.4 | 94 -
examples/peri/log.5Oct16.peri.g++.1 | 104 +
examples/peri/log.5Oct16.peri.g++.4 | 104 +
examples/pour/in.pour | 2 +-
examples/pour/in.pour.2d | 4 +-
examples/pour/in.pour.2d.molecule | 4 +-
examples/pour/log.15May15.pour.2d.g++.1 | 104 -
examples/pour/log.15May15.pour.2d.g++.4 | 104 -
examples/pour/log.15May15.pour.2d.molecule.g++.1 | 125 -
examples/pour/log.15May15.pour.2d.molecule.g++.4 | 125 -
examples/pour/log.15May15.pour.g++.1 | 151 -
examples/pour/log.15May15.pour.g++.4 | 151 -
examples/pour/log.5Oct16.pour.2d.g++.1 | 115 +
examples/pour/log.5Oct16.pour.2d.g++.4 | 115 +
examples/pour/log.5Oct16.pour.2d.molecule.g++.1 | 136 +
examples/pour/log.5Oct16.pour.2d.molecule.g++.4 | 136 +
examples/pour/log.5Oct16.pour.g++.1 | 169 +
examples/pour/log.5Oct16.pour.g++.4 | 169 +
examples/prd/README | 3 +-
examples/prd/log.5Oct16.prd.g++.4 | 22 +
examples/prd/log.5Oct16.prd.g++.8 | 22 +
examples/prd/log.prd.0.1Feb14.linux.4 | 631 -
examples/prd/log.prd.1.1Feb14.linux.4 | 631 -
examples/prd/log.prd.1Feb14.linux.4 | 12 -
examples/prd/log.prd.2.1Feb14.linux.4 | 631 -
examples/prd/log.prd.3.1Feb14.linux.4 | 631 -
examples/prd/screen.5Oct16.prd.g++.4.0 | 2328 +
examples/prd/screen.5Oct16.prd.g++.4.1 | 2204 +
examples/prd/screen.5Oct16.prd.g++.4.2 | 2349 +
examples/prd/screen.5Oct16.prd.g++.4.3 | 2183 +
examples/prd/screen.5Oct16.prd.g++.8.0 | 2328 +
examples/prd/screen.5Oct16.prd.g++.8.1 | 2204 +
examples/prd/screen.5Oct16.prd.g++.8.2 | 2349 +
examples/prd/screen.5Oct16.prd.g++.8.3 | 2183 +
examples/python/log.5Oct16.python.g++.1 | 396 +
examples/python/log.5Oct16.python.g++.4 | 396 +
examples/python/log.python.17Mar15.linux.1 | 315 -
examples/python/log.python.17Mar15.linux.4 | 315 -
examples/qeq/in.qeq.buck | 16 +-
examples/qeq/log.15May15.qeq.buck.g++.1 | 89 -
examples/qeq/log.15May15.qeq.buck.g++.4 | 89 -
examples/qeq/log.15May15.qeq.reaxc.g++.1 | 93 -
examples/qeq/log.15May15.qeq.reaxc.g++.4 | 93 -
examples/qeq/log.5Oct16.qeq.buck.g++.1 | 106 +
examples/qeq/log.5Oct16.qeq.buck.g++.4 | 106 +
examples/qeq/log.5Oct16.qeq.reaxc.g++.1 | 105 +
examples/qeq/log.5Oct16.qeq.reaxc.g++.4 | 105 +
examples/reax/AB/log.5Oct16.AB.g++.1 | 70 +
examples/reax/AB/log.5Oct16.AB.g++.4 | 70 +
examples/reax/AB/log.reaxc.AB.1Feb14.linux.1 | 54 -
examples/reax/AB/log.reaxc.AB.1Feb14.linux.4 | 54 -
examples/reax/AuO/log.5Oct16.AuO.g++.1 | 70 +
examples/reax/AuO/log.5Oct16.AuO.g++.4 | 70 +
examples/reax/AuO/log.reaxc.AuO.1Feb14.linux.1 | 54 -
examples/reax/AuO/log.reaxc.AuO.1Feb14.linux.4 | 54 -
examples/reax/CHO/log.5Oct16.CHO.g++.1 | 70 +
examples/reax/CHO/log.5Oct16.CHO.g++.4 | 70 +
examples/reax/CHO/log.reaxc.CHO.1Feb14.linux.1 | 54 -
examples/reax/CHO/log.reaxc.CHO.1Feb14.linux.4 | 54 -
examples/reax/FC/log.5Oct16.FC.g++.1 | 130 +
examples/reax/FC/log.5Oct16.FC.g++.4 | 130 +
examples/reax/FC/log.reaxc.FC.1Feb14.linux.1 | 107 -
examples/reax/FC/log.reaxc.FC.1Feb14.linux.4 | 107 -
examples/reax/FeOH3/log.5Oct16.FeOH3.g++.1 | 70 +
examples/reax/FeOH3/log.5Oct16.FeOH3.g++.4 | 70 +
examples/reax/FeOH3/log.reaxc.FeOH3.1Feb14.linux.1 | 54 -
examples/reax/FeOH3/log.reaxc.FeOH3.1Feb14.linux.4 | 54 -
examples/reax/RDX/log.5Oct16.RDX.g++.1 | 70 +
examples/reax/RDX/log.5Oct16.RDX.g++.4 | 70 +
examples/reax/RDX/log.reaxc.RDX.1Feb14.linux.1 | 54 -
examples/reax/RDX/log.reaxc.RDX.1Feb14.linux.4 | 54 -
examples/reax/VOH/log.5Oct16.VOH.g++.1 | 70 +
examples/reax/VOH/log.5Oct16.VOH.g++.4 | 70 +
examples/reax/VOH/log.reaxc.VOH.1Feb14.linux.1 | 54 -
examples/reax/VOH/log.reaxc.VOH.1Feb14.linux.4 | 54 -
examples/reax/ZnOH2/log.5Oct16.ZnOH2.g++.1 | 70 +
examples/reax/ZnOH2/log.5Oct16.ZnOH2.g++.4 | 70 +
examples/reax/ZnOH2/log.reaxc.ZnOH2.1Feb14.linux.1 | 54 -
examples/reax/ZnOH2/log.reaxc.ZnOH2.1Feb14.linux.4 | 54 -
examples/reax/log.15May15.reax.rdx.g++.1 | 89 -
examples/reax/log.15May15.reax.rdx.g++.4 | 89 -
examples/reax/log.15May15.reax.tatb.g++.1 | 85 -
examples/reax/log.15May15.reax.tatb.g++.4 | 85 -
examples/reax/log.15May15.reaxc.rdx.g++.1 | 92 -
examples/reax/log.15May15.reaxc.rdx.g++.4 | 92 -
examples/reax/log.15May15.reaxc.tatb.g++.1 | 90 -
examples/reax/log.15May15.reaxc.tatb.g++.4 | 90 -
examples/reax/log.5Oct16.reax.rdx.g++.1 | 101 +
examples/reax/log.5Oct16.reax.rdx.g++.4 | 101 +
examples/reax/log.5Oct16.reax.tatb.g++.1 | 97 +
examples/reax/log.5Oct16.reax.tatb.g++.4 | 97 +
examples/reax/log.5Oct16.reaxc.rdx.g++.1 | 104 +
examples/reax/log.5Oct16.reaxc.rdx.g++.4 | 104 +
examples/reax/log.5Oct16.reaxc.tatb.g++.1 | 102 +
examples/reax/log.5Oct16.reaxc.tatb.g++.4 | 102 +
examples/rigid/log.15May15.rigid.g++.1 | 318 -
examples/rigid/log.15May15.rigid.g++.4 | 318 -
examples/rigid/log.15May15.rigid.poems.g++.1 | 321 -
examples/rigid/log.15May15.rigid.poems.g++.4 | 321 -
examples/rigid/log.15May15.rigid.poems2.g++.1 | 325 -
examples/rigid/log.15May15.rigid.poems2.g++.4 | 325 -
examples/rigid/log.15May15.rigid.tnr.g++.1 | 399 -
examples/rigid/log.15May15.rigid.tnr.g++.4 | 399 -
examples/rigid/log.5Oct16.rigid.g++.1 | 329 +
examples/rigid/log.5Oct16.rigid.g++.4 | 329 +
examples/rigid/log.5Oct16.rigid.poems.g++.1 | 332 +
examples/rigid/log.5Oct16.rigid.poems.g++.4 | 332 +
examples/rigid/log.5Oct16.rigid.poems2.g++.1 | 336 +
examples/rigid/log.5Oct16.rigid.poems2.g++.4 | 336 +
examples/rigid/log.5Oct16.rigid.tnr.g++.1 | 452 +
examples/rigid/log.5Oct16.rigid.tnr.g++.4 | 452 +
examples/shear/log.15May15.shear.g++.1 | 172 -
examples/shear/log.15May15.shear.g++.4 | 172 -
examples/shear/log.15May15.shear.void.g++.1 | 173 -
examples/shear/log.15May15.shear.void.g++.4 | 173 -
examples/shear/log.5Oct16.shear.g++.1 | 191 +
examples/shear/log.5Oct16.shear.g++.4 | 191 +
examples/shear/log.5Oct16.shear.void.g++.1 | 192 +
examples/shear/log.5Oct16.shear.void.g++.4 | 192 +
examples/snap/Ta06A_pot.snap | 6 +-
examples/snap/log.15May15.snap.g++.1 | 120 -
examples/snap/log.15May15.snap.g++.4 | 120 -
examples/snap/log.5Oct16.snap.g++.1 | 136 +
examples/snap/log.5Oct16.snap.g++.4 | 136 +
examples/srd/log.15May15.srd.mixture.g++.1 | 245 -
examples/srd/log.15May15.srd.mixture.g++.4 | 245 -
examples/srd/log.15May15.srd.pure.g++.1 | 152 -
examples/srd/log.15May15.srd.pure.g++.4 | 152 -
examples/srd/log.5Oct16.srd.mixture.g++.1 | 269 +
examples/srd/log.5Oct16.srd.mixture.g++.4 | 269 +
examples/srd/log.5Oct16.srd.pure.g++.1 | 163 +
examples/srd/log.5Oct16.srd.pure.g++.4 | 163 +
examples/streitz/log.15May15.streitz.ewald.g++.1 | 107 -
examples/streitz/log.15May15.streitz.ewald.g++.4 | 107 -
examples/streitz/log.15May15.streitz.wolf.g++.1 | 100 -
examples/streitz/log.15May15.streitz.wolf.g++.4 | 100 -
examples/streitz/log.5Oct16.streitz.ewald.g++.1 | 119 +
examples/streitz/log.5Oct16.streitz.ewald.g++.4 | 119 +
examples/streitz/log.5Oct16.streitz.wolf.g++.1 | 111 +
examples/streitz/log.5Oct16.streitz.wolf.g++.4 | 111 +
examples/tad/README | 2 +-
examples/tad/log.5Oct16.tad.g++.3 | 39 +
examples/tad/log.tad.0.1Feb14.linux.3 | 12325 --
examples/tad/log.tad.1.1Feb14.linux.3 | 7262 -
examples/tad/log.tad.1Feb14.linux.3 | 114 -
examples/tad/log.tad.2.1Feb14.linux.3 | 7262 -
examples/tad/log.tad.neb.1Feb14.linux.3 | 1160 -
examples/threebody/BNC.tersoff | 74 +
examples/threebody/CdTeZnSeHgS0.sw | 233 +
examples/{vashishta => threebody}/InP.vashishta | 0
examples/threebody/Si.sw | 18 +
examples/threebody/in.threebody | 116 +
examples/vashishta/InP.vashishta | 0
examples/vashishta/SiO.1990.vashishta | 0
.../{in.indiumphosphide => in.vashishta.inp} | 0
examples/vashishta/{in.sio2 => in.vashishta.sio2} | 0
examples/vashishta/in.vashishta.table.inp | 75 +
examples/vashishta/in.vashishta.table.sio2 | 30 +
.../vashishta/log.5Oct16.indiumphosphide.g++.1 | 5276 +
.../vashishta/log.5Oct16.indiumphosphide.g++.4 | 128 +
examples/vashishta/log.5Oct16.sio2.g++.1 | 86 +
examples/vashishta/log.5Oct16.sio2.g++.4 | 86 +
examples/vashishta/log.5Oct16.vashishta.inp.g++.1 | 5276 +
examples/vashishta/log.5Oct16.vashishta.inp.g++.4 | 5276 +
examples/vashishta/log.5Oct16.vashishta.sio2.g++.1 | 86 +
examples/vashishta/log.5Oct16.vashishta.sio2.g++.4 | 86 +
.../vashishta/log.5Oct16.vashishta.table.inp.g++.1 | 5276 +
.../vashishta/log.5Oct16.vashishta.table.inp.g++.4 | 5276 +
.../log.5Oct16.vashishta.table.sio2.g++.1 | 89 +
.../log.5Oct16.vashishta.table.sio2.g++.4 | 89 +
examples/voronoi/in.voronoi.2d | 52 +
examples/voronoi/in.voronoi.data | 88 +
examples/voronoi/log.15May15.voronoi.g++.1 | 542 -
examples/voronoi/log.15May15.voronoi.g++.4 | 542 -
examples/voronoi/log.5Oct16.voronoi.2d.g++.1 | 130 +
examples/voronoi/log.5Oct16.voronoi.2d.g++.4 | 130 +
examples/voronoi/log.5Oct16.voronoi.data.g++.1 | 163 +
examples/voronoi/log.5Oct16.voronoi.data.g++.4 | 163 +
examples/voronoi/log.5Oct16.voronoi.g++.1 | 619 +
examples/voronoi/log.5Oct16.voronoi.g++.4 | 619 +
lib/README | 4 +-
lib/atc/LammpsInterface.cpp | 1 +
lib/atc/Makefile.icc | 2 +-
lib/atc/Makefile.mingw32-cross | 2 +-
lib/atc/Makefile.mingw32-cross-mpi | 2 +-
lib/atc/Makefile.mingw64-cross | 2 +-
lib/atc/Makefile.mingw64-cross-mpi | 2 +-
lib/atc/Makefile.mpic++ | 2 +-
lib/atc/Makefile.serial | 2 +-
lib/atc/ParDiagonalMatrix.cpp | 4 +
lib/atc/Utility.h | 4 +-
lib/atc/Vector.h | 4 +-
lib/awpmd/Makefile.mingw32-cross | 2 +-
lib/awpmd/Makefile.mingw64-cross | 2 +-
lib/awpmd/Makefile.mpicc | 2 +-
lib/colvars/Makefile.fermi | 66 +-
lib/colvars/Makefile.g++ | 60 +-
lib/colvars/Makefile.mingw32-cross | 66 +-
lib/colvars/Makefile.mingw32-cross-mpi | 4 +-
lib/colvars/Makefile.mingw64-cross | 66 +-
lib/colvars/Makefile.mingw64-cross-mpi | 4 +-
lib/colvars/colvar.cpp | 1389 +-
lib/colvars/colvar.h | 215 +-
lib/colvars/colvaratoms.cpp | 1166 +-
lib/colvars/colvaratoms.h | 368 +-
lib/colvars/colvarbias.cpp | 147 +-
lib/colvars/colvarbias.h | 47 +-
lib/colvars/colvarbias_abf.cpp | 297 +-
lib/colvars/colvarbias_abf.h | 40 +-
lib/colvars/colvarbias_alb.cpp | 49 +-
lib/colvars/colvarbias_alb.h | 15 +-
lib/colvars/colvarbias_histogram.cpp | 60 +-
lib/colvars/colvarbias_histogram.h | 13 +-
lib/colvars/colvarbias_meta.cpp | 137 +-
lib/colvars/colvarbias_meta.h | 28 +-
lib/colvars/colvarbias_restraint.cpp | 357 +-
lib/colvars/colvarbias_restraint.h | 94 +-
lib/colvars/colvarcomp.cpp | 277 +-
lib/colvars/colvarcomp.h | 219 +-
lib/colvars/colvarcomp_angles.cpp | 309 +-
lib/colvars/colvarcomp_coordnums.cpp | 246 +-
lib/colvars/colvarcomp_distances.cpp | 670 +-
lib/colvars/colvarcomp_protein.cpp | 16 +-
lib/colvars/colvarcomp_rotations.cpp | 115 +-
lib/colvars/colvardeps.cpp | 529 +
lib/colvars/colvardeps.h | 276 +
lib/colvars/colvargrid.cpp | 9 +-
lib/colvars/colvargrid.h | 224 +-
lib/colvars/colvarmodule.cpp | 631 +-
lib/colvars/colvarmodule.h | 147 +-
lib/colvars/colvarparse.cpp | 652 +-
lib/colvars/colvarparse.h | 204 +-
lib/colvars/colvarproxy.h | 563 +-
lib/colvars/colvarscript.cpp | 149 +-
lib/colvars/colvarscript.h | 3 +-
lib/colvars/colvartypes.cpp | 101 +-
lib/colvars/colvartypes.h | 46 +-
lib/colvars/colvarvalue.cpp | 2 +-
lib/colvars/colvarvalue.h | 2 +-
lib/cuda/Makefile | 4 -
lib/cuda/Makefile.common | 123 -
lib/cuda/Makefile.cudalib | 87 -
lib/cuda/Makefile.defaults | 19 -
lib/cuda/Makefile.lammps | 7 -
lib/cuda/README | 59 -
lib/cuda/atom_vec_angle_cuda.cu | 85 -
lib/cuda/atom_vec_angle_cuda_cu.h | 15 -
lib/cuda/atom_vec_atomic_cuda.cu | 85 -
lib/cuda/atom_vec_atomic_cuda_cu.h | 15 -
lib/cuda/atom_vec_charge_cuda.cu | 85 -
lib/cuda/atom_vec_charge_cuda_cu.h | 15 -
lib/cuda/atom_vec_cuda.cu | 628 -
lib/cuda/atom_vec_cuda_cu.h | 0
lib/cuda/atom_vec_cuda_kernel.cu | 512 -
lib/cuda/atom_vec_full_cuda.cu | 85 -
lib/cuda/atom_vec_full_cuda_cu.h | 15 -
lib/cuda/comm_cuda.cu | 539 -
lib/cuda/comm_cuda_cu.h | 35 -
lib/cuda/comm_cuda_kernel.cu | 394 -
lib/cuda/compute_temp_cuda.cu | 126 -
lib/cuda/compute_temp_cuda_cu.h | 28 -
lib/cuda/compute_temp_cuda_kernel.cu | 118 -
lib/cuda/compute_temp_partial_cuda.cu | 164 -
lib/cuda/compute_temp_partial_cuda_cu.h | 30 -
lib/cuda/compute_temp_partial_cuda_kernel.cu | 161 -
lib/cuda/crm_cuda_utils.cu | 919 -
lib/cuda/cuda.cu | 22 -
lib/cuda/cuda_common.h | 344 -
lib/cuda/cuda_cu.h | 1 -
lib/cuda/cuda_data.cu | 220 -
lib/cuda/cuda_data_cu.h | 13 -
lib/cuda/cuda_data_kernel.cu | 195 -
lib/cuda/cuda_kernel.cu | 0
lib/cuda/cuda_pair.cu | 1015 -
lib/cuda/cuda_pair_cu.h | 30 -
lib/cuda/cuda_pair_kernel.cu | 1437 -
lib/cuda/cuda_pair_virial_kernel_nc.cu | 126 -
lib/cuda/cuda_precision.h | 278 -
lib/cuda/cuda_shared.h | 370 -
lib/cuda/cuda_wrapper.cu | 337 -
lib/cuda/cuda_wrapper_cu.h | 52 -
lib/cuda/cuda_wrapper_kernel.cu | 24 -
lib/cuda/domain.cu | 202 -
lib/cuda/domain_cu.h | 29 -
lib/cuda/domain_kernel.cu | 293 -
lib/cuda/fft3d_cuda.cu | 103 -
lib/cuda/fft3d_cuda_cu.h | 30 -
lib/cuda/fft3d_cuda_kernel.cu | 46 -
lib/cuda/fix_addforce_cuda.cu | 93 -
lib/cuda/fix_addforce_cuda_cu.h | 27 -
lib/cuda/fix_addforce_cuda_kernel.cu | 90 -
lib/cuda/fix_aveforce_cuda.cu | 107 -
lib/cuda/fix_aveforce_cuda_cu.h | 28 -
lib/cuda/fix_aveforce_cuda_kernel.cu | 96 -
lib/cuda/fix_enforce2d_cuda.cu | 55 -
lib/cuda/fix_enforce2d_cuda_cu.h | 27 -
lib/cuda/fix_enforce2d_cuda_kernel.cu | 34 -
lib/cuda/fix_freeze_cuda.cu | 98 -
lib/cuda/fix_freeze_cuda_cu.h | 27 -
lib/cuda/fix_freeze_cuda_kernel.cu | 87 -
lib/cuda/fix_gravity_cuda.cu | 92 -
lib/cuda/fix_gravity_cuda_cu.h | 27 -
lib/cuda/fix_gravity_cuda_kernel.cu | 36 -
lib/cuda/fix_nh_cuda.cu | 255 -
lib/cuda/fix_nh_cuda_cu.h | 32 -
lib/cuda/fix_nh_cuda_kernel.cu | 205 -
lib/cuda/fix_nve_cuda.cu | 134 -
lib/cuda/fix_nve_cuda_cu.h | 28 -
lib/cuda/fix_nve_cuda_kernel.cu | 166 -
lib/cuda/fix_set_force_cuda.cu | 96 -
lib/cuda/fix_set_force_cuda_cu.h | 27 -
lib/cuda/fix_set_force_cuda_kernel.cu | 86 -
lib/cuda/fix_shake_cuda.cu | 297 -
lib/cuda/fix_shake_cuda_cu.h | 34 -
lib/cuda/fix_shake_cuda_kernel.cu | 1060 -
lib/cuda/fix_temp_berendsen_cuda.cu | 66 -
lib/cuda/fix_temp_berendsen_cuda_cu.h | 27 -
lib/cuda/fix_temp_berendsen_cuda_kernel.cu | 37 -
lib/cuda/fix_temp_rescale_cuda.cu | 64 -
lib/cuda/fix_temp_rescale_cuda_cu.h | 27 -
lib/cuda/fix_temp_rescale_cuda_kernel.cu | 37 -
lib/cuda/fix_temp_rescale_limit_cuda.cu | 64 -
lib/cuda/fix_temp_rescale_limit_cuda_cu.h | 27 -
lib/cuda/fix_temp_rescale_limit_cuda_kernel.cu | 44 -
lib/cuda/fix_viscous_cuda.cu | 67 -
lib/cuda/fix_viscous_cuda_cu.h | 27 -
lib/cuda/fix_viscous_cuda_kernel.cu | 35 -
lib/cuda/neighbor.cu | 364 -
lib/cuda/neighbor_cu.h | 32 -
lib/cuda/neighbor_kernel.cu | 660 -
lib/cuda/pair_born_coul_long_cuda.cu | 78 -
lib/cuda/pair_born_coul_long_cuda_cu.h | 30 -
lib/cuda/pair_born_coul_long_cuda_kernel_nc.cu | 36 -
lib/cuda/pair_buck_coul_cut_cuda.cu | 75 -
lib/cuda/pair_buck_coul_cut_cuda_cu.h | 30 -
lib/cuda/pair_buck_coul_long_cuda.cu | 78 -
lib/cuda/pair_buck_coul_long_cuda_cu.h | 30 -
lib/cuda/pair_buck_cuda.cu | 77 -
lib/cuda/pair_buck_cuda_cu.h | 30 -
lib/cuda/pair_buck_cuda_kernel_nc.cu | 35 -
lib/cuda/pair_eam_cuda.cu | 351 -
lib/cuda/pair_eam_cuda_cu.h | 33 -
lib/cuda/pair_eam_cuda_kernel_nc.cu | 341 -
lib/cuda/pair_gran_hooke_cuda.cu | 201 -
lib/cuda/pair_gran_hooke_cuda_cu.h | 26 -
lib/cuda/pair_gran_hooke_cuda_kernel_nc.cu | 227 -
lib/cuda/pair_lj96_cut_cuda.cu | 79 -
lib/cuda/pair_lj96_cut_cuda_cu.h | 26 -
lib/cuda/pair_lj96_cut_cuda_kernel_nc.cu | 35 -
lib/cuda/pair_lj_charmm_coul_charmm_cuda.cu | 79 -
lib/cuda/pair_lj_charmm_coul_charmm_cuda_cu.h | 26 -
.../pair_lj_charmm_coul_charmm_cuda_kernel_nc.cu | 73 -
.../pair_lj_charmm_coul_charmm_implicit_cuda.cu | 86 -
.../pair_lj_charmm_coul_charmm_implicit_cuda_cu.h | 26 -
...j_charmm_coul_charmm_implicit_cuda_kernel_nc.cu | 44 -
lib/cuda/pair_lj_charmm_coul_long_cuda.cu | 76 -
lib/cuda/pair_lj_charmm_coul_long_cuda_cu.h | 26 -
lib/cuda/pair_lj_class2_coul_cut_cuda.cu | 73 -
lib/cuda/pair_lj_class2_coul_cut_cuda_cu.h | 26 -
lib/cuda/pair_lj_class2_coul_long_cuda.cu | 73 -
lib/cuda/pair_lj_class2_coul_long_cuda_cu.h | 26 -
lib/cuda/pair_lj_class2_cuda.cu | 75 -
lib/cuda/pair_lj_class2_cuda_cu.h | 26 -
lib/cuda/pair_lj_class2_cuda_kernel_nc.cu | 35 -
lib/cuda/pair_lj_cut_coul_cut_cuda.cu | 73 -
lib/cuda/pair_lj_cut_coul_cut_cuda_cu.h | 26 -
lib/cuda/pair_lj_cut_coul_debye_cuda.cu | 72 -
lib/cuda/pair_lj_cut_coul_debye_cuda_cu.h | 26 -
lib/cuda/pair_lj_cut_coul_long_cuda.cu | 73 -
lib/cuda/pair_lj_cut_coul_long_cuda_cu.h | 30 -
lib/cuda/pair_lj_cut_cuda.cu | 75 -
lib/cuda/pair_lj_cut_cuda_cu.h | 30 -
lib/cuda/pair_lj_cut_cuda_kernel_nc.cu | 34 -
lib/cuda/pair_lj_cut_experimental_cuda.cu | 78 -
lib/cuda/pair_lj_cut_experimental_cuda_cu.h | 26 -
lib/cuda/pair_lj_expand_cuda.cu | 78 -
lib/cuda/pair_lj_expand_cuda_cu.h | 26 -
lib/cuda/pair_lj_expand_cuda_kernel_nc.cu | 35 -
lib/cuda/pair_lj_gromacs_coul_gromacs_cuda.cu | 103 -
lib/cuda/pair_lj_gromacs_coul_gromacs_cuda_cu.h | 26 -
.../pair_lj_gromacs_coul_gromacs_cuda_kernel_nc.cu | 51 -
lib/cuda/pair_lj_gromacs_cuda.cu | 84 -
lib/cuda/pair_lj_gromacs_cuda_cu.h | 26 -
lib/cuda/pair_lj_gromacs_cuda_kernel_nc.cu | 50 -
lib/cuda/pair_lj_sdk_coul_cut_cuda.cu | 81 -
lib/cuda/pair_lj_sdk_coul_cut_cuda_cu.h | 26 -
lib/cuda/pair_lj_sdk_coul_debye_cuda.cu | 81 -
lib/cuda/pair_lj_sdk_coul_debye_cuda_cu.h | 26 -
lib/cuda/pair_lj_sdk_coul_long_cuda.cu | 81 -
lib/cuda/pair_lj_sdk_coul_long_cuda_cu.h | 26 -
lib/cuda/pair_lj_sdk_cuda.cu | 87 -
lib/cuda/pair_lj_sdk_cuda_cu.h | 26 -
lib/cuda/pair_lj_sdk_cuda_kernel_nc.cu | 49 -
lib/cuda/pair_lj_smooth_cuda.cu | 84 -
lib/cuda/pair_lj_smooth_cuda_cu.h | 26 -
lib/cuda/pair_lj_smooth_cuda_kernel_nc.cu | 61 -
lib/cuda/pair_manybody_const.h | 16 -
lib/cuda/pair_morse_coul_long_cuda.cu | 79 -
lib/cuda/pair_morse_coul_long_cuda_cu.h | 30 -
lib/cuda/pair_morse_coul_long_cuda_kernel_nc.cu | 35 -
lib/cuda/pair_morse_cuda.cu | 78 -
lib/cuda/pair_morse_cuda_cu.h | 26 -
lib/cuda/pair_morse_cuda_kernel_nc.cu | 34 -
lib/cuda/pair_sw_cuda.cu | 139 -
lib/cuda/pair_sw_cuda_cu.h | 39 -
lib/cuda/pair_sw_cuda_kernel_nc.cu | 457 -
lib/cuda/pair_tersoff_cuda.cu | 154 -
lib/cuda/pair_tersoff_cuda_cu.h | 42 -
lib/cuda/pair_tersoff_cuda_kernel_nc.cu | 1097 -
lib/cuda/pair_virial_compute_cu.h | 26 -
lib/cuda/pppm_cuda.cu | 588 -
lib/cuda/pppm_cuda_cu.h | 55 -
lib/cuda/pppm_cuda_kernel.cu | 858 -
lib/gpu/Makefile.fermi | 15 +-
lib/gpu/Makefile.lammps.mingw-cross | 2 +-
lib/gpu/Makefile.lammps.standard | 10 +-
lib/gpu/Makefile.lens | 27 -
lib/gpu/Makefile.lincoln | 29 -
lib/gpu/Makefile.linux | 6 +-
lib/gpu/Makefile.longhorn | 29 -
lib/gpu/Makefile.mingw32-cross | 2 +-
lib/gpu/Makefile.mingw32-cross-mpi | 2 +-
lib/gpu/Makefile.mingw64-cross | 2 +-
lib/gpu/Makefile.mingw64-cross-mpi | 2 +-
lib/gpu/Makefile.shannon | 50 +
lib/gpu/Nvidia.makefile | 34 +-
lib/gpu/Opencl.makefile | 27 +-
lib/gpu/cudpp_mini/cudpp.h | 4 +-
lib/gpu/cudpp_mini/cudpp_globals.h | 4 +-
lib/gpu/cudpp_mini/cudpp_maximal_launch.h | 4 +-
lib/gpu/cudpp_mini/cudpp_plan.h | 2 +-
lib/gpu/cudpp_mini/cudpp_plan_manager.h | 2 +-
lib/gpu/cudpp_mini/cudpp_radixsort.h | 4 +-
lib/gpu/cudpp_mini/cudpp_scan.h | 4 +-
lib/gpu/cudpp_mini/cudpp_util.h | 4 +-
lib/gpu/cudpp_mini/sharedmem.h | 4 +-
lib/gpu/geryon/nvd_device.h | 96 +-
lib/gpu/geryon/nvd_kernel.h | 126 +-
lib/gpu/geryon/nvd_mat.h | 6 +-
lib/gpu/geryon/nvd_memory.h | 106 +-
lib/gpu/geryon/nvd_texture.h | 24 +-
lib/gpu/geryon/nvd_timer.h | 30 +-
lib/gpu/geryon/ocl_device.h | 120 +-
lib/gpu/geryon/ocl_kernel.h | 132 +-
lib/gpu/geryon/ocl_mat.h | 6 +-
lib/gpu/geryon/ocl_memory.h | 116 +-
lib/gpu/geryon/ocl_texture.h | 8 +-
lib/gpu/geryon/ocl_timer.h | 30 +-
lib/gpu/geryon/ucl_arg_kludge.h | 372 +-
lib/gpu/geryon/ucl_basemat.h | 16 +-
lib/gpu/geryon/ucl_copy.h | 162 +-
lib/gpu/geryon/ucl_d_mat.h | 112 +-
lib/gpu/geryon/ucl_d_vec.h | 98 +-
lib/gpu/geryon/ucl_h_mat.h | 164 +-
lib/gpu/geryon/ucl_h_vec.h | 144 +-
lib/gpu/geryon/ucl_matrix.h | 48 +-
lib/gpu/geryon/ucl_nv_kernel.h | 6 +-
lib/gpu/geryon/ucl_print.h | 64 +-
lib/gpu/geryon/ucl_s_obj_help.h | 30 +-
lib/gpu/geryon/ucl_types.h | 78 +-
lib/gpu/geryon/ucl_vector.h | 48 +-
lib/gpu/lal_answer.cpp | 46 +-
lib/gpu/lal_answer.h | 40 +-
lib/gpu/lal_atom.cpp | 46 +-
lib/gpu/lal_atom.cu | 6 +-
lib/gpu/lal_atom.h | 60 +-
lib/gpu/lal_balance.h | 18 +-
lib/gpu/lal_base_atomic.cpp | 20 +-
lib/gpu/lal_base_atomic.h | 22 +-
lib/gpu/lal_base_charge.cpp | 16 +-
lib/gpu/lal_base_charge.h | 12 +-
lib/gpu/lal_base_dipole.cpp | 18 +-
lib/gpu/lal_base_dipole.h | 12 +-
lib/gpu/lal_base_dpd.cpp | 18 +-
lib/gpu/lal_base_dpd.h | 12 +-
lib/gpu/lal_base_ellipsoid.cpp | 34 +-
lib/gpu/lal_base_ellipsoid.h | 28 +-
lib/gpu/lal_base_three.cpp | 56 +-
lib/gpu/lal_base_three.h | 37 +-
lib/gpu/lal_beck.cpp | 10 +-
lib/gpu/lal_beck.cu | 26 +-
lib/gpu/lal_beck.h | 12 +-
lib/gpu/lal_beck_ext.cpp | 8 +-
lib/gpu/lal_born.cpp | 26 +-
lib/gpu/lal_born.cu | 58 +-
lib/gpu/lal_born.h | 20 +-
lib/gpu/lal_born_coul_long.cpp | 28 +-
lib/gpu/lal_born_coul_long.cu | 52 +-
lib/gpu/lal_born_coul_long.h | 20 +-
lib/gpu/lal_born_coul_long_ext.cpp | 32 +-
lib/gpu/lal_born_coul_wolf.cpp | 30 +-
lib/gpu/lal_born_coul_wolf.cu | 64 +-
lib/gpu/lal_born_coul_wolf.h | 20 +-
lib/gpu/lal_born_coul_wolf_ext.cpp | 24 +-
lib/gpu/lal_born_ext.cpp | 30 +-
lib/gpu/lal_buck.cpp | 30 +-
lib/gpu/lal_buck.cu | 54 +-
lib/gpu/lal_buck.h | 18 +-
lib/gpu/lal_buck_coul.cpp | 30 +-
lib/gpu/lal_buck_coul.cu | 80 +-
lib/gpu/lal_buck_coul.h | 20 +-
lib/gpu/lal_buck_coul_ext.cpp | 24 +-
lib/gpu/lal_buck_coul_long.cpp | 26 +-
lib/gpu/lal_buck_coul_long.cu | 58 +-
lib/gpu/lal_buck_coul_long.h | 14 +-
lib/gpu/lal_buck_coul_long_ext.cpp | 20 +-
lib/gpu/lal_buck_ext.cpp | 24 +-
lib/gpu/lal_cg_cmm.cpp | 24 +-
lib/gpu/lal_cg_cmm.cu | 44 +-
lib/gpu/lal_cg_cmm.h | 10 +-
lib/gpu/lal_cg_cmm_ext.cpp | 14 +-
lib/gpu/lal_cg_cmm_long.cpp | 24 +-
lib/gpu/lal_cg_cmm_long.cu | 38 +-
lib/gpu/lal_cg_cmm_long.h | 12 +-
lib/gpu/lal_cg_cmm_long_ext.cpp | 16 +-
lib/gpu/lal_charmm_long.cpp | 20 +-
lib/gpu/lal_charmm_long.cu | 42 +-
lib/gpu/lal_charmm_long.h | 12 +-
lib/gpu/lal_charmm_long_ext.cpp | 16 +-
lib/gpu/lal_colloid.cpp | 30 +-
lib/gpu/lal_colloid.cu | 116 +-
lib/gpu/lal_colloid.h | 20 +-
lib/gpu/lal_colloid_ext.cpp | 22 +-
lib/gpu/lal_coul.cpp | 18 +-
lib/gpu/lal_coul.cu | 38 +-
lib/gpu/lal_coul.h | 12 +-
lib/gpu/lal_coul_debye.cpp | 16 +-
lib/gpu/lal_coul_debye.cu | 26 +-
lib/gpu/lal_coul_debye.h | 12 +-
lib/gpu/lal_coul_debye_ext.cpp | 16 +-
lib/gpu/lal_coul_dsf.cpp | 18 +-
lib/gpu/lal_coul_dsf.cu | 56 +-
lib/gpu/lal_coul_dsf.h | 10 +-
lib/gpu/lal_coul_dsf_ext.cpp | 22 +-
lib/gpu/lal_coul_ext.cpp | 18 +-
lib/gpu/lal_coul_long.cpp | 22 +-
lib/gpu/lal_coul_long.cu | 43 +-
lib/gpu/lal_coul_long.h | 16 +-
lib/gpu/lal_coul_long_ext.cpp | 42 +-
lib/gpu/lal_device.cpp | 112 +-
lib/gpu/lal_device.cu | 6 +-
lib/gpu/lal_device.h | 68 +-
lib/gpu/lal_dipole_lj.cpp | 16 +-
lib/gpu/lal_dipole_lj.cu | 90 +-
lib/gpu/lal_dipole_lj.h | 8 +-
lib/gpu/lal_dipole_lj_ext.cpp | 12 +-
lib/gpu/lal_dipole_lj_sf.cpp | 20 +-
lib/gpu/lal_dipole_lj_sf.cu | 122 +-
lib/gpu/lal_dipole_lj_sf.h | 8 +-
lib/gpu/lal_dipole_lj_sf_ext.cpp | 12 +-
lib/gpu/lal_dpd.cpp | 30 +-
lib/gpu/lal_dpd.cu | 84 +-
lib/gpu/lal_dpd.h | 18 +-
lib/gpu/lal_dpd_ext.cpp | 22 +-
lib/gpu/lal_eam.cpp | 134 +-
lib/gpu/lal_eam.cu | 136 +-
lib/gpu/lal_eam.h | 54 +-
lib/gpu/lal_eam_alloy_ext.cpp | 32 +-
lib/gpu/lal_eam_ext.cpp | 32 +-
lib/gpu/lal_eam_fs_ext.cpp | 32 +-
lib/gpu/lal_ellipsoid_extra.h | 16 +-
lib/gpu/lal_ellipsoid_nbor.cu | 34 +-
lib/gpu/lal_gauss.cpp | 22 +-
lib/gpu/lal_gauss.cu | 60 +-
lib/gpu/lal_gauss.h | 18 +-
lib/gpu/lal_gauss_ext.cpp | 24 +-
lib/gpu/lal_gayberne.cpp | 80 +-
lib/gpu/lal_gayberne.cu | 144 +-
lib/gpu/lal_gayberne.h | 26 +-
lib/gpu/lal_gayberne_ext.cpp | 20 +-
lib/gpu/lal_gayberne_lj.cu | 130 +-
lib/gpu/lal_lj.cpp | 30 +-
lib/gpu/lal_lj.cu | 60 +-
lib/gpu/lal_lj.h | 16 +-
lib/gpu/lal_lj96.cpp | 18 +-
lib/gpu/lal_lj96.cu | 50 +-
lib/gpu/lal_lj96.h | 10 +-
lib/gpu/lal_lj96_ext.cpp | 8 +-
lib/gpu/lal_lj_class2_long.cpp | 16 +-
lib/gpu/lal_lj_class2_long.cu | 42 +-
lib/gpu/lal_lj_class2_long.h | 8 +-
lib/gpu/lal_lj_class2_long_ext.cpp | 8 +-
lib/gpu/lal_lj_coul.cpp | 24 +-
lib/gpu/lal_lj_coul.cu | 46 +-
lib/gpu/lal_lj_coul.h | 8 +-
lib/gpu/lal_lj_coul_debye.cpp | 22 +-
lib/gpu/lal_lj_coul_debye.cu | 42 +-
lib/gpu/lal_lj_coul_debye.h | 8 +-
lib/gpu/lal_lj_coul_debye_ext.cpp | 12 +-
lib/gpu/lal_lj_coul_ext.cpp | 10 +-
lib/gpu/lal_lj_coul_long.cpp | 22 +-
lib/gpu/lal_lj_coul_long.cu | 38 +-
lib/gpu/lal_lj_coul_long.h | 10 +-
lib/gpu/lal_lj_coul_long_ext.cpp | 18 +-
lib/gpu/lal_lj_coul_msm.cpp | 24 +-
lib/gpu/lal_lj_coul_msm.cu | 30 +-
lib/gpu/lal_lj_coul_msm.h | 14 +-
lib/gpu/lal_lj_coul_msm_ext.cpp | 10 +-
lib/gpu/lal_lj_cubic.cpp | 26 +-
lib/gpu/lal_lj_cubic.cu | 64 +-
lib/gpu/lal_lj_cubic.h | 16 +-
lib/gpu/lal_lj_cubic_ext.cpp | 16 +-
lib/gpu/lal_lj_dsf.cpp | 24 +-
lib/gpu/lal_lj_dsf.cu | 46 +-
lib/gpu/lal_lj_dsf.h | 8 +-
lib/gpu/lal_lj_dsf_ext.cpp | 10 +-
lib/gpu/lal_lj_expand.cpp | 28 +-
lib/gpu/lal_lj_expand.cu | 70 +-
lib/gpu/lal_lj_expand.h | 14 +-
lib/gpu/lal_lj_expand_ext.cpp | 14 +-
lib/gpu/lal_lj_ext.cpp | 14 +-
lib/gpu/lal_lj_gromacs.cpp | 22 +-
lib/gpu/lal_lj_gromacs.cu | 26 +-
lib/gpu/lal_lj_gromacs.h | 12 +-
lib/gpu/lal_lj_gromacs_ext.cpp | 16 +-
lib/gpu/lal_mie.cpp | 16 +-
lib/gpu/lal_mie.cu | 42 +-
lib/gpu/lal_mie.h | 12 +-
lib/gpu/lal_mie_ext.cpp | 8 +-
lib/gpu/lal_morse.cpp | 24 +-
lib/gpu/lal_morse.cu | 48 +-
lib/gpu/lal_morse.h | 12 +-
lib/gpu/lal_morse_ext.cpp | 14 +-
lib/gpu/lal_neighbor.cpp | 119 +-
lib/gpu/lal_neighbor.h | 62 +-
lib/gpu/lal_neighbor_cpu.cu | 6 +-
lib/gpu/lal_neighbor_gpu.cu | 122 +-
lib/gpu/lal_neighbor_shared.cpp | 6 +-
lib/gpu/lal_neighbor_shared.h | 6 +-
lib/gpu/lal_pppm.cpp | 44 +-
lib/gpu/lal_pppm.cu | 68 +-
lib/gpu/lal_pppm.h | 28 +-
lib/gpu/lal_pppm_ext.cpp | 18 +-
lib/gpu/lal_precision.h | 16 +-
lib/gpu/lal_preprocessor.h | 20 +-
lib/gpu/lal_re_squared.cpp | 68 +-
lib/gpu/lal_re_squared.cu | 40 +-
lib/gpu/lal_re_squared.h | 20 +-
lib/gpu/lal_re_squared_ext.cpp | 20 +-
lib/gpu/lal_re_squared_lj.cu | 140 +-
lib/gpu/lal_soft.cpp | 18 +-
lib/gpu/lal_soft.cu | 32 +-
lib/gpu/lal_soft.h | 14 +-
lib/gpu/lal_soft_ext.cpp | 16 +-
lib/gpu/lal_sw.cpp | 66 +-
lib/gpu/lal_sw.cu | 132 +-
lib/gpu/lal_sw.h | 12 +-
lib/gpu/lal_sw_ext.cpp | 26 +-
lib/gpu/lal_table.cpp | 88 +-
lib/gpu/lal_table.cu | 328 +-
lib/gpu/lal_table.h | 36 +-
lib/gpu/lal_table_ext.cpp | 14 +-
lib/gpu/lal_tersoff.cpp | 151 +-
lib/gpu/lal_tersoff.cu | 732 +-
lib/gpu/lal_tersoff.h | 30 +-
lib/gpu/lal_tersoff_ext.cpp | 42 +-
lib/gpu/lal_tersoff_extra.h | 198 +-
lib/gpu/lal_tersoff_mod.cpp | 458 +
lib/gpu/lal_tersoff_mod.cu | 1080 +
lib/gpu/lal_tersoff_mod.h | 118 +
lib/gpu/lal_tersoff_mod_ext.cpp | 135 +
lib/gpu/lal_tersoff_mod_extra.h | 627 +
lib/gpu/lal_tersoff_zbl.cpp | 484 +
lib/gpu/lal_tersoff_zbl.cu | 1075 +
lib/gpu/lal_tersoff_zbl.h | 123 +
lib/gpu/lal_tersoff_zbl_ext.cpp | 146 +
lib/gpu/lal_tersoff_zbl_extra.h | 690 +
lib/gpu/lal_yukawa.cpp | 18 +-
lib/gpu/lal_yukawa.cu | 52 +-
lib/gpu/lal_yukawa.h | 16 +-
lib/gpu/lal_yukawa_colloid.cpp | 64 +-
lib/gpu/lal_yukawa_colloid.cu | 74 +-
lib/gpu/lal_yukawa_colloid.h | 28 +-
lib/gpu/lal_yukawa_colloid_ext.cpp | 26 +-
lib/gpu/lal_yukawa_ext.cpp | 22 +-
lib/gpu/lal_zbl.cpp | 30 +-
lib/gpu/lal_zbl.cu | 108 +-
lib/gpu/lal_zbl.h | 20 +-
lib/gpu/lal_zbl_ext.cpp | 20 +-
lib/h5md/src/ch5md.c | 11 +-
lib/kim/Makefile.lammps | 12 +-
lib/kim/pair-kim.release.info | 6 +-
lib/kokkos/CMakeLists.txt | 184 +
lib/kokkos/HOW_TO_SNAPSHOT | 73 +
lib/kokkos/Makefile.kokkos | 139 +-
lib/kokkos/Makefile.targets | 27 +-
lib/kokkos/README | 40 +-
lib/kokkos/algorithms/CMakeLists.txt | 10 +
lib/kokkos/algorithms/cmake/Dependencies.cmake | 5 +
.../algorithms/cmake/KokkosAlgorithms_config.h.in | 4 +
lib/kokkos/algorithms/src/CMakeLists.txt | 21 +
lib/kokkos/algorithms/src/Kokkos_Random.hpp | 403 +-
lib/kokkos/algorithms/src/Kokkos_Sort.hpp | 2 +-
lib/kokkos/algorithms/unit_tests/CMakeLists.txt | 38 +
lib/kokkos/algorithms/unit_tests/Makefile | 10 +-
lib/kokkos/algorithms/unit_tests/TestRandom.hpp | 35 +-
lib/kokkos/cmake/Dependencies.cmake | 10 +
lib/kokkos/cmake/deps/CUDA.cmake | 79 +
lib/kokkos/cmake/deps/CUSPARSE.cmake | 64 +
lib/kokkos/cmake/deps/HWLOC.cmake | 70 +
lib/kokkos/cmake/deps/Pthread.cmake | 83 +
lib/kokkos/cmake/deps/QTHREAD.cmake | 70 +
lib/kokkos/cmake/tpls/FindTPLCUSPARSE.cmake | 75 +
lib/kokkos/cmake/tpls/FindTPLHWLOC.cmake | 71 +
lib/kokkos/cmake/tpls/FindTPLPthread.cmake | 82 +
lib/kokkos/cmake/tpls/FindTPLQTHREAD.cmake | 70 +
lib/kokkos/cmake/tribits.cmake | 485 +
lib/kokkos/config/configure_compton_cpu.sh | 0
lib/kokkos/config/configure_compton_mic.sh | 0
lib/kokkos/config/configure_kokkos.sh | 0
lib/kokkos/config/configure_kokkos_nvidia.sh | 0
lib/kokkos/config/configure_shannon.sh | 0
.../kokkos-trilinos-integration-procedure.txt | 153 +
lib/kokkos/config/master_history.txt | 3 +
lib/kokkos/config/nvcc_wrapper | 183 +-
lib/kokkos/config/test_all_sandia | 386 +-
.../config/testing_scripts/obj_size_opt_check | 287 +
lib/kokkos/containers/CMakeLists.txt | 10 +
lib/kokkos/containers/cmake/Dependencies.cmake | 5 +
.../containers/cmake/KokkosContainers_config.h.in | 4 +
.../containers/performance_tests/CMakeLists.txt | 37 +
lib/kokkos/containers/performance_tests/Makefile | 10 +-
.../containers/performance_tests/TestCuda.cpp | 9 +
.../performance_tests/TestDynRankView.hpp | 265 +
.../performance_tests/TestGlobal2LocalIds.hpp | 2 +-
.../containers/performance_tests/TestOpenMP.cpp | 9 +
.../containers/performance_tests/TestThreads.cpp | 9 +
.../TestUnorderedMapPerformance.hpp | 4 +-
lib/kokkos/containers/src/CMakeLists.txt | 31 +
lib/kokkos/containers/src/Kokkos_Bitset.hpp | 4 +-
lib/kokkos/containers/src/Kokkos_DualView.hpp | 128 +-
lib/kokkos/containers/src/Kokkos_DynRankView.hpp | 1834 +
lib/kokkos/containers/src/Kokkos_DynamicView.hpp | 494 +
lib/kokkos/containers/src/Kokkos_SegmentedView.hpp | 2 +-
lib/kokkos/containers/src/Kokkos_Vector.hpp | 12 +-
.../containers/src/impl/Kokkos_Bitset_impl.hpp | 110 +-
lib/kokkos/containers/unit_tests/CMakeLists.txt | 40 +
lib/kokkos/containers/unit_tests/Makefile | 10 +-
lib/kokkos/containers/unit_tests/TestComplex.hpp | 25 +-
lib/kokkos/containers/unit_tests/TestCuda.cpp | 21 +
.../containers/unit_tests/TestDynViewAPI.hpp | 1559 +
.../containers/unit_tests/TestDynamicView.hpp | 168 +
lib/kokkos/containers/unit_tests/TestOpenMP.cpp | 20 +
.../containers/unit_tests/TestSegmentedView.hpp | 2 +-
lib/kokkos/containers/unit_tests/TestSerial.cpp | 19 +-
lib/kokkos/containers/unit_tests/TestThreads.cpp | 20 +
lib/kokkos/core/CMakeLists.txt | 11 +
lib/kokkos/core/cmake/Dependencies.cmake | 4 +
lib/kokkos/core/cmake/KokkosCore_config.h.in | 57 +
lib/kokkos/core/perf_test/CMakeLists.txt | 29 +
lib/kokkos/core/perf_test/Makefile | 10 +-
lib/kokkos/core/perf_test/PerfTestCuda.cpp | 4 +-
lib/kokkos/core/perf_test/PerfTestGramSchmidt.hpp | 2 +-
lib/kokkos/core/perf_test/PerfTestHexGrad.hpp | 2 +-
lib/kokkos/core/perf_test/test_atomic.cpp | 35 +-
lib/kokkos/core/src/CMakeLists.txt | 113 +
lib/kokkos/core/src/Cuda/KokkosExp_Cuda_View.hpp | 53 +-
lib/kokkos/core/src/Cuda/Kokkos_CudaExec.hpp | 79 +-
lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp | 351 +-
lib/kokkos/core/src/Cuda/Kokkos_Cuda_Alloc.hpp | 3 +-
.../core/src/Cuda/Kokkos_Cuda_BasicAllocators.cpp | 192 -
.../core/src/Cuda/Kokkos_Cuda_BasicAllocators.hpp | 187 -
lib/kokkos/core/src/Cuda/Kokkos_Cuda_Impl.cpp | 144 +-
lib/kokkos/core/src/Cuda/Kokkos_Cuda_Internal.hpp | 109 +-
lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp | 1430 +-
.../core/src/Cuda/Kokkos_Cuda_ReduceScan.hpp | 25 +-
lib/kokkos/core/src/Cuda/Kokkos_Cuda_Task.cpp | 179 +
lib/kokkos/core/src/Cuda/Kokkos_Cuda_Task.hpp | 519 +
.../core/src/Cuda/Kokkos_Cuda_TaskPolicy.cpp | 932 +
.../core/src/Cuda/Kokkos_Cuda_TaskPolicy.hpp | 833 +
lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp | 336 +-
lib/kokkos/core/src/KokkosExp_MDRangePolicy.hpp | 611 +
lib/kokkos/core/src/KokkosExp_View.hpp | 1989 -
lib/kokkos/core/src/Kokkos_Array.hpp | 2 +
lib/kokkos/core/src/Kokkos_Atomic.hpp | 30 +-
lib/kokkos/core/src/Kokkos_Complex.hpp | 538 +
lib/kokkos/core/src/Kokkos_Concepts.hpp | 78 +
lib/kokkos/core/src/Kokkos_Core.hpp | 141 +-
lib/kokkos/core/src/Kokkos_Core_fwd.hpp | 77 +
lib/kokkos/core/src/Kokkos_Cuda.hpp | 22 +-
lib/kokkos/core/src/Kokkos_CudaSpace.hpp | 150 +-
lib/kokkos/core/src/Kokkos_ExecPolicy.hpp | 343 +-
lib/kokkos/core/src/Kokkos_HBWSpace.hpp | 312 +
lib/kokkos/core/src/Kokkos_HostSpace.hpp | 39 +-
lib/kokkos/core/src/Kokkos_Layout.hpp | 75 +-
lib/kokkos/core/src/Kokkos_Macros.hpp | 50 +
lib/kokkos/core/src/Kokkos_MemoryPool.hpp | 1523 +
lib/kokkos/core/src/Kokkos_MemoryTraits.hpp | 4 +-
lib/kokkos/core/src/Kokkos_OpenMP.hpp | 26 +-
lib/kokkos/core/src/Kokkos_Pair.hpp | 40 +-
lib/kokkos/core/src/Kokkos_Parallel.hpp | 479 +-
lib/kokkos/core/src/Kokkos_Parallel_Reduce.hpp | 1240 +
lib/kokkos/core/src/Kokkos_Qthread.hpp | 7 +
lib/kokkos/core/src/Kokkos_ScratchSpace.hpp | 79 +-
lib/kokkos/core/src/Kokkos_Serial.hpp | 624 +-
lib/kokkos/core/src/Kokkos_TaskPolicy.hpp | 825 +-
lib/kokkos/core/src/Kokkos_Threads.hpp | 13 +-
lib/kokkos/core/src/Kokkos_View.hpp | 3324 +-
lib/kokkos/core/src/Kokkos_hwloc.hpp | 14 +-
lib/kokkos/core/src/Makefile | 19 +-
.../core/src/OpenMP/Kokkos_OpenMP_Parallel.hpp | 746 +-
lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Task.cpp | 329 +
lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Task.hpp | 356 +
lib/kokkos/core/src/OpenMP/Kokkos_OpenMPexec.cpp | 62 +-
lib/kokkos/core/src/OpenMP/Kokkos_OpenMPexec.hpp | 458 +-
lib/kokkos/core/src/Qthread/Kokkos_QthreadExec.cpp | 15 +
lib/kokkos/core/src/Qthread/Kokkos_QthreadExec.hpp | 71 +-
.../core/src/Qthread/Kokkos_Qthread_Parallel.hpp | 476 +-
.../core/src/Qthread/Kokkos_Qthread_TaskPolicy.cpp | 158 +-
.../core/src/Qthread/Kokkos_Qthread_TaskPolicy.hpp | 176 +-
lib/kokkos/core/src/Qthread/README | 21 +-
lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.cpp | 104 +-
lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.hpp | 174 +-
.../core/src/Threads/Kokkos_ThreadsExec_base.cpp | 1 +
lib/kokkos/core/src/Threads/Kokkos_ThreadsTeam.hpp | 264 +-
.../core/src/Threads/Kokkos_Threads_Parallel.hpp | 619 +-
.../core/src/Threads/Kokkos_Threads_TaskPolicy.cpp | 957 +-
.../core/src/Threads/Kokkos_Threads_TaskPolicy.hpp | 527 +-
lib/kokkos/core/src/impl/CMakeLists.txt | 18 +
lib/kokkos/core/src/impl/KokkosExp_SharedAlloc.cpp | 139 +-
lib/kokkos/core/src/impl/KokkosExp_SharedAlloc.hpp | 212 +-
.../core/src/impl/KokkosExp_ViewAllocProp.hpp | 416 -
lib/kokkos/core/src/impl/KokkosExp_ViewArray.hpp | 354 +-
lib/kokkos/core/src/impl/KokkosExp_ViewCtor.hpp | 252 +
lib/kokkos/core/src/impl/KokkosExp_ViewMapping.hpp | 2242 +-
lib/kokkos/core/src/impl/KokkosExp_ViewTile.hpp | 102 +-
.../core/src/impl/Kokkos_AllocationTracker.cpp | 844 -
.../core/src/impl/Kokkos_AllocationTracker.hpp | 586 -
lib/kokkos/core/src/impl/Kokkos_AnalyzePolicy.hpp | 197 +
.../core/src/impl/Kokkos_Atomic_Assembly.hpp | 112 +
.../core/src/impl/Kokkos_Atomic_Assembly_X86.hpp | 214 -
.../impl/Kokkos_Atomic_Compare_Exchange_Strong.hpp | 32 +-
.../core/src/impl/Kokkos_Atomic_Decrement.hpp | 117 +
.../core/src/impl/Kokkos_Atomic_Exchange.hpp | 41 +-
.../core/src/impl/Kokkos_Atomic_Fetch_Add.hpp | 66 +-
.../core/src/impl/Kokkos_Atomic_Fetch_Sub.hpp | 10 +-
lib/kokkos/core/src/impl/Kokkos_Atomic_Generic.hpp | 52 +-
.../core/src/impl/Kokkos_Atomic_Increment.hpp | 117 +
lib/kokkos/core/src/impl/Kokkos_Atomic_View.hpp | 32 -
lib/kokkos/core/src/impl/Kokkos_Atomic_Windows.hpp | 33 +-
.../core/src/impl/Kokkos_BasicAllocators.cpp | 281 -
.../core/src/impl/Kokkos_BasicAllocators.hpp | 118 -
lib/kokkos/core/src/impl/Kokkos_BitOps.hpp | 122 +
lib/kokkos/core/src/impl/Kokkos_CPUDiscovery.cpp | 124 +
lib/kokkos/core/src/impl/Kokkos_CPUDiscovery.hpp | 51 +
lib/kokkos/core/src/impl/Kokkos_Core.cpp | 15 +-
lib/kokkos/core/src/impl/Kokkos_Error.cpp | 2 +-
lib/kokkos/core/src/impl/Kokkos_Error.hpp | 4 +
lib/kokkos/core/src/impl/Kokkos_ExecPolicy.cpp | 19 +
lib/kokkos/core/src/impl/Kokkos_FunctorAdapter.hpp | 255 +-
lib/kokkos/core/src/impl/Kokkos_HBWAllocators.cpp | 108 +
lib/kokkos/core/src/impl/Kokkos_HBWAllocators.hpp | 75 +
lib/kokkos/core/src/impl/Kokkos_HBWSpace.cpp | 379 +
lib/kokkos/core/src/impl/Kokkos_HostSpace.cpp | 160 +-
lib/kokkos/core/src/impl/Kokkos_Memory_Fence.hpp | 34 +
lib/kokkos/core/src/impl/Kokkos_PhysicalLayout.hpp | 13 +-
.../core/src/impl/Kokkos_Profiling_DeviceInfo.hpp | 2 +-
.../core/src/impl/Kokkos_Profiling_Interface.cpp | 92 +-
.../core/src/impl/Kokkos_Profiling_Interface.hpp | 26 +-
lib/kokkos/core/src/impl/Kokkos_Serial_Task.cpp | 147 +
lib/kokkos/core/src/impl/Kokkos_Serial_Task.hpp | 271 +
.../core/src/impl/Kokkos_Serial_TaskPolicy.cpp | 20 +-
.../core/src/impl/Kokkos_Serial_TaskPolicy.hpp | 278 +-
lib/kokkos/core/src/impl/Kokkos_Shape.hpp | 16 +-
lib/kokkos/core/src/impl/Kokkos_Synchronic.hpp | 693 +
.../core/src/impl/Kokkos_Synchronic_Config.hpp | 169 +
.../core/src/impl/Kokkos_Synchronic_n3998.hpp | 162 +
lib/kokkos/core/src/impl/Kokkos_Tags.hpp | 120 +-
lib/kokkos/core/src/impl/Kokkos_TaskQueue.hpp | 499 +
lib/kokkos/core/src/impl/Kokkos_TaskQueue_impl.hpp | 569 +
lib/kokkos/core/src/impl/Kokkos_Timer.hpp | 3 +
lib/kokkos/core/src/impl/Kokkos_Traits.hpp | 171 +-
lib/kokkos/core/src/impl/Kokkos_ViewDefault.hpp | 18 +-
lib/kokkos/core/src/impl/Kokkos_ViewOffset.hpp | 2 +-
lib/kokkos/core/src/impl/Kokkos_ViewSupport.hpp | 131 +-
lib/kokkos/core/src/impl/Kokkos_ViewTileLeft.hpp | 153 -
lib/kokkos/core/src/impl/Kokkos_hwloc.cpp | 30 +-
lib/kokkos/core/src/impl/Kokkos_spinwait.cpp | 9 +-
lib/kokkos/core/unit_test/CMakeLists.txt | 105 +
lib/kokkos/core/unit_test/Makefile | 61 +-
lib/kokkos/core/unit_test/TestAggregate.hpp | 686 +-
.../core/unit_test/TestAggregateReduction.hpp | 16 +-
.../core/unit_test/TestAllocationTracker.cpp | 145 -
lib/kokkos/core/unit_test/TestAtomic.hpp | 48 +-
lib/kokkos/core/unit_test/TestAtomicOperations.hpp | 841 +
lib/kokkos/core/unit_test/TestCXX11.hpp | 81 +-
lib/kokkos/core/unit_test/TestCuda.cpp | 285 +-
lib/kokkos/core/unit_test/TestCuda_a.cpp | 182 +
lib/kokkos/core/unit_test/TestCuda_b.cpp | 191 +
lib/kokkos/core/unit_test/TestCuda_c.cpp | 375 +
.../core/unit_test/TestDefaultDeviceType.cpp | 8 +-
.../core/unit_test/TestDefaultDeviceTypeInit.cpp | 390 -
.../core/unit_test/TestDefaultDeviceTypeInit.hpp | 419 +
.../core/unit_test/TestDefaultDeviceTypeInit_1.cpp | 2 +
.../unit_test/TestDefaultDeviceTypeInit_10.cpp | 2 +
.../unit_test/TestDefaultDeviceTypeInit_11.cpp | 2 +
.../unit_test/TestDefaultDeviceTypeInit_12.cpp | 2 +
.../unit_test/TestDefaultDeviceTypeInit_13.cpp | 2 +
.../unit_test/TestDefaultDeviceTypeInit_14.cpp | 2 +
.../unit_test/TestDefaultDeviceTypeInit_15.cpp | 2 +
.../unit_test/TestDefaultDeviceTypeInit_16.cpp | 2 +
.../core/unit_test/TestDefaultDeviceTypeInit_2.cpp | 2 +
.../core/unit_test/TestDefaultDeviceTypeInit_3.cpp | 2 +
.../core/unit_test/TestDefaultDeviceTypeInit_4.cpp | 2 +
.../core/unit_test/TestDefaultDeviceTypeInit_5.cpp | 2 +
.../core/unit_test/TestDefaultDeviceTypeInit_6.cpp | 2 +
.../core/unit_test/TestDefaultDeviceTypeInit_7.cpp | 2 +
.../core/unit_test/TestDefaultDeviceTypeInit_8.cpp | 2 +
.../core/unit_test/TestDefaultDeviceTypeInit_9.cpp | 2 +
.../core/unit_test/TestDefaultDeviceType_a.cpp | 76 +
lib/kokkos/core/unit_test/TestMDRange.hpp | 555 +
lib/kokkos/core/unit_test/TestMemoryPool.hpp | 820 +
.../core/unit_test/TestMemorySpaceTracking.hpp | 2 +-
lib/kokkos/core/unit_test/TestOpenMP.cpp | 303 +-
lib/kokkos/core/unit_test/TestOpenMP_a.cpp | 150 +
lib/kokkos/core/unit_test/TestOpenMP_b.cpp | 185 +
lib/kokkos/core/unit_test/TestOpenMP_c.cpp | 262 +
.../core/unit_test/TestPolicyConstruction.hpp | 493 +
lib/kokkos/core/unit_test/TestQthread.cpp | 38 +-
lib/kokkos/core/unit_test/TestRange.hpp | 91 +-
lib/kokkos/core/unit_test/TestReduce.hpp | 1494 +-
lib/kokkos/core/unit_test/TestScan.hpp | 6 +
lib/kokkos/core/unit_test/TestSerial.cpp | 198 +-
lib/kokkos/core/unit_test/TestSharedAlloc.hpp | 17 +-
lib/kokkos/core/unit_test/TestSynchronic.cpp | 448 +
lib/kokkos/core/unit_test/TestSynchronic.hpp | 240 +
lib/kokkos/core/unit_test/TestTaskPolicy.hpp | 803 +-
lib/kokkos/core/unit_test/TestTeam.hpp | 504 +-
lib/kokkos/core/unit_test/TestThreads.cpp | 218 +-
lib/kokkos/core/unit_test/TestViewAPI.hpp | 526 +-
lib/kokkos/core/unit_test/TestViewImpl.hpp | 2 +-
lib/kokkos/core/unit_test/TestViewMapping.hpp | 393 +-
lib/kokkos/core/unit_test/TestViewOfClass.hpp | 81 +-
lib/kokkos/core/unit_test/TestViewSubview.hpp | 230 +-
lib/kokkos/doc/Doxyfile | 127 +
lib/kokkos/doc/Kokkos_PG.pdf | Bin 0 -> 1359256 bytes
lib/kokkos/doc/README | 32 +
lib/kokkos/doc/build_docs | 15 +
lib/kokkos/doc/index.doc | 72 +
lib/kokkos/example/CMakeLists.txt | 20 +
lib/kokkos/example/cmake/Dependencies.cmake | 4 +
lib/kokkos/example/feint/CMakeLists.txt | 18 +
lib/kokkos/example/feint/ElemFunctor.hpp | 2 +-
lib/kokkos/example/feint/Makefile | 7 +-
lib/kokkos/example/fenl/CGSolve.hpp | 4 +-
lib/kokkos/example/fenl/CMakeLists.txt | 17 +
lib/kokkos/example/fenl/Makefile | 28 +-
lib/kokkos/example/fenl/fenl_functors.hpp | 2 +-
lib/kokkos/example/fenl/fenl_impl.hpp | 2 +-
lib/kokkos/example/fixture/CMakeLists.txt | 13 +
lib/kokkos/example/fixture/Makefile | 9 +-
.../example/global_2_local_ids/CMakeLists.txt | 17 +
lib/kokkos/example/global_2_local_ids/G2L.hpp | 2 +-
lib/kokkos/example/global_2_local_ids/Makefile | 53 +
lib/kokkos/example/grow_array/CMakeLists.txt | 14 +
lib/kokkos/example/grow_array/Makefile | 53 +
lib/kokkos/example/ichol/Makefile | 63 +
.../example/example_chol_performance_device.hpp | 240 +
.../example_chol_performance_device_cuda.cpp | 70 +
.../example_chol_performance_device_pthread.cpp | 67 +
lib/kokkos/example/ichol/src/chol.hpp | 92 +
lib/kokkos/example/ichol/src/chol_u.hpp | 23 +
.../ichol/src/chol_u_right_look_by_blocks.hpp | 394 +
.../example/ichol/src/chol_u_unblocked_opt1.hpp | 90 +
.../example/ichol/src/chol_u_unblocked_opt2.hpp | 154 +
lib/kokkos/example/ichol/src/control.hpp | 110 +
lib/kokkos/example/ichol/src/coo.hpp | 75 +
lib/kokkos/example/ichol/src/crs_matrix_base.hpp | 598 +
.../example/ichol/src/crs_matrix_base_import.hpp | 104 +
lib/kokkos/example/ichol/src/crs_matrix_helper.hpp | 71 +
.../example/ichol/src/crs_matrix_helper_impl.hpp | 364 +
lib/kokkos/example/ichol/src/crs_matrix_view.hpp | 226 +
lib/kokkos/example/ichol/src/crs_row_view.hpp | 185 +
lib/kokkos/example/ichol/src/dot.hpp | 74 +
lib/kokkos/example/ichol/src/gemm.hpp | 99 +
lib/kokkos/example/ichol/src/gemm_ct_nt.hpp | 12 +
.../ichol/src/gemm_ct_nt_for_factor_blocked.hpp | 108 +
.../example/ichol/src/graph_helper_scotch.hpp | 427 +
lib/kokkos/example/ichol/src/herk.hpp | 91 +
lib/kokkos/example/ichol/src/herk_u_ct.hpp | 11 +
.../ichol/src/herk_u_ct_for_factor_blocked.hpp | 103 +
lib/kokkos/example/ichol/src/norm.hpp | 82 +
lib/kokkos/example/ichol/src/partition.hpp | 381 +
lib/kokkos/example/ichol/src/scale.hpp | 92 +
.../example/ichol/src/symbolic_factor_helper.hpp | 379 +
lib/kokkos/example/ichol/src/symbolic_task.hpp | 118 +
lib/kokkos/example/ichol/src/task_factory.hpp | 77 +
lib/kokkos/example/ichol/src/task_view.hpp | 104 +
lib/kokkos/example/ichol/src/trsm.hpp | 92 +
lib/kokkos/example/ichol/src/trsm_l_u_ct.hpp | 14 +
.../ichol/src/trsm_l_u_ct_for_factor_blocked.hpp | 185 +
lib/kokkos/example/ichol/src/util.cpp | 4 +
lib/kokkos/example/ichol/src/util.hpp | 237 +
lib/kokkos/example/md_skeleton/CMakeLists.txt | 16 +
lib/kokkos/example/md_skeleton/Makefile | 53 +
lib/kokkos/example/md_skeleton/main.cpp | 4 +-
lib/kokkos/example/multi_fem/CMakeLists.txt | 16 +
lib/kokkos/example/multi_fem/Explicit.hpp | 2 +-
lib/kokkos/example/multi_fem/Implicit.hpp | 2 +-
lib/kokkos/example/multi_fem/Makefile | 53 +
lib/kokkos/example/multi_fem/Nonlinear.hpp | 2 +-
.../example/multi_fem/SparseLinearSystem.hpp | 2 +-
lib/kokkos/example/query_device/CMakeLists.txt | 14 +
lib/kokkos/example/query_device/Makefile | 53 +
lib/kokkos/example/sort_array/CMakeLists.txt | 14 +
lib/kokkos/example/sort_array/Makefile | 53 +
lib/kokkos/example/sort_array/sort_array.hpp | 2 +-
.../example/tutorial/01_hello_world/CMakeLists.txt | 11 +
.../example/tutorial/01_hello_world/Makefile | 2 +-
.../tutorial/01_hello_world_lambda/CMakeLists.txt | 13 +
.../tutorial/01_hello_world_lambda/Makefile | 2 +-
.../tutorial/02_simple_reduce/CMakeLists.txt | 10 +
.../example/tutorial/02_simple_reduce/Makefile | 2 +-
.../02_simple_reduce_lambda/CMakeLists.txt | 12 +
.../tutorial/02_simple_reduce_lambda/Makefile | 2 +-
.../example/tutorial/03_simple_view/CMakeLists.txt | 10 +
.../example/tutorial/03_simple_view/Makefile | 2 +-
.../tutorial/03_simple_view_lambda/CMakeLists.txt | 12 +
.../tutorial/03_simple_view_lambda/Makefile | 2 +-
.../tutorial/04_simple_memoryspaces/CMakeLists.txt | 10 +
.../tutorial/04_simple_memoryspaces/Makefile | 2 +-
.../tutorial/05_simple_atomics/CMakeLists.txt | 10 +
.../example/tutorial/05_simple_atomics/Makefile | 2 +-
.../Advanced_Views/01_data_layouts/CMakeLists.txt | 10 +
.../Advanced_Views/01_data_layouts/Makefile | 2 +-
.../01_data_layouts/data_layouts.cpp | 4 +-
.../Advanced_Views/02_memory_traits/CMakeLists.txt | 10 +
.../Advanced_Views/02_memory_traits/Makefile | 2 +-
.../02_memory_traits/memory_traits.cpp | 4 +-
.../Advanced_Views/03_subviews/CMakeLists.txt | 10 +
.../tutorial/Advanced_Views/03_subviews/Makefile | 2 +-
.../Advanced_Views/04_dualviews/CMakeLists.txt | 10 +
.../tutorial/Advanced_Views/04_dualviews/Makefile | 2 +-
.../Advanced_Views/04_dualviews/dual_view.cpp | 10 +-
.../Advanced_Views/05_NVIDIA_UVM/CMakeLists.txt | 13 +
.../tutorial/Advanced_Views/05_NVIDIA_UVM/Makefile | 2 +-
.../Advanced_Views/05_NVIDIA_UVM/uvm_example.cpp | 2 +-
.../Advanced_Views/06_AtomicViews/Makefile | 2 +-
.../07_Overlapping_DeepCopy/Makefile | 2 +-
.../overlapping_deepcopy.cpp | 2 +-
.../example/tutorial/Advanced_Views/CMakeLists.txt | 9 +
.../tutorial/Algorithms/01_random_numbers/Makefile | 2 +-
.../01_random_numbers/random_numbers.cpp | 2 +-
lib/kokkos/example/tutorial/CMakeLists.txt | 17 +
.../01_thread_teams/CMakeLists.txt | 10 +
.../01_thread_teams/Makefile | 2 +-
.../01_thread_teams_lambda/CMakeLists.txt | 13 +
.../01_thread_teams_lambda/Makefile | 3 +-
.../01_thread_teams_lambda/thread_teams_lambda.cpp | 3 +-
.../02_nested_parallel_for/CMakeLists.txt | 10 +
.../02_nested_parallel_for/Makefile | 2 +-
.../03_vectorization/CMakeLists.txt | 16 +
.../03_vectorization/Makefile | 2 +-
.../03_vectorization/vectorization.cpp | 6 +-
.../04_team_scan/CMakeLists.txt | 10 +
.../Hierarchical_Parallelism/04_team_scan/Makefile | 2 +-
.../04_team_scan/team_scan.cpp | 2 +-
.../Hierarchical_Parallelism/CMakeLists.txt | 8 +
lib/kokkos/generate_makefile.bash | 198 +-
lib/kokkos/tpls/gtest/gtest/LICENSE | 28 +
lib/kokkos/tpls/gtest/gtest/README | 13 +
lib/kokkos/tpls/gtest/gtest/gtest-all.cc | 9594 ++
lib/kokkos/tpls/gtest/gtest/gtest-test-part.h | 1 +
lib/kokkos/tpls/gtest/gtest/gtest.h | 20065 +++
lib/linalg/Makefile.gfortran | 0
lib/linalg/Makefile.mingw32-cross | 0
lib/linalg/Makefile.mingw32-cross-mpi | 4 +-
lib/linalg/Makefile.mingw64-cross | 0
lib/linalg/Makefile.mingw64-cross-mpi | 4 +-
lib/meam/.depend | 9 +
lib/meam/Makefile.g95 | 6 +-
lib/meam/Makefile.gfortran | 9 +-
lib/meam/Makefile.ifort | 6 +-
lib/meam/Makefile.mingw32-cross | 6 +-
lib/meam/Makefile.mingw32-cross-mpi | 4 +-
lib/meam/Makefile.mingw64-cross | 6 +-
lib/meam/Makefile.mingw64-cross-mpi | 4 +-
lib/meam/Makefile.pgf90 | 6 +-
lib/meam/Makefile.tbird | 6 +-
lib/meam/fm_exp.c | 133 +
lib/meam/meam_data.F | 5 +-
lib/meam/meam_dens_final.F | 34 +-
lib/meam/meam_dens_init.F | 60 +-
lib/meam/meam_force.F | 90 +-
lib/meam/meam_setup_done.F | 182 +-
lib/meam/meam_setup_global.F | 2 +-
lib/meam/meam_setup_param.F | 22 +-
lib/netcdf/Makefile.lammps | 19 +
lib/netcdf/README | 43 +
lib/poems/.depend | 128 +
lib/poems/Makefile.g++ | 4 +-
lib/poems/Makefile.icc | 4 +-
lib/poems/Makefile.mingw32-cross | 5 +-
lib/poems/Makefile.mingw32-cross-mpi | 4 +-
lib/poems/Makefile.mingw64-cross | 5 +-
lib/poems/Makefile.mingw64-cross-mpi | 4 +-
lib/poems/system.cpp | 6 +-
lib/python/Makefile.lammps.python2.7 | 2 +-
lib/qmmm/Makefile.gfortran | 17 +-
lib/qmmm/Makefile.ifort | 66 +
lib/qmmm/README | 28 +-
lib/qmmm/example-ec/README | 1 +
lib/qmmm/example-ec/mm-master/data.water | 233 +
lib/qmmm/example-ec/mm-master/water.in | 31 +
lib/qmmm/example-ec/mm-slave/data.single_water | 33 +
lib/qmmm/example-ec/mm-slave/water_single.in | 28 +
lib/qmmm/example-ec/qm-pw/pseudo/H.blyp-vbc.UPF | 359 +
.../qm-pw/pseudo/H.pbe-van_ak.UPF | 0
lib/qmmm/example-ec/qm-pw/pseudo/O.blyp-mt.UPF | 557 +
.../qm-pw/pseudo/O.pbe-van_bm.UPF | 0
lib/qmmm/example-ec/qm-pw/water.in | 45 +
lib/qmmm/example-ec/qmmm.inp | 24 +
lib/qmmm/example-mc/README | 1 +
.../{example1 => example-mc}/mm-master/data.water | 0
.../{example1 => example-mc}/mm-master/water.in | 0
.../mm-slave/data.single_water | 0
.../mm-slave/water_single.in | 0
.../qm-pw/pseudo/H.pbe-van_ak.UPF | 0
.../qm-pw/pseudo/O.pbe-van_bm.UPF | 0
lib/qmmm/{example1 => example-mc}/qm-pw/water.in | 0
lib/qmmm/example-mc/qmmm.inp | 24 +
lib/qmmm/example1/qmmm.inp | 24 -
lib/qmmm/pwqmmm.c | 53 +-
lib/quip/Makefile.lammps | 18 +-
lib/quip/README | 23 +-
lib/reax/Makefile.g95 | 0
lib/reax/Makefile.gfortran | 0
lib/vtk/Makefile.lammps | 13 +
lib/vtk/Makefile.lammps.arch_vtk6 | 4 +
lib/vtk/Makefile.lammps.centos6_vtk5 | 16 +
lib/vtk/Makefile.lammps.centos7_vtk6 | 16 +
lib/vtk/Makefile.lammps.ubuntu14.04_vtk5 | 12 +
lib/vtk/Makefile.lammps.ubuntu14.04_vtk6 | 12 +
lib/vtk/README | 28 +
potentials/CH.airebo-m | 37604 +++++
potentials/CdTe.sw | 8 +-
potentials/CdTeZnSeHgS0.sw | 14 +-
potentials/CuTa.eam.alloy | 2807 +
potentials/CuTa_eam.poly | 6426 +-
potentials/GaN_sw.poly | 1226 +-
potentials/GaN_tersoff.poly | 826 +-
potentials/MOH.nb3b.harmonic | 27 +-
potentials/SiC_Erhart-Albe.tersoff | 96 +-
potentials/charmm22.cmap | 1023 +
potentials/charmm36.cmap | 1023 +
python/README | 46 +-
python/examples/demo.py | 33 +-
python/examples/gui.py | 10 +-
python/examples/ipython/interface_usage.ipynb | 517 +
.../examples/ipython/interface_usage_bonds.ipynb | 498 +
python/examples/ipython/simple.ipynb | 152 +
python/examples/mc.py | 19 +-
python/examples/pizza/dump.py | 232 +-
python/examples/pizza/gl.py | 31 +-
python/examples/pizza/gnu.py | 19 +-
python/examples/pizza/pdbfile.py | 33 +-
python/examples/pizza/vmd.py | 19 +-
python/examples/plot.py | 5 +-
python/examples/simple.py | 55 +-
python/examples/split.py | 80 +
python/examples/trivial.py | 15 +-
python/examples/viz_atomeye.py | 5 +-
python/examples/viz_gl.py | 11 +-
python/examples/viz_pymol.py | 5 +-
python/examples/viz_vmd.py | 7 +-
python/examples/vizplotgui_atomeye.py | 10 +-
python/examples/vizplotgui_gl.py | 15 +-
python/examples/vizplotgui_pymol.py | 10 +-
python/examples/vizplotgui_vmd.py | 10 +-
python/install.py | 75 +-
python/lammps.py | 747 +-
regress/benchmark.py | 235 -
regress/melt/in.melt | 20 -
regress/melt/log.melt.linux.4 | 60 -
regress/min/in.min | 26 -
regress/min/in.min.box | 31 -
regress/min/log.min.box.linux.4 | 335 -
regress/min/log.min.linux.4 | 97 -
regress/regression.sh | 14 -
src/.gitignore | 14 -
src/ASPHERE/compute_temp_asphere.cpp | 3 +-
src/ASPHERE/compute_temp_asphere.h | 5 +
src/ASPHERE/fix_nph_asphere.cpp | 7 +-
src/ASPHERE/fix_npt_asphere.cpp | 4 +-
src/ASPHERE/fix_npt_asphere.h | 0
src/ASPHERE/fix_nve_asphere.cpp | 0
src/ASPHERE/fix_nve_asphere.h | 0
src/ASPHERE/fix_nve_asphere_noforce.h | 0
src/ASPHERE/fix_nvt_asphere.cpp | 2 +-
src/ASPHERE/fix_nvt_asphere.h | 0
src/ASPHERE/pair_gayberne.cpp | 4 +-
src/ASPHERE/pair_gayberne.h | 0
src/ASPHERE/pair_line_lj.cpp | 97 +-
src/ASPHERE/pair_line_lj.h | 13 +-
src/ASPHERE/pair_resquared.cpp | 4 +-
src/ASPHERE/pair_resquared.h | 0
src/ASPHERE/pair_tri_lj.cpp | 6 +-
src/BODY/body_nparticle.cpp | 107 +-
src/BODY/body_nparticle.h | 13 +-
src/BODY/compute_body_local.cpp | 24 +-
src/BODY/compute_body_local.h | 2 -
src/BODY/compute_temp_body.cpp | 394 +
src/BODY/compute_temp_body.h | 92 +
src/BODY/fix_nh_body.cpp | 153 +
src/BODY/fix_nh_body.h | 50 +
src/BODY/fix_nph_body.cpp | 72 +
src/BODY/fix_nph_body.h | 48 +
src/BODY/fix_npt_body.cpp | 72 +
src/BODY/fix_npt_body.h | 48 +
src/BODY/fix_nvt_body.cpp | 53 +
src/BODY/fix_nvt_body.h | 48 +
src/BODY/pair_body.cpp | 4 +-
src/CLASS2/angle_class2.cpp | 2 +-
src/CLASS2/bond_class2.cpp | 2 +-
src/CLASS2/dihedral_class2.cpp | 14 +-
src/CLASS2/improper_class2.cpp | 8 +-
src/CLASS2/pair_lj_class2.cpp | 4 +-
src/CLASS2/pair_lj_class2_coul_cut.cpp | 4 +-
src/CLASS2/pair_lj_class2_coul_long.cpp | 4 +-
src/COLLOID/pair_brownian.cpp | 733 +
src/{FLD => COLLOID}/pair_brownian.h | 0
src/{FLD => COLLOID}/pair_brownian_poly.cpp | 0
src/{FLD => COLLOID}/pair_brownian_poly.h | 0
src/COLLOID/pair_colloid.cpp | 4 +-
src/COLLOID/pair_lubricate.cpp | 820 +
src/{FLD => COLLOID}/pair_lubricate.h | 0
src/COLLOID/pair_lubricateU.cpp | 2061 +
src/{FLD => COLLOID}/pair_lubricateU.h | 0
src/COLLOID/pair_lubricateU_poly.cpp | 1246 +
src/{FLD => COLLOID}/pair_lubricateU_poly.h | 0
src/COLLOID/pair_lubricate_poly.cpp | 563 +
src/{FLD => COLLOID}/pair_lubricate_poly.h | 0
src/COMPRESS/Install.sh | 4 +
src/COMPRESS/dump_atom_gz.h | 4 +
src/COMPRESS/dump_cfg_gz.h | 4 +
src/COMPRESS/dump_custom_gz.cpp | 12 +-
src/COMPRESS/dump_custom_gz.h | 4 +
src/COMPRESS/dump_xyz_gz.h | 4 +
src/CORESHELL/Install.sh | 6 +
src/CORESHELL/compute_temp_cs.cpp | 13 +-
src/CORESHELL/compute_temp_cs.h | 5 +
src/CORESHELL/pair_born_coul_dsf_cs.cpp | 162 +
src/CORESHELL/pair_born_coul_dsf_cs.h | 59 +
src/DEPEND/fastdep.c | 697 +
src/DIPOLE/pair_lj_cut_dipole_cut.cpp | 4 +-
src/DIPOLE/pair_lj_cut_dipole_cut.h | 0
src/DIPOLE/pair_lj_cut_dipole_long.cpp | 4 +-
src/DIPOLE/pair_lj_cut_dipole_long.h | 0
src/DIPOLE/pair_lj_long_dipole_long.cpp | 4 +-
src/DIPOLE/pair_lj_long_dipole_long.h | 0
src/Depend.sh | 14 +-
src/FLD/pair_brownian.cpp | 733 -
src/FLD/pair_lubricate.cpp | 820 -
src/FLD/pair_lubricateU.cpp | 2061 -
src/FLD/pair_lubricateU_poly.cpp | 1234 -
src/FLD/pair_lubricate_poly.cpp | 555 -
src/GPU/Install.sh | 8 +
src/GPU/fix_gpu.cpp | 3 -
src/GPU/pair_born_coul_long_gpu.cpp | 4 +-
src/GPU/pair_born_coul_wolf_gpu.cpp | 2 +-
src/GPU/pair_born_gpu.cpp | 2 +-
src/GPU/pair_coul_long_gpu.cpp | 9 +-
src/GPU/pair_eam_alloy_gpu.cpp | 2 +-
src/GPU/pair_eam_alloy_gpu.h | 10 +
src/GPU/pair_eam_fs_gpu.cpp | 2 +-
src/GPU/pair_eam_fs_gpu.h | 10 +
src/GPU/pair_eam_gpu.h | 1 +
src/GPU/pair_lj_cubic_gpu.h | 2 +-
src/GPU/pair_lj_cut_dipole_cut_gpu.cpp | 0
src/GPU/pair_lj_cut_dipole_cut_gpu.h | 0
src/GPU/pair_lj_gromacs_gpu.cpp | 30 +-
src/GPU/pair_lj_sf_dipole_sf_gpu.cpp | 0
src/GPU/pair_lj_sf_dipole_sf_gpu.h | 0
src/GPU/pair_sw_gpu.cpp | 2 +-
src/GPU/pair_tersoff_gpu.cpp | 5 +-
src/GPU/pair_tersoff_gpu.h | 9 +-
src/GPU/pair_tersoff_mod_gpu.cpp | 252 +
src/GPU/pair_tersoff_mod_gpu.h | 67 +
src/GPU/pair_tersoff_zbl_gpu.cpp | 274 +
src/GPU/pair_tersoff_zbl_gpu.h | 67 +
src/GPU/pair_zbl_gpu.cpp | 26 +-
src/GPU/pair_zbl_gpu.h | 4 +-
src/GPU/pppm_gpu.cpp | 2 +-
src/GRANULAR/fix_pour.cpp | 68 +-
src/GRANULAR/fix_pour.h | 1 +
src/GRANULAR/fix_wall_gran.cpp | 553 +-
src/GRANULAR/fix_wall_gran.h | 65 +-
src/GRANULAR/fix_wall_gran_region.cpp | 510 +
src/GRANULAR/fix_wall_gran_region.h | 105 +
src/GRANULAR/pair_gran_hertz_history.cpp | 43 +-
src/GRANULAR/pair_gran_hooke.cpp | 38 +-
src/GRANULAR/pair_gran_hooke_history.cpp | 76 +-
src/GRANULAR/pair_gran_hooke_history.h | 9 +-
src/Install.sh | 4 +
src/KIM/Install.sh | 4 +
src/KIM/pair_kim.cpp | 214 +-
src/KIM/pair_kim.h | 10 +-
src/KIM/pair_kim_version.h | 4 +-
src/KOKKOS/Install.sh | 40 +-
src/KOKKOS/angle_charmm_kokkos.cpp | 120 +-
src/KOKKOS/angle_charmm_kokkos.h | 28 +-
src/KOKKOS/angle_harmonic_kokkos.cpp | 34 +-
src/KOKKOS/angle_harmonic_kokkos.h | 16 +-
src/KOKKOS/atom_kokkos.cpp | 22 +-
src/KOKKOS/atom_kokkos.h | 7 +
src/KOKKOS/atom_vec_angle_kokkos.cpp | 94 +
src/KOKKOS/atom_vec_angle_kokkos.h | 1 +
src/KOKKOS/atom_vec_atomic_kokkos.cpp | 41 +
src/KOKKOS/atom_vec_atomic_kokkos.h | 1 +
src/KOKKOS/atom_vec_bond_kokkos.cpp | 71 +
src/KOKKOS/atom_vec_bond_kokkos.h | 1 +
src/KOKKOS/atom_vec_charge_kokkos.cpp | 46 +-
src/KOKKOS/atom_vec_charge_kokkos.h | 1 +
src/KOKKOS/atom_vec_full_kokkos.cpp | 174 +-
src/KOKKOS/atom_vec_full_kokkos.h | 1 +
src/KOKKOS/atom_vec_kokkos.cpp | 3 +
src/KOKKOS/atom_vec_kokkos.h | 69 +
src/KOKKOS/atom_vec_molecular_kokkos.cpp | 147 +
src/KOKKOS/atom_vec_molecular_kokkos.h | 1 +
src/KOKKOS/bond_fene_kokkos.cpp | 5 +-
src/KOKKOS/bond_fene_kokkos.h | 0
src/KOKKOS/bond_harmonic_kokkos.cpp | 99 +-
src/KOKKOS/bond_harmonic_kokkos.h | 22 +-
src/KOKKOS/comm_kokkos.cpp | 44 +-
src/KOKKOS/comm_tiled_kokkos.cpp | 266 +
src/KOKKOS/comm_tiled_kokkos.h | 59 +
src/KOKKOS/compute_temp_kokkos.cpp | 7 +-
src/KOKKOS/compute_temp_kokkos.h | 7 +-
src/KOKKOS/dihedral_charmm_kokkos.cpp | 198 +-
src/KOKKOS/dihedral_charmm_kokkos.h | 58 +-
src/KOKKOS/dihedral_opls_kokkos.cpp | 5 +-
src/KOKKOS/dihedral_opls_kokkos.h | 6 +-
src/KOKKOS/domain_kokkos.cpp | 187 +-
src/KOKKOS/domain_kokkos.h | 5 +
src/KOKKOS/fix_deform_kokkos.cpp | 2 +
src/KOKKOS/fix_deform_kokkos.h | 55 +-
src/KOKKOS/fix_langevin_kokkos.cpp | 6 +-
src/KOKKOS/fix_nh_kokkos.cpp | 7 +-
src/KOKKOS/fix_nh_kokkos.h | 9 +
src/KOKKOS/fix_nph_kokkos.cpp | 10 +-
src/KOKKOS/fix_nph_kokkos.h | 8 +
src/KOKKOS/fix_npt_kokkos.cpp | 8 +-
src/KOKKOS/fix_npt_kokkos.h | 8 +
src/KOKKOS/fix_nve_kokkos.cpp | 4 +
src/KOKKOS/fix_nvt_kokkos.cpp | 8 +-
src/KOKKOS/fix_nvt_kokkos.h | 8 +
src/KOKKOS/fix_qeq_reax_kokkos.cpp | 1265 +
src/KOKKOS/fix_qeq_reax_kokkos.h | 498 +
src/KOKKOS/fix_reaxc_bonds_kokkos.cpp | 127 +
src/KOKKOS/fix_reaxc_bonds_kokkos.h | 42 +
src/KOKKOS/fix_reaxc_species_kokkos.cpp | 159 +
src/KOKKOS/fix_reaxc_species_kokkos.h | 41 +
src/KOKKOS/fix_setforce_kokkos.cpp | 189 +
src/KOKKOS/fix_setforce_kokkos.h | 100 +
src/KOKKOS/fix_wall_reflect_kokkos.cpp | 4 +
src/KOKKOS/fix_wall_reflect_kokkos.h | 2 -
src/KOKKOS/gridcomm_kokkos.cpp | 614 +
src/KOKKOS/gridcomm_kokkos.h | 96 +
src/KOKKOS/improper_harmonic_kokkos.cpp | 119 +-
src/KOKKOS/improper_harmonic_kokkos.h | 24 +-
src/KOKKOS/kokkos.cpp | 48 +-
src/KOKKOS/kokkos.h | 17 +-
src/KOKKOS/kokkos_type.h | 187 +-
src/KOKKOS/math_special_kokkos.cpp | 534 +
src/KOKKOS/math_special_kokkos.h | 100 +
src/KOKKOS/modify_kokkos.cpp | 154 +-
src/KOKKOS/neigh_bond_kokkos.cpp | 31 +-
src/KOKKOS/neigh_bond_kokkos.h | 2 +-
src/KOKKOS/neigh_full_kokkos.h | 38 +-
src/KOKKOS/neigh_list_kokkos.cpp | 8 +-
src/KOKKOS/neigh_list_kokkos.h | 3 +-
src/KOKKOS/neighbor_kokkos.cpp | 53 +-
src/KOKKOS/neighbor_kokkos.h | 19 +-
src/KOKKOS/pair_buck_coul_cut_kokkos.cpp | 5 +-
src/KOKKOS/pair_buck_coul_cut_kokkos.h | 14 +
src/KOKKOS/pair_buck_coul_long_kokkos.cpp | 5 +-
src/KOKKOS/pair_buck_coul_long_kokkos.h | 14 +
src/KOKKOS/pair_buck_kokkos.cpp | 6 +-
src/KOKKOS/pair_buck_kokkos.h | 2 +-
src/KOKKOS/pair_coul_cut_kokkos.cpp | 5 +-
src/KOKKOS/pair_coul_debye_kokkos.cpp | 5 +-
src/KOKKOS/pair_coul_debye_kokkos.h | 14 +
src/KOKKOS/pair_coul_dsf_kokkos.cpp | 9 +-
src/KOKKOS/pair_coul_dsf_kokkos.h | 1 -
src/KOKKOS/pair_coul_long_kokkos.cpp | 5 +-
src/KOKKOS/pair_coul_long_kokkos.h | 14 +
src/KOKKOS/pair_coul_wolf_kokkos.cpp | 9 +-
src/KOKKOS/pair_coul_wolf_kokkos.h | 1 -
src/KOKKOS/pair_eam_alloy_kokkos.cpp | 12 +-
src/KOKKOS/pair_eam_alloy_kokkos.h | 21 +-
src/KOKKOS/pair_eam_fs_kokkos.cpp | 7 +-
src/KOKKOS/pair_eam_fs_kokkos.h | 21 +-
src/KOKKOS/pair_eam_kokkos.cpp | 196 +-
src/KOKKOS/pair_eam_kokkos.h | 15 +-
src/KOKKOS/pair_kokkos.h | 42 +-
.../pair_lj_charmm_coul_charmm_implicit_kokkos.cpp | 5 +-
.../pair_lj_charmm_coul_charmm_implicit_kokkos.h | 14 +
src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp | 9 +-
src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.h | 14 +
src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp | 41 +-
src/KOKKOS/pair_lj_charmm_coul_long_kokkos.h | 9 +-
src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp | 6 +-
src/KOKKOS/pair_lj_class2_coul_cut_kokkos.h | 14 +
src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp | 6 +-
src/KOKKOS/pair_lj_class2_coul_long_kokkos.h | 14 +
src/KOKKOS/pair_lj_class2_kokkos.cpp | 5 +-
src/KOKKOS/pair_lj_class2_kokkos.h | 14 +
src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp | 5 +-
src/KOKKOS/pair_lj_cut_coul_cut_kokkos.h | 2 +-
src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp | 5 +-
src/KOKKOS/pair_lj_cut_coul_debye_kokkos.h | 14 +
src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp | 5 +-
src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.h | 8 +
src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp | 33 +-
src/KOKKOS/pair_lj_cut_coul_long_kokkos.h | 5 +-
src/KOKKOS/pair_lj_cut_kokkos.cpp | 33 +-
src/KOKKOS/pair_lj_cut_kokkos.h | 5 +-
src/KOKKOS/pair_lj_expand_kokkos.cpp | 4 +-
src/KOKKOS/pair_lj_expand_kokkos.h | 14 +
src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp | 5 +-
src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.h | 14 +
src/KOKKOS/pair_lj_gromacs_kokkos.cpp | 5 +-
src/KOKKOS/pair_lj_gromacs_kokkos.h | 14 +
src/KOKKOS/pair_lj_sdk_kokkos.cpp | 5 +-
src/KOKKOS/pair_lj_sdk_kokkos.h | 2 +-
src/KOKKOS/pair_reax_c_kokkos.cpp | 4198 +
src/KOKKOS/pair_reax_c_kokkos.h | 498 +
src/KOKKOS/pair_sw_kokkos.cpp | 83 +-
src/KOKKOS/pair_sw_kokkos.h | 14 +-
src/KOKKOS/pair_table_kokkos.cpp | 8 +-
src/KOKKOS/pair_tersoff_kokkos.cpp | 283 +-
src/KOKKOS/pair_tersoff_kokkos.h | 16 +-
src/KOKKOS/pair_tersoff_mod_kokkos.cpp | 250 +-
src/KOKKOS/pair_tersoff_mod_kokkos.h | 16 +-
src/KOKKOS/pair_tersoff_zbl_kokkos.cpp | 248 +-
src/KOKKOS/pair_tersoff_zbl_kokkos.h | 19 +-
src/KOKKOS/pppm_kokkos.cpp | 3193 +
src/KOKKOS/pppm_kokkos.h | 552 +
src/KOKKOS/region_block_kokkos.cpp | 173 +
src/KOKKOS/region_block_kokkos.h | 83 +
src/KOKKOS/verlet_kokkos.cpp | 198 +-
src/KOKKOS/verlet_kokkos.h | 11 +-
src/KSPACE/ewald.cpp | 14 +-
src/KSPACE/ewald_disp.cpp | 39 +-
src/KSPACE/ewald_disp.h | 4 +-
src/KSPACE/fix_tune_kspace.cpp | 1 +
src/KSPACE/msm.cpp | 20 +-
src/KSPACE/msm_cg.cpp | 8 +-
src/KSPACE/pair_born_coul_long.cpp | 4 +-
src/KSPACE/pair_buck_coul_long.cpp | 4 +-
src/KSPACE/pair_buck_long_coul_long.cpp | 11 +-
src/KSPACE/pair_coul_long.cpp | 4 +-
src/KSPACE/pair_lj_charmm_coul_long.cpp | 84 +-
src/KSPACE/pair_lj_charmm_coul_long.h | 6 +-
src/KSPACE/pair_lj_charmm_coul_msm.cpp | 26 +-
src/KSPACE/pair_lj_cut_coul_long.cpp | 4 +-
src/KSPACE/pair_lj_long_coul_long.cpp | 9 +-
src/KSPACE/pair_lj_long_tip4p_long.cpp | 0
src/KSPACE/pair_lj_long_tip4p_long.h | 0
src/KSPACE/pppm.cpp | 23 +-
src/KSPACE/pppm_cg.cpp | 8 +-
src/KSPACE/pppm_disp.cpp | 50 +-
src/KSPACE/pppm_disp.h | 0
src/KSPACE/pppm_disp_tip4p.cpp | 2 +-
src/KSPACE/pppm_disp_tip4p.h | 0
src/KSPACE/pppm_stagger.cpp | 7 +-
src/KSPACE/pppm_stagger.h | 0
src/KSPACE/pppm_tip4p.cpp | 2 +-
src/MAKE/MACHINES/Makefile.beacon | 11 +-
src/MAKE/MACHINES/Makefile.bgl | 9 +-
src/MAKE/MACHINES/Makefile.bgq | 9 +-
src/MAKE/MACHINES/Makefile.bgq.details | 7 +
src/MAKE/MACHINES/Makefile.chama | 9 +-
src/MAKE/MACHINES/Makefile.cygwin | 9 +-
src/MAKE/MACHINES/Makefile.glory | 9 +-
src/MAKE/MACHINES/Makefile.jaguar | 9 +-
src/MAKE/MACHINES/Makefile.mac | 9 +-
src/MAKE/MACHINES/Makefile.mac_mpi | 9 +-
src/MAKE/MACHINES/Makefile.mingw32-cross | 9 +-
src/MAKE/MACHINES/Makefile.mingw32-cross-mpi | 9 +-
src/MAKE/MACHINES/Makefile.mingw64-cross | 9 +-
src/MAKE/MACHINES/Makefile.mingw64-cross-mpi | 9 +-
src/MAKE/MACHINES/Makefile.myrinet | 9 +-
src/MAKE/MACHINES/Makefile.power | 9 +-
src/MAKE/MACHINES/Makefile.redsky | 9 +-
src/MAKE/MACHINES/Makefile.serial | 9 +-
src/MAKE/MACHINES/Makefile.stampede | 11 +-
src/MAKE/MACHINES/Makefile.storm | 9 +-
src/MAKE/MACHINES/Makefile.tacc | 9 +-
src/MAKE/MACHINES/Makefile.ubuntu | 9 +-
src/MAKE/MACHINES/Makefile.ubuntu_simple | 9 +-
src/MAKE/MACHINES/Makefile.xe6 | 13 +-
src/MAKE/MACHINES/Makefile.xt3 | 9 +-
src/MAKE/MACHINES/Makefile.xt5 | 9 +-
src/MAKE/Makefile.mpi | 19 +-
src/MAKE/Makefile.serial | 21 +-
src/MAKE/OPTIONS/Makefile.big | 120 +
src/MAKE/OPTIONS/Makefile.fftw | 11 +-
src/MAKE/OPTIONS/Makefile.g++_mpich | 120 +
src/MAKE/OPTIONS/Makefile.g++_mpich_link | 120 +
src/MAKE/OPTIONS/Makefile.g++_openmpi | 121 +
src/MAKE/OPTIONS/Makefile.g++_openmpi_link | 120 +
src/MAKE/OPTIONS/Makefile.g++_serial | 120 +
src/MAKE/OPTIONS/Makefile.gpu | 120 +
src/MAKE/OPTIONS/Makefile.icc_mpich | 120 +
src/MAKE/OPTIONS/Makefile.icc_mpich_link | 120 +
src/MAKE/OPTIONS/Makefile.icc_openmpi | 121 +
src/MAKE/OPTIONS/Makefile.icc_openmpi_link | 120 +
src/MAKE/OPTIONS/Makefile.icc_serial | 120 +
src/MAKE/OPTIONS/Makefile.intel_coprocessor | 123 +
src/MAKE/OPTIONS/Makefile.intel_cpu | 117 -
src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi | 123 +
src/MAKE/OPTIONS/Makefile.intel_cpu_mpich | 122 +
src/MAKE/OPTIONS/Makefile.intel_cpu_openmpi | 123 +
src/MAKE/OPTIONS/Makefile.intel_phi | 118 -
src/MAKE/OPTIONS/Makefile.jpeg | 9 +-
src/MAKE/OPTIONS/Makefile.knl | 121 +
src/MAKE/OPTIONS/Makefile.kokkos_cuda | 120 -
src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpich | 123 +
src/MAKE/OPTIONS/Makefile.kokkos_cuda_openmpi | 124 +
src/MAKE/OPTIONS/Makefile.kokkos_mpi_only | 121 +
src/MAKE/OPTIONS/Makefile.kokkos_omp | 13 +-
src/MAKE/OPTIONS/Makefile.kokkos_phi | 17 +-
src/MAKE/OPTIONS/Makefile.mgptfast | 120 +
src/MAKE/OPTIONS/Makefile.mpi_fastmgpt | 113 -
src/MAKE/OPTIONS/Makefile.mpich_g++ | 115 -
src/MAKE/OPTIONS/Makefile.mpich_icc | 115 -
src/MAKE/OPTIONS/Makefile.mpich_native_g++ | 115 -
src/MAKE/OPTIONS/Makefile.mpich_native_icc | 115 -
src/MAKE/OPTIONS/Makefile.omp | 11 +-
src/MAKE/OPTIONS/Makefile.ompi_g++ | 116 -
src/MAKE/OPTIONS/Makefile.ompi_icc | 116 -
src/MAKE/OPTIONS/Makefile.ompi_native_g++ | 115 -
src/MAKE/OPTIONS/Makefile.ompi_native_icc | 115 -
src/MAKE/OPTIONS/Makefile.opt | 11 +-
src/MAKE/OPTIONS/Makefile.pgi | 116 -
src/MAKE/OPTIONS/Makefile.pgi_mpich_link | 120 +
src/MAKE/OPTIONS/Makefile.png | 9 +-
src/MAKE/OPTIONS/Makefile.serial_icc | 115 -
src/MAKE/README | 109 +-
src/MANYBODY/fix_qeq_comb.cpp | 21 +-
src/MANYBODY/fix_qeq_comb.h | 2 +-
src/MANYBODY/pair_adp.cpp | 2 +-
src/MANYBODY/pair_airebo.cpp | 165 +-
src/MANYBODY/pair_airebo.h | 8 +-
src/MANYBODY/pair_airebo_morse.cpp | 40 +
src/MANYBODY/pair_airebo_morse.h | 46 +
src/MANYBODY/pair_bop.cpp | 8 +-
src/MANYBODY/pair_bop.h | 4 +
src/MANYBODY/pair_comb.cpp | 5 +-
src/MANYBODY/pair_comb.h | 3 +-
src/MANYBODY/pair_comb3.cpp | 15 +-
src/MANYBODY/pair_comb3.h | 3 +-
src/MANYBODY/pair_eam.cpp | 27 +-
src/MANYBODY/pair_eam.h | 2 +
src/MANYBODY/pair_eam_alloy.cpp | 3 +-
src/MANYBODY/pair_eam_fs.cpp | 3 +-
src/MANYBODY/pair_eim.cpp | 56 +-
src/MANYBODY/pair_nb3b_harmonic.cpp | 6 +-
src/MANYBODY/pair_nb3b_harmonic.h | 2 +-
src/MANYBODY/pair_polymorphic.cpp | 948 +-
src/MANYBODY/pair_polymorphic.h | 423 +-
src/MANYBODY/pair_rebo.cpp | 6 +-
src/MANYBODY/pair_sw.cpp | 82 +-
src/MANYBODY/pair_sw.h | 4 +-
src/MANYBODY/pair_tersoff.cpp | 105 +-
src/MANYBODY/pair_tersoff.h | 4 +-
src/MANYBODY/pair_tersoff_mod.cpp | 2 +-
src/MANYBODY/pair_tersoff_mod.h | 2 +-
src/MANYBODY/pair_tersoff_zbl.h | 2 +-
src/MANYBODY/pair_vashishta.cpp | 97 +-
src/MANYBODY/pair_vashishta.h | 25 +-
src/MANYBODY/pair_vashishta_table.cpp | 302 +
src/MANYBODY/pair_vashishta_table.h | 100 +
src/MC/fix_atom_swap.cpp | 26 +-
src/MC/fix_atom_swap.h | 4 +
src/MC/fix_bond_break.cpp | 6 +-
src/MC/fix_bond_break.h | 0
src/MC/fix_bond_create.cpp | 4 +-
src/MC/fix_bond_create.h | 0
src/MC/fix_bond_swap.cpp | 6 +-
src/MC/fix_gcmc.cpp | 78 +-
src/MC/fix_gcmc.h | 22 +-
src/MC/fix_tfmc.cpp | 17 +-
src/MC/fix_tfmc.h | 0
src/MC/pair_dsmc.cpp | 4 +-
src/MEAM/Install.sh | 4 +
src/MEAM/pair_meam.cpp | 18 +-
src/MISC/compute_ti.cpp | 5 +-
src/MISC/dump_xtc.cpp | 1215 +
src/MISC/dump_xtc.h | 118 +
src/MISC/fix_deposit.cpp | 70 +-
src/MISC/fix_deposit.h | 12 +-
src/MISC/fix_efield.cpp | 27 +-
src/MISC/fix_efield.h | 2 +-
src/MISC/fix_evaporate.cpp | 4 +-
src/MISC/fix_gld.cpp | 3 +-
src/MISC/fix_orient_bcc.cpp | 612 +
src/MISC/fix_orient_bcc.h | 115 +
src/MISC/fix_orient_fcc.cpp | 22 +-
src/MISC/fix_orient_fcc.h | 2 +-
src/MISC/fix_thermal_conductivity.cpp | 3 +-
src/MISC/fix_ttm.cpp | 13 +-
src/MISC/fix_viscosity.cpp | 3 +-
src/MISC/pair_nm_cut.cpp | 4 +-
src/MISC/pair_nm_cut_coul_cut.cpp | 4 +-
src/MISC/pair_nm_cut_coul_long.cpp | 4 +-
src/{XTC => MISC}/xdr_compat.cpp | 0
src/{XTC => MISC}/xdr_compat.h | 0
src/MOLECULE/angle_charmm.cpp | 2 +-
src/MOLECULE/angle_cosine.cpp | 2 +-
src/MOLECULE/angle_cosine_periodic.cpp | 2 +-
src/MOLECULE/angle_cosine_squared.cpp | 2 +-
src/MOLECULE/angle_harmonic.cpp | 2 +-
src/MOLECULE/angle_table.cpp | 2 +-
src/MOLECULE/bond_fene.cpp | 2 +-
src/MOLECULE/bond_fene_expand.cpp | 2 +-
src/MOLECULE/bond_harmonic.cpp | 2 +-
src/MOLECULE/bond_morse.cpp | 2 +-
src/MOLECULE/bond_nonlinear.cpp | 2 +-
src/MOLECULE/bond_quartic.cpp | 2 +-
src/MOLECULE/bond_table.cpp | 81 +-
src/MOLECULE/dihedral_charmm.cpp | 2 +-
src/MOLECULE/dihedral_harmonic.cpp | 2 +-
src/MOLECULE/dihedral_helix.cpp | 2 +-
src/MOLECULE/dihedral_multi_harmonic.cpp | 2 +-
src/MOLECULE/dihedral_opls.cpp | 2 +-
src/MOLECULE/fix_cmap.cpp | 1451 +
src/MOLECULE/fix_cmap.h | 129 +
src/MOLECULE/improper_cvff.cpp | 2 +-
src/MOLECULE/improper_harmonic.cpp | 2 +-
src/MOLECULE/improper_umbrella.cpp | 25 +-
src/MOLECULE/pair_hbond_dreiding_lj.cpp | 6 +-
src/MOLECULE/pair_hbond_dreiding_morse.cpp | 6 +-
src/MOLECULE/pair_lj_charmm_coul_charmm.cpp | 12 +-
src/MOLECULE/pair_lj_cut_tip4p_cut.cpp | 4 +-
src/MOLECULE/pair_tip4p_cut.cpp | 4 +-
src/MPIIO/Install.sh | 4 +
src/MPIIO/dump_atom_mpiio.cpp | 9 +-
src/MPIIO/dump_custom_mpiio.cpp | 40 +-
src/MPIIO/dump_xyz_mpiio.cpp | 4 +-
src/Make.py | 891 +-
src/Make.sh | 6 +
src/Makefile | 36 +-
src/OPT/Install.sh | 4 +
src/OPT/pair_eam_opt.cpp | 7 +-
src/PERI/atom_vec_peri.h | 0
src/PERI/compute_damage_atom.cpp | 5 +-
src/PERI/compute_dilatation_atom.cpp | 2 +-
src/PERI/compute_plasticity_atom.cpp | 2 +-
src/PERI/pair_peri_eps.cpp | 4 +-
src/PERI/pair_peri_lps.cpp | 4 +-
src/PERI/pair_peri_pmb.cpp | 4 +-
src/PERI/pair_peri_ves.cpp | 4 +-
src/POEMS/Install.sh | 4 +
src/POEMS/fix_poems.cpp | 2 +-
src/PYTHON/Install.sh | 4 +
src/Package.sh | 4 +
src/Purge.list | 150 +
src/QEQ/fix_qeq.cpp | 20 +-
src/QEQ/fix_qeq.h | 3 +
src/QEQ/fix_qeq_fire.cpp | 356 +
src/QEQ/fix_qeq_fire.h | 75 +
src/QEQ/fix_qeq_slater.cpp | 8 -
src/REAX/Install.sh | 4 +
src/REAX/pair_reax.cpp | 7 +-
src/REAX/pair_reax.h | 8 +-
src/REPLICA/compute_event_displace.cpp | 2 +-
src/REPLICA/fix_event.cpp | 11 +-
src/REPLICA/fix_neb.cpp | 357 +-
src/REPLICA/fix_neb.h | 23 +-
src/REPLICA/neb.cpp | 11 +-
src/REPLICA/prd.cpp | 166 +-
src/REPLICA/prd.h | 5 +-
src/REPLICA/tad.cpp | 21 +-
src/REPLICA/temper.cpp | 33 +-
src/REPLICA/verlet_split.cpp | 4 +-
src/RIGID/compute_erotate_rigid.cpp | 19 +-
src/RIGID/compute_ke_rigid.cpp | 18 +-
src/RIGID/compute_rigid_local.cpp | 319 +
src/RIGID/compute_rigid_local.h | 74 +
src/RIGID/fix_ehex.cpp | 622 +
src/RIGID/fix_ehex.h | 130 +
src/RIGID/fix_rattle.cpp | 376 +-
src/RIGID/fix_rattle.h | 41 +-
src/RIGID/fix_rigid.cpp | 45 +-
src/RIGID/fix_rigid.h | 1 +
src/RIGID/fix_rigid_nh.cpp | 20 +-
src/RIGID/fix_rigid_nh.h | 2 +-
src/RIGID/fix_rigid_nh_small.cpp | 18 +-
src/RIGID/fix_rigid_nh_small.h | 2 +-
src/RIGID/fix_rigid_small.cpp | 44 +-
src/RIGID/fix_rigid_small.h | 9 +-
src/RIGID/fix_shake.cpp | 190 +-
src/RIGID/fix_shake.h | 12 +-
src/SHOCK/fix_append_atoms.cpp | 3 +-
src/SHOCK/fix_append_atoms.h | 3 +-
src/SHOCK/fix_msst.cpp | 4 +-
src/SHOCK/fix_nphug.cpp | 7 +-
src/SHOCK/fix_wall_piston.cpp | 4 +-
src/SNAP/compute_sna_atom.cpp | 5 +-
src/SNAP/compute_snad_atom.cpp | 5 +-
src/SNAP/compute_snav_atom.cpp | 7 +-
src/SNAP/sna.cpp | 2 +-
src/SNAP/sna.h | 2 +-
src/SRD/fix_srd.cpp | 10 +-
src/SRD/fix_wall_srd.cpp | 2 +-
src/STUBS/Makefile | 2 +-
src/STUBS/Makefile.mingw32-cross | 2 +-
src/STUBS/Makefile.mingw64-cross | 2 +-
src/STUBS/mpi.c | 11 +-
src/STUBS/mpi.h | 8 +-
src/USER-ATC/Install.sh | 4 +
src/USER-AWPMD/Install.sh | 4 +
src/USER-AWPMD/pair_awpmd_cut.cpp | 4 +-
src/USER-CG-CMM/Install.sh | 4 +
src/USER-CG-CMM/angle_sdk.cpp | 2 +-
src/USER-CG-CMM/pair_lj_sdk.cpp | 4 +-
src/USER-CG-CMM/pair_lj_sdk_coul_long.cpp | 4 +-
src/USER-COLVARS/Install.sh | 4 +
src/USER-COLVARS/colvarproxy_lammps.cpp | 312 +-
src/USER-COLVARS/colvarproxy_lammps.h | 82 +-
src/USER-COLVARS/fix_colvars.cpp | 58 +-
src/USER-COLVARS/fix_colvars.h | 12 +-
src/USER-COLVARS/ndx_group.cpp | 248 +
src/USER-COLVARS/ndx_group.h | 56 +
src/USER-CUDA/Install.sh | 202 -
src/USER-CUDA/README | 21 -
src/USER-CUDA/atom_vec_angle_cuda.cpp | 467 -
src/USER-CUDA/atom_vec_angle_cuda.h | 69 -
src/USER-CUDA/atom_vec_atomic_cuda.cpp | 394 -
src/USER-CUDA/atom_vec_atomic_cuda.h | 81 -
src/USER-CUDA/atom_vec_charge_cuda.cpp | 394 -
src/USER-CUDA/atom_vec_charge_cuda.h | 69 -
src/USER-CUDA/atom_vec_full_cuda.cpp | 508 -
src/USER-CUDA/atom_vec_full_cuda.h | 69 -
src/USER-CUDA/comm_cuda.cpp | 1375 -
src/USER-CUDA/comm_cuda.h | 69 -
src/USER-CUDA/compute_pe_cuda.cpp | 61 -
src/USER-CUDA/compute_pe_cuda.h | 59 -
src/USER-CUDA/compute_pressure_cuda.cpp | 97 -
src/USER-CUDA/compute_pressure_cuda.h | 63 -
src/USER-CUDA/compute_temp_cuda.cpp | 215 -
src/USER-CUDA/compute_temp_cuda.h | 76 -
src/USER-CUDA/compute_temp_partial_cuda.cpp | 360 -
src/USER-CUDA/compute_temp_partial_cuda.h | 84 -
src/USER-CUDA/cuda.cpp | 1067 -
src/USER-CUDA/cuda_data.h | 796 -
src/USER-CUDA/cuda_modify_flags.h | 45 -
src/USER-CUDA/cuda_neigh_list.cpp | 184 -
src/USER-CUDA/cuda_neigh_list.h | 83 -
src/USER-CUDA/domain_cuda.cpp | 345 -
src/USER-CUDA/domain_cuda.h | 41 -
src/USER-CUDA/fft3d_cuda.cpp | 609 -
src/USER-CUDA/fft3d_cuda.h | 148 -
src/USER-CUDA/fft3d_wrap_cuda.cpp | 111 -
src/USER-CUDA/fft3d_wrap_cuda.h | 68 -
src/USER-CUDA/fix_addforce_cuda.cpp | 193 -
src/USER-CUDA/fix_addforce_cuda.h | 64 -
src/USER-CUDA/fix_aveforce_cuda.cpp | 262 -
src/USER-CUDA/fix_aveforce_cuda.h | 68 -
src/USER-CUDA/fix_enforce2d_cuda.cpp | 171 -
src/USER-CUDA/fix_enforce2d_cuda.h | 55 -
src/USER-CUDA/fix_freeze_cuda.cpp | 137 -
src/USER-CUDA/fix_freeze_cuda.h | 57 -
src/USER-CUDA/fix_gravity_cuda.cpp | 180 -
src/USER-CUDA/fix_gravity_cuda.h | 60 -
src/USER-CUDA/fix_nh_cuda.cpp | 2072 -
src/USER-CUDA/fix_nh_cuda.h | 126 -
src/USER-CUDA/fix_npt_cuda.cpp | 75 -
src/USER-CUDA/fix_npt_cuda.h | 36 -
src/USER-CUDA/fix_nve_cuda.cpp | 157 -
src/USER-CUDA/fix_nve_cuda.h | 63 -
src/USER-CUDA/fix_nvt_cuda.cpp | 52 -
src/USER-CUDA/fix_nvt_cuda.h | 36 -
src/USER-CUDA/fix_set_force_cuda.cpp | 184 -
src/USER-CUDA/fix_set_force_cuda.h | 63 -
src/USER-CUDA/fix_shake_cuda.cpp | 2885 -
src/USER-CUDA/fix_shake_cuda.h | 130 -
src/USER-CUDA/fix_temp_berendsen_cuda.cpp | 219 -
src/USER-CUDA/fix_temp_berendsen_cuda.h | 58 -
src/USER-CUDA/fix_temp_rescale_cuda.cpp | 224 -
src/USER-CUDA/fix_temp_rescale_cuda.h | 61 -
src/USER-CUDA/fix_temp_rescale_limit_cuda.cpp | 237 -
src/USER-CUDA/fix_temp_rescale_limit_cuda.h | 61 -
src/USER-CUDA/fix_viscous_cuda.cpp | 105 -
src/USER-CUDA/fix_viscous_cuda.h | 55 -
src/USER-CUDA/modify_cuda.cpp | 437 -
src/USER-CUDA/modify_cuda.h | 83 -
src/USER-CUDA/neigh_full_cuda.cpp | 307 -
src/USER-CUDA/neighbor_cuda.cpp | 240 -
src/USER-CUDA/neighbor_cuda.h | 39 -
src/USER-CUDA/pair_born_coul_long_cuda.cpp | 183 -
src/USER-CUDA/pair_born_coul_long_cuda.h | 57 -
src/USER-CUDA/pair_buck_coul_cut_cuda.cpp | 170 -
src/USER-CUDA/pair_buck_coul_cut_cuda.h | 57 -
src/USER-CUDA/pair_buck_coul_long_cuda.cpp | 181 -
src/USER-CUDA/pair_buck_coul_long_cuda.h | 57 -
src/USER-CUDA/pair_buck_cuda.cpp | 166 -
src/USER-CUDA/pair_buck_cuda.h | 57 -
src/USER-CUDA/pair_eam_alloy_cuda.cpp | 326 -
src/USER-CUDA/pair_eam_alloy_cuda.h | 44 -
src/USER-CUDA/pair_eam_cuda.cpp | 265 -
src/USER-CUDA/pair_eam_cuda.h | 80 -
src/USER-CUDA/pair_eam_fs_cuda.cpp | 335 -
src/USER-CUDA/pair_eam_fs_cuda.h | 44 -
src/USER-CUDA/pair_gran_hooke_cuda.cpp | 250 -
src/USER-CUDA/pair_gran_hooke_cuda.h | 57 -
src/USER-CUDA/pair_lj96_cut_cuda.cpp | 179 -
src/USER-CUDA/pair_lj96_cut_cuda.h | 57 -
src/USER-CUDA/pair_lj_charmm_coul_charmm_cuda.cpp | 188 -
src/USER-CUDA/pair_lj_charmm_coul_charmm_cuda.h | 63 -
.../pair_lj_charmm_coul_charmm_implicit_cuda.cpp | 183 -
.../pair_lj_charmm_coul_charmm_implicit_cuda.h | 62 -
src/USER-CUDA/pair_lj_charmm_coul_long_cuda.cpp | 196 -
src/USER-CUDA/pair_lj_charmm_coul_long_cuda.h | 62 -
src/USER-CUDA/pair_lj_class2_coul_cut_cuda.cpp | 162 -
src/USER-CUDA/pair_lj_class2_coul_cut_cuda.h | 57 -
src/USER-CUDA/pair_lj_class2_coul_long_cuda.cpp | 175 -
src/USER-CUDA/pair_lj_class2_coul_long_cuda.h | 57 -
src/USER-CUDA/pair_lj_class2_cuda.cpp | 167 -
src/USER-CUDA/pair_lj_class2_cuda.h | 57 -
src/USER-CUDA/pair_lj_cut_coul_cut_cuda.cpp | 162 -
src/USER-CUDA/pair_lj_cut_coul_cut_cuda.h | 57 -
src/USER-CUDA/pair_lj_cut_coul_debye_cuda.cpp | 163 -
src/USER-CUDA/pair_lj_cut_coul_debye_cuda.h | 57 -
src/USER-CUDA/pair_lj_cut_coul_long_cuda.cpp | 216 -
src/USER-CUDA/pair_lj_cut_coul_long_cuda.h | 57 -
src/USER-CUDA/pair_lj_cut_cuda.cpp | 179 -
src/USER-CUDA/pair_lj_cut_cuda.h | 57 -
src/USER-CUDA/pair_lj_cut_experimental_cuda.cpp | 178 -
src/USER-CUDA/pair_lj_cut_experimental_cuda.h | 57 -
src/USER-CUDA/pair_lj_expand_cuda.cpp | 180 -
src/USER-CUDA/pair_lj_expand_cuda.h | 57 -
.../pair_lj_gromacs_coul_gromacs_cuda.cpp | 194 -
src/USER-CUDA/pair_lj_gromacs_coul_gromacs_cuda.h | 68 -
src/USER-CUDA/pair_lj_gromacs_cuda.cpp | 177 -
src/USER-CUDA/pair_lj_gromacs_cuda.h | 68 -
src/USER-CUDA/pair_lj_sdk_coul_long_cuda.cpp | 193 -
src/USER-CUDA/pair_lj_sdk_coul_long_cuda.h | 59 -
src/USER-CUDA/pair_lj_sdk_cuda.cpp | 184 -
src/USER-CUDA/pair_lj_sdk_cuda.h | 65 -
src/USER-CUDA/pair_lj_smooth_cuda.cpp | 177 -
src/USER-CUDA/pair_lj_smooth_cuda.h | 68 -
src/USER-CUDA/pair_morse_cuda.cpp | 177 -
src/USER-CUDA/pair_morse_cuda.h | 57 -
src/USER-CUDA/pair_sw_cuda.cpp | 207 -
src/USER-CUDA/pair_sw_cuda.h | 66 -
src/USER-CUDA/pair_tersoff_cuda.cpp | 204 -
src/USER-CUDA/pair_tersoff_cuda.h | 66 -
src/USER-CUDA/pair_tersoff_zbl_cuda.cpp | 220 -
src/USER-CUDA/pair_tersoff_zbl_cuda.h | 53 -
src/USER-CUDA/pppm_cuda.cpp | 1420 -
src/USER-CUDA/pppm_cuda.h | 113 -
src/USER-CUDA/pppm_old.cpp | 2839 -
src/USER-CUDA/pppm_old.h | 271 -
src/USER-CUDA/user_cuda.h | 159 -
src/USER-CUDA/verlet_cuda.cpp | 1242 -
src/USER-CUDA/verlet_cuda.h | 63 -
src/USER-DIFFRACTION/compute_saed.cpp | 2 +-
src/USER-DIFFRACTION/compute_xrd.cpp | 2 +-
src/USER-DIFFRACTION/fix_saed_vtk.cpp | 5 +-
src/USER-DPD/README | 35 +
src/USER-DPD/atom_vec_dpd.cpp | 939 +
src/USER-DPD/atom_vec_dpd.h | 92 +
src/USER-DPD/compute_dpd.cpp | 89 +
src/USER-DPD/compute_dpd.h | 56 +
src/USER-DPD/compute_dpd_atom.cpp | 108 +
src/USER-DPD/compute_dpd_atom.h | 61 +
src/USER-DPD/fix_dpd_energy.cpp | 90 +
src/USER-DPD/fix_dpd_energy.h | 52 +
src/USER-DPD/fix_eos_cv.cpp | 113 +
src/USER-DPD/fix_eos_cv.h | 61 +
src/USER-DPD/fix_eos_table.cpp | 442 +
src/USER-DPD/fix_eos_table.h | 126 +
src/USER-DPD/fix_eos_table_rx.cpp | 811 +
src/USER-DPD/fix_eos_table_rx.h | 157 +
src/USER-DPD/fix_rx.cpp | 1813 +
src/USER-DPD/fix_rx.h | 191 +
src/USER-DPD/fix_shardlow.cpp | 648 +
src/USER-DPD/fix_shardlow.h | 108 +
src/USER-DPD/pair_dpd_fdt.cpp | 452 +
src/USER-DPD/pair_dpd_fdt.h | 88 +
src/USER-DPD/pair_dpd_fdt_energy.cpp | 574 +
src/USER-DPD/pair_dpd_fdt_energy.h | 90 +
src/USER-DPD/pair_exp6_rx.cpp | 1131 +
src/USER-DPD/pair_exp6_rx.h | 138 +
src/USER-DPD/pair_multi_lucy.cpp | 834 +
src/USER-DPD/pair_multi_lucy.h | 149 +
src/USER-DPD/pair_multi_lucy_rx.cpp | 1024 +
src/USER-DPD/pair_multi_lucy_rx.h | 161 +
src/USER-DPD/pair_table_rx.cpp | 1186 +
src/USER-DPD/pair_table_rx.h | 172 +
src/USER-DRUDE/compute_temp_drude.cpp | 7 +
src/USER-DRUDE/compute_temp_drude.h | 1 +
src/USER-DRUDE/fix_drude.cpp | 45 +-
src/USER-DRUDE/fix_langevin_drude.cpp | 6 +-
src/USER-DRUDE/pair_lj_cut_thole_long.cpp | 8 +-
src/USER-DRUDE/pair_thole.cpp | 4 +-
src/USER-EFF/compute_ke_atom_eff.cpp | 2 +-
src/USER-EFF/compute_temp_deform_eff.cpp | 2 +-
src/USER-EFF/compute_temp_region_eff.cpp | 2 +-
src/USER-EFF/fix_langevin_eff.cpp | 6 +-
src/USER-EFF/fix_nph_eff.cpp | 4 +-
src/USER-EFF/fix_npt_eff.cpp | 4 +-
src/USER-EFF/fix_nvt_eff.cpp | 2 +-
src/USER-EFF/fix_nvt_sllod_eff.cpp | 2 +-
src/USER-EFF/pair_eff_cut.cpp | 4 +-
src/USER-FEP/Install.sh | 10 +-
src/USER-FEP/README | 5 +
src/USER-FEP/compute_fep.cpp | 6 +-
src/USER-FEP/fix_adapt_fep.cpp | 15 +-
src/USER-FEP/pair_coul_cut_soft.cpp | 4 +-
src/USER-FEP/pair_coul_long_soft.cpp | 4 +-
src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp | 4 +-
src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp | 4 +-
src/USER-FEP/pair_lj_cut_coul_long_soft.cpp | 4 +-
src/USER-FEP/pair_lj_cut_soft.cpp | 4 +-
src/USER-FEP/pair_morse_soft.cpp | 424 +
src/USER-FEP/pair_morse_soft.h | 59 +
src/USER-H5MD/Install.sh | 4 +
src/USER-H5MD/dump_h5md.cpp | 4 +-
src/USER-INTEL/Install.sh | 10 +-
src/USER-INTEL/README | 36 +-
src/USER-INTEL/TEST/README | 161 +-
src/USER-INTEL/TEST/in.intel.lc | 66 +-
src/USER-INTEL/TEST/in.intel.lj | 43 +
src/USER-INTEL/TEST/in.intel.rhodo | 34 +-
src/USER-INTEL/TEST/in.intel.sw | 45 +
src/USER-INTEL/TEST/in.intel.tersoff | 45 +
src/USER-INTEL/TEST/in.intel.water | 45 +
src/USER-INTEL/TEST/in.lc_generate_restart | 57 +
src/USER-INTEL/TEST/mW.sw | 18 +
src/USER-INTEL/TEST/mW_32k_cube.data | 64018 +++++++++
src/USER-INTEL/angle_charmm_intel.cpp | 332 +
src/USER-INTEL/angle_charmm_intel.h | 88 +
src/USER-INTEL/angle_harmonic_intel.cpp | 312 +
src/USER-INTEL/angle_harmonic_intel.h | 84 +
src/USER-INTEL/bond_fene_intel.cpp | 295 +
src/USER-INTEL/bond_fene_intel.h | 88 +
src/USER-INTEL/bond_harmonic_intel.cpp | 261 +
src/USER-INTEL/bond_harmonic_intel.h | 88 +
src/USER-INTEL/dihedral_charmm_intel.cpp | 1001 +
src/USER-INTEL/dihedral_charmm_intel.h | 84 +
src/USER-INTEL/dihedral_harmonic_intel.cpp | 411 +
src/USER-INTEL/dihedral_harmonic_intel.h | 81 +
src/USER-INTEL/dihedral_opls_intel.cpp | 438 +
src/USER-INTEL/dihedral_opls_intel.h | 80 +
src/USER-INTEL/fix_intel.cpp | 424 +-
src/USER-INTEL/fix_intel.h | 352 +-
src/USER-INTEL/fix_nh_intel.cpp | 525 +
src/USER-INTEL/fix_nh_intel.h | 163 +
src/USER-INTEL/fix_npt_intel.cpp | 68 +
src/USER-INTEL/fix_npt_intel.h | 52 +
src/USER-INTEL/fix_nve_asphere_intel.cpp | 238 +
src/USER-INTEL/fix_nve_asphere_intel.h | 62 +
src/USER-INTEL/fix_nve_intel.cpp | 198 +
src/USER-INTEL/fix_nve_intel.h | 59 +
src/USER-INTEL/fix_nvt_intel.cpp | 50 +
src/USER-INTEL/fix_nvt_intel.h | 52 +
src/USER-INTEL/fix_nvt_sllod_intel.cpp | 126 +
src/USER-INTEL/fix_nvt_sllod_intel.h | 72 +
src/USER-INTEL/improper_cvff_intel.cpp | 423 +
src/USER-INTEL/improper_cvff_intel.h | 90 +
src/USER-INTEL/improper_harmonic_intel.cpp | 383 +
src/USER-INTEL/improper_harmonic_intel.h | 94 +
src/USER-INTEL/intel_buffers.cpp | 74 +-
src/USER-INTEL/intel_buffers.h | 44 +-
src/USER-INTEL/intel_intrinsics.h | 2187 +
src/USER-INTEL/intel_preprocess.h | 143 +-
src/USER-INTEL/intel_simd.h | 1918 +
src/USER-INTEL/math_extra_intel.h | 124 +
src/USER-INTEL/neigh_half_bin_intel.cpp | 998 +-
src/USER-INTEL/pair_buck_coul_cut_intel.cpp | 556 +
src/USER-INTEL/pair_buck_coul_cut_intel.h | 91 +
src/USER-INTEL/pair_buck_coul_long_intel.cpp | 657 +
src/USER-INTEL/pair_buck_coul_long_intel.h | 92 +
src/USER-INTEL/pair_buck_intel.cpp | 498 +
src/USER-INTEL/pair_buck_intel.h | 89 +
src/USER-INTEL/pair_gayberne_intel.cpp | 59 +-
src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp | 39 +-
src/USER-INTEL/pair_lj_charmm_coul_long_intel.h | 2 +-
src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp | 54 +-
src/USER-INTEL/pair_lj_cut_coul_long_intel.h | 2 +-
src/USER-INTEL/pair_lj_cut_intel.cpp | 188 +-
src/USER-INTEL/pair_lj_cut_intel.h | 5 +-
src/USER-INTEL/pair_sw_intel.cpp | 883 +-
src/USER-INTEL/pair_sw_intel.h | 17 +-
src/USER-INTEL/pair_tersoff_intel.cpp | 1504 +
src/USER-INTEL/pair_tersoff_intel.h | 156 +
src/USER-INTEL/pppm_intel.cpp | 669 +
src/USER-INTEL/pppm_intel.h | 76 +
src/USER-INTEL/verlet_intel.cpp | 449 -
src/USER-INTEL/verlet_intel.h | 67 -
src/USER-INTEL/verlet_lrt_intel.cpp | 420 +
src/USER-INTEL/verlet_lrt_intel.h | 78 +
src/USER-INTEL/verlet_split_intel.cpp | 595 -
src/USER-INTEL/verlet_split_intel.h | 89 -
src/USER-LB/README | 0
src/USER-LB/fix_lb_fluid.cpp | 0
src/USER-LB/fix_lb_fluid.h | 0
src/USER-LB/fix_lb_momentum.cpp | 0
src/USER-LB/fix_lb_momentum.h | 0
src/USER-LB/fix_lb_pc.cpp | 0
src/USER-LB/fix_lb_pc.h | 0
src/USER-LB/fix_lb_rigid_pc_sphere.cpp | 4 +-
src/USER-LB/fix_lb_rigid_pc_sphere.h | 0
src/USER-LB/fix_lb_viscous.cpp | 2 +-
src/USER-LB/fix_lb_viscous.h | 0
src/USER-MANIFOLD/README | 84 +
src/USER-MANIFOLD/fix_manifoldforce.cpp | 185 +
src/USER-MANIFOLD/fix_manifoldforce.h | 81 +
src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp | 644 +
src/USER-MANIFOLD/fix_nve_manifold_rattle.h | 172 +
src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp | 416 +
src/USER-MANIFOLD/fix_nvt_manifold_rattle.h | 155 +
src/USER-MANIFOLD/manifold.h | 100 +
src/USER-MANIFOLD/manifold_cylinder.cpp | 27 +
src/USER-MANIFOLD/manifold_cylinder.h | 29 +
src/USER-MANIFOLD/manifold_cylinder_dent.cpp | 44 +
src/USER-MANIFOLD/manifold_cylinder_dent.h | 27 +
src/USER-MANIFOLD/manifold_dumbbell.cpp | 43 +
src/USER-MANIFOLD/manifold_dumbbell.h | 31 +
src/USER-MANIFOLD/manifold_ellipsoid.cpp | 28 +
src/USER-MANIFOLD/manifold_ellipsoid.h | 28 +
src/USER-MANIFOLD/manifold_factory.cpp | 73 +
src/USER-MANIFOLD/manifold_factory.h | 110 +
src/USER-MANIFOLD/manifold_plane.cpp | 24 +
src/USER-MANIFOLD/manifold_plane.h | 30 +
src/USER-MANIFOLD/manifold_plane_wiggle.cpp | 28 +
src/USER-MANIFOLD/manifold_plane_wiggle.h | 28 +
src/USER-MANIFOLD/manifold_sphere.h | 59 +
src/USER-MANIFOLD/manifold_spine.cpp | 163 +
src/USER-MANIFOLD/manifold_spine.h | 43 +
src/USER-MANIFOLD/manifold_supersphere.h | 58 +
src/USER-MANIFOLD/manifold_thylakoid.cpp | 618 +
src/USER-MANIFOLD/manifold_thylakoid.h | 71 +
src/USER-MANIFOLD/manifold_thylakoid_shared.cpp | 228 +
src/USER-MANIFOLD/manifold_thylakoid_shared.h | 63 +
src/USER-MANIFOLD/manifold_torus.cpp | 40 +
src/USER-MANIFOLD/manifold_torus.h | 32 +
src/USER-MGPT/pair_mgpt.cpp | 2 +-
src/USER-MISC/Install.sh | 4 +
src/USER-MISC/README | 9 +-
src/USER-MISC/angle_cosine_shift.cpp | 2 +-
src/USER-MISC/angle_cosine_shift_exp.cpp | 2 +-
src/USER-MISC/angle_dipole.cpp | 52 +-
src/USER-MISC/angle_fourier.cpp | 2 +-
src/USER-MISC/angle_fourier_simple.cpp | 2 +-
src/USER-MISC/angle_quartic.cpp | 2 +-
src/USER-MISC/bond_harmonic_shift.cpp | 2 +-
src/USER-MISC/bond_harmonic_shift_cut.cpp | 2 +-
src/USER-MISC/compute_ackland_atom.cpp | 2 +-
src/USER-MISC/compute_basal_atom.cpp | 2 +-
src/USER-MISC/compute_temp_rotate.cpp | 4 +-
src/USER-MISC/dihedral_cosine_shift_exp.cpp | 2 +-
src/USER-MISC/dihedral_fourier.cpp | 22 +-
src/USER-MISC/dihedral_fourier.h | 1 +
src/USER-MISC/dihedral_nharmonic.cpp | 2 +-
src/USER-MISC/dihedral_quadratic.cpp | 2 +-
src/USER-MISC/dihedral_spherical.cpp | 876 +
src/USER-MISC/dihedral_spherical.h | 59 +
src/USER-MISC/dihedral_table.cpp | 2 +-
src/USER-MISC/fix_addtorque.cpp | 18 +-
src/USER-MISC/fix_addtorque.h | 2 +-
src/USER-MISC/fix_ave_spatial_sphere.cpp | 1063 -
src/USER-MISC/fix_ave_spatial_sphere.h | 186 -
src/USER-MISC/fix_flow_gauss.cpp | 246 +
src/USER-MISC/fix_flow_gauss.h | 56 +
src/USER-MISC/fix_smd.cpp | 35 +-
src/USER-MISC/fix_smd.h | 2 +-
src/USER-MISC/fix_srp.cpp | 227 +-
src/USER-MISC/fix_srp.h | 2 -
src/USER-MISC/fix_ti_rs.cpp | 199 -
src/USER-MISC/fix_ti_rs.h | 66 -
src/USER-MISC/fix_ti_spring.cpp | 56 +-
src/USER-MISC/fix_ti_spring.h | 9 +-
src/USER-MISC/fix_ttm_mod.cpp | 258 +-
src/USER-MISC/fix_ttm_mod.h | 4 +-
src/USER-MISC/improper_cossq.cpp | 2 +-
src/USER-MISC/improper_distance.cpp | 261 +
src/USER-MISC/improper_distance.h | 47 +
src/USER-MISC/improper_fourier.cpp | 2 +-
src/USER-MISC/improper_ring.cpp | 2 +-
src/USER-MISC/pair_buck_mdf.cpp | 433 +
src/USER-MISC/pair_buck_mdf.h | 73 +
src/USER-MISC/pair_cdeam.h | 2 +
src/USER-MISC/pair_coul_diel.cpp | 4 +-
src/USER-MISC/pair_edip.cpp | 4 +-
src/USER-MISC/pair_edip.h | 2 +-
src/USER-MISC/pair_gauss_cut.cpp | 43 +-
src/USER-MISC/pair_gauss_cut.h | 2 +
src/USER-MISC/pair_lennard_mdf.cpp | 395 +
src/USER-MISC/pair_lennard_mdf.h | 69 +
src/USER-MISC/pair_list.cpp | 4 +-
src/USER-MISC/pair_lj_mdf.cpp | 395 +
src/USER-MISC/pair_lj_mdf.h | 69 +
src/USER-MISC/pair_lj_sf.cpp | 4 +-
src/USER-MISC/pair_lj_sf_dipole_sf.cpp | 166 +-
src/USER-MISC/pair_lj_sf_dipole_sf.h | 3 +
src/USER-MISC/pair_morse_smooth_linear.cpp | 370 +
src/USER-MISC/pair_morse_smooth_linear.h | 80 +
src/USER-MISC/pair_srp.cpp | 92 +-
src/USER-MISC/pair_tersoff_table.cpp | 4 +-
src/USER-MISC/pair_tersoff_table.h | 2 +-
src/USER-MOLFILE/Install.sh | 4 +
src/USER-NC-DUMP/Install.sh | 63 +
src/USER-NC-DUMP/README | 39 +
src/USER-NC-DUMP/dump_nc.cpp | 1147 +
src/USER-NC-DUMP/dump_nc.h | 143 +
src/USER-NC-DUMP/dump_nc_mpiio.cpp | 1077 +
src/USER-NC-DUMP/dump_nc_mpiio.h | 140 +
src/USER-OMP/Install.sh | 4 +
src/USER-OMP/angle_dipole_omp.cpp | 54 +-
src/USER-OMP/ewald_omp.cpp | 2 +-
src/USER-OMP/fix_gravity_omp.cpp | 2 +-
src/USER-OMP/fix_nh_sphere_omp.cpp | 3 +-
src/USER-OMP/fix_nph_asphere_omp.cpp | 4 +-
src/USER-OMP/fix_nph_omp.cpp | 4 +-
src/USER-OMP/fix_nph_sphere_omp.cpp | 4 +-
src/USER-OMP/fix_nphug_omp.cpp | 6 +-
src/USER-OMP/fix_npt_asphere_omp.cpp | 4 +-
src/USER-OMP/fix_npt_omp.cpp | 4 +-
src/USER-OMP/fix_npt_sphere_omp.cpp | 4 +-
src/USER-OMP/fix_nve_sphere_omp.cpp | 135 +-
src/USER-OMP/fix_nvt_asphere_omp.cpp | 2 +-
src/USER-OMP/fix_nvt_omp.cpp | 2 +-
src/USER-OMP/fix_nvt_sllod_omp.cpp | 2 +-
src/USER-OMP/fix_nvt_sphere_omp.cpp | 2 +-
src/USER-OMP/fix_omp.cpp | 28 +-
src/USER-OMP/fix_qeq_comb_omp.cpp | 6 +-
src/USER-OMP/fix_shear_history_omp.cpp | 22 +-
src/USER-OMP/fix_wall_gran_omp.cpp | 72 +-
src/USER-OMP/improper_class2_omp.cpp | 5 +-
src/USER-OMP/improper_umbrella_omp.cpp | 18 +-
src/USER-OMP/msm_cg_omp.cpp | 8 +-
src/USER-OMP/msm_omp.cpp | 0
src/USER-OMP/msm_omp.h | 0
src/USER-OMP/neigh_gran_omp.cpp | 43 +-
src/USER-OMP/pair_airebo_morse_omp.cpp | 40 +
src/USER-OMP/pair_airebo_morse_omp.h | 36 +
src/USER-OMP/pair_airebo_omp.cpp | 91 +-
src/USER-OMP/pair_airebo_omp.h | 7 +-
src/USER-OMP/pair_born_coul_msm_omp.cpp | 0
src/USER-OMP/pair_born_coul_msm_omp.h | 0
src/USER-OMP/pair_buck_coul_msm_omp.cpp | 0
src/USER-OMP/pair_buck_coul_msm_omp.h | 0
src/USER-OMP/pair_coul_msm_omp.cpp | 0
src/USER-OMP/pair_coul_msm_omp.h | 0
src/USER-OMP/pair_eam_alloy_omp.cpp | 3 +-
src/USER-OMP/pair_eam_fs_omp.cpp | 3 +-
src/USER-OMP/pair_eam_omp.cpp | 7 +-
src/USER-OMP/pair_gran_hertz_history_omp.cpp | 44 +-
src/USER-OMP/pair_gran_hertz_history_omp.h | 2 +-
src/USER-OMP/pair_gran_hooke_history_omp.cpp | 40 +-
src/USER-OMP/pair_gran_hooke_history_omp.h | 2 +-
src/USER-OMP/pair_line_lj_omp.cpp | 343 -
src/USER-OMP/pair_line_lj_omp.h | 48 -
src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp | 4 +-
src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp | 0
src/USER-OMP/pair_lj_charmm_coul_msm_omp.h | 0
src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp | 0
src/USER-OMP/pair_lj_cut_coul_msm_omp.h | 0
src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp | 0
src/USER-OMP/pair_lj_cut_dipole_cut_omp.h | 0
src/USER-OMP/pair_lj_cut_thole_long_omp.cpp | 266 +
src/USER-OMP/pair_lj_cut_thole_long_omp.h | 70 +
src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp | 22 +-
src/USER-OMP/pair_lj_sf_dipole_sf_omp.h | 0
src/USER-OMP/pair_lubricate_poly_omp.cpp | 14 +-
src/USER-OMP/pair_morse_smooth_linear_omp.cpp | 169 +
src/USER-OMP/pair_morse_smooth_linear_omp.h | 62 +
src/USER-OMP/pair_sw_omp.cpp | 50 +-
src/USER-OMP/pair_tersoff_omp.cpp | 54 +-
src/USER-OMP/pair_tri_lj_omp.cpp | 413 -
src/USER-OMP/pair_tri_lj_omp.h | 48 -
src/USER-OMP/pair_vashishta_omp.cpp | 41 +-
src/USER-OMP/pair_vashishta_table_omp.cpp | 224 +
src/USER-OMP/pair_vashishta_table_omp.h | 48 +
src/USER-OMP/pppm_disp_omp.cpp | 9 +-
src/USER-OMP/pppm_disp_omp.h | 2 +-
src/USER-OMP/pppm_disp_tip4p_omp.cpp | 2 +-
src/USER-OMP/pppm_tip4p_omp.cpp | 2 +-
src/USER-OMP/respa_omp.cpp | 13 +-
src/USER-PHONON/Install.sh | 4 +
src/USER-PHONON/README | 6 +
src/USER-PHONON/fix_phonon.cpp | 140 +-
src/USER-PHONON/fix_phonon.h | 11 +-
src/USER-QMMM/Install.sh | 4 +
src/USER-QMMM/fix_qmmm.cpp | 279 +-
src/USER-QMMM/fix_qmmm.h | 3 +-
src/USER-QUIP/Install.sh | 4 +
src/USER-REAXC/compute_spec_atom.cpp | 4 +-
src/USER-REAXC/compute_spec_atom.h | 2 -
src/USER-REAXC/fix_qeq_reax.cpp | 13 +-
src/USER-REAXC/fix_qeq_reax.h | 2 +-
src/USER-REAXC/fix_reaxc_bonds.cpp | 3 +
src/USER-REAXC/fix_reaxc_bonds.h | 10 +-
src/USER-REAXC/fix_reaxc_species.cpp | 17 +-
src/USER-REAXC/fix_reaxc_species.h | 9 +-
src/USER-REAXC/pair_reax_c.cpp | 11 +-
src/USER-REAXC/pair_reax_c.h | 25 +-
src/USER-REAXC/reaxc_ffield.cpp | 5 +
src/USER-REAXC/reaxc_hydrogen_bonds.cpp | 1 +
src/USER-REAXC/reaxc_lookup.h | 11 +
src/USER-REAXC/reaxc_tool_box.cpp | 10 +-
src/USER-REAXC/reaxc_tool_box.h | 4 +-
src/USER-REAXC/reaxc_traj.cpp | 2 +-
src/USER-REAXC/reaxc_traj.h | 1 +
src/USER-REAXC/reaxc_types.h | 41 +-
src/USER-SMD/Install.sh | 4 +
src/USER-SMD/README | 20 +
src/USER-SMD/compute_smd_contact_radius.cpp | 2 +-
src/USER-SMD/compute_smd_contact_radius.h | 2 +-
src/USER-SMD/compute_smd_damage.cpp | 2 +-
src/USER-SMD/compute_smd_hourglass_error.cpp | 2 +-
src/USER-SMD/compute_smd_hourglass_error.h | 2 +-
src/USER-SMD/compute_smd_internal_energy.cpp | 2 +-
src/USER-SMD/compute_smd_internal_energy.h | 2 +-
src/USER-SMD/compute_smd_plastic_strain.cpp | 2 +-
src/USER-SMD/compute_smd_plastic_strain.h | 2 +-
src/USER-SMD/compute_smd_plastic_strain_rate.cpp | 2 +-
src/USER-SMD/compute_smd_plastic_strain_rate.h | 2 +-
src/USER-SMD/compute_smd_rho.cpp | 2 +-
src/USER-SMD/compute_smd_tlsph_defgrad.cpp | 2 +-
src/USER-SMD/compute_smd_tlsph_defgrad.h | 2 +-
src/USER-SMD/compute_smd_tlsph_dt.cpp | 2 +-
src/USER-SMD/compute_smd_tlsph_dt.h | 2 +-
src/USER-SMD/compute_smd_tlsph_num_neighs.cpp | 2 +-
src/USER-SMD/compute_smd_tlsph_num_neighs.h | 2 +-
src/USER-SMD/compute_smd_tlsph_shape.cpp | 2 +-
src/USER-SMD/compute_smd_tlsph_shape.h | 2 +-
src/USER-SMD/compute_smd_tlsph_strain.cpp | 2 +-
src/USER-SMD/compute_smd_tlsph_strain.h | 2 +-
src/USER-SMD/compute_smd_tlsph_strain_rate.cpp | 2 +-
src/USER-SMD/compute_smd_tlsph_strain_rate.h | 2 +-
src/USER-SMD/compute_smd_tlsph_stress.cpp | 2 +-
src/USER-SMD/compute_smd_tlsph_stress.h | 2 +-
.../compute_smd_triangle_mesh_vertices.cpp | 2 +-
src/USER-SMD/compute_smd_triangle_mesh_vertices.h | 2 +-
src/USER-SMD/compute_smd_ulsph_effm.cpp | 2 +-
src/USER-SMD/compute_smd_ulsph_effm.h | 2 +-
src/USER-SMD/compute_smd_ulsph_num_neighs.cpp | 2 +-
src/USER-SMD/compute_smd_ulsph_num_neighs.h | 2 +-
src/USER-SMD/compute_smd_ulsph_strain.cpp | 2 +-
src/USER-SMD/compute_smd_ulsph_strain.h | 2 +-
src/USER-SMD/compute_smd_ulsph_strain_rate.cpp | 2 +-
src/USER-SMD/compute_smd_ulsph_strain_rate.h | 2 +-
src/USER-SMD/compute_smd_ulsph_stress.cpp | 2 +-
src/USER-SMD/compute_smd_ulsph_stress.h | 2 +-
src/USER-SMD/compute_smd_vol.cpp | 2 +-
src/USER-SMD/fix_smd_setvel.cpp | 12 +-
src/USER-SMD/pair_smd_hertz.cpp | 4 +-
src/USER-SMD/pair_smd_triangulated_surface.cpp | 4 +-
src/USER-SMTBQ/pair_smtbq.cpp | 2526 +-
src/USER-SMTBQ/pair_smtbq.h | 392 +-
src/USER-SPH/compute_meso_e_atom.cpp | 6 +-
src/USER-SPH/compute_meso_e_atom.h | 2 +-
src/USER-SPH/compute_meso_rho_atom.cpp | 6 +-
src/USER-SPH/compute_meso_rho_atom.h | 2 +-
src/USER-SPH/compute_meso_t_atom.cpp | 10 +-
src/USER-SPH/compute_meso_t_atom.h | 2 +-
src/USER-SPH/pair_sph_heatconduction.cpp | 4 +-
src/USER-SPH/pair_sph_idealgas.cpp | 4 +-
src/USER-SPH/pair_sph_lj.cpp | 4 +-
src/USER-SPH/pair_sph_rhosum.cpp | 4 +-
src/USER-SPH/pair_sph_taitwater.cpp | 4 +-
src/USER-SPH/pair_sph_taitwater_morris.cpp | 4 +-
src/USER-TALLY/compute_force_tally.cpp | 1 +
src/USER-TALLY/compute_pe_mol_tally.cpp | 129 +
src/USER-TALLY/compute_pe_mol_tally.h | 59 +
src/USER-TALLY/compute_pe_tally.cpp | 1 +
src/USER-TALLY/compute_stress_tally.cpp | 1 +
src/USER-VTK/Install.sh | 64 +
src/USER-VTK/README | 17 +
src/USER-VTK/dump_custom_vtk.cpp | 2398 +
src/USER-VTK/dump_custom_vtk.h | 320 +
src/VORONOI/Install.sh | 4 +
src/VORONOI/README | 2 +-
src/VORONOI/compute_voronoi_atom.cpp | 179 +-
src/VORONOI/compute_voronoi_atom.h | 5 +-
src/XTC/dump_xtc.cpp | 1214 -
src/XTC/dump_xtc.h | 119 -
src/accelerator_cuda.h | 88 -
src/accelerator_intel.h | 3 +-
src/accelerator_kokkos.h | 14 +
src/angle.cpp | 7 +-
src/angle.h | 6 +-
src/angle_hybrid.cpp | 2 +-
src/angle_zero.cpp | 154 +
src/angle_zero.h | 61 +
src/atom.cpp | 267 +-
src/atom.h | 69 +-
src/atom_vec.cpp | 4 +-
src/atom_vec.h | 6 -
src/atom_vec_body.cpp | 71 +-
src/atom_vec_body.h | 12 +-
src/atom_vec_ellipsoid.cpp | 0
src/atom_vec_ellipsoid.h | 0
src/atom_vec_line.cpp | 76 +-
src/atom_vec_line.h | 2 +-
src/atom_vec_tri.cpp | 186 +-
src/atom_vec_tri.h | 4 +-
src/balance.cpp | 414 +-
src/balance.h | 33 +-
src/body.h | 5 +-
src/bond.cpp | 74 +-
src/bond.h | 6 +-
src/bond_hybrid.cpp | 2 +-
src/bond_zero.cpp | 156 +
src/bond_zero.h | 61 +
src/comm.cpp | 15 +-
src/comm.h | 15 +-
src/comm_brick.cpp | 63 +-
src/comm_brick.h | 2 +
src/comm_tiled.cpp | 49 +-
src/comm_tiled.h | 30 +-
src/compute.cpp | 29 +-
src/compute.h | 11 +-
src/compute_angle.cpp | 81 +
src/compute_angle.h | 67 +
src/compute_angle_local.cpp | 4 +-
src/compute_angle_local.h | 2 -
src/compute_angmom_chunk.cpp | 14 +-
src/compute_bond.cpp | 81 +
src/compute_bond.h | 67 +
src/compute_bond_local.cpp | 210 +-
src/compute_bond_local.h | 6 +-
src/compute_centro_atom.cpp | 187 +-
src/compute_centro_atom.h | 3 +-
src/compute_chunk_atom.cpp | 538 +-
src/compute_chunk_atom.h | 49 +-
src/compute_cluster_atom.cpp | 6 +-
src/compute_cna_atom.cpp | 10 +-
src/compute_com.cpp | 1 +
src/compute_com_chunk.cpp | 5 +-
src/compute_com_chunk.h | 6 +-
src/compute_contact_atom.cpp | 4 +-
src/compute_coord_atom.cpp | 9 +-
src/compute_dihedral.cpp | 83 +
src/compute_dihedral.h | 67 +
src/compute_dihedral_local.cpp | 2 -
src/compute_dihedral_local.h | 2 -
src/compute_dipole_chunk.cpp | 294 +
src/compute_dipole_chunk.h | 77 +
src/compute_displace_atom.cpp | 15 +-
src/compute_erotate_sphere_atom.cpp | 6 +-
src/compute_group_group.cpp | 3 +-
src/compute_gyration.cpp | 6 +-
src/compute_gyration_chunk.cpp | 28 +-
src/compute_heat_flux.cpp | 3 +-
src/compute_hexorder_atom.cpp | 8 +-
src/compute_hexorder_atom.h | 4 +
src/compute_improper.cpp | 83 +
src/compute_improper.h | 67 +
src/compute_improper_local.cpp | 2 -
src/compute_improper_local.h | 2 -
src/compute_inertia_chunk.cpp | 15 +-
src/compute_ke_atom.cpp | 6 +-
src/compute_msd.cpp | 82 +-
src/compute_msd.h | 4 +-
src/compute_msd_chunk.cpp | 69 +-
src/compute_msd_chunk.h | 11 +-
src/compute_omega_chunk.cpp | 157 +-
src/compute_orientorder_atom.cpp | 14 +-
src/compute_orientorder_atom.h | 4 +
src/compute_pair.cpp | 4 +-
src/compute_pair_local.cpp | 45 +-
src/compute_pair_local.h | 5 +-
src/compute_pe.cpp | 7 +-
src/compute_pe.h | 2 +-
src/compute_pe_atom.cpp | 15 +-
src/compute_pe_atom.h | 3 +-
src/compute_pressure.cpp | 3 +-
src/compute_property_atom.cpp | 7 +-
src/compute_property_atom.h | 2 -
src/compute_property_chunk.cpp | 6 +-
src/compute_property_local.cpp | 52 +-
src/compute_property_local.h | 4 +-
src/compute_rdf.cpp | 8 +-
src/compute_reduce.cpp | 41 +-
src/compute_reduce_region.cpp | 12 +-
src/compute_slice.cpp | 67 +-
src/compute_stress_atom.cpp | 4 +-
src/compute_temp.h | 5 +
src/compute_temp_chunk.cpp | 41 +-
src/compute_temp_chunk.h | 5 +
src/compute_temp_com.h | 5 +
src/compute_temp_deform.cpp | 2 +-
src/compute_temp_deform.h | 5 +
src/compute_temp_partial.cpp | 10 +-
src/compute_temp_partial.h | 5 +
src/compute_temp_profile.cpp | 6 +-
src/compute_temp_profile.h | 5 +
src/compute_temp_ramp.cpp | 2 +-
src/compute_temp_ramp.h | 5 +
src/compute_temp_region.cpp | 5 +-
src/compute_temp_region.h | 5 +
src/compute_temp_sphere.cpp | 4 +-
src/compute_temp_sphere.h | 5 +
src/compute_torque_chunk.cpp | 14 +-
src/compute_vacf.cpp | 12 +-
src/compute_vacf.h | 0
src/compute_vcm_chunk.cpp | 13 +-
src/create_atoms.cpp | 102 +-
src/create_bonds.cpp | 1 +
src/create_box.cpp | 3 +-
src/delete_atoms.cpp | 56 +-
src/delete_atoms.h | 6 +-
src/delete_bonds.cpp | 4 +-
src/dihedral.cpp | 7 +-
src/dihedral.h | 6 +-
src/dihedral_hybrid.cpp | 2 +-
src/dihedral_zero.cpp | 122 +
src/dihedral_zero.h | 54 +
src/displace_atoms.cpp | 74 +-
src/displace_atoms.h | 8 +
src/domain.cpp | 149 +-
src/domain.h | 11 +
src/dump.cpp | 137 +-
src/dump.h | 22 +-
src/dump_atom.cpp | 21 +-
src/dump_cfg.cpp | 75 +-
src/dump_cfg.h | 0
src/dump_custom.cpp | 424 +-
src/dump_custom.h | 30 +-
src/dump_dcd.cpp | 5 +-
src/dump_dcd.h | 3 +-
src/dump_image.cpp | 278 +-
src/dump_image.h | 37 +-
src/dump_local.cpp | 75 +-
src/dump_xyz.cpp | 7 +-
src/error.cpp | 79 +-
src/error.h | 14 +
src/exceptions.h | 58 +
src/finish.cpp | 33 +-
src/fix.cpp | 116 +-
src/fix.h | 28 +-
src/fix_adapt.cpp | 58 +-
src/fix_adapt.h | 5 +
src/fix_addforce.cpp | 24 +-
src/fix_addforce.h | 2 +-
src/fix_ave_atom.cpp | 135 +-
src/fix_ave_chunk.cpp | 106 +-
src/fix_ave_chunk.h | 12 +
src/fix_ave_correlate.cpp | 67 +-
src/fix_ave_correlate.h | 8 +
src/fix_ave_histo.cpp | 282 +-
src/fix_ave_histo.h | 11 +-
src/fix_ave_histo_weight.cpp | 13 +-
src/fix_ave_histo_weight.h | 133 +-
src/fix_ave_spatial.cpp | 1538 -
src/fix_ave_spatial.h | 192 -
src/fix_ave_time.cpp | 261 +-
src/fix_ave_time.h | 15 +-
src/fix_aveforce.cpp | 16 +-
src/fix_aveforce.h | 2 +-
src/fix_balance.cpp | 96 +-
src/fix_balance.h | 8 +-
src/fix_box_relax.cpp | 3 +-
src/fix_controller.cpp | 274 +
src/fix_controller.h | 58 +
src/fix_deform.cpp | 12 +-
src/fix_deprecated.cpp | 42 +
src/fix_deprecated.h | 51 +
src/fix_drag.cpp | 16 +-
src/fix_drag.h | 2 +-
src/fix_dt_reset.cpp | 1 +
src/fix_enforce2d.cpp | 35 +-
src/fix_enforce2d.h | 5 +
src/fix_external.cpp | 4 +-
src/fix_gravity.cpp | 19 +-
src/fix_gravity.h | 2 +-
src/fix_group.cpp | 17 +-
src/fix_group.h | 3 +
src/fix_halt.cpp | 220 +
src/fix_halt.h | 62 +
src/fix_heat.cpp | 12 +-
src/fix_indent.cpp | 19 +-
src/fix_indent.h | 2 +-
src/fix_langevin.cpp | 19 +-
src/fix_langevin.h | 1 +
src/fix_minimize.cpp | 7 +-
src/fix_momentum.cpp | 21 +-
src/fix_momentum.h | 1 +
src/fix_move.cpp | 308 +-
src/fix_move.h | 20 +-
src/fix_nh.cpp | 68 +-
src/fix_nh.h | 17 +-
src/fix_nh_sphere.cpp | 147 +-
src/fix_nh_sphere.h | 1 +
src/fix_nph.cpp | 4 +-
src/fix_nph_sphere.cpp | 4 +-
src/fix_npt.cpp | 4 +-
src/fix_npt_sphere.cpp | 4 +-
src/fix_nve_limit.h | 5 +-
src/fix_nve_sphere.cpp | 164 +-
src/fix_nve_sphere.h | 8 +-
src/fix_nvt.cpp | 2 +-
src/fix_nvt_sllod.cpp | 2 +-
src/fix_nvt_sphere.cpp | 2 +-
src/fix_press_berendsen.cpp | 3 +-
src/fix_print.cpp | 5 +-
src/fix_property_atom.cpp | 70 +-
src/fix_property_atom.h | 10 +-
src/fix_read_restart.cpp | 5 +-
src/fix_recenter.cpp | 6 +-
src/fix_respa.cpp | 3 +-
src/fix_restrain.cpp | 25 +-
src/fix_restrain.h | 2 +-
src/fix_setforce.cpp | 19 +-
src/fix_setforce.h | 11 +-
src/fix_shear_history.cpp | 455 +-
src/fix_shear_history.h | 33 +-
src/fix_spring.cpp | 60 +-
src/fix_spring.h | 2 +-
src/fix_spring_chunk.cpp | 253 +
src/fix_spring_chunk.h | 78 +
src/fix_spring_rg.cpp | 33 +-
src/fix_spring_rg.h | 2 +-
src/fix_spring_self.cpp | 18 +-
src/fix_spring_self.h | 2 +-
src/fix_store.cpp | 223 +-
src/fix_store.h | 21 +-
src/fix_store_force.cpp | 5 +-
src/fix_store_state.cpp | 181 +-
src/fix_store_state.h | 9 +
src/fix_temp_berendsen.cpp | 3 +-
src/fix_temp_csld.cpp | 3 +-
src/fix_temp_csvr.cpp | 10 +-
src/fix_temp_csvr.h | 1 -
src/fix_temp_rescale.cpp | 5 +-
src/fix_tmd.cpp | 34 +-
src/fix_vector.cpp | 22 +-
src/fix_viscous.cpp | 22 +-
src/fix_viscous.h | 2 +-
src/fix_wall.cpp | 22 +-
src/fix_wall.h | 3 +-
src/fix_wall_reflect.cpp | 3 +-
src/fix_wall_region.cpp | 19 +-
src/fix_wall_region.h | 8 +-
src/force.cpp | 359 +-
src/force.h | 38 +-
src/group.cpp | 96 +-
src/group.h | 4 +
src/imbalance.cpp | 20 +
src/imbalance.h | 45 +
src/imbalance_group.cpp | 88 +
src/imbalance_group.h | 41 +
src/imbalance_neigh.cpp | 114 +
src/imbalance_neigh.h | 41 +
src/imbalance_store.cpp | 69 +
src/imbalance_store.h | 40 +
src/imbalance_time.cpp | 111 +
src/imbalance_time.h | 43 +
src/imbalance_var.cpp | 96 +
src/imbalance_var.h | 43 +
src/improper.cpp | 9 +-
src/improper.h | 7 +-
src/improper_hybrid.cpp | 13 +-
src/improper_hybrid.h | 1 +
src/improper_zero.cpp | 122 +
src/improper_zero.h | 57 +
src/info.cpp | 458 +-
src/info.h | 58 +-
src/input.cpp | 183 +-
src/input.h | 22 +-
src/integrate.cpp | 6 +-
src/integrate.h | 1 +
src/kspace.cpp | 16 +-
src/kspace.h | 11 +-
src/lammps.cpp | 210 +-
src/lammps.h | 12 +-
src/lattice.cpp | 10 +-
src/library.cpp | 790 +-
src/library.h | 10 +
src/lmptype.h | 5 +
src/main.cpp | 17 +-
src/math_const.h | 2 +
src/math_extra.cpp | 46 +
src/math_extra.h | 89 +-
src/math_special.cpp | 533 +
src/math_special.h | 29 +
src/memory.cpp | 19 +
src/min.cpp | 37 +-
src/min.h | 4 +
src/min_cg.cpp | 7 +-
src/min_fire.cpp | 7 +-
src/min_hftn.cpp | 21 +-
src/min_hftn.h | 24 +-
src/min_linesearch.cpp | 4 -
src/min_quickmin.cpp | 7 +-
src/min_sd.cpp | 7 +-
src/minimize.cpp | 7 +
src/minimize.h | 4 +
src/modify.cpp | 150 +-
src/modify.h | 22 +-
src/molecule.cpp | 149 +-
src/molecule.h | 115 +-
src/mpiio.h | 2 +-
src/my_pool_chunk.h | 4 +-
src/neigh_derive.cpp | 430 +-
src/neigh_gran.cpp | 321 +-
src/neigh_list.cpp | 40 +-
src/neigh_list.h | 14 +-
src/neigh_request.cpp | 69 +-
src/neigh_request.h | 40 +-
src/neigh_shardlow.cpp | 438 +
src/neigh_shardlow.h | 22 +
src/neighbor.cpp | 198 +-
src/neighbor.h | 43 +-
src/output.cpp | 43 +-
src/output.h | 10 +
src/pair.cpp | 53 +-
src/pair.h | 43 +-
src/pair_beck.cpp | 4 +-
src/pair_born.cpp | 4 +-
src/pair_born_coul_dsf.cpp | 495 +
src/pair_born_coul_dsf.h | 81 +
src/pair_born_coul_wolf.cpp | 4 +-
src/pair_buck.cpp | 4 +-
src/pair_buck_coul_cut.cpp | 4 +-
src/pair_coul_cut.cpp | 4 +-
src/pair_coul_dsf.cpp | 9 +-
src/pair_coul_streitz.cpp | 4 +-
src/pair_coul_streitz.h | 2 +-
src/pair_coul_wolf.cpp | 6 +-
src/pair_dpd.cpp | 12 +-
src/pair_dpd_tstat.cpp | 4 +-
src/pair_gauss.cpp | 58 +-
src/pair_gauss.h | 2 +
src/pair_hybrid.cpp | 122 +-
src/pair_hybrid.h | 15 +
src/pair_hybrid_overlay.cpp | 4 +-
src/pair_lj96_cut.cpp | 4 +-
src/pair_lj_cubic.cpp | 4 +-
src/pair_lj_cut.cpp | 4 +-
src/pair_lj_cut_coul_cut.cpp | 4 +-
src/pair_lj_cut_coul_dsf.cpp | 4 +-
src/pair_lj_expand.cpp | 4 +-
src/pair_lj_gromacs.cpp | 4 +-
src/pair_lj_gromacs_coul_gromacs.cpp | 4 +-
src/pair_lj_smooth.cpp | 4 +-
src/pair_lj_smooth_linear.cpp | 4 +-
src/pair_mie_cut.cpp | 4 +-
src/pair_morse.cpp | 7 +-
src/pair_soft.cpp | 4 +-
src/pair_table.cpp | 111 +-
src/pair_yukawa.cpp | 4 +-
src/pair_zbl.cpp | 4 +-
src/pair_zero.cpp | 233 +
src/pair_zero.h | 82 +
src/random_mars.cpp | 9 +-
src/random_park.cpp | 6 +-
src/random_park.h | 1 -
src/read_data.cpp | 144 +-
src/read_data.h | 96 +-
src/read_dump.cpp | 28 +-
src/read_restart.cpp | 16 +-
src/read_restart.h | 16 +
src/region.cpp | 227 +-
src/region.h | 53 +-
src/region_block.cpp | 242 +-
src/region_block.h | 7 +-
src/region_cone.cpp | 234 +-
src/region_cone.h | 4 -
src/region_cylinder.cpp | 374 +-
src/region_cylinder.h | 2 +
src/region_intersect.cpp | 104 +-
src/region_intersect.h | 7 +-
src/region_plane.cpp | 6 +-
src/region_prism.cpp | 143 +-
src/region_prism.h | 6 -
src/region_sphere.cpp | 46 +
src/region_sphere.h | 3 +
src/region_union.cpp | 105 +-
src/region_union.h | 8 +-
src/replicate.cpp | 4 +-
src/rerun.cpp | 3 +-
src/respa.cpp | 34 +-
src/respa.h | 12 +-
src/run.cpp | 10 +
src/set.cpp | 121 +-
src/set.h | 26 +-
src/special.cpp | 5 +
src/suffix.h | 5 +-
src/thermo.cpp | 178 +-
src/thermo.h | 9 +-
src/timer.cpp | 125 +-
src/timer.h | 51 +-
src/universe.cpp | 54 +-
src/update.cpp | 117 +-
src/update.h | 25 +-
src/variable.cpp | 670 +-
src/variable.h | 48 +-
src/velocity.cpp | 3 +-
src/verlet.cpp | 15 +-
src/verlet.h | 5 +
src/version.h | 2 +-
src/write_coeff.cpp | 113 +
src/write_coeff.h | 61 +
src/write_data.cpp | 8 +-
src/write_dump.cpp | 3 +-
src/write_restart.cpp | 50 +-
src/write_restart.h | 1 +
tools/ch2lmp/README | 131 +-
tools/ch2lmp/charmm2lammps.pl | 2062 +-
tools/ch2lmp/example-cmap/1gb1.data | 10614 ++
tools/ch2lmp/example-cmap/1gb1.in | 36 +
tools/ch2lmp/example-cmap/1gb1.log | 256 +
tools/ch2lmp/example-cmap/1gb1.pdb | 860 +
tools/ch2lmp/example-cmap/1gb1.psf | 3223 +
tools/ch2lmp/example-cmap/1gb1_ctrl.pdb | 2838 +
tools/ch2lmp/example-cmap/1gb1_ctrl.psf | 5330 +
tools/ch2lmp/example-cmap/par_all36_prot.prm | 3399 +
tools/ch2lmp/example-cmap/top_all36_prot.rtf | 1777 +
tools/ch2lmp/example/1ac7.data | 6990 +-
tools/ch2lmp/example/1ac7.dump | 5931 -
tools/ch2lmp/example/1ac7.in | 25 +-
tools/ch2lmp/example/1ac7.log | 256 +
tools/ch2lmp/example/1ac7.pdb | 0
tools/ch2lmp/example/1ac7.pdb1 | 0
tools/ch2lmp/example/1ac7.pgn | 0
tools/ch2lmp/example/1ac7.psf | 0
tools/ch2lmp/example/1ac7_ctrl.pdb | 3248 +-
tools/ch2lmp/example/1ac7_ctrl.psf | 2332 +-
tools/ch2lmp/example/1ac7_pared.pdb | 0
tools/ch2lmp/example/par_all27_na.prm | 0
tools/ch2lmp/example/top_all27_na.rtf | 0
tools/ch2lmp/lammps2pdb.pl | 194 +-
tools/ch2lmp/other/in_mkpdb | 0
tools/moltemplate/common/spce_ice_rect16.lt | 162 +-
tools/moltemplate/common/spce_ice_rect32.lt | 258 +-
tools/moltemplate/common/spce_ice_rect8.lt | 114 +-
.../moltemplate_files/spce_ice_rect16.lt | 162 +-
.../moltemplate_files/spce_ice_rect32.lt | 258 +-
.../moltemplate_files/spce_ice_rect8.lt | 114 +-
.../moltemplate_files/lipid.lt | 156 +-
.../moltemplate_files/system.lt | 48 +-
.../moltemplate_files/water.lt | 34 +-
.../packmol_files/lipid.xyz | 28 +-
.../moltemplate_files/lipid.lt | 156 +-
.../moltemplate_files/system.lt | 54 +-
.../moltemplate_files/water.lt | 34 +-
tools/moltemplate/src/bonds_by_type.py | 43 +-
tools/moltemplate/src/ltemplify.py | 18 +-
tools/moltemplate/src/lttree.py | 1 -
tools/moltemplate/src/moltemplate.sh | 24 +-
tools/moltemplate/src/ttree.py | 16 +-
tools/msi2lmp/README | 7 +-
tools/msi2lmp/frc_files/clayff.frc | 61 +-
tools/msi2lmp/src/ReadMdfFile.c | 16 +-
tools/msi2lmp/src/SearchAndFill.c | 14 +-
tools/msi2lmp/src/msi2lmp.c | 3 +
tools/msi2lmp/src/msi2lmp.h | 4 +-
tools/msi2lmp/test/PyAC_bulk-clayff.car | 2574 +-
tools/msi2lmp/test/PyAC_bulk-clayff.mdf | 2616 +-
tools/msi2lmp/test/reference/PyAC_bulk-clayff.data | 2 +-
.../msi2lmp/test/reference/PyAC_bulk-clayff.data2 | 2562 +-
tools/phonon/Makefile | 25 +-
tools/phonon/README | 79 +-
tools/phonon/disp.cpp | 2854 +
tools/phonon/dynmat.cpp | 219 +-
tools/phonon/dynmat.h | 2 +-
tools/phonon/global.h | 13 +
tools/phonon/green.cpp | 47 +-
tools/phonon/interpolate.cpp | 53 +-
tools/phonon/phonon.cpp | 515 +-
tools/phonon/phonon.h | 2 +
tools/phonon/timer.cpp | 16 +-
tools/phonon/version.h | 2 +-
tools/polybond/lmpsdata.py | 3890 +-
tools/pymol_asphere/src/cartesian.cpp | 0
tools/pymol_asphere/src/cartesian.h | 0
tools/pymol_asphere/src/colors.cpp | 0
tools/pymol_asphere/src/colors.h | 0
tools/pymol_asphere/src/commandline.cpp | 0
tools/pymol_asphere/src/commandline.h | 0
tools/pymol_asphere/src/error.cpp | 0
tools/pymol_asphere/src/error.h | 0
tools/pymol_asphere/src/glsurface.cpp | 0
tools/pymol_asphere/src/glsurface.h | 0
tools/pymol_asphere/src/m_constants.h | 0
tools/pymol_asphere/src/misc.cpp | 0
tools/pymol_asphere/src/misc.h | 0
tools/pymol_asphere/src/miscm.cpp | 0
tools/pymol_asphere/src/miscm.h | 0
tools/pymol_asphere/src/spherical.cpp | 0
tools/pymol_asphere/src/spherical.h | 0
tools/xmovie/control.c | 0
tools/xmovie/dummy.c | 0
tools/xmovie/hpsort.c | 0
tools/xmovie/read.c | 0
tools/xmovie/resource.h | 0
tools/xmovie/scene.c | 0
tools/xmovie/toascii.c | 0
tools/xmovie/tobinary.c | 0
tools/xmovie/version.c | 0
tools/xmovie/xmovie.c | 0
tools/xmovie/xmovie.h | 0
6868 files changed, 1092516 insertions(+), 888059 deletions(-)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-science/packages/lammps.git
More information about the debian-science-commits
mailing list