[lammps] 01/12: Merge tag 'upstream/0_20151116.git27798d4'
Anton Gladky
gladk at moszumanska.debian.org
Wed Nov 18 21:19:40 UTC 2015
This is an automated email from the git hooks/post-receive script.
gladk pushed a commit to branch master
in repository lammps.
commit 0438b9c2de7393d222e9326f6c366b2571433129
Merge: ff7d03f 7ff7818
Author: Anton Gladky <gladk at debian.org>
Date: Tue Nov 17 22:24:42 2015 +0100
Merge tag 'upstream/0_20151116.git27798d4'
Upstream version 0~20151116.git27798d4
bench/Cu_u3.eam | 2 +-
bench/POTENTIALS/in.dpd | 2 +-
bench/README | 2 +-
bench/in.chute.scaled | 2 +-
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.1Feb14.chain.fixed.linux.1 | 63 -
bench/log.1Feb14.chain.fixed.linux.4 | 63 -
bench/log.1Feb14.chain.scaled.linux.4 | 79 -
bench/log.1Feb14.chute.fixed.linux.1 | 65 -
bench/log.1Feb14.chute.fixed.linux.4 | 65 -
bench/log.1Feb14.chute.scaled.linux.4 | 75 -
bench/log.1Feb14.eam.fixed.linux.1 | 67 -
bench/log.1Feb14.eam.fixed.linux.4 | 67 -
bench/log.1Feb14.eam.scaled.linux.4 | 67 -
bench/log.1Feb14.lj.fixed.linux.1 | 64 -
bench/log.1Feb14.lj.fixed.linux.4 | 64 -
bench/log.1Feb14.lj.scaled.linux.4 | 64 -
bench/log.1Feb14.rhodo.fixed.linux.1 | 109 -
bench/log.1Feb14.rhodo.fixed.linux.4 | 109 -
bench/log.1Feb14.rhodo.scaled.linux.4 | 130 -
doc/Eqs/compute_saed1.jpg | Bin 0 -> 1471 bytes
doc/Eqs/compute_saed1.tex | 10 +
doc/Eqs/compute_saed2.jpg | Bin 0 -> 4911 bytes
doc/Eqs/compute_saed2.tex | 9 +
doc/Eqs/compute_saed3.jpg | Bin 0 -> 7048 bytes
doc/Eqs/compute_saed3.tex | 10 +
doc/Eqs/compute_xrd1.jpg | Bin 0 -> 2363 bytes
doc/Eqs/compute_xrd1.tex | 10 +
doc/Eqs/compute_xrd2.jpg | Bin 0 -> 4778 bytes
doc/Eqs/compute_xrd2.tex | 9 +
doc/Eqs/compute_xrd3.jpg | Bin 0 -> 4745 bytes
doc/Eqs/compute_xrd3.tex | 9 +
doc/Eqs/compute_xrd4.jpg | Bin 0 -> 2278 bytes
doc/Eqs/compute_xrd4.tex | 9 +
doc/Eqs/compute_xrd5.jpg | Bin 0 -> 7603 bytes
doc/Eqs/compute_xrd5.tex | 10 +
doc/Eqs/hexorder.jpg | Bin 0 -> 16870 bytes
doc/Eqs/hexorder.tex | 8 +
doc/Eqs/orientorder.jpg | Bin 0 -> 34695 bytes
doc/Eqs/orientorder.tex | 12 +
doc/Eqs/pair_mgpt.jpg | Bin 0 -> 12874 bytes
doc/Eqs/pair_mgpt.tex | 12 +
doc/Eqs/pair_smtbq1.jpg | Bin 0 -> 27807 bytes
doc/Eqs/pair_smtbq1.tex | 13 +
doc/Eqs/pair_smtbq2.jpg | Bin 0 -> 15544 bytes
doc/Eqs/pair_smtbq2.tex | 12 +
doc/Eqs/pair_smtbq3.jpg | Bin 0 -> 6832 bytes
doc/Eqs/pair_smtbq3.tex | 10 +
doc/Eqs/pair_vashishta.jpg | Bin 0 -> 73306 bytes
doc/Eqs/pair_vashishta.tex | 22 +
doc/Eqs/polymorphic1.jpg | Bin 0 -> 9186 bytes
doc/Eqs/polymorphic1.tex | 9 +
doc/Eqs/polymorphic2.jpg | Bin 0 -> 7156 bytes
doc/Eqs/polymorphic2.tex | 10 +
doc/Eqs/polymorphic3.jpg | Bin 0 -> 2425 bytes
doc/Eqs/polymorphic3.tex | 10 +
doc/Eqs/polymorphic4.jpg | Bin 0 -> 27028 bytes
doc/Eqs/polymorphic4.tex | 17 +
doc/Eqs/polymorphic5.jpg | Bin 0 -> 30052 bytes
doc/Eqs/polymorphic5.tex | 17 +
doc/Eqs/polymorphic6.jpg | Bin 0 -> 9063 bytes
doc/Eqs/polymorphic6.tex | 13 +
doc/Eqs/polymorphic7.jpg | Bin 0 -> 58111 bytes
doc/Eqs/polymorphic7.tex | 25 +
doc/Eqs/polymorphic8.jpg | Bin 0 -> 10249 bytes
doc/Eqs/polymorphic8.tex | 13 +
doc/Eqs/polymorphic9.jpg | Bin 0 -> 13704 bytes
doc/Eqs/polymorphic9.tex | 17 +
doc/JPG/qbmsst_init.jpg | Bin 0 -> 38407 bytes
doc/JPG/qbmsst_shock.jpg | Bin 0 -> 79334 bytes
doc/JPG/saed_ewald_intersect.jpg | Bin 0 -> 112619 bytes
doc/JPG/saed_ewald_intersect_small.jpg | Bin 0 -> 41372 bytes
doc/JPG/saed_mesh.jpg | Bin 0 -> 110946 bytes
doc/JPG/saed_mesh_small.jpg | Bin 0 -> 43053 bytes
doc/JPG/xrd_mesh.jpg | Bin 0 -> 121055 bytes
doc/JPG/xrd_mesh_small.jpg | Bin 0 -> 46491 bytes
doc/Manual.html | 80 +-
doc/Manual.html.html | 318 +
doc/Manual.pdf | Bin 9325726 -> 10368659 bytes
doc/Manual.txt | 63 +-
doc/PDF/SMD_LAMMPS_userguide.pdf | Bin 0 -> 3435420 bytes
doc/{USER/sph => PDF}/SPH_LAMMPS_userguide.pdf | Bin
doc/PDF/colvars-refman-lammps.pdf | Bin 528423 -> 632477 bytes
doc/Section_accelerate.html | 809 +-
doc/Section_accelerate.txt | 40 +-
doc/Section_commands.html | 2010 +-
doc/Section_commands.txt | 198 +-
doc/Section_errors.html | 15764 ++-
doc/Section_errors.txt | 2076 +-
doc/Section_example.html | 473 +-
doc/Section_example.txt | 11 +-
doc/Section_history.html | 394 +-
doc/Section_howto.html | 4129 +-
doc/Section_howto.txt | 259 +-
doc/Section_intro.html | 1079 +-
doc/Section_intro.txt | 38 +-
doc/Section_modify.html | 1645 +-
doc/Section_modify.txt | 9 +
doc/Section_packages.html | 1950 +-
doc/Section_packages.txt | 336 +-
doc/Section_perf.html | 314 +-
doc/Section_python.html | 1401 +-
doc/Section_python.txt | 293 +-
doc/Section_start.html | 2808 +-
doc/Section_start.txt | 304 +-
doc/Section_tools.html | 1123 +-
doc/_images/angle_charmm.jpg | Bin 0 -> 3932 bytes
doc/_images/angle_class2.jpg | Bin 0 -> 16202 bytes
doc/_images/angle_cosine.jpg | Bin 0 -> 2380 bytes
doc/_images/angle_cosine_delta.jpg | Bin 0 -> 2576 bytes
doc/_images/angle_cosine_periodic.jpg | Bin 0 -> 3362 bytes
doc/_images/angle_cosine_shift.jpg | Bin 0 -> 3933 bytes
doc/_images/angle_cosine_shift_exp.jpg | Bin 0 -> 7884 bytes
doc/_images/angle_cosine_squared.jpg | Bin 0 -> 3265 bytes
doc/_images/angle_dipole_gamma.jpg | Bin 0 -> 2709 bytes
doc/_images/angle_dipole_potential.jpg | Bin 0 -> 2616 bytes
doc/_images/angle_dipole_torque.jpg | Bin 0 -> 5110 bytes
doc/_images/angle_fourier.jpg | Bin 0 -> 4618 bytes
doc/_images/angle_fourier_simple.jpg | Bin 0 -> 2761 bytes
doc/_images/angle_harmonic.jpg | Bin 0 -> 2005 bytes
doc/_images/angle_quartic.jpg | Bin 0 -> 5273 bytes
doc/_images/atc_nanotube.jpg | Bin 0 -> 13402 bytes
doc/_images/balance_nonuniform.jpg | Bin 0 -> 78857 bytes
doc/_images/balance_rcb.jpg | Bin 0 -> 72941 bytes
doc/_images/balance_uniform.jpg | Bin 0 -> 79281 bytes
doc/_images/bond_class2.jpg | Bin 0 -> 5142 bytes
doc/_images/bond_fene.jpg | Bin 0 -> 8322 bytes
doc/_images/bond_fene_expand.jpg | Bin 0 -> 11506 bytes
doc/_images/bond_harmonic.jpg | Bin 0 -> 1861 bytes
doc/_images/bond_harmonic_shift.jpg | Bin 0 -> 5078 bytes
doc/_images/bond_harmonic_shift_cut.jpg | Bin 0 -> 5184 bytes
doc/_images/bond_morse.jpg | Bin 0 -> 2509 bytes
doc/_images/bond_nonlinear.jpg | Bin 0 -> 3593 bytes
doc/_images/bond_quartic.jpg | Bin 0 -> 9554 bytes
doc/_images/bondswap.jpg | Bin 0 -> 10548 bytes
doc/_images/box.jpg | Bin 0 -> 11093 bytes
doc/_images/box_inverse.jpg | Bin 0 -> 10250 bytes
doc/_images/centro_symmetry.jpg | Bin 0 -> 4111 bytes
doc/_images/cna_cutoff1.jpg | Bin 0 -> 13431 bytes
doc/_images/cna_cutoff2.jpg | Bin 0 -> 2518 bytes
doc/_images/compute_fep_bar.jpg | Bin 0 -> 18106 bytes
doc/_images/compute_fep_fdti.jpg | Bin 0 -> 15544 bytes
doc/_images/compute_fep_fep.jpg | Bin 0 -> 18055 bytes
doc/_images/compute_fep_lambda.jpg | Bin 0 -> 10511 bytes
doc/_images/compute_fep_ti.jpg | Bin 0 -> 18149 bytes
doc/_images/compute_fep_u.jpg | Bin 0 -> 9337 bytes
doc/_images/compute_fep_vol.jpg | Bin 0 -> 15209 bytes
doc/_images/compute_gyration.jpg | Bin 0 -> 3658 bytes
doc/_images/compute_msd_nongauss.jpg | Bin 0 -> 7277 bytes
doc/_images/compute_saed1.jpg | Bin 0 -> 1471 bytes
doc/_images/compute_saed2.jpg | Bin 0 -> 4911 bytes
doc/_images/compute_saed3.jpg | Bin 0 -> 7048 bytes
doc/_images/compute_sna_atom1.jpg | Bin 0 -> 19001 bytes
doc/_images/compute_sna_atom2.jpg | Bin 0 -> 17114 bytes
doc/_images/compute_sna_atom3.jpg | Bin 0 -> 19644 bytes
doc/_images/compute_sna_atom4.jpg | Bin 0 -> 35933 bytes
doc/_images/compute_sna_atom5.jpg | Bin 0 -> 14734 bytes
doc/_images/compute_sna_atom6.jpg | Bin 0 -> 17274 bytes
doc/_images/compute_xrd1.jpg | Bin 0 -> 2363 bytes
doc/_images/compute_xrd2.jpg | Bin 0 -> 4778 bytes
doc/_images/compute_xrd3.jpg | Bin 0 -> 4745 bytes
doc/_images/compute_xrd4.jpg | Bin 0 -> 2278 bytes
doc/_images/compute_xrd5.jpg | Bin 0 -> 7603 bytes
doc/_images/coul_soft.jpg | Bin 0 -> 12676 bytes
doc/_images/dihedral_charmm.jpg | Bin 0 -> 3118 bytes
doc/_images/dihedral_class2.jpg | Bin 0 -> 47795 bytes
doc/_images/dihedral_cosine_shift_exp.jpg | Bin 0 -> 8004 bytes
doc/_images/dihedral_fourier.jpg | Bin 0 -> 4544 bytes
doc/_images/dihedral_harmonic.jpg | Bin 0 -> 2937 bytes
doc/_images/dihedral_helix.jpg | Bin 0 -> 6810 bytes
doc/_images/dihedral_multi_harmonic.jpg | Bin 0 -> 3103 bytes
doc/_images/dihedral_nharmonic.jpg | Bin 0 -> 3231 bytes
doc/_images/dihedral_opls.jpg | Bin 0 -> 10755 bytes
doc/_images/dihedral_quadratic.jpg | Bin 0 -> 2067 bytes
doc/_images/dihedral_sign.jpg | Bin 0 -> 19297 bytes
doc/_images/dreiding_hbond.jpg | Bin 0 -> 21369 bytes
doc/_images/dump1.jpg | Bin 0 -> 608016 bytes
doc/_images/dump2.jpg | Bin 0 -> 172441 bytes
doc/_images/eff_ECP1.jpg | Bin 0 -> 5146 bytes
doc/_images/eff_ECP2.jpg | Bin 0 -> 9744 bytes
doc/_images/eff_KE.jpg | Bin 0 -> 3385 bytes
doc/_images/eff_NN.jpg | Bin 0 -> 4153 bytes
doc/_images/eff_Ne.jpg | Bin 0 -> 6425 bytes
doc/_images/eff_Pauli.jpg | Bin 0 -> 5676 bytes
doc/_images/eff_ee.jpg | Bin 0 -> 6829 bytes
doc/_images/eff_energy_expression.jpg | Bin 0 -> 9538 bytes
doc/_images/fix_box_relax1.jpg | Bin 0 -> 3375 bytes
doc/_images/fix_box_relax2.jpg | Bin 0 -> 3029 bytes
doc/_images/fix_gld1.jpg | Bin 0 -> 14274 bytes
doc/_images/fix_lb_fluid_boltzmann.jpg | Bin 0 -> 4643 bytes
doc/_images/fix_lb_fluid_fluidforce.jpg | Bin 0 -> 2358 bytes
doc/_images/fix_lb_fluid_gammadefault.jpg | Bin 0 -> 4793 bytes
doc/_images/fix_lb_fluid_navierstokes.jpg | Bin 0 -> 9311 bytes
doc/_images/fix_lb_fluid_properties.jpg | Bin 0 -> 3471 bytes
doc/_images/fix_lb_fluid_stress.jpg | Bin 0 -> 2530 bytes
doc/_images/fix_lb_fluid_viscosity.jpg | Bin 0 -> 6522 bytes
doc/_images/fix_nh1.jpg | Bin 0 -> 31088 bytes
doc/_images/fix_nphug.jpg | Bin 0 -> 7506 bytes
doc/_images/fix_orient_fcc.jpg | Bin 0 -> 26005 bytes
doc/_images/fix_pimd.jpg | Bin 0 -> 14569 bytes
doc/_images/fix_rattle_constraints.jpg | Bin 0 -> 4556 bytes
doc/_images/fix_rattle_rij.jpg | Bin 0 -> 1812 bytes
doc/_images/fix_spring_rg.jpg | Bin 0 -> 16204 bytes
doc/_images/fix_ti_rs_force.jpg | Bin 0 -> 1777 bytes
doc/_images/fix_ti_rs_function_1.jpg | Bin 0 -> 2534 bytes
doc/_images/fix_ti_rs_function_2.jpg | Bin 0 -> 3233 bytes
doc/_images/fix_ti_rs_function_3.jpg | Bin 0 -> 4801 bytes
doc/_images/fix_ti_spring_force.jpg | Bin 0 -> 3627 bytes
doc/_images/fix_ti_spring_function_1.jpg | Bin 0 -> 1040 bytes
doc/_images/fix_ti_spring_function_2.jpg | Bin 0 -> 5753 bytes
doc/_images/fix_ttm.jpg | Bin 0 -> 5869 bytes
doc/_images/fix_ttm_blast.jpg | Bin 0 -> 4449 bytes
doc/_images/fix_ttm_blast1.jpg | Bin 0 -> 8657 bytes
doc/_images/fix_ttm_ce.jpg | Bin 0 -> 7446 bytes
doc/_images/fix_ttm_mod.jpg | Bin 0 -> 10179 bytes
doc/_images/fix_wall_colloid.jpg | Bin 0 -> 17879 bytes
doc/_images/fix_wall_harmonic.jpg | Bin 0 -> 2413 bytes
doc/_images/fix_wall_lj1043.jpg | Bin 0 -> 10996 bytes
doc/_images/fix_wall_lj93.jpg | Bin 0 -> 4883 bytes
doc/_images/fld.jpg | Bin 0 -> 3640 bytes
doc/_images/fld2.jpg | Bin 0 -> 4161 bytes
doc/_images/heat_flux_J.jpg | Bin 0 -> 15205 bytes
doc/_images/heat_flux_k.jpg | Bin 0 -> 8760 bytes
doc/_images/hop1.jpg | Bin 0 -> 52996 bytes
doc/_images/hop2.jpg | Bin 0 -> 53149 bytes
doc/_images/improper_class2.jpg | Bin 0 -> 15728 bytes
doc/_images/improper_cossq.jpg | Bin 0 -> 2995 bytes
doc/_images/improper_cvff.jpg | Bin 0 -> 2826 bytes
doc/_images/improper_fourier.jpg | Bin 0 -> 4746 bytes
doc/_images/improper_harmonic.jpg | Bin 0 -> 2005 bytes
doc/_images/improper_ring.jpg | Bin 0 -> 11101 bytes
doc/_images/improper_umbrella.jpg | Bin 0 -> 9598 bytes
doc/_images/lj_soft.jpg | Bin 0 -> 12313 bytes
doc/_images/min_energy.jpg | Bin 0 -> 19599 bytes
doc/_images/pair_adp.jpg | Bin 0 -> 20391 bytes
doc/_images/pair_airebo.jpg | Bin 0 -> 9380 bytes
doc/_images/pair_beck.jpg | Bin 0 -> 9451 bytes
doc/_images/pair_bop.jpg | Bin 0 -> 13202 bytes
doc/_images/pair_born.jpg | Bin 0 -> 5099 bytes
doc/_images/pair_buck.jpg | Bin 0 -> 2861 bytes
doc/_images/pair_charmm.jpg | Bin 0 -> 25138 bytes
doc/_images/pair_class2.jpg | Bin 0 -> 5093 bytes
doc/_images/pair_cmm.jpg | Bin 0 -> 11921 bytes
doc/_images/pair_colloid_cc.jpg | Bin 0 -> 43501 bytes
doc/_images/pair_colloid_cs.jpg | Bin 0 -> 11599 bytes
doc/_images/pair_colloid_ss.jpg | Bin 0 -> 5573 bytes
doc/_images/pair_comb1.jpg | Bin 0 -> 18596 bytes
doc/_images/pair_comb2.jpg | Bin 0 -> 39601 bytes
doc/_images/pair_coul_diel.jpg | Bin 0 -> 10587 bytes
doc/_images/pair_coul_dsf.jpg | Bin 0 -> 12261 bytes
doc/_images/pair_coul_soft.jpg | Bin 0 -> 11309 bytes
doc/_images/pair_coul_wolf.jpg | Bin 0 -> 8758 bytes
doc/_images/pair_coulomb.jpg | Bin 0 -> 2505 bytes
doc/_images/pair_cs.jpg | Bin 0 -> 3500 bytes
doc/_images/pair_debye.jpg | Bin 0 -> 3641 bytes
doc/_images/pair_dipole.jpg | Bin 0 -> 47516 bytes
doc/_images/pair_dipole_sf.jpg | Bin 0 -> 93270 bytes
doc/_images/pair_dipole_sf2.jpg | Bin 0 -> 40855 bytes
doc/_images/pair_dpd.jpg | Bin 0 -> 12376 bytes
doc/_images/pair_eam.jpg | Bin 0 -> 6693 bytes
doc/_images/pair_eam_fs.jpg | Bin 0 -> 6547 bytes
doc/_images/pair_edip.jpg | Bin 0 -> 42939 bytes
doc/_images/pair_eim1.jpg | Bin 0 -> 6824 bytes
doc/_images/pair_eim2.jpg | Bin 0 -> 8494 bytes
doc/_images/pair_eim3.jpg | Bin 0 -> 40993 bytes
doc/_images/pair_gauss.jpg | Bin 0 -> 2835 bytes
doc/_images/pair_gauss_cut.jpg | Bin 0 -> 3855 bytes
doc/_images/pair_gayberne.jpg | Bin 0 -> 13814 bytes
doc/_images/pair_gayberne2.jpg | Bin 0 -> 4203 bytes
doc/_images/pair_gran_hertz.jpg | Bin 0 -> 12512 bytes
doc/_images/pair_gran_hooke.jpg | Bin 0 -> 5737 bytes
doc/_images/pair_gromacs.jpg | Bin 0 -> 50447 bytes
doc/_images/pair_hbond_dreiding.jpg | Bin 0 -> 32047 bytes
doc/_images/pair_lj.jpg | Bin 0 -> 4547 bytes
doc/_images/pair_lj96.jpg | Bin 0 -> 4851 bytes
doc/_images/pair_lj_cubic.jpg | Bin 0 -> 9352 bytes
doc/_images/pair_lj_expand.jpg | Bin 0 -> 5905 bytes
doc/_images/pair_lj_sf.jpg | Bin 0 -> 15535 bytes
doc/_images/pair_lj_smooth.jpg | Bin 0 -> 11580 bytes
doc/_images/pair_lj_smooth_linear.jpg | Bin 0 -> 10372 bytes
doc/_images/pair_lj_soft.jpg | Bin 0 -> 17984 bytes
doc/_images/pair_lubricate.jpg | Bin 0 -> 14321 bytes
doc/_images/pair_meam.jpg | Bin 0 -> 6110 bytes
doc/_images/pair_meam_spline.jpg | Bin 0 -> 10530 bytes
doc/_images/pair_meam_sw_spline.jpg | Bin 0 -> 17215 bytes
doc/_images/pair_mgpt.jpg | Bin 0 -> 12874 bytes
doc/_images/pair_mie.jpg | Bin 0 -> 4686 bytes
doc/_images/pair_mie2.jpg | Bin 0 -> 6502 bytes
doc/_images/pair_morse.jpg | Bin 0 -> 4042 bytes
doc/_images/pair_nb3b_harmonic.jpg | Bin 0 -> 1918 bytes
doc/_images/pair_nm.jpg | Bin 0 -> 6304 bytes
doc/_images/pair_resquared.jpg | Bin 0 -> 2683 bytes
doc/_images/pair_resquared2.jpg | Bin 0 -> 2303 bytes
doc/_images/pair_resquared3.jpg | Bin 0 -> 1156 bytes
doc/_images/pair_resquared4.jpg | Bin 0 -> 4779 bytes
doc/_images/pair_smtbq1.jpg | Bin 0 -> 27807 bytes
doc/_images/pair_smtbq2.jpg | Bin 0 -> 15544 bytes
doc/_images/pair_smtbq3.jpg | Bin 0 -> 6832 bytes
doc/_images/pair_snap.jpg | Bin 0 -> 32505 bytes
doc/_images/pair_soft.jpg | Bin 0 -> 4085 bytes
doc/_images/pair_sph_ideal.jpg | Bin 0 -> 1540 bytes
doc/_images/pair_sph_tait.jpg | Bin 0 -> 2303 bytes
doc/_images/pair_srp1.jpg | Bin 0 -> 3537 bytes
doc/_images/pair_srp2.jpg | Bin 0 -> 5648 bytes
doc/_images/pair_sw.jpg | Bin 0 -> 28707 bytes
doc/_images/pair_tersoff_1.jpg | Bin 0 -> 36584 bytes
doc/_images/pair_tersoff_2.jpg | Bin 0 -> 13756 bytes
doc/_images/pair_tersoff_mod.jpg | Bin 0 -> 91727 bytes
doc/_images/pair_tersoff_zbl.jpg | Bin 0 -> 392677 bytes
doc/_images/pair_vashishta.jpg | Bin 0 -> 73306 bytes
doc/_images/pair_yukawa.jpg | Bin 0 -> 2189 bytes
doc/_images/pair_yukawa_colloid.jpg | Bin 0 -> 3067 bytes
doc/_images/pair_zbl.jpg | Bin 0 -> 32209 bytes
doc/_images/pimd.jpg | Bin 0 -> 29560 bytes
doc/_images/polymorphic1.jpg | Bin 0 -> 9186 bytes
doc/_images/polymorphic2.jpg | Bin 0 -> 7156 bytes
doc/_images/polymorphic3.jpg | Bin 0 -> 2425 bytes
doc/_images/polymorphic4.jpg | Bin 0 -> 27028 bytes
doc/_images/polymorphic5.jpg | Bin 0 -> 30052 bytes
doc/_images/polymorphic6.jpg | Bin 0 -> 9063 bytes
doc/_images/polymorphic7.jpg | Bin 0 -> 58111 bytes
doc/_images/polymorphic8.jpg | Bin 0 -> 10249 bytes
doc/_images/polymorphic9.jpg | Bin 0 -> 13704 bytes
doc/_images/pressure.jpg | Bin 0 -> 4097 bytes
doc/_images/pressure_tensor.jpg | Bin 0 -> 5038 bytes
doc/_images/qbmsst_init.jpg | Bin 0 -> 38407 bytes
doc/_images/qbmsst_shock.jpg | Bin 0 -> 79334 bytes
doc/_images/rhodo_staggered.jpg | Bin 0 -> 42303 bytes
doc/_images/rotate.jpg | Bin 0 -> 17991 bytes
doc/_images/saed_ewald_intersect.jpg | Bin 0 -> 112619 bytes
doc/_images/saed_mesh.jpg | Bin 0 -> 110946 bytes
doc/_images/screenshot_atomeye.jpg | Bin 0 -> 426608 bytes
doc/_images/screenshot_gl.jpg | Bin 0 -> 306252 bytes
doc/_images/screenshot_pymol.jpg | Bin 0 -> 417093 bytes
doc/_images/screenshot_vmd.jpg | Bin 0 -> 327211 bytes
doc/_images/sinusoid.jpg | Bin 0 -> 128596 bytes
doc/_images/stress_tensor.jpg | Bin 0 -> 22403 bytes
doc/_images/transform.jpg | Bin 0 -> 60790 bytes
doc/_images/umbrella.jpg | Bin 0 -> 20442 bytes
doc/_images/xrd_mesh.jpg | Bin 0 -> 121055 bytes
doc/_static/ajax-loader.gif | Bin 0 -> 673 bytes
doc/_static/basic.css | 599 +
doc/_static/comment-bright.png | Bin 0 -> 3500 bytes
doc/_static/comment-close.png | Bin 0 -> 3578 bytes
doc/_static/comment.png | Bin 0 -> 3445 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/doctools.js | 263 +
doc/_static/down-pressed.png | Bin 0 -> 347 bytes
doc/_static/down.png | Bin 0 -> 347 bytes
doc/_static/file.png | Bin 0 -> 358 bytes
doc/_static/fonts/FontAwesome.otf | Bin 0 -> 62856 bytes
doc/_static/fonts/Inconsolata-Bold.ttf | Bin 0 -> 47064 bytes
doc/_static/fonts/Inconsolata.ttf | Bin 0 -> 63184 bytes
doc/_static/fonts/Lato-Bold.ttf | Bin 0 -> 82368 bytes
doc/_static/fonts/Lato-Regular.ttf | Bin 0 -> 81980 bytes
doc/_static/fonts/RobotoSlab-Bold.ttf | Bin 0 -> 36596 bytes
doc/_static/fonts/RobotoSlab-Regular.ttf | Bin 0 -> 36276 bytes
doc/_static/fonts/fontawesome-webfont.eot | Bin 0 -> 38205 bytes
doc/_static/fonts/fontawesome-webfont.svg | 414 +
doc/_static/fonts/fontawesome-webfont.ttf | Bin 0 -> 80652 bytes
doc/_static/fonts/fontawesome-webfont.woff | Bin 0 -> 44432 bytes
doc/_static/jquery-1.11.1.js | 10308 ++
doc/_static/jquery.js | 4 +
doc/_static/js/modernizr.min.js | 4 +
doc/_static/js/theme.js | 113 +
doc/_static/minus.png | Bin 0 -> 173 bytes
doc/_static/plus.png | Bin 0 -> 173 bytes
doc/_static/pygments.css | 63 +
doc/_static/searchtools.js | 622 +
.../lightbox2-customize/jquery-noconflict.js | 1 +
.../LightBox2/lightbox2/css/lightbox.css | 210 +
.../LightBox2/lightbox2/img/close.png | Bin 0 -> 280 bytes
.../LightBox2/lightbox2/img/loading.gif | Bin 0 -> 8476 bytes
.../LightBox2/lightbox2/img/next.png | Bin 0 -> 1350 bytes
.../LightBox2/lightbox2/img/prev.png | Bin 0 -> 1360 bytes
.../LightBox2/lightbox2/js/jquery-1.11.0.min.js | 4 +
.../LightBox2/lightbox2/js/lightbox.min.js | 10 +
.../LightBox2/lightbox2/js/lightbox.min.map | 1 +
doc/_static/underscore-1.3.1.js | 999 +
doc/_static/underscore.js | 31 +
doc/_static/up-pressed.png | Bin 0 -> 345 bytes
doc/_static/up.png | Bin 0 -> 345 bytes
doc/_static/websupport.js | 808 +
doc/accelerate_cuda.html | 498 +-
doc/accelerate_cuda.txt | 2 +-
doc/accelerate_gpu.html | 542 +-
doc/accelerate_gpu.txt | 2 +-
doc/accelerate_intel.html | 719 +-
doc/accelerate_intel.txt | 386 +-
doc/accelerate_kokkos.html | 924 +-
doc/accelerate_kokkos.txt | 287 +-
doc/accelerate_omp.html | 472 +-
doc/accelerate_omp.txt | 145 +-
doc/accelerate_opt.html | 304 +-
doc/accelerate_opt.txt | 49 +-
doc/angle_charmm.html | 333 +-
doc/angle_charmm.txt | 1 +
doc/angle_class2.html | 381 +-
doc/angle_coeff.html | 337 +-
doc/angle_cosine.html | 316 +-
doc/angle_cosine_delta.html | 326 +-
doc/angle_cosine_periodic.html | 346 +-
doc/angle_cosine_shift.html | 309 +-
doc/angle_cosine_shift_exp.html | 341 +-
doc/angle_cosine_squared.html | 325 +-
doc/angle_dipole.html | 406 +-
doc/angle_fourier.html | 318 +-
doc/angle_fourier_simple.html | 316 +-
doc/angle_harmonic.html | 330 +-
doc/angle_harmonic.txt | 1 +
doc/angle_hybrid.html | 328 +-
doc/angle_none.html | 236 +-
doc/angle_quartic.html | 330 +-
doc/angle_sdk.html | 300 +-
doc/angle_style.html | 345 +-
doc/angle_table.html | 394 +-
doc/atom_modify.html | 412 +-
doc/atom_modify.txt | 24 +-
doc/atom_style.html | 620 +-
doc/atom_style.txt | 13 +-
doc/balance.html | 593 +-
doc/balance.txt | 2 +-
doc/body.html | 388 +-
doc/bond_class2.html | 334 +-
doc/bond_coeff.html | 332 +-
doc/bond_fene.html | 344 +-
doc/bond_fene.txt | 1 +
doc/bond_fene_expand.html | 350 +-
doc/bond_harmonic.html | 323 +-
doc/bond_harmonic.txt | 1 +
doc/bond_harmonic_shift.html | 329 +-
doc/bond_harmonic_shift_cut.html | 331 +-
doc/bond_hybrid.html | 304 +-
doc/bond_morse.html | 322 +-
doc/bond_none.html | 236 +-
doc/bond_nonlinear.html | 330 +-
doc/bond_quartic.html | 355 +-
doc/bond_style.html | 354 +-
doc/bond_table.html | 394 +-
doc/boundary.html | 324 +-
doc/boundary.txt | 22 +-
doc/box.html | 287 +-
doc/change_box.html | 648 +-
doc/clear.html | 247 +-
doc/comm_modify.html | 400 +-
doc/comm_modify.txt | 42 +-
doc/comm_style.html | 283 +-
doc/compute.html | 593 +-
doc/compute.txt | 7 +-
doc/compute_ackland_atom.html | 304 +-
doc/compute_angle_local.html | 293 +-
doc/compute_angmom_chunk.html | 270 +
doc/compute_angmom_chunk.txt | 89 +
doc/compute_basal_atom.html | 300 +-
doc/compute_body_local.html | 317 +-
doc/compute_bond_local.html | 308 +-
doc/compute_centro_atom.html | 351 +-
doc/compute_chunk_atom.html | 968 +-
doc/compute_cluster_atom.html | 276 +-
doc/compute_cna_atom.html | 334 +-
doc/compute_com.html | 286 +-
doc/compute_com.txt | 2 +-
doc/compute_com_chunk.html | 338 +-
doc/compute_contact_atom.html | 276 +-
doc/compute_coord_atom.html | 317 +-
doc/compute_damage_atom.html | 304 +-
doc/compute_dihedral_local.html | 282 +-
doc/compute_dilatation_atom.html | 303 +-
doc/compute_displace_atom.html | 296 +-
doc/compute_erotate_asphere.html | 295 +-
doc/compute_erotate_rigid.html | 294 +-
doc/compute_erotate_sphere.html | 298 +-
doc/compute_erotate_sphere_atom.html | 293 +-
doc/compute_event_displace.html | 287 +-
doc/compute_fep.html | 624 +-
doc/compute_fep.txt | 2 +-
doc/compute_group_group.html | 348 +-
doc/compute_gyration.html | 303 +-
doc/compute_gyration.txt | 2 +-
doc/compute_gyration_chunk.html | 350 +-
doc/compute_heat_flux.html | 441 +-
doc/compute_heat_flux.txt | 2 +-
doc/compute_hexorder_atom.html | 125 +
doc/compute_hexorder_atom.txt | 116 +
doc/compute_improper_local.html | 282 +-
doc/compute_inertia_chunk.html | 338 +-
doc/compute_inertia_chunk.txt | 2 +-
doc/compute_ke.html | 297 +-
doc/compute_ke_atom.html | 285 +-
doc/compute_ke_atom_eff.html | 309 +-
doc/compute_ke_eff.html | 304 +-
doc/compute_ke_rigid.html | 295 +-
doc/compute_meso_e_atom.html | 280 +-
doc/compute_meso_rho_atom.html | 296 +-
doc/compute_meso_t_atom.html | 283 +-
doc/compute_modify.html | 300 +-
doc/compute_msd.html | 322 +-
doc/compute_msd.txt | 2 +-
doc/compute_msd_chunk.html | 383 +-
doc/compute_msd_chunk.txt | 2 +-
doc/compute_msd_nongauss.html | 306 +-
doc/compute_omega_chunk.html | 270 +
doc/compute_omega_chunk.txt | 89 +
doc/compute_orientorder_atom.txt | 119 +
doc/compute_pair.html | 320 +-
doc/compute_pair_local.html | 341 +-
doc/compute_pe.html | 372 +-
doc/compute_pe.txt | 20 +-
doc/compute_pe_atom.html | 331 +-
doc/compute_plasticity_atom.html | 311 +-
doc/compute_pressure.html | 414 +-
doc/compute_pressure.txt | 20 +-
doc/compute_property_atom.html | 487 +-
doc/compute_property_chunk.html | 362 +-
doc/compute_property_local.html | 406 +-
doc/compute_rdf.html | 409 +-
doc/compute_rdf.txt | 14 +-
doc/compute_reduce.html | 453 +-
doc/compute_reduce.txt | 28 +-
doc/compute_saed.html | 364 +
doc/compute_saed.txt | 177 +
doc/compute_slice.html | 334 +-
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 | 530 +-
doc/compute_stress_atom.html | 411 +-
doc/compute_tally.html | 269 +
doc/compute_tally.txt | 85 +
doc/compute_temp.html | 366 +-
doc/compute_temp.txt | 21 +-
doc/compute_temp_asphere.html | 389 +-
doc/compute_temp_chunk.html | 493 +-
doc/compute_temp_chunk.txt | 19 +-
doc/compute_temp_com.html | 313 +-
doc/compute_temp_cs.html | 337 +-
doc/compute_temp_cs.txt | 16 +-
doc/compute_temp_deform.html | 356 +-
doc/compute_temp_deform_eff.html | 294 +-
doc/compute_temp_drude.html | 259 +
doc/compute_temp_drude.txt | 82 +
doc/compute_temp_eff.html | 323 +-
doc/compute_temp_partial.html | 360 +-
doc/compute_temp_partial.txt | 20 +-
doc/compute_temp_profile.html | 426 +-
doc/compute_temp_profile.txt | 11 +-
doc/compute_temp_ramp.html | 370 +-
doc/compute_temp_region.html | 333 +-
doc/compute_temp_region.txt | 8 +-
doc/compute_temp_region_eff.html | 287 +-
doc/compute_temp_rotate.html | 315 +-
doc/compute_temp_sphere.html | 381 +-
doc/compute_ti.html | 391 +-
doc/compute_torque_chunk.html | 337 +-
doc/compute_torque_chunk.txt | 2 +-
doc/compute_vacf.html | 295 +-
doc/compute_vcm_chunk.html | 316 +-
doc/compute_voronoi_atom.html | 405 +-
doc/compute_voronoi_atom.txt | 2 +-
doc/compute_xrd.html | 390 +
doc/compute_xrd.txt | 200 +
doc/create_atoms.html | 672 +-
doc/create_bonds.html | 343 +-
doc/create_box.html | 381 +-
doc/create_box.txt | 2 +-
doc/delete_atoms.html | 377 +-
doc/delete_atoms.txt | 2 +-
doc/delete_bonds.html | 389 +-
doc/dielectric.html | 255 +-
doc/dihedral_charmm.html | 357 +-
doc/dihedral_charmm.txt | 1 +
doc/dihedral_class2.html | 488 +-
doc/dihedral_coeff.html | 347 +-
doc/dihedral_cosine_shift_exp.html | 337 +-
doc/dihedral_fourier.html | 328 +-
doc/dihedral_harmonic.html | 338 +-
doc/dihedral_helix.html | 316 +-
doc/dihedral_hybrid.html | 328 +-
doc/dihedral_multi_harmonic.html | 321 +-
doc/dihedral_nharmonic.html | 322 +-
doc/dihedral_none.html | 236 +-
doc/dihedral_opls.html | 324 +-
doc/dihedral_opls.txt | 1 +
doc/dihedral_quadratic.html | 321 +-
doc/dihedral_style.html | 367 +-
doc/dihedral_table.html | 461 +-
doc/dimension.html | 271 +-
doc/displace_atoms.html | 408 +-
doc/displace_atoms.txt | 20 +-
doc/doc2/Eqs/.log | 30 +
doc/doc2/Eqs/angle_charmm.jpg | Bin 0 -> 3932 bytes
doc/doc2/Eqs/angle_charmm.tex | 9 +
doc/doc2/Eqs/angle_class2.jpg | Bin 0 -> 16202 bytes
doc/doc2/Eqs/angle_class2.tex | 12 +
doc/doc2/Eqs/angle_cosine.jpg | Bin 0 -> 2380 bytes
doc/doc2/Eqs/angle_cosine.tex | 9 +
doc/doc2/Eqs/angle_cosine_delta.jpg | Bin 0 -> 2576 bytes
doc/doc2/Eqs/angle_cosine_delta.tex | 9 +
doc/doc2/Eqs/angle_cosine_periodic.jpg | Bin 0 -> 3362 bytes
doc/doc2/Eqs/angle_cosine_periodic.tex | 9 +
doc/doc2/Eqs/angle_cosine_shift.jpg | Bin 0 -> 3933 bytes
doc/doc2/Eqs/angle_cosine_shift.tex | 9 +
doc/doc2/Eqs/angle_cosine_shift_exp.jpg | Bin 0 -> 7884 bytes
doc/doc2/Eqs/angle_cosine_shift_exp.tex | 13 +
doc/doc2/Eqs/angle_cosine_squared.jpg | Bin 0 -> 3265 bytes
doc/doc2/Eqs/angle_cosine_squared.tex | 9 +
doc/doc2/Eqs/angle_dipole_gamma.jpg | Bin 0 -> 2709 bytes
doc/doc2/Eqs/angle_dipole_gamma.tex | 9 +
doc/doc2/Eqs/angle_dipole_potential.jpg | Bin 0 -> 2616 bytes
doc/doc2/Eqs/angle_dipole_potential.tex | 9 +
doc/doc2/Eqs/angle_dipole_torque.jpg | Bin 0 -> 5110 bytes
doc/doc2/Eqs/angle_dipole_torque.tex | 9 +
doc/doc2/Eqs/angle_fourier.jpg | Bin 0 -> 4618 bytes
doc/doc2/Eqs/angle_fourier.tex | 9 +
doc/doc2/Eqs/angle_fourier_simple.jpg | Bin 0 -> 2761 bytes
doc/doc2/Eqs/angle_fourier_simple.tex | 9 +
doc/doc2/Eqs/angle_harmonic.jpg | Bin 0 -> 2005 bytes
doc/doc2/Eqs/angle_harmonic.tex | 9 +
doc/doc2/Eqs/angle_quartic.jpg | Bin 0 -> 5273 bytes
doc/doc2/Eqs/angle_quartic.tex | 9 +
doc/doc2/Eqs/bond_class2.jpg | Bin 0 -> 5142 bytes
doc/doc2/Eqs/bond_class2.tex | 9 +
doc/doc2/Eqs/bond_fene.jpg | Bin 0 -> 8322 bytes
doc/doc2/Eqs/bond_fene.tex | 11 +
doc/doc2/Eqs/bond_fene_expand.jpg | Bin 0 -> 11506 bytes
doc/doc2/Eqs/bond_fene_expand.tex | 13 +
doc/doc2/Eqs/bond_harmonic.jpg | Bin 0 -> 1861 bytes
doc/doc2/Eqs/bond_harmonic.tex | 9 +
doc/doc2/Eqs/bond_harmonic_shift.jpg | Bin 0 -> 5078 bytes
doc/doc2/Eqs/bond_harmonic_shift.tex | 9 +
doc/doc2/Eqs/bond_harmonic_shift_cut.jpg | Bin 0 -> 5184 bytes
doc/doc2/Eqs/bond_harmonic_shift_cut.tex | 9 +
doc/doc2/Eqs/bond_morse.jpg | Bin 0 -> 2509 bytes
doc/doc2/Eqs/bond_morse.tex | 10 +
doc/doc2/Eqs/bond_nonlinear.jpg | Bin 0 -> 3593 bytes
doc/doc2/Eqs/bond_nonlinear.tex | 9 +
doc/doc2/Eqs/bond_quartic.jpg | Bin 0 -> 9554 bytes
doc/doc2/Eqs/bond_quartic.tex | 11 +
doc/doc2/Eqs/box.jpg | Bin 0 -> 11093 bytes
doc/doc2/Eqs/box.tex | 14 +
doc/doc2/Eqs/box_inverse.jpg | Bin 0 -> 10250 bytes
doc/doc2/Eqs/box_inverse.tex | 14 +
doc/doc2/Eqs/centro_symmetry.jpg | Bin 0 -> 4111 bytes
doc/doc2/Eqs/centro_symmetry.tex | 9 +
doc/doc2/Eqs/cna_cutoff1.jpg | Bin 0 -> 13431 bytes
doc/doc2/Eqs/cna_cutoff1.tex | 14 +
doc/doc2/Eqs/cna_cutoff2.jpg | Bin 0 -> 2518 bytes
doc/doc2/Eqs/cna_cutoff2.tex | 12 +
doc/doc2/Eqs/compute_fep_bar.jpg | Bin 0 -> 18106 bytes
doc/doc2/Eqs/compute_fep_bar.tex | 7 +
doc/doc2/Eqs/compute_fep_fdti.jpg | Bin 0 -> 15544 bytes
doc/doc2/Eqs/compute_fep_fdti.tex | 10 +
doc/doc2/Eqs/compute_fep_fep.jpg | Bin 0 -> 18055 bytes
doc/doc2/Eqs/compute_fep_fep.tex | 9 +
doc/doc2/Eqs/compute_fep_lambda.jpg | Bin 0 -> 10511 bytes
doc/doc2/Eqs/compute_fep_lambda.tex | 10 +
doc/doc2/Eqs/compute_fep_ti.jpg | Bin 0 -> 18149 bytes
doc/doc2/Eqs/compute_fep_ti.tex | 10 +
doc/doc2/Eqs/compute_fep_u.jpg | Bin 0 -> 9337 bytes
doc/doc2/Eqs/compute_fep_u.tex | 7 +
doc/doc2/Eqs/compute_fep_vol.jpg | Bin 0 -> 15209 bytes
doc/doc2/Eqs/compute_fep_vol.tex | 9 +
doc/doc2/Eqs/compute_gyration.jpg | Bin 0 -> 3658 bytes
doc/doc2/Eqs/compute_gyration.tex | 9 +
doc/doc2/Eqs/compute_msd_nongauss.jpg | Bin 0 -> 7277 bytes
doc/doc2/Eqs/compute_msd_nongauss.tex | 9 +
doc/doc2/Eqs/compute_saed1.jpg | Bin 0 -> 1471 bytes
doc/doc2/Eqs/compute_saed1.tex | 10 +
doc/doc2/Eqs/compute_saed2.jpg | Bin 0 -> 4911 bytes
doc/doc2/Eqs/compute_saed2.tex | 9 +
doc/doc2/Eqs/compute_saed3.jpg | Bin 0 -> 7048 bytes
doc/doc2/Eqs/compute_saed3.tex | 10 +
doc/doc2/Eqs/compute_sna_atom1.jpg | Bin 0 -> 19001 bytes
doc/doc2/Eqs/compute_sna_atom1.tex | 11 +
doc/doc2/Eqs/compute_sna_atom2.jpg | Bin 0 -> 17114 bytes
doc/doc2/Eqs/compute_sna_atom2.tex | 11 +
doc/doc2/Eqs/compute_sna_atom3.jpg | Bin 0 -> 19644 bytes
doc/doc2/Eqs/compute_sna_atom3.tex | 16 +
doc/doc2/Eqs/compute_sna_atom4.jpg | Bin 0 -> 35933 bytes
doc/doc2/Eqs/compute_sna_atom4.tex | 14 +
doc/doc2/Eqs/compute_sna_atom5.jpg | Bin 0 -> 14734 bytes
doc/doc2/Eqs/compute_sna_atom5.tex | 12 +
doc/doc2/Eqs/compute_sna_atom6.jpg | Bin 0 -> 17274 bytes
doc/doc2/Eqs/compute_sna_atom6.tex | 12 +
doc/doc2/Eqs/compute_xrd1.jpg | Bin 0 -> 2363 bytes
doc/doc2/Eqs/compute_xrd1.tex | 10 +
doc/doc2/Eqs/compute_xrd2.jpg | Bin 0 -> 4778 bytes
doc/doc2/Eqs/compute_xrd2.tex | 9 +
doc/doc2/Eqs/compute_xrd3.jpg | Bin 0 -> 4745 bytes
doc/doc2/Eqs/compute_xrd3.tex | 9 +
doc/doc2/Eqs/compute_xrd4.jpg | Bin 0 -> 2278 bytes
doc/doc2/Eqs/compute_xrd4.tex | 9 +
doc/doc2/Eqs/compute_xrd5.jpg | Bin 0 -> 7603 bytes
doc/doc2/Eqs/compute_xrd5.tex | 10 +
doc/doc2/Eqs/dihedral_charmm.jpg | Bin 0 -> 3118 bytes
doc/doc2/Eqs/dihedral_charmm.tex | 9 +
doc/doc2/Eqs/dihedral_class2.jpg | Bin 0 -> 47795 bytes
doc/doc2/Eqs/dihedral_class2.tex | 17 +
doc/doc2/Eqs/dihedral_cosine_shift_exp.jpg | Bin 0 -> 8004 bytes
doc/doc2/Eqs/dihedral_cosine_shift_exp.tex | 13 +
doc/doc2/Eqs/dihedral_fourier.jpg | Bin 0 -> 4544 bytes
doc/doc2/Eqs/dihedral_fourier.tex | 9 +
doc/doc2/Eqs/dihedral_harmonic.jpg | Bin 0 -> 2937 bytes
doc/doc2/Eqs/dihedral_harmonic.tex | 9 +
doc/doc2/Eqs/dihedral_helix.jpg | Bin 0 -> 6810 bytes
doc/doc2/Eqs/dihedral_helix.tex | 10 +
doc/doc2/Eqs/dihedral_multi_harmonic.jpg | Bin 0 -> 3103 bytes
doc/doc2/Eqs/dihedral_multi_harmonic.tex | 9 +
doc/doc2/Eqs/dihedral_nharmonic.jpg | Bin 0 -> 3231 bytes
doc/doc2/Eqs/dihedral_nharmonic.tex | 9 +
doc/doc2/Eqs/dihedral_opls.jpg | Bin 0 -> 10755 bytes
doc/doc2/Eqs/dihedral_opls.tex | 10 +
doc/doc2/Eqs/dihedral_quadratic.jpg | Bin 0 -> 2067 bytes
doc/doc2/Eqs/dihedral_quadratic.tex | 9 +
doc/doc2/Eqs/dihedral_sign.jpg | Bin 0 -> 19297 bytes
doc/doc2/Eqs/dreiding_hbond.jpg | Bin 0 -> 21369 bytes
doc/doc2/Eqs/eff_ECP1.jpg | Bin 0 -> 5146 bytes
doc/doc2/Eqs/eff_ECP1.tex | 9 +
doc/doc2/Eqs/eff_ECP2.jpg | Bin 0 -> 9744 bytes
doc/doc2/Eqs/eff_ECP2.tex | 8 +
doc/doc2/Eqs/eff_KE.jpg | Bin 0 -> 3385 bytes
doc/doc2/Eqs/eff_KE.tex | 9 +
doc/doc2/Eqs/eff_NN.jpg | Bin 0 -> 4153 bytes
doc/doc2/Eqs/eff_NN.tex | 9 +
doc/doc2/Eqs/eff_Ne.jpg | Bin 0 -> 6425 bytes
doc/doc2/Eqs/eff_Ne.tex | 9 +
doc/doc2/Eqs/eff_Pauli.jpg | Bin 0 -> 5676 bytes
doc/doc2/Eqs/eff_Pauli.tex | 9 +
doc/doc2/Eqs/eff_ee.jpg | Bin 0 -> 6829 bytes
doc/doc2/Eqs/eff_ee.tex | 9 +
doc/doc2/Eqs/eff_energy_expression.gif | Bin 0 -> 2471 bytes
doc/doc2/Eqs/eff_energy_expression.jpg | Bin 0 -> 9538 bytes
doc/doc2/Eqs/eff_energy_expression.tex | 9 +
doc/doc2/Eqs/fix_box_relax1.jpg | Bin 0 -> 3375 bytes
doc/doc2/Eqs/fix_box_relax1.tex | 9 +
doc/doc2/Eqs/fix_box_relax2.jpg | Bin 0 -> 3029 bytes
doc/doc2/Eqs/fix_box_relax2.tex | 9 +
doc/doc2/Eqs/fix_gld1.jpg | Bin 0 -> 14274 bytes
doc/doc2/Eqs/fix_gld1.tex | 13 +
doc/doc2/Eqs/fix_lb_fluid_boltzmann.jpg | Bin 0 -> 4643 bytes
doc/doc2/Eqs/fix_lb_fluid_boltzmann.tex | 14 +
doc/doc2/Eqs/fix_lb_fluid_fluidforce.jpg | Bin 0 -> 2358 bytes
doc/doc2/Eqs/fix_lb_fluid_fluidforce.tex | 14 +
doc/doc2/Eqs/fix_lb_fluid_gammadefault.jpg | Bin 0 -> 4793 bytes
doc/doc2/Eqs/fix_lb_fluid_gammadefault.tex | 14 +
doc/doc2/Eqs/fix_lb_fluid_navierstokes.jpg | Bin 0 -> 9311 bytes
doc/doc2/Eqs/fix_lb_fluid_navierstokes.tex | 16 +
doc/doc2/Eqs/fix_lb_fluid_properties.jpg | Bin 0 -> 3471 bytes
doc/doc2/Eqs/fix_lb_fluid_properties.tex | 17 +
doc/doc2/Eqs/fix_lb_fluid_stress.jpg | Bin 0 -> 2530 bytes
doc/doc2/Eqs/fix_lb_fluid_stress.tex | 14 +
doc/doc2/Eqs/fix_lb_fluid_viscosity.jpg | Bin 0 -> 6522 bytes
doc/doc2/Eqs/fix_lb_fluid_viscosity.tex | 14 +
doc/doc2/Eqs/fix_nh1.jpg | Bin 0 -> 31088 bytes
doc/doc2/Eqs/fix_nh1.tex | 35 +
doc/doc2/Eqs/fix_nphug.jpg | Bin 0 -> 7506 bytes
doc/doc2/Eqs/fix_nphug.tex | 9 +
doc/doc2/Eqs/fix_orient_fcc.jpg | Bin 0 -> 26005 bytes
doc/doc2/Eqs/fix_orient_fcc.tex | 30 +
doc/doc2/Eqs/fix_pimd.jpg | Bin 0 -> 14569 bytes
doc/doc2/Eqs/fix_pimd.tex | 17 +
doc/doc2/Eqs/fix_rattle_constraints.jpg | Bin 0 -> 4556 bytes
doc/doc2/Eqs/fix_rattle_constraints.tex | 9 +
doc/doc2/Eqs/fix_rattle_rij.jpg | Bin 0 -> 1812 bytes
doc/doc2/Eqs/fix_rattle_rij.tex | 8 +
doc/doc2/Eqs/fix_spring_rg.jpg | Bin 0 -> 16204 bytes
doc/doc2/Eqs/fix_spring_rg.tex | 19 +
doc/doc2/Eqs/fix_ti_rs_force.jpg | Bin 0 -> 1777 bytes
doc/doc2/Eqs/fix_ti_rs_force.tex | 11 +
doc/doc2/Eqs/fix_ti_rs_function_1.jpg | Bin 0 -> 2534 bytes
doc/doc2/Eqs/fix_ti_rs_function_1.tex | 9 +
doc/doc2/Eqs/fix_ti_rs_function_2.jpg | Bin 0 -> 3233 bytes
doc/doc2/Eqs/fix_ti_rs_function_2.tex | 9 +
doc/doc2/Eqs/fix_ti_rs_function_3.jpg | Bin 0 -> 4801 bytes
doc/doc2/Eqs/fix_ti_rs_function_3.tex | 9 +
doc/doc2/Eqs/fix_ti_spring_force.jpg | Bin 0 -> 3627 bytes
doc/doc2/Eqs/fix_ti_spring_force.tex | 11 +
doc/doc2/Eqs/fix_ti_spring_function_1.jpg | Bin 0 -> 1040 bytes
doc/doc2/Eqs/fix_ti_spring_function_1.tex | 9 +
doc/doc2/Eqs/fix_ti_spring_function_2.jpg | Bin 0 -> 5753 bytes
doc/doc2/Eqs/fix_ti_spring_function_2.tex | 9 +
doc/doc2/Eqs/fix_ttm.jpg | Bin 0 -> 5869 bytes
doc/doc2/Eqs/fix_ttm.tex | 15 +
doc/doc2/Eqs/fix_ttm_blast.jpg | Bin 0 -> 4449 bytes
doc/doc2/Eqs/fix_ttm_blast.tex | 13 +
doc/doc2/Eqs/fix_ttm_blast1.jpg | Bin 0 -> 8657 bytes
doc/doc2/Eqs/fix_ttm_blast1.tex | 13 +
doc/doc2/Eqs/fix_ttm_ce.jpg | Bin 0 -> 7446 bytes
doc/doc2/Eqs/fix_ttm_ce.tex | 13 +
doc/doc2/Eqs/fix_ttm_mod.jpg | Bin 0 -> 10179 bytes
doc/doc2/Eqs/fix_ttm_mod.tex | 15 +
doc/doc2/Eqs/fix_wall_colloid.jpg | Bin 0 -> 17879 bytes
doc/doc2/Eqs/fix_wall_colloid.tex | 14 +
doc/doc2/Eqs/fix_wall_harmonic.jpg | Bin 0 -> 2413 bytes
doc/doc2/Eqs/fix_wall_harmonic.tex | 9 +
doc/doc2/Eqs/fix_wall_lj1043.jpg | Bin 0 -> 10996 bytes
doc/doc2/Eqs/fix_wall_lj1043.tex | 12 +
doc/doc2/Eqs/fix_wall_lj93.jpg | Bin 0 -> 4883 bytes
doc/doc2/Eqs/fix_wall_lj93.tex | 11 +
doc/doc2/Eqs/fld.jpg | Bin 0 -> 3640 bytes
doc/doc2/Eqs/fld.tex | 9 +
doc/doc2/Eqs/fld2.jpg | Bin 0 -> 4161 bytes
doc/doc2/Eqs/fld2.tex | 9 +
doc/doc2/Eqs/heat_flux_J.jpg | Bin 0 -> 15205 bytes
doc/doc2/Eqs/heat_flux_J.tex | 11 +
doc/doc2/Eqs/heat_flux_k.jpg | Bin 0 -> 8760 bytes
doc/doc2/Eqs/heat_flux_k.tex | 11 +
doc/doc2/Eqs/improper_class2.jpg | Bin 0 -> 15728 bytes
doc/doc2/Eqs/improper_class2.tex | 13 +
doc/doc2/Eqs/improper_cossq.jpg | Bin 0 -> 2995 bytes
doc/doc2/Eqs/improper_cossq.tex | 9 +
doc/doc2/Eqs/improper_cvff.jpg | Bin 0 -> 2826 bytes
doc/doc2/Eqs/improper_cvff.tex | 9 +
doc/doc2/Eqs/improper_fourier.jpg | Bin 0 -> 4746 bytes
doc/doc2/Eqs/improper_fourier.tex | 9 +
doc/doc2/Eqs/improper_harmonic.jpg | Bin 0 -> 2005 bytes
doc/doc2/Eqs/improper_harmonic.tex | 9 +
doc/doc2/Eqs/improper_ring.jpg | Bin 0 -> 11101 bytes
doc/doc2/Eqs/improper_ring.tex | 12 +
doc/doc2/Eqs/improper_umbrella.jpg | Bin 0 -> 9598 bytes
doc/doc2/Eqs/improper_umbrella.tex | 13 +
doc/doc2/Eqs/min_energy.jpg | Bin 0 -> 19599 bytes
doc/doc2/Eqs/min_energy.tex | 15 +
doc/doc2/Eqs/pair_adp.jpg | Bin 0 -> 20391 bytes
doc/doc2/Eqs/pair_adp.tex | 16 +
doc/doc2/Eqs/pair_airebo.jpg | Bin 0 -> 9380 bytes
doc/doc2/Eqs/pair_airebo.tex | 11 +
doc/doc2/Eqs/pair_beck.jpg | Bin 0 -> 9451 bytes
doc/doc2/Eqs/pair_beck.tex | 11 +
doc/doc2/Eqs/pair_bop.jpg | Bin 0 -> 13202 bytes
doc/doc2/Eqs/pair_bop.tex | 9 +
doc/doc2/Eqs/pair_born.jpg | Bin 0 -> 5099 bytes
doc/doc2/Eqs/pair_born.tex | 10 +
doc/doc2/Eqs/pair_buck.jpg | Bin 0 -> 2861 bytes
doc/doc2/Eqs/pair_buck.tex | 9 +
doc/doc2/Eqs/pair_charmm.jpg | Bin 0 -> 25138 bytes
doc/doc2/Eqs/pair_charmm.tex | 22 +
doc/doc2/Eqs/pair_class2.jpg | Bin 0 -> 5093 bytes
doc/doc2/Eqs/pair_class2.tex | 11 +
doc/doc2/Eqs/pair_cmm.jpg | Bin 0 -> 11921 bytes
doc/doc2/Eqs/pair_cmm.tex | 16 +
doc/doc2/Eqs/pair_colloid_cc.jpg | Bin 0 -> 43501 bytes
doc/doc2/Eqs/pair_colloid_cc.tex | 31 +
doc/doc2/Eqs/pair_colloid_cs.jpg | Bin 0 -> 11599 bytes
doc/doc2/Eqs/pair_colloid_cs.tex | 12 +
doc/doc2/Eqs/pair_colloid_ss.jpg | Bin 0 -> 5573 bytes
doc/doc2/Eqs/pair_colloid_ss.tex | 12 +
doc/doc2/Eqs/pair_comb1.jpg | Bin 0 -> 18596 bytes
doc/doc2/Eqs/pair_comb1.tex | 7 +
doc/doc2/Eqs/pair_comb2.jpg | Bin 0 -> 39601 bytes
doc/doc2/Eqs/pair_comb2.tex | 23 +
doc/doc2/Eqs/pair_coul_diel.jpg | Bin 0 -> 10587 bytes
doc/doc2/Eqs/pair_coul_diel.tex | 9 +
doc/doc2/Eqs/pair_coul_dsf.jpg | Bin 0 -> 12261 bytes
doc/doc2/Eqs/pair_coul_dsf.tex | 10 +
doc/doc2/Eqs/pair_coul_soft.jpg | Bin 0 -> 11309 bytes
doc/doc2/Eqs/pair_coul_soft.tex | 10 +
doc/doc2/Eqs/pair_coul_wolf.jpg | Bin 0 -> 8758 bytes
doc/doc2/Eqs/pair_coul_wolf.tex | 11 +
doc/doc2/Eqs/pair_coulomb.jpg | Bin 0 -> 2505 bytes
doc/doc2/Eqs/pair_coulomb.tex | 9 +
doc/doc2/Eqs/pair_cs.jpg | Bin 0 -> 3500 bytes
doc/doc2/Eqs/pair_cs.tex | 9 +
doc/doc2/Eqs/pair_debye.jpg | Bin 0 -> 3641 bytes
doc/doc2/Eqs/pair_debye.tex | 8 +
doc/doc2/Eqs/pair_dipole.jpg | Bin 0 -> 47516 bytes
doc/doc2/Eqs/pair_dipole.tex | 38 +
doc/doc2/Eqs/pair_dipole_sf.jpg | Bin 0 -> 93270 bytes
doc/doc2/Eqs/pair_dipole_sf.tex | 51 +
doc/doc2/Eqs/pair_dipole_sf2.jpg | Bin 0 -> 40855 bytes
doc/doc2/Eqs/pair_dipole_sf2.tex | 24 +
doc/doc2/Eqs/pair_dpd.jpg | Bin 0 -> 12376 bytes
doc/doc2/Eqs/pair_dpd.tex | 13 +
doc/doc2/Eqs/pair_eam.jpg | Bin 0 -> 6693 bytes
doc/doc2/Eqs/pair_eam.tex | 10 +
doc/doc2/Eqs/pair_eam_fs.jpg | Bin 0 -> 6547 bytes
doc/doc2/Eqs/pair_eam_fs.tex | 11 +
doc/doc2/Eqs/pair_edip.jpg | Bin 0 -> 42939 bytes
doc/doc2/Eqs/pair_edip.tex | 22 +
doc/doc2/Eqs/pair_eim1.jpg | Bin 0 -> 6824 bytes
doc/doc2/Eqs/pair_eim1.tex | 9 +
doc/doc2/Eqs/pair_eim2.jpg | Bin 0 -> 8494 bytes
doc/doc2/Eqs/pair_eim2.tex | 11 +
doc/doc2/Eqs/pair_eim3.jpg | Bin 0 -> 40993 bytes
doc/doc2/Eqs/pair_eim3.tex | 25 +
doc/doc2/Eqs/pair_gauss.jpg | Bin 0 -> 2835 bytes
doc/doc2/Eqs/pair_gauss.tex | 9 +
doc/doc2/Eqs/pair_gauss_cut.jpg | Bin 0 -> 3855 bytes
doc/doc2/Eqs/pair_gauss_cut.tex | 8 +
doc/doc2/Eqs/pair_gayberne.jpg | Bin 0 -> 13814 bytes
doc/doc2/Eqs/pair_gayberne.tex | 14 +
doc/doc2/Eqs/pair_gayberne2.jpg | Bin 0 -> 4203 bytes
doc/doc2/Eqs/pair_gayberne2.tex | 9 +
doc/doc2/Eqs/pair_gran_hertz.jpg | Bin 0 -> 12512 bytes
doc/doc2/Eqs/pair_gran_hertz.tex | 14 +
doc/doc2/Eqs/pair_gran_hooke.jpg | Bin 0 -> 5737 bytes
doc/doc2/Eqs/pair_gran_hooke.tex | 12 +
doc/doc2/Eqs/pair_gromacs.jpg | Bin 0 -> 50447 bytes
doc/doc2/Eqs/pair_gromacs.tex | 17 +
doc/doc2/Eqs/pair_hbond_dreiding.jpg | Bin 0 -> 32047 bytes
doc/doc2/Eqs/pair_hbond_dreiding.tex | 18 +
doc/doc2/Eqs/pair_lj.jpg | Bin 0 -> 4547 bytes
doc/doc2/Eqs/pair_lj.tex | 11 +
doc/doc2/Eqs/pair_lj96.jpg | Bin 0 -> 4851 bytes
doc/doc2/Eqs/pair_lj96.tex | 11 +
doc/doc2/Eqs/pair_lj_cubic.jpg | Bin 0 -> 9352 bytes
doc/doc2/Eqs/pair_lj_cubic.tex | 12 +
doc/doc2/Eqs/pair_lj_expand.jpg | Bin 0 -> 5905 bytes
doc/doc2/Eqs/pair_lj_expand.tex | 11 +
doc/doc2/Eqs/pair_lj_sf.jpg | Bin 0 -> 15535 bytes
doc/doc2/Eqs/pair_lj_sf.tex | 11 +
doc/doc2/Eqs/pair_lj_smooth.jpg | Bin 0 -> 11580 bytes
doc/doc2/Eqs/pair_lj_smooth.tex | 15 +
doc/doc2/Eqs/pair_lj_smooth_linear.jpg | Bin 0 -> 10372 bytes
doc/doc2/Eqs/pair_lj_smooth_linear.tex | 13 +
doc/doc2/Eqs/pair_lj_soft.jpg | Bin 0 -> 17984 bytes
doc/doc2/Eqs/pair_lj_soft.tex | 15 +
doc/doc2/Eqs/pair_lubricate.jpg | Bin 0 -> 14321 bytes
doc/doc2/Eqs/pair_lubricate.tex | 17 +
doc/doc2/Eqs/pair_meam.jpg | Bin 0 -> 6110 bytes
doc/doc2/Eqs/pair_meam.tex | 10 +
doc/doc2/Eqs/pair_meam_spline.jpg | Bin 0 -> 10530 bytes
doc/doc2/Eqs/pair_meam_spline.tex | 13 +
doc/doc2/Eqs/pair_meam_sw_spline.jpg | Bin 0 -> 17215 bytes
doc/doc2/Eqs/pair_meam_sw_spline.tex | 23 +
doc/doc2/Eqs/pair_mgpt.jpg | Bin 0 -> 12874 bytes
doc/doc2/Eqs/pair_mgpt.tex | 12 +
doc/doc2/Eqs/pair_mie.jpg | Bin 0 -> 4686 bytes
doc/doc2/Eqs/pair_mie.tex | 10 +
doc/doc2/Eqs/pair_mie2.jpg | Bin 0 -> 6502 bytes
doc/doc2/Eqs/pair_mie2.tex | 9 +
doc/doc2/Eqs/pair_morse.jpg | Bin 0 -> 4042 bytes
doc/doc2/Eqs/pair_morse.tex | 10 +
doc/doc2/Eqs/pair_nb3b_harmonic.jpg | Bin 0 -> 1918 bytes
doc/doc2/Eqs/pair_nb3b_harmonic.tex | 9 +
doc/doc2/Eqs/pair_nm.jpg | Bin 0 -> 6304 bytes
doc/doc2/Eqs/pair_nm.tex | 10 +
doc/doc2/Eqs/pair_resquared.jpg | Bin 0 -> 2683 bytes
doc/doc2/Eqs/pair_resquared.tex | 7 +
doc/doc2/Eqs/pair_resquared2.jpg | Bin 0 -> 2303 bytes
doc/doc2/Eqs/pair_resquared2.tex | 7 +
doc/doc2/Eqs/pair_resquared3.jpg | Bin 0 -> 1156 bytes
doc/doc2/Eqs/pair_resquared3.tex | 7 +
doc/doc2/Eqs/pair_resquared4.jpg | Bin 0 -> 4779 bytes
doc/doc2/Eqs/pair_resquared4.tex | 9 +
doc/doc2/Eqs/pair_smtbq1.jpg | Bin 0 -> 27807 bytes
doc/doc2/Eqs/pair_smtbq1.tex | 13 +
doc/doc2/Eqs/pair_smtbq2.jpg | Bin 0 -> 15544 bytes
doc/doc2/Eqs/pair_smtbq2.tex | 12 +
doc/doc2/Eqs/pair_smtbq3.jpg | Bin 0 -> 6832 bytes
doc/doc2/Eqs/pair_smtbq3.tex | 10 +
doc/doc2/Eqs/pair_snap.jpg | Bin 0 -> 32505 bytes
doc/doc2/Eqs/pair_snap.tex | 9 +
doc/doc2/Eqs/pair_soft.jpg | Bin 0 -> 4085 bytes
doc/doc2/Eqs/pair_soft.tex | 10 +
doc/doc2/Eqs/pair_sph_ideal.jpg | Bin 0 -> 1540 bytes
doc/doc2/Eqs/pair_sph_ideal.tex | 9 +
doc/doc2/Eqs/pair_sph_tait.jpg | Bin 0 -> 2303 bytes
doc/doc2/Eqs/pair_sph_tait.tex | 9 +
doc/doc2/Eqs/pair_srp1.jpg | Bin 0 -> 3537 bytes
doc/doc2/Eqs/pair_srp1.tex | 9 +
doc/doc2/Eqs/pair_srp2.jpg | Bin 0 -> 5648 bytes
doc/doc2/Eqs/pair_srp2.tex | 10 +
doc/doc2/Eqs/pair_sw.jpg | Bin 0 -> 28707 bytes
doc/doc2/Eqs/pair_sw.tex | 18 +
doc/doc2/Eqs/pair_tersoff.jpg | Bin 0 -> 36139 bytes
doc/doc2/Eqs/pair_tersoff_1.jpg | Bin 0 -> 36584 bytes
doc/doc2/Eqs/pair_tersoff_1.tex | 24 +
doc/doc2/Eqs/pair_tersoff_2.jpg | Bin 0 -> 13756 bytes
doc/doc2/Eqs/pair_tersoff_2.tex | 14 +
doc/doc2/Eqs/pair_tersoff_mod.jpg | Bin 0 -> 91727 bytes
doc/doc2/Eqs/pair_tersoff_mod.tex | 24 +
doc/doc2/Eqs/pair_tersoff_zbl.jpg | Bin 0 -> 392677 bytes
doc/doc2/Eqs/pair_tersoff_zbl.tex | 33 +
doc/doc2/Eqs/pair_vashishta.jpg | Bin 0 -> 73306 bytes
doc/doc2/Eqs/pair_vashishta.tex | 22 +
doc/doc2/Eqs/pair_yukawa.jpg | Bin 0 -> 2189 bytes
doc/doc2/Eqs/pair_yukawa.tex | 9 +
doc/doc2/Eqs/pair_yukawa_colloid.jpg | Bin 0 -> 3067 bytes
doc/doc2/Eqs/pair_yukawa_colloid.tex | 9 +
doc/doc2/Eqs/pair_zbl.jpg | Bin 0 -> 32209 bytes
doc/doc2/Eqs/pair_zbl.tex | 11 +
doc/doc2/Eqs/polymorphic1.jpg | Bin 0 -> 9186 bytes
doc/doc2/Eqs/polymorphic1.tex | 9 +
doc/doc2/Eqs/polymorphic2.jpg | Bin 0 -> 7156 bytes
doc/doc2/Eqs/polymorphic2.tex | 10 +
doc/doc2/Eqs/polymorphic3.jpg | Bin 0 -> 2425 bytes
doc/doc2/Eqs/polymorphic3.tex | 10 +
doc/doc2/Eqs/polymorphic4.jpg | Bin 0 -> 27028 bytes
doc/doc2/Eqs/polymorphic4.tex | 17 +
doc/doc2/Eqs/polymorphic5.jpg | Bin 0 -> 30052 bytes
doc/doc2/Eqs/polymorphic5.tex | 17 +
doc/doc2/Eqs/polymorphic6.jpg | Bin 0 -> 9063 bytes
doc/doc2/Eqs/polymorphic6.tex | 13 +
doc/doc2/Eqs/polymorphic7.jpg | Bin 0 -> 58111 bytes
doc/doc2/Eqs/polymorphic7.tex | 25 +
doc/doc2/Eqs/polymorphic8.jpg | Bin 0 -> 10249 bytes
doc/doc2/Eqs/polymorphic8.tex | 13 +
doc/doc2/Eqs/polymorphic9.jpg | Bin 0 -> 13704 bytes
doc/doc2/Eqs/polymorphic9.tex | 17 +
doc/doc2/Eqs/pressure.jpg | Bin 0 -> 4097 bytes
doc/doc2/Eqs/pressure.tex | 9 +
doc/doc2/Eqs/pressure_tensor.jpg | Bin 0 -> 5038 bytes
doc/doc2/Eqs/pressure_tensor.tex | 10 +
doc/doc2/Eqs/rotate.jpg | Bin 0 -> 17991 bytes
doc/doc2/Eqs/rotate.tex | 26 +
doc/doc2/Eqs/stress_tensor.jpg | Bin 0 -> 22403 bytes
doc/doc2/Eqs/stress_tensor.tex | 20 +
doc/doc2/Eqs/transform.jpg | Bin 0 -> 60790 bytes
doc/doc2/Eqs/transform.tex | 27 +
doc/doc2/Eqs/umbrella.jpg | Bin 0 -> 20442 bytes
doc/doc2/JPG/atc_nanotube.jpg | Bin 0 -> 13402 bytes
doc/doc2/JPG/balance_nonuniform.jpg | Bin 0 -> 78857 bytes
doc/doc2/JPG/balance_nonuniform_small.jpg | Bin 0 -> 16588 bytes
doc/doc2/JPG/balance_rcb.jpg | Bin 0 -> 72941 bytes
doc/doc2/JPG/balance_rcb_small.jpg | Bin 0 -> 15571 bytes
doc/doc2/JPG/balance_uniform.jpg | Bin 0 -> 79281 bytes
doc/doc2/JPG/balance_uniform_small.jpg | Bin 0 -> 17279 bytes
doc/doc2/JPG/bondswap.jpg | Bin 0 -> 10548 bytes
doc/doc2/JPG/coul_soft.jpg | Bin 0 -> 12676 bytes
doc/doc2/JPG/dump1.jpg | Bin 0 -> 608016 bytes
doc/doc2/JPG/dump1_small.jpg | Bin 0 -> 16529 bytes
doc/doc2/JPG/dump2.jpg | Bin 0 -> 172441 bytes
doc/doc2/JPG/dump2_small.jpg | Bin 0 -> 6506 bytes
doc/doc2/JPG/hop1.jpg | Bin 0 -> 52996 bytes
doc/doc2/JPG/hop1_small.jpg | Bin 0 -> 4302 bytes
doc/doc2/JPG/hop2.jpg | Bin 0 -> 53149 bytes
doc/doc2/JPG/hop2_small.jpg | Bin 0 -> 4214 bytes
doc/doc2/JPG/lj_soft.jpg | Bin 0 -> 12313 bytes
doc/doc2/JPG/pimd.jpg | Bin 0 -> 29560 bytes
doc/doc2/JPG/qbmsst_init.jpg | Bin 0 -> 38407 bytes
doc/doc2/JPG/qbmsst_shock.jpg | Bin 0 -> 79334 bytes
doc/doc2/JPG/rhodo_staggered.jpg | Bin 0 -> 42303 bytes
doc/doc2/JPG/saed_ewald_intersect.jpg | Bin 0 -> 112619 bytes
doc/doc2/JPG/saed_ewald_intersect_small.jpg | Bin 0 -> 41372 bytes
doc/doc2/JPG/saed_mesh.jpg | Bin 0 -> 110946 bytes
doc/doc2/JPG/saed_mesh_small.jpg | Bin 0 -> 43053 bytes
doc/doc2/JPG/screenshot_atomeye.jpg | Bin 0 -> 426608 bytes
doc/doc2/JPG/screenshot_atomeye_small.jpg | Bin 0 -> 7498 bytes
doc/doc2/JPG/screenshot_gl.jpg | Bin 0 -> 306252 bytes
doc/doc2/JPG/screenshot_gl_small.jpg | Bin 0 -> 5875 bytes
doc/doc2/JPG/screenshot_pymol.jpg | Bin 0 -> 417093 bytes
doc/doc2/JPG/screenshot_pymol_small.jpg | Bin 0 -> 7660 bytes
doc/doc2/JPG/screenshot_vmd.jpg | Bin 0 -> 327211 bytes
doc/doc2/JPG/screenshot_vmd_small.jpg | Bin 0 -> 6787 bytes
doc/doc2/JPG/sinusoid.jpg | Bin 0 -> 128596 bytes
doc/doc2/JPG/sinusoid_small.jpg | Bin 0 -> 29397 bytes
doc/doc2/JPG/xrd_mesh.jpg | Bin 0 -> 121055 bytes
doc/doc2/JPG/xrd_mesh_small.jpg | Bin 0 -> 46491 bytes
doc/doc2/Manual.html | 478 +
doc/doc2/Manual.html.html | 318 +
doc/doc2/PDF/PDLammps_EPS.pdf | Bin 0 -> 79021 bytes
doc/doc2/PDF/PDLammps_VES.pdf | Bin 0 -> 74846 bytes
doc/doc2/PDF/PDLammps_overview.pdf | Bin 0 -> 254253 bytes
doc/doc2/PDF/colvars-refman-lammps.pdf | 8124 ++
doc/doc2/PDF/kspace.pdf | Bin 0 -> 158427 bytes
doc/doc2/PDF/pair_gayberne_extra.aux | 1 +
doc/doc2/PDF/pair_gayberne_extra.dvi | Bin 0 -> 8508 bytes
doc/doc2/PDF/pair_gayberne_extra.log | 148 +
doc/doc2/PDF/pair_gayberne_extra.pdf | Bin 0 -> 55448 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 0 -> 6264 bytes
doc/doc2/PDF/pair_resquared_extra.log | 154 +
doc/doc2/PDF/pair_resquared_extra.pdf | Bin 0 -> 55733 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 | 0
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 | 0
doc/doc2/Section_python.html | 794 +
doc/doc2/Section_start.html | 1940 +
doc/{ => doc2}/Section_tools.html | 0
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 | 0
doc/{ => doc2}/angle_coeff.html | 0
doc/{ => doc2}/angle_cosine.html | 0
doc/{ => doc2}/angle_cosine_delta.html | 0
doc/{ => doc2}/angle_cosine_periodic.html | 0
doc/{ => doc2}/angle_cosine_shift.html | 0
doc/{ => doc2}/angle_cosine_shift_exp.html | 0
doc/{ => doc2}/angle_cosine_squared.html | 0
doc/{ => doc2}/angle_dipole.html | 0
doc/{ => doc2}/angle_fourier.html | 0
doc/{ => doc2}/angle_fourier_simple.html | 0
doc/doc2/angle_harmonic.html | 84 +
doc/{ => doc2}/angle_hybrid.html | 0
doc/{ => doc2}/angle_none.html | 0
doc/{ => doc2}/angle_quartic.html | 0
doc/{ => doc2}/angle_sdk.html | 0
doc/{ => doc2}/angle_style.html | 0
doc/{ => doc2}/angle_table.html | 0
doc/doc2/atom_modify.html | 179 +
doc/doc2/atom_style.html | 276 +
doc/doc2/balance.html | 360 +
doc/{ => doc2}/body.html | 0
doc/{ => doc2}/bond_class2.html | 0
doc/{ => doc2}/bond_coeff.html | 0
doc/doc2/bond_fene.html | 96 +
doc/{ => doc2}/bond_fene_expand.html | 0
doc/doc2/bond_harmonic.html | 81 +
doc/{ => doc2}/bond_harmonic_shift.html | 0
doc/{ => doc2}/bond_harmonic_shift_cut.html | 0
doc/{ => doc2}/bond_hybrid.html | 0
doc/{ => doc2}/bond_morse.html | 0
doc/{ => doc2}/bond_none.html | 0
doc/{ => doc2}/bond_nonlinear.html | 0
doc/{ => doc2}/bond_quartic.html | 0
doc/{ => doc2}/bond_style.html | 0
doc/{ => doc2}/bond_table.html | 0
doc/doc2/boundary.html | 106 +
doc/{ => doc2}/box.html | 0
doc/{ => doc2}/change_box.html | 0
doc/{ => doc2}/clear.html | 0
doc/doc2/comm_modify.html | 167 +
doc/{ => doc2}/comm_style.html | 0
doc/doc2/compute.html | 267 +
doc/{ => doc2}/compute_ackland_atom.html | 0
doc/{ => doc2}/compute_angle_local.html | 0
doc/doc2/compute_angmom_chunk.html | 94 +
doc/{ => doc2}/compute_basal_atom.html | 0
doc/{ => doc2}/compute_body_local.html | 0
doc/{ => doc2}/compute_bond_local.html | 0
doc/{ => doc2}/compute_centro_atom.html | 0
doc/{ => doc2}/compute_chunk_atom.html | 0
doc/{ => doc2}/compute_cluster_atom.html | 0
doc/{ => doc2}/compute_cna_atom.html | 0
doc/doc2/compute_com.html | 62 +
doc/{ => doc2}/compute_com_chunk.html | 0
doc/{ => doc2}/compute_contact_atom.html | 0
doc/{ => doc2}/compute_coord_atom.html | 0
doc/{ => doc2}/compute_damage_atom.html | 0
doc/{ => doc2}/compute_dihedral_local.html | 0
doc/{ => doc2}/compute_dilatation_atom.html | 0
doc/{ => doc2}/compute_displace_atom.html | 0
doc/{ => doc2}/compute_erotate_asphere.html | 0
doc/{ => doc2}/compute_erotate_rigid.html | 0
doc/{ => doc2}/compute_erotate_sphere.html | 0
doc/{ => doc2}/compute_erotate_sphere_atom.html | 0
doc/{ => doc2}/compute_event_displace.html | 0
doc/doc2/compute_fep.html | 279 +
doc/{ => doc2}/compute_group_group.html | 0
doc/doc2/compute_gyration.html | 78 +
doc/{ => doc2}/compute_gyration_chunk.html | 0
doc/doc2/compute_heat_flux.html | 192 +
doc/doc2/compute_hexorder_atom.html | 115 +
doc/{ => doc2}/compute_improper_local.html | 0
doc/doc2/compute_inertia_chunk.html | 93 +
doc/{ => doc2}/compute_ke.html | 0
doc/{ => doc2}/compute_ke_atom.html | 0
doc/{ => doc2}/compute_ke_atom_eff.html | 0
doc/{ => doc2}/compute_ke_eff.html | 0
doc/{ => doc2}/compute_ke_rigid.html | 0
doc/{ => doc2}/compute_meso_e_atom.html | 0
doc/{ => doc2}/compute_meso_rho_atom.html | 0
doc/{ => doc2}/compute_meso_t_atom.html | 0
doc/{ => doc2}/compute_modify.html | 0
doc/doc2/compute_msd.html | 99 +
doc/doc2/compute_msd_chunk.html | 125 +
doc/{ => doc2}/compute_msd_nongauss.html | 0
doc/doc2/compute_omega_chunk.html | 94 +
doc/{ => doc2}/compute_pair.html | 0
doc/{ => doc2}/compute_pair_local.html | 0
doc/doc2/compute_pe.html | 109 +
doc/{ => doc2}/compute_pe_atom.html | 0
doc/{ => doc2}/compute_plasticity_atom.html | 0
doc/doc2/compute_pressure.html | 155 +
doc/{ => doc2}/compute_property_atom.html | 0
doc/{ => doc2}/compute_property_chunk.html | 0
doc/{ => doc2}/compute_property_local.html | 0
doc/doc2/compute_rdf.html | 160 +
doc/doc2/compute_reduce.html | 200 +
doc/doc2/compute_saed.html | 191 +
doc/{ => doc2}/compute_slice.html | 0
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 | 0
doc/{ => doc2}/compute_stress_atom.html | 0
doc/doc2/compute_tally.html | 92 +
doc/doc2/compute_temp.html | 121 +
doc/{ => doc2}/compute_temp_asphere.html | 0
doc/doc2/compute_temp_chunk.html | 251 +
doc/{ => doc2}/compute_temp_com.html | 0
doc/doc2/compute_temp_cs.html | 125 +
doc/{ => doc2}/compute_temp_deform.html | 0
doc/{ => doc2}/compute_temp_deform_eff.html | 0
doc/doc2/compute_temp_drude.html | 87 +
doc/{ => doc2}/compute_temp_eff.html | 0
doc/doc2/compute_temp_partial.html | 127 +
doc/doc2/compute_temp_profile.html | 195 +
doc/{ => doc2}/compute_temp_ramp.html | 0
doc/doc2/compute_temp_region.html | 115 +
doc/{ => doc2}/compute_temp_region_eff.html | 0
doc/{ => doc2}/compute_temp_rotate.html | 0
doc/{ => doc2}/compute_temp_sphere.html | 0
doc/{ => doc2}/compute_ti.html | 0
doc/doc2/compute_torque_chunk.html | 92 +
doc/{ => doc2}/compute_vacf.html | 0
doc/{ => doc2}/compute_vcm_chunk.html | 0
doc/doc2/compute_voronoi_atom.html | 183 +
doc/doc2/compute_xrd.html | 214 +
doc/{ => doc2}/create_atoms.html | 0
doc/{ => doc2}/create_bonds.html | 0
doc/doc2/create_box.html | 162 +
doc/doc2/delete_atoms.html | 154 +
doc/{ => doc2}/delete_bonds.html | 0
doc/{ => doc2}/dielectric.html | 0
doc/doc2/dihedral_charmm.html | 123 +
doc/{ => doc2}/dihedral_class2.html | 0
doc/{ => doc2}/dihedral_coeff.html | 0
doc/{ => doc2}/dihedral_cosine_shift_exp.html | 0
doc/{ => doc2}/dihedral_fourier.html | 0
doc/{ => doc2}/dihedral_harmonic.html | 0
doc/{ => doc2}/dihedral_helix.html | 0
doc/{ => doc2}/dihedral_hybrid.html | 0
doc/{ => doc2}/dihedral_multi_harmonic.html | 0
doc/{ => doc2}/dihedral_nharmonic.html | 0
doc/{ => doc2}/dihedral_none.html | 0
doc/doc2/dihedral_opls.html | 93 +
doc/{ => doc2}/dihedral_quadratic.html | 0
doc/{ => doc2}/dihedral_style.html | 0
doc/{ => doc2}/dihedral_table.html | 0
doc/{ => doc2}/dimension.html | 0
doc/doc2/displace_atoms.html | 143 +
doc/doc2/dump.html | 649 +
doc/doc2/dump_h5md.html | 136 +
doc/{ => doc2}/dump_image.html | 0
doc/doc2/dump_modify.html | 817 +
doc/{ => doc2}/dump_molfile.html | 0
doc/{ => doc2}/echo.html | 0
doc/doc2/fix.html | 285 +
doc/doc2/fix_adapt.html | 267 +
doc/doc2/fix_adapt_fep.html | 275 +
doc/{ => doc2}/fix_addforce.html | 0
doc/{ => doc2}/fix_addtorque.html | 0
doc/{ => doc2}/fix_append_atoms.html | 0
doc/{ => doc2}/fix_atc.html | 0
doc/doc2/fix_atom_swap.html | 201 +
doc/{ => doc2}/fix_ave_atom.html | 0
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 | 0
doc/{ => doc2}/fix_ave_spatial_sphere.html | 0
doc/doc2/fix_ave_time.html | 341 +
doc/{ => doc2}/fix_aveforce.html | 0
doc/doc2/fix_balance.html | 361 +
doc/{ => doc2}/fix_bond_break.html | 0
doc/{ => doc2}/fix_bond_create.html | 0
doc/{ => doc2}/fix_bond_swap.html | 0
doc/{ => doc2}/fix_box_relax.html | 0
doc/{ => doc2}/fix_colvars.html | 0
doc/doc2/fix_deform.html | 607 +
doc/doc2/fix_deposit.html | 292 +
doc/{ => doc2}/fix_drag.html | 0
doc/doc2/fix_drude.html | 60 +
doc/doc2/fix_drude_transform.html | 171 +
doc/{ => doc2}/fix_dt_reset.html | 0
doc/{ => doc2}/fix_efield.html | 0
doc/{ => doc2}/fix_enforce2d.html | 0
doc/{ => doc2}/fix_evaporate.html | 0
doc/{ => doc2}/fix_external.html | 0
doc/{ => doc2}/fix_freeze.html | 0
doc/doc2/fix_gcmc.html | 369 +
doc/{ => doc2}/fix_gld.html | 0
doc/doc2/fix_gle.html | 170 +
doc/{ => doc2}/fix_gravity.html | 0
doc/{ => doc2}/fix_heat.html | 0
doc/{ => doc2}/fix_imd.html | 0
doc/{ => doc2}/fix_indent.html | 0
doc/{ => doc2}/fix_ipi.html | 0
doc/doc2/fix_langevin.html | 362 +
doc/doc2/fix_langevin_drude.html | 280 +
doc/{ => doc2}/fix_langevin_eff.html | 0
doc/{ => doc2}/fix_lb_fluid.html | 0
doc/{ => doc2}/fix_lb_momentum.html | 0
doc/{ => doc2}/fix_lb_pc.html | 0
doc/{ => doc2}/fix_lb_rigid_pc_sphere.html | 0
doc/{ => doc2}/fix_lb_viscous.html | 0
doc/{ => doc2}/fix_lineforce.html | 0
doc/{ => doc2}/fix_meso.html | 0
doc/{ => doc2}/fix_meso_stationary.html | 0
doc/{ => doc2}/fix_modify.html | 0
doc/doc2/fix_momentum.html | 85 +
doc/{ => doc2}/fix_move.html | 0
doc/{ => doc2}/fix_msst.html | 0
doc/{ => doc2}/fix_neb.html | 0
doc/doc2/fix_nh.html | 633 +
doc/{ => doc2}/fix_nh_eff.html | 0
doc/{ => doc2}/fix_nph_asphere.html | 0
doc/{ => doc2}/fix_nph_sphere.html | 0
doc/{ => doc2}/fix_nphug.html | 0
doc/{ => doc2}/fix_npt_asphere.html | 0
doc/{ => doc2}/fix_npt_sphere.html | 0
doc/{ => doc2}/fix_nve.html | 0
doc/{ => doc2}/fix_nve_asphere.html | 0
doc/{ => doc2}/fix_nve_asphere_noforce.html | 0
doc/{ => doc2}/fix_nve_body.html | 0
doc/{ => doc2}/fix_nve_eff.html | 0
doc/{ => doc2}/fix_nve_limit.html | 0
doc/{ => doc2}/fix_nve_line.html | 0
doc/{ => doc2}/fix_nve_noforce.html | 0
doc/{ => doc2}/fix_nve_sphere.html | 0
doc/{ => doc2}/fix_nve_tri.html | 0
doc/{ => doc2}/fix_nvt_asphere.html | 0
doc/{ => doc2}/fix_nvt_sllod.html | 0
doc/{ => doc2}/fix_nvt_sllod_eff.html | 0
doc/{ => doc2}/fix_nvt_sphere.html | 0
doc/{ => doc2}/fix_oneway.html | 0
doc/{ => doc2}/fix_orient_fcc.html | 0
doc/{ => doc2}/fix_phonon.html | 0
doc/{ => doc2}/fix_pimd.html | 0
doc/{ => doc2}/fix_planeforce.html | 0
doc/{ => doc2}/fix_poems.html | 0
doc/{ => doc2}/fix_pour.html | 0
doc/{ => doc2}/fix_press_berendsen.html | 0
doc/doc2/fix_print.html | 102 +
doc/doc2/fix_property_atom.html | 226 +
doc/doc2/fix_qbmsst.html | 232 +
doc/{ => doc2}/fix_qeq.html | 0
doc/{ => doc2}/fix_qeq_comb.html | 0
doc/{ => doc2}/fix_qeq_reax.html | 0
doc/{ => doc2}/fix_qmmm.html | 0
doc/doc2/fix_qtb.html | 194 +
doc/{ => doc2}/fix_reax_bonds.html | 0
doc/{ => doc2}/fix_reaxc_species.html | 0
doc/{ => doc2}/fix_recenter.html | 0
doc/doc2/fix_restrain.html | 193 +
doc/doc2/fix_rigid.html | 814 +
doc/doc2/fix_saed_vtk.html | 199 +
doc/{ => doc2}/fix_setforce.html | 0
doc/doc2/fix_shake.html | 247 +
doc/{ => doc2}/fix_smd.html | 0
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 | 0
doc/{ => doc2}/fix_spring_rg.html | 0
doc/{ => doc2}/fix_spring_self.html | 0
doc/doc2/fix_srd.html | 410 +
doc/{ => doc2}/fix_store_force.html | 0
doc/{ => doc2}/fix_store_state.html | 0
doc/{ => doc2}/fix_temp_berendsen.html | 0
doc/doc2/fix_temp_csvr.html | 182 +
doc/{ => doc2}/fix_temp_rescale.html | 0
doc/{ => doc2}/fix_temp_rescale_eff.html | 0
doc/{ => doc2}/fix_tfmc.html | 0
doc/doc2/fix_thermal_conductivity.html | 177 +
doc/{ => doc2}/fix_ti_rs.html | 0
doc/{ => doc2}/fix_ti_spring.html | 0
doc/{ => doc2}/fix_tmd.html | 0
doc/{ => doc2}/fix_ttm.html | 0
doc/{ => doc2}/fix_tune_kspace.html | 0
doc/doc2/fix_vector.html | 171 +
doc/{ => doc2}/fix_viscosity.html | 0
doc/{ => doc2}/fix_viscous.html | 0
doc/{ => doc2}/fix_wall.html | 0
doc/{ => doc2}/fix_wall_gran.html | 0
doc/{ => doc2}/fix_wall_piston.html | 0
doc/doc2/fix_wall_reflect.html | 199 +
doc/{ => doc2}/fix_wall_region.html | 0
doc/{ => doc2}/fix_wall_srd.html | 0
doc/doc2/genindex.html | 2240 +
doc/doc2/group.html | 289 +
doc/{ => doc2}/group2ndx.html | 0
doc/{ => doc2}/if.html | 0
doc/{ => doc2}/improper_class2.html | 0
doc/{ => doc2}/improper_coeff.html | 0
doc/{ => doc2}/improper_cossq.html | 0
doc/{ => doc2}/improper_cvff.html | 0
doc/{ => doc2}/improper_fourier.html | 0
doc/doc2/improper_harmonic.html | 97 +
doc/{ => doc2}/improper_hybrid.html | 0
doc/{ => doc2}/improper_none.html | 0
doc/{ => doc2}/improper_ring.html | 0
doc/{ => doc2}/improper_style.html | 0
doc/{ => doc2}/improper_umbrella.html | 0
doc/{ => doc2}/include.html | 0
doc/doc2/info.html | 91 +
doc/{ => doc2}/jump.html | 0
doc/{ => doc2}/kspace_modify.html | 0
doc/{ => doc2}/kspace_style.html | 0
doc/{ => doc2}/label.html | 0
doc/doc2/lattice.html | 300 +
doc/{ => doc2}/log.html | 0
doc/doc2/mass.html | 89 +
doc/{ => doc2}/min_modify.html | 0
doc/{ => doc2}/min_style.html | 0
doc/{ => doc2}/minimize.html | 0
doc/doc2/molecule.html | 473 +
doc/{ => doc2}/neb.html | 0
doc/doc2/neigh_modify.html | 219 +
doc/doc2/neighbor.html | 88 +
doc/{ => doc2}/newton.html | 0
doc/{ => doc2}/next.html | 0
doc/doc2/package.html | 675 +
doc/{ => doc2}/pair_adp.html | 0
doc/{ => doc2}/pair_airebo.html | 0
doc/{ => doc2}/pair_awpmd.html | 0
doc/{ => doc2}/pair_beck.html | 0
doc/{ => doc2}/pair_body.html | 0
doc/doc2/pair_bop.html | 460 +
doc/doc2/pair_born.html | 210 +
doc/{ => doc2}/pair_brownian.html | 0
doc/doc2/pair_buck.html | 220 +
doc/{ => doc2}/pair_buck_long.html | 0
doc/{ => doc2}/pair_charmm.html | 0
doc/doc2/pair_class2.html | 193 +
doc/{ => doc2}/pair_coeff.html | 0
doc/doc2/pair_colloid.html | 213 +
doc/doc2/pair_comb.html | 204 +
doc/doc2/pair_coul.html | 373 +
doc/{ => doc2}/pair_coul_diel.html | 0
doc/{ => doc2}/pair_cs.html | 0
doc/{ => doc2}/pair_dipole.html | 0
doc/{ => doc2}/pair_dpd.html | 0
doc/doc2/pair_dsmc.html | 154 +
doc/doc2/pair_eam.html | 480 +
doc/{ => doc2}/pair_edip.html | 0
doc/{ => doc2}/pair_eff.html | 0
doc/{ => doc2}/pair_eim.html | 0
doc/{ => doc2}/pair_gauss.html | 0
doc/{ => doc2}/pair_gayberne.html | 0
doc/{ => doc2}/pair_gran.html | 0
doc/{ => doc2}/pair_gromacs.html | 0
doc/{ => doc2}/pair_hbond_dreiding.html | 0
doc/doc2/pair_hybrid.html | 390 +
doc/doc2/pair_kim.html | 123 +
doc/{ => doc2}/pair_lcbop.html | 0
doc/{ => doc2}/pair_line_lj.html | 0
doc/{ => doc2}/pair_list.html | 0
doc/doc2/pair_lj.html | 366 +
doc/{ => doc2}/pair_lj96.html | 0
doc/doc2/pair_lj_cubic.html | 138 +
doc/doc2/pair_lj_cut_smooth.html | 111 +
doc/{ => doc2}/pair_lj_expand.html | 0
doc/{ => doc2}/pair_lj_long.html | 0
doc/{ => doc2}/pair_lj_sf.html | 0
doc/{ => doc2}/pair_lj_smooth.html | 0
doc/{ => doc2}/pair_lj_smooth_linear.html | 0
doc/doc2/pair_lj_soft.html | 299 +
doc/{ => doc2}/pair_lubricate.html | 0
doc/{ => doc2}/pair_lubricateU.html | 0
doc/{ => doc2}/pair_meam.html | 0
doc/{ => doc2}/pair_meam_spline.html | 0
doc/{ => doc2}/pair_meam_sw_spline.html | 0
doc/doc2/pair_mgpt.html | 229 +
doc/{ => doc2}/pair_mie.html | 0
doc/doc2/pair_modify.html | 271 +
doc/{ => doc2}/pair_morse.html | 0
doc/{ => doc2}/pair_nb3b_harmonic.html | 0
doc/{ => doc2}/pair_nm.html | 0
doc/{ => doc2}/pair_none.html | 0
doc/{ => doc2}/pair_peri.html | 0
doc/doc2/pair_polymorphic.html | 245 +
doc/{ => doc2}/pair_quip.html | 0
doc/doc2/pair_reax.html | 218 +
doc/{ => doc2}/pair_reax_c.html | 0
doc/{ => doc2}/pair_resquared.html | 0
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 | 0
doc/{ => doc2}/pair_soft.html | 0
doc/{ => doc2}/pair_sph_heatconduction.html | 0
doc/{ => doc2}/pair_sph_idealgas.html | 0
doc/{ => doc2}/pair_sph_lj.html | 0
doc/{ => doc2}/pair_sph_rhosum.html | 0
doc/{ => doc2}/pair_sph_taitwater.html | 0
doc/{ => doc2}/pair_sph_taitwater_morris.html | 0
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 | 0
doc/doc2/pair_vashishta.html | 236 +
doc/{ => doc2}/pair_write.html | 0
doc/{ => doc2}/pair_yukawa.html | 0
doc/{ => doc2}/pair_yukawa_colloid.html | 0
doc/doc2/pair_zbl.html | 148 +
doc/{ => doc2}/partition.html | 0
doc/doc2/prd.html | 339 +
doc/doc2/print.html | 86 +
doc/{ => doc2}/processors.html | 0
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 | 0
doc/{ => doc2}/replicate.html | 0
doc/doc2/rerun.html | 210 +
doc/{ => doc2}/reset_timestep.html | 0
doc/doc2/restart.html | 187 +
doc/{ => doc2}/run.html | 0
doc/doc2/run_style.html | 298 +
doc/doc2/search.html | 206 +
doc/doc2/set.html | 415 +
doc/{ => doc2}/shell.html | 0
doc/doc2/special_bonds.html | 276 +
doc/doc2/suffix.html | 111 +
doc/{ => doc2}/tad.html | 0
doc/doc2/temper.html | 137 +
doc/{ => doc2}/thermo.html | 0
doc/{ => doc2}/thermo_modify.html | 0
doc/{ => doc2}/thermo_style.html | 0
doc/doc2/timer.html | 79 +
doc/doc2/timestep.html | 58 +
doc/doc2/tutorial_drude.html | 467 +
doc/{ => doc2}/uncompute.html | 0
doc/{ => doc2}/undump.html | 0
doc/{ => doc2}/unfix.html | 0
doc/doc2/units.html | 223 +
doc/doc2/variable.html | 1218 +
doc/{ => doc2}/velocity.html | 0
doc/doc2/write_data.html | 131 +
doc/{ => doc2}/write_dump.html | 0
doc/doc2/write_restart.html | 130 +
doc/dump.html | 1025 +-
doc/dump.txt | 37 +-
doc/dump_h5md.html | 299 +
doc/dump_h5md.txt | 124 +
doc/dump_image.html | 1045 +-
doc/dump_modify.html | 1506 +-
doc/dump_modify.txt | 2 +-
doc/dump_molfile.html | 339 +-
doc/echo.html | 255 +-
doc/fix.html | 638 +-
doc/fix.txt | 2 +-
doc/fix_adapt.html | 612 +-
doc/fix_adapt.txt | 15 +-
doc/fix_adapt_fep.html | 629 +-
doc/fix_adapt_fep.txt | 3 -
doc/fix_addforce.html | 442 +-
doc/fix_addtorque.html | 325 +-
doc/fix_append_atoms.html | 366 +-
doc/fix_atc.html | 668 +-
doc/fix_atom_swap.html | 538 +-
doc/fix_atom_swap.txt | 138 +-
doc/fix_ave_atom.html | 397 +-
doc/fix_ave_chunk.html | 780 +-
doc/fix_ave_chunk.txt | 24 +-
doc/fix_ave_correlate.html | 706 +-
doc/fix_ave_correlate.txt | 8 +-
doc/fix_ave_correlate_long.html | 317 +
doc/fix_ave_correlate_long.txt | 144 +
doc/fix_ave_histo.html | 695 +-
doc/fix_ave_histo.txt | 31 +-
doc/fix_ave_spatial.html | 784 +-
doc/fix_ave_spatial_sphere.html | 625 +-
doc/fix_ave_time.html | 665 +-
doc/fix_ave_time.txt | 11 +-
doc/fix_aveforce.html | 362 +-
doc/fix_balance.html | 588 +-
doc/fix_balance.txt | 4 +-
doc/fix_bond_break.html | 390 +-
doc/fix_bond_create.html | 543 +-
doc/fix_bond_swap.html | 416 +-
doc/fix_box_relax.html | 659 +-
doc/fix_colvars.html | 387 +-
doc/fix_deform.html | 892 +-
doc/fix_deform.txt | 24 +
doc/fix_deposit.html | 597 +-
doc/fix_deposit.txt | 26 +-
doc/fix_drag.html | 290 +-
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 | 352 +-
doc/fix_efield.html | 408 +-
doc/fix_enforce2d.html | 299 +-
doc/fix_evaporate.html | 326 +-
doc/fix_external.html | 421 +-
doc/fix_freeze.html | 322 +-
doc/fix_gcmc.html | 695 +-
doc/fix_gcmc.txt | 176 +-
doc/fix_gld.html | 396 +-
doc/fix_gle.html | 419 +-
doc/fix_gle.txt | 2 +-
doc/fix_gravity.html | 395 +-
doc/fix_heat.html | 365 +-
doc/fix_imd.html | 387 +-
doc/fix_indent.html | 484 +-
doc/fix_ipi.html | 329 +-
doc/fix_langevin.html | 600 +-
doc/fix_langevin.txt | 4 +
doc/fix_langevin_drude.html | 434 +
doc/fix_langevin_drude.txt | 261 +
doc/fix_langevin_eff.html | 370 +-
doc/fix_lb_fluid.html | 690 +-
doc/fix_lb_momentum.html | 307 +-
doc/fix_lb_pc.html | 306 +-
doc/fix_lb_rigid_pc_sphere.html | 397 +-
doc/fix_lb_viscous.html | 331 +-
doc/fix_lineforce.html | 274 +-
doc/fix_meso.html | 273 +-
doc/fix_meso_stationary.html | 273 +-
doc/fix_modify.html | 291 +-
doc/fix_momentum.html | 304 +-
doc/fix_momentum.txt | 7 +-
doc/fix_move.html | 506 +-
doc/fix_msst.html | 418 +-
doc/fix_neb.html | 343 +-
doc/fix_nh.html | 972 +-
doc/fix_nh.txt | 3 +
doc/fix_nh_eff.html | 388 +-
doc/fix_nph_asphere.html | 412 +-
doc/fix_nph_sphere.html | 407 +-
doc/fix_nphug.html | 538 +-
doc/fix_npt_asphere.html | 437 +-
doc/fix_npt_sphere.html | 432 +-
doc/fix_nve.html | 325 +-
doc/fix_nve_asphere.html | 285 +-
doc/fix_nve_asphere_noforce.html | 287 +-
doc/fix_nve_body.html | 289 +-
doc/fix_nve_eff.html | 292 +-
doc/fix_nve_limit.html | 308 +-
doc/fix_nve_line.html | 280 +-
doc/fix_nve_noforce.html | 278 +-
doc/fix_nve_sphere.html | 333 +-
doc/fix_nve_tri.html | 280 +-
doc/fix_nvt_asphere.html | 410 +-
doc/fix_nvt_sllod.html | 440 +-
doc/fix_nvt_sllod_eff.html | 332 +-
doc/fix_nvt_sphere.html | 405 +-
doc/fix_oneway.html | 279 +-
doc/fix_orient_fcc.html | 413 +-
doc/fix_phonon.html | 490 +-
doc/fix_pimd.html | 431 +-
doc/fix_planeforce.html | 274 +-
doc/fix_poems.html | 362 +-
doc/fix_pour.html | 544 +-
doc/fix_press_berendsen.html | 493 +-
doc/fix_print.html | 324 +-
doc/fix_print.txt | 2 +
doc/fix_property_atom.html | 498 +-
doc/fix_property_atom.txt | 9 +
doc/fix_qbmsst.html | 379 +
doc/fix_qbmsst.txt | 219 +
doc/fix_qeq.html | 501 +-
doc/fix_qeq_comb.html | 379 +-
doc/fix_qeq_reax.html | 353 +-
doc/fix_qmmm.html | 280 +-
doc/fix_qtb.html | 342 +
doc/fix_qtb.txt | 182 +
doc/fix_reax_bonds.html | 310 +-
doc/fix_reaxc_species.html | 399 +-
doc/fix_recenter.html | 360 +-
doc/fix_restrain.html | 444 +-
doc/fix_restrain.txt | 4 +-
doc/fix_rigid.html | 1291 +-
doc/fix_rigid.txt | 146 +-
doc/fix_saed_vtk.html | 354 +
doc/fix_saed_vtk.txt | 189 +
doc/fix_setforce.html | 360 +-
doc/fix_shake.html | 474 +-
doc/fix_shake.txt | 3 +
doc/fix_smd.html | 410 +-
doc/fix_smd.rst | 168 +
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 +
.../fix_smd_tlsph_reference_configuration.txt | 0
doc/fix_smd_wall_surface.html | 244 +
doc/fix_smd_wall_surface.txt | 58 +
doc/fix_spring.html | 375 +-
doc/fix_spring_rg.html | 309 +-
doc/fix_spring_self.html | 308 +-
doc/fix_srd.html | 731 +-
doc/fix_srd.txt | 2 +-
doc/fix_store_force.html | 293 +-
doc/fix_store_state.html | 431 +-
doc/fix_temp_berendsen.html | 445 +-
doc/fix_temp_csvr.html | 437 +-
doc/fix_temp_csvr.txt | 76 +-
doc/fix_temp_rescale.html | 445 +-
doc/fix_temp_rescale_eff.html | 324 +-
doc/fix_tfmc.html | 384 +-
doc/fix_thermal_conductivity.html | 400 +-
doc/fix_thermal_conductivity.txt | 10 +-
doc/fix_ti_rs.html | 404 +-
doc/fix_ti_spring.html | 425 +-
doc/fix_tmd.html | 378 +-
doc/fix_ttm.html | 615 +-
doc/fix_tune_kspace.html | 328 +-
doc/fix_vector.html | 410 +-
doc/fix_vector.txt | 2 +-
doc/fix_viscosity.html | 405 +-
doc/fix_viscous.html | 360 +-
doc/fix_wall.html | 652 +-
doc/fix_wall_gran.html | 412 +-
doc/fix_wall_piston.html | 370 +-
doc/fix_wall_reflect.html | 448 +-
doc/fix_wall_reflect.txt | 24 +
doc/fix_wall_region.html | 487 +-
doc/fix_wall_srd.html | 471 +-
doc/genindex.html | 2240 +
doc/group.html | 565 +-
doc/group.txt | 7 +-
doc/group2ndx.html | 268 +-
doc/if.html | 475 +-
doc/improper_class2.html | 376 +-
doc/improper_coeff.html | 330 +-
doc/improper_cossq.html | 338 +-
doc/improper_cvff.html | 332 +-
doc/improper_fourier.html | 333 +-
doc/improper_harmonic.html | 340 +-
doc/improper_harmonic.txt | 1 +
doc/improper_hybrid.html | 290 +-
doc/improper_none.html | 236 +-
doc/improper_ring.html | 350 +-
doc/improper_style.html | 335 +-
doc/improper_umbrella.html | 329 +-
doc/include.html | 253 +-
doc/info.html | 266 +
doc/info.txt | 86 +
doc/jump.html | 376 +-
doc/kspace_modify.html | 577 +-
doc/kspace_style.html | 738 +-
doc/label.html | 245 +-
doc/lattice.html | 554 +-
doc/lattice.txt | 33 +
doc/log.html | 266 +-
doc/mass.html | 308 +-
doc/mass.txt | 7 +-
doc/min_modify.html | 299 +-
doc/min_style.html | 332 +-
doc/minimize.html | 551 +-
doc/molecule.html | 861 +-
doc/molecule.txt | 117 +-
doc/neb.html | 688 +-
doc/neigh_modify.html | 456 +-
doc/neigh_modify.txt | 2 +-
doc/neighbor.html | 313 +-
doc/neighbor.txt | 8 +-
doc/newton.html | 305 +-
doc/next.html | 385 +-
doc/package.html | 1101 +-
doc/package.txt | 11 +-
doc/pair_adp.html | 463 +-
doc/pair_airebo.html | 456 +-
doc/pair_awpmd.html | 385 +-
doc/pair_beck.html | 371 +-
doc/pair_body.html | 357 +-
doc/pair_bop.html | 946 +-
doc/pair_bop.txt | 326 +-
doc/pair_born.html | 534 +-
doc/pair_born.txt | 14 +-
doc/pair_brownian.html | 434 +-
doc/pair_buck.html | 548 +-
doc/pair_buck.txt | 21 +-
doc/pair_buck_long.html | 440 +-
doc/pair_charmm.html | 538 +-
doc/pair_class2.html | 503 +-
doc/pair_class2.txt | 3 +
doc/pair_coeff.html | 375 +-
doc/pair_colloid.html | 481 +-
doc/pair_colloid.txt | 2 +-
doc/pair_comb.html | 476 +-
doc/pair_comb.txt | 8 +-
doc/pair_coul.html | 769 +-
doc/pair_coul.txt | 22 +-
doc/pair_coul_diel.html | 360 +-
doc/pair_cs.html | 335 +-
doc/pair_dipole.html | 585 +-
doc/pair_dpd.html | 521 +-
doc/pair_dsmc.html | 404 +-
doc/pair_dsmc.txt | 2 +-
doc/pair_eam.html | 935 +-
doc/pair_eam.txt | 12 +-
doc/pair_edip.html | 435 +-
doc/pair_eff.html | 523 +-
doc/pair_eim.html | 427 +-
doc/pair_gauss.html | 452 +-
doc/pair_gayberne.html | 523 +-
doc/pair_gran.html | 540 +-
doc/pair_gromacs.html | 463 +-
doc/pair_hbond_dreiding.html | 584 +-
doc/pair_hybrid.html | 673 +-
doc/pair_hybrid.txt | 58 +-
doc/pair_kim.html | 370 +-
doc/pair_kim.txt | 12 +-
doc/pair_lcbop.html | 338 +-
doc/pair_line_lj.html | 364 +-
doc/pair_list.html | 431 +-
doc/pair_lj.html | 780 +-
doc/pair_lj.txt | 12 +-
doc/pair_lj96.html | 367 +-
doc/pair_lj_cubic.html | 417 +-
doc/pair_lj_cubic.txt | 36 +-
doc/pair_lj_expand.html | 371 +-
doc/pair_lj_long.html | 532 +-
doc/pair_lj_sf.html | 364 +-
doc/pair_lj_smooth.html | 380 +-
doc/pair_lj_smooth_linear.html | 353 +-
doc/pair_lj_soft.html | 670 +-
doc/pair_lj_soft.txt | 86 +-
doc/pair_lubricate.html | 546 +-
doc/pair_lubricateU.html | 503 +-
doc/pair_meam.html | 613 +-
doc/pair_meam_spline.html | 404 +-
doc/pair_meam_sw_spline.html | 397 +-
doc/pair_mgpt.html | 378 +
doc/pair_mgpt.txt | 219 +
doc/pair_mie.html | 348 +-
doc/pair_modify.html | 516 +-
doc/pair_modify.txt | 62 +-
doc/pair_morse.html | 368 +-
doc/pair_nb3b_harmonic.html | 380 +-
doc/pair_nm.html | 481 +-
doc/pair_none.html | 248 +-
doc/pair_peri.html | 547 +-
doc/pair_polymorphic.html | 380 +
doc/pair_polymorphic.txt | 229 +
doc/pair_quip.html | 328 +-
doc/pair_reax.html | 494 +-
doc/pair_reax.txt | 8 +-
doc/pair_reax_c.html | 639 +-
doc/pair_resquared.html | 528 +-
doc/pair_sdk.html | 458 +-
doc/pair_sdk.txt | 1 +
doc/pair_smd_hertz.html | 233 +
doc/pair_smd_hertz.txt | 56 +
doc/pair_smd_tlsph.html | 243 +
doc/pair_smd_tlsph.txt | 67 +
doc/pair_smd_triangulated_surface.html | 234 +
doc/pair_smd_triangulated_surface.txt | 57 +
doc/pair_smd_ulsph.html | 248 +
doc/pair_smd_ulsph.txt | 71 +
doc/pair_smtbq.html | 428 +
doc/pair_smtbq.txt | 261 +
doc/pair_snap.html | 500 +-
doc/pair_soft.html | 393 +-
doc/pair_sph_heatconduction.html | 308 +-
doc/pair_sph_idealgas.html | 314 +-
doc/pair_sph_lj.html | 318 +-
doc/pair_sph_rhosum.html | 311 +-
doc/pair_sph_taitwater.html | 335 +-
doc/pair_sph_taitwater_morris.html | 331 +-
doc/pair_srp.html | 454 +-
doc/pair_srp.txt | 56 +-
doc/pair_style.html | 568 +-
doc/pair_style.txt | 10 +-
doc/pair_sw.html | 470 +-
doc/pair_sw.txt | 1 +
doc/pair_table.html | 551 +-
doc/pair_table.txt | 6 +-
doc/pair_tersoff.html | 538 +-
doc/pair_tersoff.txt | 4 +-
doc/pair_tersoff_mod.html | 476 +-
doc/pair_tersoff_mod.txt | 1 +
doc/pair_tersoff_zbl.html | 534 +-
doc/pair_tersoff_zbl.txt | 1 +
doc/pair_thole.html | 285 +
doc/pair_thole.txt | 126 +
doc/pair_tri_lj.html | 366 +-
doc/pair_vashishta.html | 384 +
doc/pair_vashishta.txt | 228 +
doc/pair_write.html | 322 +-
doc/pair_yukawa.html | 358 +-
doc/pair_yukawa_colloid.html | 435 +-
doc/pair_zbl.html | 403 +-
doc/pair_zbl.txt | 38 +-
doc/partition.html | 299 +-
doc/prd.html | 584 +-
doc/prd.txt | 8 +-
doc/print.html | 306 +-
doc/print.txt | 19 +-
doc/processors.html | 657 +-
doc/python.html | 640 +
doc/python.txt | 482 +
doc/quit.html | 272 +-
doc/quit.txt | 21 +-
doc/read_data.html | 2072 +-
doc/read_data.txt | 184 +-
doc/read_dump.html | 631 +-
doc/read_dump.txt | 4 +-
doc/read_restart.html | 477 +-
doc/read_restart.txt | 40 +-
doc/region.html | 654 +-
doc/replicate.html | 283 +-
doc/rerun.html | 457 +-
doc/rerun.txt | 4 +-
doc/reset_timestep.html | 279 +-
doc/restart.html | 421 +-
doc/restart.txt | 15 +-
doc/run.html | 472 +-
doc/run_style.html | 594 +-
doc/run_style.txt | 32 +-
doc/search.html | 206 +
doc/searchindex.js | 1 +
doc/set.html | 711 +-
doc/set.txt | 33 +-
doc/shell.html | 342 +-
doc/special_bonds.html | 499 +-
doc/special_bonds.txt | 33 +-
doc/suffix.html | 339 +-
doc/suffix.txt | 26 +-
doc/tad.html | 556 +-
doc/temper.html | 384 +-
doc/temper.txt | 2 +-
doc/thermo.html | 283 +-
doc/thermo_modify.html | 422 +-
doc/thermo_style.html | 747 +-
doc/timer.html | 265 +
doc/timer.txt | 73 +
doc/timestep.html | 326 +-
doc/timestep.txt | 21 +-
doc/tutorial_drude.html | 595 +
doc/tutorial_drude.txt | 463 +
doc/uncompute.html | 248 +-
doc/undump.html | 262 +-
doc/unfix.html | 248 +-
doc/units.html | 574 +-
doc/units.txt | 18 +
doc/variable.html | 1719 +-
doc/variable.txt | 178 +-
doc/velocity.html | 553 +-
doc/write_data.html | 355 +-
doc/write_data.txt | 8 +-
doc/write_dump.html | 320 +-
doc/write_restart.html | 356 +-
doc/write_restart.txt | 7 +-
examples/ASPHERE/box/in.box | 4 +
examples/ASPHERE/box/in.box.mp | 4 +
examples/ASPHERE/star/in.star | 4 +
examples/ASPHERE/star/in.star.mp | 4 +
examples/COUPLE/README | 15 +-
examples/COUPLE/multiple/README | 35 +
examples/COUPLE/multiple/data.chain | 95710 +++++++++++++++++++
examples/COUPLE/multiple/in.chain | 25 +
examples/COUPLE/multiple/multiple.cpp | 134 +
examples/COUPLE/simple/README | 47 +-
examples/ELASTIC/Si.sw | 1 +
examples/ELASTIC/displace.mod | 16 +-
examples/ELASTIC/displace_restart.mod | 134 -
examples/ELASTIC/displace_reverse.mod | 162 -
examples/ELASTIC/in.elastic | 31 +-
examples/ELASTIC/init.mod | 4 +
examples/ELASTIC_T/Si.sw | 18 +
examples/ELASTIC_T/displace.mod | 140 +
examples/ELASTIC_T/in.elastic | 210 +
examples/ELASTIC_T/init.mod | 40 +
examples/ELASTIC_T/potential.mod | 28 +
examples/README | 13 +-
examples/USER/diffraction/BulkNi.in | 34 +
examples/USER/diffraction/Output/BulkNi.in | 35 +
.../diffraction/Output/bulkNi.hist.xrd.correct | 204 +
.../USER/diffraction/Output/bulkNi.log.correct | 63 +
.../Output/bulkNi_001.saed.0.vtk.correct | 17966 ++++
.../Output/bulkNi_001.saed.0_VisIt_Image.png | Bin 0 -> 91543 bytes
examples/USER/diffraction/Output/log.cite | 26 +
examples/USER/diffraction/README | 88 +
examples/USER/drude/README | 13 +
examples/USER/drude/butane/data.butane | 21561 +++++
examples/USER/drude/butane/in.butane.lang | 58 +
examples/USER/drude/butane/in.butane.nh | 62 +
.../drude/butane/log.butane.lang.18Jul15.linux.1 | 171 +
.../drude/butane/log.butane.lang.18Jul15.linux.4 | 171 +
.../drude/butane/log.butane.nh.18Jul15.linux.3 | 177 +
.../drude/butane/log.butane.nh.18Jul15.linux.4 | 177 +
examples/USER/drude/ethanol/data.ethanol | 12067 +++
examples/USER/drude/ethanol/in.ethanol.lang | 80 +
examples/USER/drude/ethanol/in.ethanol.nh | 86 +
.../drude/ethanol/log.ethanol.lang.8Jul15.linux.1 | 254 +
.../drude/ethanol/log.ethanol.lang.8Jul15.linux.4 | 254 +
.../drude/ethanol/log.ethanol.nh.8Jul15.linux.1 | 263 +
.../drude/ethanol/log.ethanol.nh.8Jul15.linux.4 | 263 +
examples/USER/drude/swm4-ndp/data.swm4-ndp | 5037 +
examples/USER/drude/swm4-ndp/in.swm4-ndp.lang | 47 +
examples/USER/drude/swm4-ndp/in.swm4-ndp.nh | 50 +
.../swm4-ndp/log.swm4-ndp.lang.8Jul15.linux.1 | 230 +
.../swm4-ndp/log.swm4-ndp.lang.8Jul15.linux.4 | 230 +
.../drude/swm4-ndp/log.swm4-ndp.nh.8Jul15.linux.1 | 236 +
.../drude/swm4-ndp/log.swm4-ndp.nh.8Jul15.linux.4 | 236 +
examples/USER/fep/CH4hyd/fdti01/fdti01.lmp | 44 +-
examples/USER/fep/CH4hyd/fdti01/in.fdti01.lmp | 53 +-
examples/USER/fep/CH4hyd/fdti01/log.lammps | 7682 +-
examples/USER/fep/CH4hyd/fdti10/fdti10.lmp | 44 +-
examples/USER/fep/CH4hyd/fdti10/in.fdti10.lmp | 52 +-
examples/USER/fep/CH4hyd/fdti10/log.lammps | 7674 +-
examples/USER/fep/CH4hyd/fep01/fep01.lmp | 44 +-
examples/USER/fep/CH4hyd/fep01/in.fep01.lmp | 53 +-
examples/USER/fep/CH4hyd/fep01/log.lammps | 7682 +-
examples/USER/fep/CH4hyd/fep10/fep10.lmp | 44 +-
examples/USER/fep/CH4hyd/fep10/in.fep10.lmp | 52 +-
examples/USER/fep/CH4hyd/fep10/log.lammps | 7674 +-
examples/USER/lb/polymer/in.polymer | 105 -
examples/USER/lb/polymer/in.polymer_default_gamma | 107 +
examples/USER/lb/polymer/in.polymer_setgamma | 105 +
examples/USER/lb/polymer/out.polymer | 19 -
examples/USER/lb/polymer/out.polymer_default_gamma | 83 +
examples/USER/lb/polymer/out.polymer_setgamma | 83 +
examples/USER/mgpt/Ta6.8x.mgpt.README | 57 +
examples/USER/mgpt/Ta6.8x.mgpt.parmin | 2 +
examples/USER/mgpt/Ta6.8x.mgpt.potin | 11253 +++
examples/USER/mgpt/in.bcc0 | 68 +
examples/USER/mgpt/in.vac0-bcc | 76 +
examples/USER/mgpt/in.vacmin-bcc | 71 +
examples/USER/mgpt/log.bcc0 | 53 +
examples/USER/mgpt/log.lammps | 78 +
examples/USER/mgpt/log.vac0-bcc | 55 +
examples/USER/mgpt/log.vacmin-bcc | 78 +
examples/USER/qtb/README | 10 +
.../alpha_quartz_qbmsst/alpha_quartz_potential.mod | 15 +
.../qtb/alpha_quartz_qbmsst/alpha_quartz_qbmsst.in | 55 +
.../qtb/alpha_quartz_qbmsst/alpha_quartz_qtb.mod | 62 +
.../qtb/alpha_quartz_qbmsst/potential_SiO2.TPF | 79811 ++++++++++++++++
.../USER/qtb/alpha_quartz_qtb/alpha_quartz_qtb.in | 79 +
examples/USER/qtb/methane_qbmsst/ffield.reax | 183 +
examples/USER/qtb/methane_qbmsst/methane_qbmsst.in | 33 +
examples/USER/qtb/methane_qbmsst/methane_qtb.mod | 63 +
examples/USER/qtb/methane_qtb/ffield.reax | 183 +
examples/USER/qtb/methane_qtb/methane_qtb.in | 69 +
examples/USER/smd/README | 7 +
.../aluminum_strip_pull/aluminum_strip_pull.lmp | 139 +
.../fluid_structure_interaction.lmp | 156 +
examples/USER/smd/funnel_flow/boundary.stl | 66306 +++++++++++++
examples/USER/smd/funnel_flow/funnel_flow.lmp | 130 +
.../USER/smd/rubber_rings_3d/rubber_rings_3d.lmp | 112 +
.../smd/rubber_rings_3d/washer_hex_adjusted.data | 973 +
examples/USER/smd/rubber_strip_pull/plot.gpl | 13 +
.../smd/rubber_strip_pull/rubber_strip_pull.lmp | 109 +
examples/USER/smtbq/data.Alpha | 1811 +
examples/USER/smtbq/ffield.smtbq.Al | 34 +
examples/USER/smtbq/ffield.smtbq.Al2O3 | 56 +
examples/USER/smtbq/ffield.smtbq.TiO2 | 53 +
examples/USER/smtbq/in.smtbq.Al | 77 +
examples/USER/smtbq/in.smtbq.Al2O3 | 55 +
examples/USER/smtbq/in.smtbq.TiO2 | 97 +
examples/USER/smtbq/log.smtbq.Al | 279 +
examples/USER/smtbq/log.smtbq.Al2O3 | 210 +
examples/USER/smtbq/log.smtbq.TiO2 | 255 +
examples/USER/tally/README | 6 +
examples/USER/tally/data.spce | 9029 ++
examples/USER/tally/in.force | 57 +
examples/USER/tally/in.pe | 63 +
examples/USER/tally/in.stress | 55 +
examples/USER/tally/log.21Aug15.force.1 | 136 +
examples/USER/tally/log.21Aug15.force.4 | 136 +
examples/USER/tally/log.21Aug15.pe.1 | 144 +
examples/USER/tally/log.21Aug15.pe.4 | 144 +
examples/USER/tally/log.21Aug15.stress.1 | 135 +
examples/USER/tally/log.21Aug15.stress.4 | 135 +
.../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 +
examples/balance/log.balance.8Aug14.linux.1 | 187 -
examples/balance/log.balance.8Aug14.linux.4 | 187 -
.../balance/log.balance.bond.fast.21Jan15.linux.1 | 203 -
.../balance/log.balance.bond.fast.21Jan15.linux.4 | 203 -
.../balance/log.balance.bond.slow.21Jan15.linux.1 | 502 -
.../balance/log.balance.bond.slow.21Jan15.linux.4 | 502 -
examples/body/log.15May15.body.g++.1 | 75 +
examples/body/log.15May15.body.g++.4 | 75 +
examples/body/log.body.1Feb14.linux.1 | 71 -
examples/body/log.body.1Feb14.linux.4 | 71 -
examples/colloid/log.15May15.colloid.g++.1 | 135 +
examples/colloid/log.15May15.colloid.g++.4 | 135 +
examples/colloid/log.colloid.1Feb14.linux.1 | 131 -
examples/colloid/log.colloid.1Feb14.linux.4 | 131 -
examples/comb/ffield.comb | 108 +-
examples/comb/ffield.comb3 | 866 +-
examples/comb/lib.comb3 | 4104 +-
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.comb.Cu.1Feb14.linux.1 | 76 -
examples/comb/log.comb.Cu.1Feb14.linux.4 | 76 -
examples/comb/log.comb.Cu2O.elastic.1Feb14.linux.1 | 316 -
examples/comb/log.comb.Cu2O.elastic.1Feb14.linux.4 | 316 -
examples/comb/log.comb.HfO2.1Feb14.linux.1 | 185 -
examples/comb/log.comb.HfO2.1Feb14.linux.4 | 185 -
examples/comb/log.comb.Si.1Feb14.linux.1 | 76 -
examples/comb/log.comb.Si.1Feb14.linux.4 | 76 -
examples/comb/log.comb.Si.elastic.1Feb14.linux.1 | 274 -
examples/comb/log.comb.Si.elastic.1Feb14.linux.4 | 274 -
examples/comb/log.comb3.1Feb14.linux.1 | 73 -
examples/comb/log.comb3.1Feb14.linux.4 | 73 -
examples/crack/log.15May15.crack.g++.1 | 142 +
examples/crack/log.15May15.crack.g++.4 | 142 +
examples/crack/log.crack.1Feb14.linux.1 | 138 -
examples/crack/log.crack.1Feb14.linux.4 | 138 -
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/dipole/log.15May15.dipole.g++.1 | 93 +
examples/dipole/log.15May15.dipole.g++.4 | 93 +
examples/dipole/log.dipole.1Feb14.linux.1 | 89 -
examples/dipole/log.dipole.1Feb14.linux.4 | 89 -
examples/dreiding/log.15May15.dreiding.g++.1 | 107 +
examples/dreiding/log.15May15.dreiding.g++.4 | 107 +
examples/dreiding/log.dreiding.1Feb14.linux.1 | 106 -
examples/dreiding/log.dreiding.1Feb14.linux.4 | 106 -
examples/eim/ffield.eim | 2 +-
examples/eim/log.15May15.eim.g++.1 | 76 +
examples/eim/log.15May15.eim.g++.4 | 76 +
examples/eim/log.eim.1Feb14.linux.1 | 72 -
examples/eim/log.eim.1Feb14.linux.4 | 72 -
.../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 +
.../ellipse/log.ellipse.gayberne.1Feb14.linux.1 | 163 -
.../ellipse/log.ellipse.gayberne.1Feb14.linux.4 | 163 -
.../ellipse/log.ellipse.resquared.1Feb14.linux.1 | 160 -
.../ellipse/log.ellipse.resquared.1Feb14.linux.4 | 160 -
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.flow.couette.1Feb14.linux.1 | 130 -
examples/flow/log.flow.couette.1Feb14.linux.4 | 130 -
examples/flow/log.flow.pois.1Feb14.linux.1 | 130 -
examples/flow/log.flow.pois.1Feb14.linux.4 | 130 -
examples/friction/log.15May15.friction.g++.1 | 153 +
examples/friction/log.15May15.friction.g++.4 | 153 +
examples/friction/log.friction.1Feb14.linux.1 | 149 -
examples/friction/log.friction.1Feb14.linux.4 | 149 -
examples/hugoniostat/log.15May15.hugoniostat.g++.1 | 98 +
examples/hugoniostat/log.15May15.hugoniostat.g++.4 | 98 +
.../hugoniostat/log.hugoniostat.1Feb14.linux.1 | 90 -
.../hugoniostat/log.hugoniostat.1Feb14.linux.4 | 90 -
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.indent.1Feb14.linux.1 | 179 -
examples/indent/log.indent.1Feb14.linux.4 | 179 -
examples/indent/log.indent.min.1Feb14.linux.1 | 404 -
examples/indent/log.indent.min.1Feb14.linux.4 | 405 -
examples/kim/log.kim.lj.27Jul14.ubuntu.1 | 29 -
examples/kim/log.kim.lj.27Jul14.ubuntu.4 | 29 -
examples/kim/log.kim.lj.28jun15.ubuntu.1 | 33 +
examples/kim/log.kim.lj.28jun15.ubuntu.4 | 33 +
examples/kim/log.kim.lj.lmp.27Jul14.ubuntu.1 | 29 -
examples/kim/log.kim.lj.lmp.27Jul14.ubuntu.4 | 29 -
examples/kim/log.kim.lj.lmp.28jun15.ubuntu.1 | 33 +
examples/kim/log.kim.lj.lmp.28jun15.ubuntu.4 | 33 +
examples/meam/Ni.meam | 1 +
examples/meam/SiC.meam | 1 +
examples/meam/library.meam | 16 +
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.meam.1Feb14.linux.1 | 67 -
examples/meam/log.meam.1Feb14.linux.4 | 67 -
examples/meam/log.meam.shear.1Feb14.linux.1 | 172 -
examples/meam/log.meam.shear.1Feb14.linux.4 | 172 -
examples/melt/log.15May15.melt.g++.1 | 67 +
examples/melt/log.15May15.melt.g++.4 | 67 +
examples/melt/log.melt.1Feb14.linux.1 | 63 -
examples/melt/log.melt.1Feb14.linux.4 | 63 -
examples/micelle/log.15May15.micelle.g++.1 | 223 +
examples/micelle/log.15May15.micelle.g++.4 | 223 +
examples/micelle/log.micelle.1Feb14.linux.1 | 215 -
examples/micelle/log.micelle.1Feb14.linux.4 | 215 -
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.min.1Feb14.linux.1 | 118 -
examples/min/log.min.1Feb14.linux.4 | 118 -
examples/min/log.min.box.1Feb14.linux.1 | 356 -
examples/min/log.min.box.1Feb14.linux.4 | 356 -
examples/msst/log.15May15.msst.g++.1 | 142 +
examples/msst/log.15May15.msst.g++.4 | 142 +
examples/msst/log.msst.1Feb14.linux.1 | 138 -
examples/msst/log.msst.1Feb14.linux.4 | 138 -
examples/nb3b/MOH.nb3b.harmonic | 11 +-
examples/nb3b/log.15May15.nb3b.g++.1 | 152 +
examples/nb3b/log.15May15.nb3b.g++.4 | 152 +
examples/nb3b/log.nb3b.1Feb14.linux.1 | 144 -
examples/nb3b/log.nb3b.1Feb14.linux.4 | 144 -
examples/neb/Si.sw | 1 +
examples/nemd/log.15May15.nemd.g++.1 | 119 +
examples/nemd/log.15May15.nemd.g++.4 | 119 +
examples/nemd/log.nemd.1Feb14.linux.1 | 115 -
examples/nemd/log.nemd.1Feb14.linux.4 | 115 -
examples/obstacle/log.15May15.obstacle.g++.1 | 144 +
examples/obstacle/log.15May15.obstacle.g++.4 | 144 +
examples/obstacle/log.obstacle.1Feb14.linux.1 | 140 -
examples/obstacle/log.obstacle.1Feb14.linux.4 | 140 -
examples/peptide/log.15May15.peptide.g++.1 | 178 +
examples/peptide/log.15May15.peptide.g++.4 | 178 +
examples/peptide/log.peptide.1Feb14.linux.1 | 177 -
examples/peptide/log.peptide.1Feb14.linux.4 | 177 -
examples/peri/log.15May15.peri.g++.1 | 94 +
examples/peri/log.15May15.peri.g++.4 | 94 +
examples/peri/log.peri.1Feb14.linux.1 | 90 -
examples/peri/log.peri.1Feb14.linux.4 | 90 -
examples/pour/in.pour.2d.molecule | 8 +-
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.pour.1Feb14.linux.1 | 147 -
examples/pour/log.pour.1Feb14.linux.4 | 147 -
examples/pour/log.pour.2d.1Feb14.linux.1 | 100 -
examples/pour/log.pour.2d.1Feb14.linux.4 | 100 -
examples/pour/log.pour.2d.molecule.1Feb14.linux.1 | 113 -
examples/pour/log.pour.2d.molecule.1Feb14.linux.4 | 113 -
examples/prd/Si.sw | 1 +
examples/python/funcs.py | 22 +
examples/python/in.python | 64 +
examples/python/log.python.17Mar15.linux.1 | 315 +
examples/python/log.python.17Mar15.linux.4 | 315 +
examples/qeq/ffield.reax.cho | 2 +-
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.qeq.buck.8Sep14.linux.1 | 85 -
examples/qeq/log.qeq.buck.8Sep14.linux.4 | 85 -
examples/qeq/log.qeq.reaxc.8Sep14.linux.1 | 89 -
examples/qeq/log.qeq.reaxc.8Sep14.linux.4 | 89 -
examples/reax/AB/ffield.reax.AB | 2 +-
examples/reax/AuO/ffield.reax.AuO | 2 +-
examples/reax/CHO/ffield.reax.cho | 2 +-
examples/reax/FC/ffield.reax.FC | 2 +-
examples/reax/FeOH3/ffield.reax.Fe_O_C_H | 2 +-
examples/reax/RDX/ffield.reax.rdx | 2 +-
examples/reax/VOH/ffield.reax.V_O_C_H | 2 +-
examples/reax/ZnOH2/ffield.reax.ZnOH | 2 +-
examples/reax/ffield.reax | 2 +-
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.reax.rdx.1Feb14.linux.1 | 85 -
examples/reax/log.reax.rdx.1Feb14.linux.4 | 85 -
examples/reax/log.reax.tatb.1Feb14.linux.1 | 81 -
examples/reax/log.reax.tatb.1Feb14.linux.4 | 81 -
examples/reax/log.reaxc.rdx.1Feb14.linux.1 | 88 -
examples/reax/log.reaxc.rdx.1Feb14.linux.4 | 88 -
examples/reax/log.reaxc.tatb.1Feb14.linux.1 | 86 -
examples/reax/log.reaxc.tatb.1Feb14.linux.4 | 86 -
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.rigid.1Feb14.linux.1 | 314 -
examples/rigid/log.rigid.1Feb14.linux.4 | 314 -
examples/rigid/log.rigid.poems.1Feb14.linux.1 | 317 -
examples/rigid/log.rigid.poems.1Feb14.linux.4 | 317 -
examples/rigid/log.rigid.poems2.1Feb14.linux.1 | 321 -
examples/rigid/log.rigid.poems2.1Feb14.linux.4 | 321 -
examples/rigid/log.rigid.tnr.1Feb14.linux.1 | 401 -
examples/rigid/log.rigid.tnr.1Feb14.linux.4 | 401 -
examples/shear/Ni_u3.eam | 2 +-
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.shear.1Feb14.linux.1 | 168 -
examples/shear/log.shear.1Feb14.linux.4 | 168 -
examples/shear/log.shear.void.1Feb14.linux.1 | 169 -
examples/shear/log.shear.void.1Feb14.linux.4 | 169 -
examples/snap/Ta06A.snapcoeff | 1 +
examples/snap/Ta06A.snapparam | 2 +
examples/snap/Ta06A_pot.snap | 5 +-
examples/snap/log.15May15.snap.g++.1 | 120 +
examples/snap/log.15May15.snap.g++.4 | 120 +
examples/snap/log.snap.5Sep14.linux.1 | 116 -
examples/snap/log.snap.5Sep14.linux.4 | 116 -
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.srd.mixture.1Feb14.linux.1 | 232 -
examples/srd/log.srd.mixture.1Feb14.linux.4 | 232 -
examples/srd/log.srd.pure.1Feb14.linux.1 | 148 -
examples/srd/log.srd.pure.1Feb14.linux.4 | 148 -
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.streitz.ewald.19Feb15.linux.1 | 111 -
examples/streitz/log.streitz.ewald.19Feb15.linux.4 | 107 -
examples/streitz/log.streitz.wolf.19Feb15.linux.1 | 100 -
examples/streitz/log.streitz.wolf.19Feb15.linux.4 | 100 -
examples/tad/Si.sw | 1 +
examples/vashishta/InP.vashishta | 38 +
examples/vashishta/SiO.1990.vashishta | 41 +
examples/vashishta/data.quartz | 26 +
examples/vashishta/in.indiumphosphide | 75 +
examples/vashishta/in.sio2 | 28 +
examples/voronoi/log.15May15.voronoi.g++.1 | 542 +
examples/voronoi/log.15May15.voronoi.g++.4 | 542 +
lib/README | 8 +
lib/atc/ATC_Error.h | 2 +-
lib/atc/ATC_TypeDefs.h | 14 +-
lib/atc/DependencyManager.h | 2 +-
lib/atc/ExtrinsicModel.h | 2 +-
lib/atc/FE_Element.h | 2 +-
lib/atc/FE_Mesh.h | 2 +-
lib/atc/MatrixDef.h | 4 +-
lib/atc/MeshReader.h | 2 +-
lib/atc/PaqAtcUtility.h | 2 +-
lib/atc/PerPairQuantity.cpp | 2 +
lib/atc/PhysicsModel.h | 2 +-
lib/atc/TimeFilter.h | 2 +-
lib/atc/WeakEquation.h | 2 +-
lib/awpmd/ivutils/include/logexc.h | 2 +-
lib/awpmd/ivutils/include/pairhash.h | 1 -
lib/awpmd/ivutils/include/vector_3.h | 10 +-
lib/awpmd/systems/interact/TCP/wpmd_split.h | 1 +
lib/colvars/Makefile.fermi | 25 +-
lib/colvars/Makefile.g++ | 35 +-
lib/colvars/Makefile.mingw32-cross | 20 +-
lib/colvars/Makefile.mingw64-cross | 20 +-
lib/colvars/colvar.cpp | 214 +-
lib/colvars/colvar.h | 7 +-
lib/colvars/colvaratoms.cpp | 6 +-
lib/colvars/colvaratoms.h | 4 -
lib/colvars/colvarbias.cpp | 7 +
lib/colvars/colvarbias.h | 16 +-
lib/colvars/colvarbias_abf.cpp | 205 +-
lib/colvars/colvarbias_abf.h | 36 +-
lib/colvars/colvarbias_histogram.cpp | 253 +
lib/colvars/colvarbias_histogram.h | 43 +
lib/colvars/colvarbias_meta.cpp | 573 +-
lib/colvars/colvarbias_meta.h | 2 +
lib/colvars/colvarbias_restraint.h | 2 +-
lib/colvars/colvarcomp.cpp | 8 +-
lib/colvars/colvarcomp.h | 9 +-
lib/colvars/colvarcomp_distances.cpp | 37 +-
lib/colvars/colvarcomp_rotations.cpp | 4 +-
lib/colvars/colvargrid.cpp | 103 +-
lib/colvars/colvargrid.h | 135 +-
lib/colvars/colvarmodule.cpp | 65 +-
lib/colvars/colvarmodule.h | 36 +-
lib/colvars/colvarparse.cpp | 16 +-
lib/colvars/colvarparse.h | 7 +-
lib/colvars/colvarscript.cpp | 165 +-
lib/colvars/colvarscript.h | 4 +
lib/colvars/colvartypes.cpp | 1 -
lib/compress/Makefile.lammps | 21 +
lib/compress/README | 7 +
lib/gpu/Nvidia.makefile | 53 +-
lib/gpu/Opencl.makefile | 46 +-
lib/gpu/cudpp_mini/license.txt | 2 +-
lib/gpu/geryon/ocl_kernel.h | 8 +-
lib/gpu/lal_answer.cpp | 2 +-
lib/gpu/lal_base_three.cpp | 8 +-
lib/gpu/lal_base_three.h | 4 +-
lib/gpu/lal_coul_dsf.cu | 24 +-
lib/gpu/lal_device.cpp | 4 +-
lib/gpu/lal_eam_alloy_ext.cpp | 143 +
lib/gpu/lal_eam_fs_ext.cpp | 143 +
lib/gpu/lal_lj_cubic.cpp | 159 +
lib/gpu/lal_lj_cubic.cu | 229 +
lib/gpu/lal_lj_cubic.h | 81 +
lib/gpu/lal_lj_cubic_ext.cpp | 124 +
lib/gpu/lal_lj_dsf.cu | 16 +-
lib/gpu/lal_sw.cu | 10 +-
lib/gpu/lal_tersoff.cpp | 451 +
lib/gpu/lal_tersoff.cu | 1090 +
lib/gpu/lal_tersoff.h | 116 +
lib/gpu/lal_tersoff_ext.cpp | 139 +
lib/gpu/lal_tersoff_extra.h | 612 +
lib/gpu/lal_zbl.cpp | 159 +
lib/gpu/lal_zbl.cu | 276 +
lib/gpu/lal_zbl.h | 84 +
lib/gpu/lal_zbl_ext.cpp | 123 +
lib/h5md/LICENSE | 25 +
lib/h5md/Makefile | 33 +
lib/h5md/Makefile.lammps.empty | 7 +
lib/h5md/README | 27 +
lib/h5md/include/ch5md.h | 74 +
lib/h5md/src/ch5md.c | 445 +
lib/kim/Makefile.lammps | 23 +-
lib/kim/README | 71 +-
lib/kim/pair-kim.release.info | 6 +
lib/kokkos/Copyright.txt | 40 +
lib/kokkos/LICENSE | 40 +
lib/kokkos/Makefile.kokkos | 377 +
lib/kokkos/Makefile.lammps | 170 -
lib/kokkos/Makefile.targets | 57 +
lib/kokkos/README | 168 +-
lib/kokkos/TPL/cmake/Dependencies.cmake | 9 -
lib/kokkos/TPL/cub/block/block_discontinuity.cuh | 587 -
lib/kokkos/TPL/cub/block/block_exchange.cuh | 918 -
lib/kokkos/TPL/cub/block/block_histogram.cuh | 414 -
lib/kokkos/TPL/cub/block/block_load.cuh | 1122 -
lib/kokkos/TPL/cub/block/block_radix_rank.cuh | 479 -
lib/kokkos/TPL/cub/block/block_radix_sort.cuh | 608 -
lib/kokkos/TPL/cub/block/block_raking_layout.cuh | 145 -
lib/kokkos/TPL/cub/block/block_reduce.cuh | 563 -
lib/kokkos/TPL/cub/block/block_scan.cuh | 2233 -
lib/kokkos/TPL/cub/block/block_store.cuh | 926 -
.../specializations/block_histogram_atomic.cuh | 85 -
.../block/specializations/block_histogram_sort.cuh | 197 -
.../block/specializations/block_reduce_raking.cuh | 214 -
.../block_reduce_warp_reductions.cuh | 198 -
.../block/specializations/block_scan_raking.cuh | 761 -
.../specializations/block_scan_warp_scans.cuh | 342 -
lib/kokkos/TPL/cub/cub.cuh | 84 -
.../TPL/cub/device/block/block_histo_tiles.cuh | 322 -
.../TPL/cub/device/block/block_partition_tiles.cuh | 381 -
.../block/block_radix_sort_downsweep_tiles.cuh | 713 -
.../block/block_radix_sort_upsweep_tiles.cuh | 464 -
.../cub/device/block/block_reduce_by_key_tiles.cuh | 399 -
.../TPL/cub/device/block/block_reduce_tiles.cuh | 375 -
.../TPL/cub/device/block/block_scan_tiles.cuh | 509 -
.../TPL/cub/device/block/scan_tiles_types.cuh | 318 -
.../specializations/block_histo_tiles_gatomic.cuh | 184 -
.../specializations/block_histo_tiles_satomic.cuh | 237 -
.../specializations/block_histo_tiles_sort.cuh | 364 -
lib/kokkos/TPL/cub/device/device_histogram.cuh | 1062 -
lib/kokkos/TPL/cub/device/device_radix_sort.cuh | 890 -
lib/kokkos/TPL/cub/device/device_reduce.cuh | 775 -
lib/kokkos/TPL/cub/device/device_reduce_by_key.cuh | 633 -
lib/kokkos/TPL/cub/device/device_reorder.cuh | 550 -
lib/kokkos/TPL/cub/device/device_scan.cuh | 812 -
lib/kokkos/TPL/cub/grid/grid_barrier.cuh | 211 -
lib/kokkos/TPL/cub/grid/grid_even_share.cuh | 197 -
lib/kokkos/TPL/cub/grid/grid_mapping.cuh | 95 -
lib/kokkos/TPL/cub/grid/grid_queue.cuh | 207 -
lib/kokkos/TPL/cub/host/spinlock.cuh | 123 -
lib/kokkos/TPL/cub/thread/thread_load.cuh | 429 -
lib/kokkos/TPL/cub/thread/thread_operators.cuh | 145 -
lib/kokkos/TPL/cub/thread/thread_reduce.cuh | 145 -
lib/kokkos/TPL/cub/thread/thread_scan.cuh | 231 -
lib/kokkos/TPL/cub/thread/thread_store.cuh | 412 -
lib/kokkos/TPL/cub/util_allocator.cuh | 661 -
lib/kokkos/TPL/cub/util_arch.cuh | 295 -
lib/kokkos/TPL/cub/util_debug.cuh | 115 -
lib/kokkos/TPL/cub/util_device.cuh | 378 -
lib/kokkos/TPL/cub/util_iterator.cuh | 718 -
lib/kokkos/TPL/cub/util_macro.cuh | 107 -
lib/kokkos/TPL/cub/util_namespace.cuh | 41 -
lib/kokkos/TPL/cub/util_ptx.cuh | 380 -
lib/kokkos/TPL/cub/util_type.cuh | 685 -
lib/kokkos/TPL/cub/util_vector.cuh | 166 -
.../cub/warp/specializations/warp_reduce_shfl.cuh | 358 -
.../cub/warp/specializations/warp_reduce_smem.cuh | 291 -
.../cub/warp/specializations/warp_scan_shfl.cuh | 371 -
.../cub/warp/specializations/warp_scan_smem.cuh | 327 -
lib/kokkos/TPL/cub/warp/warp_reduce.cuh | 677 -
lib/kokkos/TPL/cub/warp/warp_scan.cuh | 1297 -
.../algorithms/src/KokkosAlgorithms_dummy.cpp | 0
lib/kokkos/algorithms/src/Kokkos_Random.hpp | 83 +-
lib/kokkos/algorithms/src/Kokkos_Sort.hpp | 46 +-
lib/kokkos/algorithms/unit_tests/Makefile | 92 +
lib/kokkos/algorithms/unit_tests/TestCuda.cpp | 110 +
lib/kokkos/algorithms/unit_tests/TestOpenMP.cpp | 102 +
lib/kokkos/algorithms/unit_tests/TestRandom.hpp | 476 +
lib/kokkos/algorithms/unit_tests/TestSerial.cpp | 99 +
lib/kokkos/algorithms/unit_tests/TestSort.hpp | 206 +
lib/kokkos/algorithms/unit_tests/TestThreads.cpp | 113 +
lib/kokkos/algorithms/unit_tests/UnitTestMain.cpp | 50 +
lib/kokkos/config/configure_compton_cpu.sh | 190 +
lib/kokkos/config/configure_compton_mic.sh | 186 +
lib/kokkos/config/configure_kokkos.sh | 293 +
lib/kokkos/config/configure_kokkos_bgq.sh | 88 +
lib/kokkos/config/configure_kokkos_dev.sh | 216 +
lib/kokkos/config/configure_kokkos_nvidia.sh | 204 +
lib/kokkos/config/configure_shannon.sh | 190 +
.../configure_tpetra_kokkos_cuda_nvcc_wrapper.sh | 140 +
lib/kokkos/config/kokkos_dev/config-core-all.sh | 113 +
.../kokkos_dev/config-core-cuda-omp-hwloc.sh | 104 +
lib/kokkos/config/kokkos_dev/config-core-cuda.sh | 88 +
.../config/kokkos_dev/config-core-cxx11-omp.sh | 84 +
.../config/kokkos_dev/config-core-dbg-none.sh | 78 +
.../kokkos_dev/config-core-intel-cuda-omp.sh | 89 +
.../config/kokkos_dev/config-core-intel-omp.sh | 84 +
lib/kokkos/config/kokkos_dev/config-core-omp.sh | 77 +
.../config/kokkos_dev/config-core-threads-hwloc.sh | 87 +
lib/kokkos/config/nvcc_wrapper | 185 +
lib/kokkos/config/snapshot.py | 279 +
lib/kokkos/config/test_all_sandia | 305 +
lib/kokkos/config/testing_scripts/README | 5 +
.../config/testing_scripts/jenkins_test_driver | 83 +
lib/kokkos/containers/performance_tests/Makefile | 81 +
.../containers/performance_tests/TestCuda.cpp | 100 +
.../performance_tests/TestGlobal2LocalIds.hpp | 231 +
.../containers/performance_tests/TestMain.cpp | 50 +
.../containers/performance_tests/TestOpenMP.cpp | 131 +
.../containers/performance_tests/TestThreads.cpp | 126 +
.../TestUnorderedMapPerformance.hpp | 262 +
lib/kokkos/containers/src/Kokkos_Bitset.hpp | 42 +-
lib/kokkos/containers/src/Kokkos_DualView.hpp | 392 +-
lib/kokkos/containers/src/Kokkos_Functional.hpp | 41 +
lib/kokkos/containers/src/Kokkos_SegmentedView.hpp | 165 +-
.../containers/src/Kokkos_StaticCrsGraph.hpp | 21 +-
lib/kokkos/containers/src/Kokkos_UnorderedMap.hpp | 80 +-
lib/kokkos/containers/src/Kokkos_Vector.hpp | 59 +-
.../containers/src/impl/Kokkos_Bitset_impl.hpp | 16 +-
.../containers/src/impl/Kokkos_Functional_impl.hpp | 41 +
.../src/impl/Kokkos_StaticCrsGraph_factory.hpp | 41 +-
.../src/impl/Kokkos_UnorderedMap_impl.cpp | 12 +-
.../src/impl/Kokkos_UnorderedMap_impl.hpp | 34 +-
lib/kokkos/containers/unit_tests/Makefile | 92 +
lib/kokkos/containers/unit_tests/TestBitset.hpp | 285 +
lib/kokkos/containers/unit_tests/TestComplex.hpp | 264 +
lib/kokkos/containers/unit_tests/TestCuda.cpp | 206 +
lib/kokkos/containers/unit_tests/TestDualView.hpp | 121 +
lib/kokkos/containers/unit_tests/TestOpenMP.cpp | 162 +
.../containers/unit_tests/TestSegmentedView.hpp | 708 +
lib/kokkos/containers/unit_tests/TestSerial.cpp | 158 +
.../containers/unit_tests/TestStaticCrsGraph.hpp | 149 +
lib/kokkos/containers/unit_tests/TestThreads.cpp | 168 +
.../containers/unit_tests/TestUnorderedMap.hpp | 313 +
lib/kokkos/containers/unit_tests/TestVector.hpp | 131 +
lib/kokkos/containers/unit_tests/UnitTestMain.cpp | 50 +
lib/kokkos/core/perf_test/Makefile | 66 +
lib/kokkos/core/perf_test/PerfTestBlasKernels.hpp | 309 +
lib/kokkos/core/perf_test/PerfTestCuda.cpp | 189 +
lib/kokkos/core/perf_test/PerfTestDriver.hpp | 152 +
lib/kokkos/core/perf_test/PerfTestGramSchmidt.hpp | 226 +
lib/kokkos/core/perf_test/PerfTestHexGrad.hpp | 268 +
lib/kokkos/core/perf_test/PerfTestHost.cpp | 104 +
lib/kokkos/core/perf_test/PerfTestMain.cpp | 49 +
lib/kokkos/core/perf_test/test_atomic.cpp | 504 +
lib/kokkos/core/src/Cuda/KokkosExp_Cuda_View.hpp | 283 +
lib/kokkos/core/src/Cuda/Kokkos_CudaExec.hpp | 68 +-
lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp | 853 +-
lib/kokkos/core/src/Cuda/Kokkos_Cuda_Alloc.hpp | 183 +
.../core/src/Cuda/Kokkos_Cuda_BasicAllocators.cpp | 192 +
.../core/src/Cuda/Kokkos_Cuda_BasicAllocators.hpp | 187 +
lib/kokkos/core/src/Cuda/Kokkos_Cuda_Error.hpp | 69 +
lib/kokkos/core/src/Cuda/Kokkos_Cuda_Impl.cpp | 66 +-
lib/kokkos/core/src/Cuda/Kokkos_Cuda_Internal.hpp | 34 +-
lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp | 715 +-
.../core/src/Cuda/Kokkos_Cuda_ReduceScan.hpp | 11 +-
.../core/src/Cuda/Kokkos_Cuda_Vectorization.hpp | 29 +-
lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp | 266 +-
lib/kokkos/core/src/Cuda/Kokkos_Cuda_abort.hpp | 12 +-
lib/kokkos/core/src/KokkosExp_View.hpp | 1989 +
lib/kokkos/core/src/Kokkos_Array.hpp | 300 +
lib/kokkos/core/src/Kokkos_Atomic.hpp | 75 +-
lib/kokkos/core/src/Kokkos_Core.hpp | 147 +-
lib/kokkos/core/src/Kokkos_Core_fwd.hpp | 40 +-
lib/kokkos/core/src/Kokkos_CrsArray.hpp | 171 -
lib/kokkos/core/src/Kokkos_Cuda.hpp | 45 +-
lib/kokkos/core/src/Kokkos_CudaSpace.hpp | 604 +-
lib/kokkos/core/src/Kokkos_CudaTypes.hpp | 139 -
lib/kokkos/core/src/Kokkos_ExecPolicy.hpp | 114 +-
lib/kokkos/core/src/Kokkos_HostSpace.hpp | 201 +-
lib/kokkos/core/src/Kokkos_Layout.hpp | 16 +-
lib/kokkos/core/src/Kokkos_Macros.hpp | 111 +-
lib/kokkos/core/src/Kokkos_MemoryTraits.hpp | 16 +-
lib/kokkos/core/src/Kokkos_OpenMP.hpp | 21 +-
lib/kokkos/core/src/Kokkos_Pair.hpp | 41 +
lib/kokkos/core/src/Kokkos_Parallel.hpp | 370 +-
lib/kokkos/core/src/Kokkos_Qthread.hpp | 20 +-
lib/kokkos/core/src/Kokkos_ScratchSpace.hpp | 26 +-
lib/kokkos/core/src/Kokkos_Serial.hpp | 133 +-
lib/kokkos/core/src/Kokkos_TaskPolicy.hpp | 137 +-
lib/kokkos/core/src/Kokkos_Threads.hpp | 23 +-
lib/kokkos/core/src/Kokkos_Vectorization.hpp | 61 +-
lib/kokkos/core/src/Kokkos_View.hpp | 649 +-
lib/kokkos/core/src/Kokkos_hwloc.hpp | 6 +-
lib/kokkos/core/src/Makefile | 127 +
.../core/src/OpenMP/Kokkos_OpenMP_Parallel.hpp | 12 +-
lib/kokkos/core/src/OpenMP/Kokkos_OpenMPexec.cpp | 67 +-
lib/kokkos/core/src/OpenMP/Kokkos_OpenMPexec.hpp | 95 +-
lib/kokkos/core/src/Qthread/Kokkos_QthreadExec.cpp | 162 +-
lib/kokkos/core/src/Qthread/Kokkos_QthreadExec.hpp | 71 +-
.../core/src/Qthread/Kokkos_Qthread_Parallel.hpp | 237 +-
.../core/src/Qthread/Kokkos_Qthread_TaskPolicy.cpp | 312 +-
.../core/src/Qthread/Kokkos_Qthread_TaskPolicy.hpp | 462 +-
lib/kokkos/core/src/Qthread/README | 28 +
lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.cpp | 121 +-
lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.hpp | 704 +-
.../core/src/Threads/Kokkos_ThreadsExec_base.cpp | 12 +-
lib/kokkos/core/src/Threads/Kokkos_ThreadsTeam.hpp | 730 +
.../core/src/Threads/Kokkos_Threads_Parallel.hpp | 16 +-
.../core/src/Threads/Kokkos_Threads_TaskPolicy.cpp | 599 +
.../core/src/Threads/Kokkos_Threads_TaskPolicy.hpp | 584 +
lib/kokkos/core/src/build.cuda.mac | 28 -
lib/kokkos/core/src/build_common.sh | 281 -
lib/kokkos/core/src/impl/KokkosExp_SharedAlloc.cpp | 275 +
lib/kokkos/core/src/impl/KokkosExp_SharedAlloc.hpp | 292 +
.../core/src/impl/KokkosExp_ViewAllocProp.hpp | 416 +
lib/kokkos/core/src/impl/KokkosExp_ViewArray.hpp | 616 +
lib/kokkos/core/src/impl/KokkosExp_ViewMapping.hpp | 2830 +
lib/kokkos/core/src/impl/KokkosExp_ViewTile.hpp | 219 +
.../core/src/impl/Kokkos_AllocationTracker.cpp | 844 +
.../core/src/impl/Kokkos_AllocationTracker.hpp | 586 +
lib/kokkos/core/src/impl/Kokkos_AnalyzeShape.hpp | 6 +-
.../core/src/impl/Kokkos_Atomic_Assembly_X86.hpp | 62 +-
.../impl/Kokkos_Atomic_Compare_Exchange_Strong.hpp | 68 +-
.../core/src/impl/Kokkos_Atomic_Exchange.hpp | 105 +-
.../core/src/impl/Kokkos_Atomic_Fetch_Add.hpp | 69 +-
.../core/src/impl/Kokkos_Atomic_Fetch_And.hpp | 14 +-
.../core/src/impl/Kokkos_Atomic_Fetch_Or.hpp | 14 +-
.../core/src/impl/Kokkos_Atomic_Fetch_Sub.hpp | 233 +
lib/kokkos/core/src/impl/Kokkos_Atomic_Generic.hpp | 124 +-
lib/kokkos/core/src/impl/Kokkos_Atomic_View.hpp | 46 +-
lib/kokkos/core/src/impl/Kokkos_Atomic_Windows.hpp | 211 +
.../core/src/impl/Kokkos_BasicAllocators.cpp | 281 +
.../core/src/impl/Kokkos_BasicAllocators.hpp | 118 +
lib/kokkos/core/src/impl/Kokkos_Core.cpp | 24 +-
.../core/src/impl/Kokkos_CrsArray_factory.hpp | 223 -
lib/kokkos/core/src/impl/Kokkos_Error.cpp | 16 +-
lib/kokkos/core/src/impl/Kokkos_Error.hpp | 16 +-
lib/kokkos/core/src/impl/Kokkos_FunctorAdapter.hpp | 270 +-
lib/kokkos/core/src/impl/Kokkos_HostSpace.cpp | 416 +-
lib/kokkos/core/src/impl/Kokkos_MemoryTracking.hpp | 374 -
lib/kokkos/core/src/impl/Kokkos_Memory_Fence.hpp | 18 +-
lib/kokkos/core/src/impl/Kokkos_PhysicalLayout.hpp | 12 +-
.../core/src/impl/Kokkos_Profiling_DeviceInfo.hpp | 57 +
.../core/src/impl/Kokkos_Profiling_Interface.cpp | 148 +
.../core/src/impl/Kokkos_Profiling_Interface.hpp | 98 +
lib/kokkos/core/src/impl/Kokkos_Serial.cpp | 14 +-
.../core/src/impl/Kokkos_Serial_TaskPolicy.cpp | 44 +-
.../core/src/impl/Kokkos_Serial_TaskPolicy.hpp | 166 +-
lib/kokkos/core/src/impl/Kokkos_Shape.cpp | 6 +-
lib/kokkos/core/src/impl/Kokkos_Shape.hpp | 14 +-
lib/kokkos/core/src/impl/Kokkos_Singleton.hpp | 55 +
lib/kokkos/core/src/impl/Kokkos_StaticAssert.hpp | 6 +-
lib/kokkos/core/src/impl/Kokkos_Tags.hpp | 73 +-
lib/kokkos/core/src/impl/Kokkos_Timer.hpp | 6 +-
lib/kokkos/core/src/impl/Kokkos_Traits.hpp | 14 +-
lib/kokkos/core/src/impl/Kokkos_ViewDefault.hpp | 2144 +-
lib/kokkos/core/src/impl/Kokkos_ViewOffset.hpp | 124 +-
lib/kokkos/core/src/impl/Kokkos_ViewSupport.hpp | 77 +-
lib/kokkos/core/src/impl/Kokkos_ViewTileLeft.hpp | 28 +-
lib/kokkos/core/src/impl/Kokkos_Volatile_Load.hpp | 14 +-
lib/kokkos/core/src/impl/Kokkos_hwloc.cpp | 12 +-
lib/kokkos/core/src/impl/Kokkos_spinwait.cpp | 20 +-
lib/kokkos/core/src/impl/Kokkos_spinwait.hpp | 14 +-
lib/kokkos/core/unit_test/Makefile | 146 +
lib/kokkos/core/unit_test/TestAggregate.hpp | 753 +
.../core/unit_test/TestAggregateReduction.hpp | 195 +
.../core/unit_test/TestAllocationTracker.cpp | 145 +
lib/kokkos/core/unit_test/TestAtomic.hpp | 376 +
lib/kokkos/core/unit_test/TestCXX11.hpp | 319 +
lib/kokkos/core/unit_test/TestCXX11Deduction.hpp | 94 +
lib/kokkos/core/unit_test/TestCompilerMacros.hpp | 93 +
lib/kokkos/core/unit_test/TestCuda.cpp | 491 +
.../core/unit_test/TestDefaultDeviceType.cpp | 248 +
.../core/unit_test/TestDefaultDeviceTypeInit.cpp | 390 +
lib/kokkos/core/unit_test/TestHWLOC.cpp | 69 +
.../core/unit_test/TestMemorySpaceTracking.hpp | 100 +
lib/kokkos/core/unit_test/TestOpenMP.cpp | 373 +
lib/kokkos/core/unit_test/TestQthread.cpp | 280 +
lib/kokkos/core/unit_test/TestRange.hpp | 171 +
lib/kokkos/core/unit_test/TestReduce.hpp | 384 +
lib/kokkos/core/unit_test/TestScan.hpp | 97 +
lib/kokkos/core/unit_test/TestSerial.cpp | 407 +
lib/kokkos/core/unit_test/TestSharedAlloc.hpp | 204 +
lib/kokkos/core/unit_test/TestTaskPolicy.hpp | 490 +
lib/kokkos/core/unit_test/TestTeam.hpp | 466 +
lib/kokkos/core/unit_test/TestTeamVector.hpp | 646 +
.../core/unit_test/TestTemplateMetaFunctions.hpp | 219 +
lib/kokkos/core/unit_test/TestThreads.cpp | 436 +
lib/kokkos/core/unit_test/TestTile.hpp | 153 +
lib/kokkos/core/unit_test/TestViewAPI.hpp | 1370 +
lib/kokkos/core/unit_test/TestViewImpl.hpp | 289 +
lib/kokkos/core/unit_test/TestViewMapping.hpp | 1080 +
lib/kokkos/core/unit_test/TestViewOfClass.hpp | 126 +
lib/kokkos/core/unit_test/TestViewSubview.hpp | 646 +
lib/kokkos/core/unit_test/UnitTestMain.cpp | 50 +
lib/kokkos/example/README | 16 +
lib/kokkos/example/common/VectorImport.hpp | 294 +
lib/kokkos/example/common/WrapMPI.hpp | 103 +
lib/kokkos/example/feint/ElemFunctor.hpp | 489 +
lib/kokkos/example/feint/Makefile | 62 +
lib/kokkos/example/feint/feint.hpp | 165 +
lib/kokkos/example/feint/feint_cuda.cpp | 67 +
lib/kokkos/example/feint/feint_fwd.hpp | 60 +
lib/kokkos/example/feint/feint_openmp.cpp | 67 +
lib/kokkos/example/feint/feint_threads.cpp | 66 +
lib/kokkos/example/feint/main.cpp | 110 +
lib/kokkos/example/fenl/CGSolve.hpp | 296 +
lib/kokkos/example/fenl/Makefile | 50 +
lib/kokkos/example/fenl/fenl.cpp | 117 +
lib/kokkos/example/fenl/fenl.hpp | 89 +
lib/kokkos/example/fenl/fenl_functors.hpp | 1173 +
lib/kokkos/example/fenl/fenl_impl.hpp | 598 +
lib/kokkos/example/fenl/main.cpp | 422 +
lib/kokkos/example/fixture/BoxElemFixture.hpp | 355 +
lib/kokkos/example/fixture/BoxElemPart.cpp | 413 +
lib/kokkos/example/fixture/BoxElemPart.hpp | 320 +
lib/kokkos/example/fixture/HexElement.hpp | 270 +
lib/kokkos/example/fixture/Main.cpp | 304 +
lib/kokkos/example/fixture/Makefile | 49 +
lib/kokkos/example/fixture/TestFixture.cpp | 58 +
lib/kokkos/example/fixture/TestFixture.hpp | 156 +
lib/kokkos/example/global_2_local_ids/G2L.hpp | 266 +
lib/kokkos/example/global_2_local_ids/G2L_Main.cpp | 149 +
lib/kokkos/example/grow_array/grow_array.hpp | 257 +
lib/kokkos/example/grow_array/main.cpp | 110 +
lib/kokkos/example/md_skeleton/README | 3 +
lib/kokkos/example/md_skeleton/force.cpp | 192 +
lib/kokkos/example/md_skeleton/main.cpp | 205 +
lib/kokkos/example/md_skeleton/neighbor.cpp | 430 +
lib/kokkos/example/md_skeleton/setup.cpp | 271 +
lib/kokkos/example/md_skeleton/system.h | 92 +
lib/kokkos/example/md_skeleton/types.h | 118 +
lib/kokkos/example/multi_fem/BoxMeshFixture.hpp | 610 +
lib/kokkos/example/multi_fem/BoxMeshPartition.cpp | 381 +
lib/kokkos/example/multi_fem/BoxMeshPartition.hpp | 210 +
lib/kokkos/example/multi_fem/Explicit.hpp | 452 +
lib/kokkos/example/multi_fem/ExplicitFunctors.hpp | 1471 +
lib/kokkos/example/multi_fem/FEMesh.hpp | 86 +
lib/kokkos/example/multi_fem/HexElement.hpp | 268 +
.../example/multi_fem/HexExplicitFunctions.hpp | 443 +
lib/kokkos/example/multi_fem/Implicit.hpp | 341 +
lib/kokkos/example/multi_fem/ImplicitFunctors.hpp | 585 +
lib/kokkos/example/multi_fem/LinAlgBLAS.hpp | 567 +
lib/kokkos/example/multi_fem/Nonlinear.hpp | 573 +
.../example/multi_fem/NonlinearElement_Cuda.hpp | 390 +
lib/kokkos/example/multi_fem/NonlinearFunctors.hpp | 482 +
lib/kokkos/example/multi_fem/ParallelComm.hpp | 167 +
lib/kokkos/example/multi_fem/ParallelDataMap.hpp | 517 +
lib/kokkos/example/multi_fem/ParallelMachine.cpp | 178 +
lib/kokkos/example/multi_fem/ParallelMachine.hpp | 118 +
.../example/multi_fem/SparseLinearSystem.hpp | 400 +
.../example/multi_fem/SparseLinearSystemFill.hpp | 276 +
.../example/multi_fem/SparseLinearSystem_Cuda.hpp | 164 +
.../example/multi_fem/TestBoxMeshFixture.hpp | 242 +
.../example/multi_fem/TestBoxMeshPartition.cpp | 172 +
lib/kokkos/example/multi_fem/TestCuda.cpp | 192 +
lib/kokkos/example/multi_fem/TestHost.cpp | 137 +
lib/kokkos/example/multi_fem/TestHybridFEM.cpp | 348 +
lib/kokkos/example/query_device/query_device.cpp | 100 +
lib/kokkos/example/sort_array/main.cpp | 95 +
lib/kokkos/example/sort_array/sort_array.hpp | 190 +
.../example/tutorial/01_hello_world/Makefile | 43 +
.../tutorial/01_hello_world/hello_world.cpp | 130 +
.../tutorial/01_hello_world_lambda/Makefile | 44 +
.../01_hello_world_lambda/hello_world_lambda.cpp | 109 +
.../example/tutorial/02_simple_reduce/Makefile | 43 +
.../tutorial/02_simple_reduce/simple_reduce.cpp | 101 +
.../tutorial/02_simple_reduce_lambda/Makefile | 44 +
.../simple_reduce_lambda.cpp | 86 +
.../example/tutorial/03_simple_view/Makefile | 43 +
.../tutorial/03_simple_view/simple_view.cpp | 142 +
.../tutorial/03_simple_view_lambda/Makefile | 44 +
.../03_simple_view_lambda/simple_view_lambda.cpp | 116 +
.../tutorial/04_simple_memoryspaces/Makefile | 43 +
.../04_simple_memoryspaces/simple_memoryspaces.cpp | 101 +
.../example/tutorial/05_simple_atomics/Makefile | 43 +
.../tutorial/05_simple_atomics/simple_atomics.cpp | 137 +
.../Advanced_Views/01_data_layouts/Makefile | 43 +
.../01_data_layouts/data_layouts.cpp | 171 +
.../Advanced_Views/02_memory_traits/Makefile | 43 +
.../02_memory_traits/memory_traits.cpp | 141 +
.../tutorial/Advanced_Views/03_subviews/Makefile | 43 +
.../Advanced_Views/03_subviews/subviews.cpp | 190 +
.../tutorial/Advanced_Views/04_dualviews/Makefile | 43 +
.../Advanced_Views/04_dualviews/dual_view.cpp | 214 +
.../tutorial/Advanced_Views/05_NVIDIA_UVM/Makefile | 43 +
.../Advanced_Views/05_NVIDIA_UVM/uvm_example.cpp | 134 +
.../Advanced_Views/06_AtomicViews/Makefile | 43 +
.../07_Overlapping_DeepCopy/Makefile | 43 +
.../overlapping_deepcopy.cpp | 148 +
.../example/tutorial/Advanced_Views/Makefile | 84 +
.../tutorial/Algorithms/01_random_numbers/Makefile | 43 +
.../01_random_numbers/random_numbers.cpp | 152 +
lib/kokkos/example/tutorial/Algorithms/Makefile | 24 +
.../01_thread_teams/Makefile | 43 +
.../01_thread_teams/thread_teams.cpp | 94 +
.../01_thread_teams_lambda/Makefile | 43 +
.../01_thread_teams_lambda/thread_teams_lambda.cpp | 93 +
.../02_nested_parallel_for/Makefile | 43 +
.../02_nested_parallel_for/nested_parallel_for.cpp | 89 +
.../03_vectorization/Makefile | 43 +
.../03_vectorization/vectorization.cpp | 162 +
.../Hierarchical_Parallelism/04_team_scan/Makefile | 43 +
.../04_team_scan/team_scan.cpp | 141 +
.../tutorial/Hierarchical_Parallelism/Makefile | 72 +
lib/kokkos/example/tutorial/Makefile | 144 +
lib/kokkos/example/tutorial/README | 17 +
lib/kokkos/generate_makefile.bash | 212 +
lib/python/Makefile.lammps | 6 +
lib/python/Makefile.lammps.python2 | 6 +
lib/python/Makefile.lammps.python2.7 | 6 +
lib/python/README | 58 +
lib/quip/Makefile.lammps | 6 +-
lib/quip/README | 6 +-
lib/smd/Makefile.lammps | 5 +
lib/smd/README | 41 +
potentials/AlCu.bop.table | 5684 ++
potentials/CCu_v2.bop.table | 6039 ++
potentials/CdTe.bop | 44 -
potentials/CdTeSe.bop.table | 9664 ++
potentials/CdTeZnSeHgS0.sw | 225 +
potentials/CdZnTe_v1.bop.table | 9664 ++
potentials/CdZnTe_v2.bop.table | 9664 ++
potentials/CuH.bop.table | 6039 ++
potentials/CuTa_eam.poly | 2830 +
potentials/GaAs.bop | 45 -
potentials/GaAs.bop.table | 2 +-
potentials/GaN_sw.poly | 6836 ++
potentials/GaN_tersoff.poly | 8430 ++
potentials/InP.vashishta | 38 +
potentials/Mo5.2.mgpt.README | 55 +
potentials/Mo5.2.mgpt.parmin | 2 +
potentials/Mo5.2.mgpt.potin | 9701 ++
potentials/README | 32 +-
potentials/Si.tersoff.mod | 54 +-
potentials/SiC.vashishta | 41 +
potentials/SiO.1990.vashishta | 41 +
potentials/SiO.1994.vashishta | 38 +
potentials/SiO.1997.vashishta | 37 +
potentials/Ta06A_pot.snap | 3 +-
potentials/Ta4.mgpt.README | 49 +
potentials/Ta4.mgpt.parmin | 2 +
potentials/Ta4.mgpt.potin | 6597 ++
potentials/Ta6.8x.mgpt.README | 57 +
potentials/Ta6.8x.mgpt.parmin | 2 +
potentials/Ta6.8x.mgpt.potin | 11253 +++
potentials/V6.1.mgpt.README | 56 +
potentials/V6.1.mgpt.parmin | 2 +
potentials/V6.1.mgpt.potin | 9701 ++
potentials/ffield.comb | 196 +-
potentials/ffield.smtbq.Al | 34 +
potentials/ffield.smtbq.Al2O3 | 56 +
potentials/ffield.smtbq.TiO2 | 53 +
potentials/lib.comb3 | 3 +-
python/README | 12 +-
python/install.py | 37 +-
python/lammps.py | 14 +-
src/ASPHERE/compute_erotate_asphere.cpp | 2 +-
src/ASPHERE/compute_temp_asphere.cpp | 21 +-
src/ASPHERE/fix_nh_asphere.cpp | 6 +-
src/ASPHERE/fix_nph_asphere.cpp | 2 +-
src/ASPHERE/fix_npt_asphere.cpp | 2 +-
src/ASPHERE/fix_nve_asphere.cpp | 6 +-
src/ASPHERE/fix_nve_asphere_noforce.cpp | 6 +-
src/ASPHERE/fix_nve_line.cpp | 6 +-
src/ASPHERE/fix_nve_tri.cpp | 6 +-
src/ASPHERE/fix_nvt_asphere.cpp | 2 +-
src/ASPHERE/pair_gayberne.cpp | 8 +-
src/ASPHERE/pair_line_lj.cpp | 8 +-
src/ASPHERE/pair_resquared.cpp | 8 +-
src/ASPHERE/pair_tri_lj.cpp | 10 +-
src/BODY/body_nparticle.cpp | 22 +-
src/BODY/compute_body_local.cpp | 8 +-
src/BODY/fix_nve_body.cpp | 6 +-
src/BODY/pair_body.cpp | 12 +-
src/CLASS2/angle_class2.cpp | 6 +-
src/CLASS2/angle_class2.h | 2 +-
src/CLASS2/bond_class2.cpp | 4 +-
src/CLASS2/bond_class2.h | 2 +-
src/CLASS2/dihedral_class2.cpp | 10 +-
src/CLASS2/dihedral_class2.h | 2 +-
src/CLASS2/improper_class2.cpp | 12 +-
src/CLASS2/improper_class2.h | 2 +-
src/CLASS2/pair_lj_class2.cpp | 32 +-
src/CLASS2/pair_lj_class2.h | 6 +-
src/CLASS2/pair_lj_class2_coul_cut.cpp | 38 +-
src/CLASS2/pair_lj_class2_coul_cut.h | 8 +-
src/CLASS2/pair_lj_class2_coul_long.cpp | 74 +-
src/CLASS2/pair_lj_class2_coul_long.h | 8 +-
src/COLLOID/fix_wall_colloid.cpp | 4 +-
src/COLLOID/pair_colloid.cpp | 12 +-
src/COLLOID/pair_yukawa_colloid.cpp | 4 +-
src/COMPRESS/Install.sh | 60 +
src/COMPRESS/README | 13 +
src/COMPRESS/dump_atom_gz.cpp | 144 +
src/COMPRESS/dump_atom_gz.h | 53 +
src/COMPRESS/dump_cfg_gz.cpp | 153 +
src/COMPRESS/dump_cfg_gz.h | 53 +
src/COMPRESS/dump_custom_gz.cpp | 144 +
src/COMPRESS/dump_custom_gz.h | 53 +
src/COMPRESS/dump_xyz_gz.cpp | 124 +
src/COMPRESS/dump_xyz_gz.h | 53 +
src/CORESHELL/Install.sh | 4 +
src/CORESHELL/compute_temp_cs.cpp | 64 +-
src/CORESHELL/compute_temp_cs.h | 40 +-
src/CORESHELL/pair_born_coul_long_cs.cpp | 33 +-
src/CORESHELL/pair_born_coul_long_cs.h | 4 -
src/CORESHELL/pair_buck_coul_long_cs.cpp | 33 +-
src/CORESHELL/pair_buck_coul_long_cs.h | 4 -
src/CORESHELL/pair_coul_long_cs.cpp | 185 +
src/CORESHELL/pair_coul_long_cs.h | 58 +
src/CORESHELL/pair_lj_cut_coul_long_cs.cpp | 572 +
src/CORESHELL/pair_lj_cut_coul_long_cs.h | 67 +
src/DIPOLE/atom_vec_dipole.cpp | 4 +-
src/DIPOLE/pair_lj_cut_dipole_cut.cpp | 6 +-
src/DIPOLE/pair_lj_cut_dipole_long.cpp | 46 +-
src/DIPOLE/pair_lj_cut_dipole_long.h | 2 +-
src/DIPOLE/pair_lj_long_dipole_long.cpp | 44 +-
src/DIPOLE/pair_lj_long_dipole_long.h | 9 +-
src/Depend.sh | 10 +
src/FLD/pair_brownian.cpp | 10 +-
src/FLD/pair_brownian_poly.cpp | 10 +-
src/FLD/pair_lubricate.cpp | 10 +-
src/FLD/pair_lubricateU.cpp | 12 +-
src/FLD/pair_lubricateU_poly.cpp | 12 +-
src/FLD/pair_lubricate_poly.cpp | 10 +-
src/GPU/Install.sh | 6 +
src/GPU/fix_gpu.cpp | 21 +-
src/GPU/fix_gpu.h | 19 +-
src/GPU/pair_beck_gpu.cpp | 28 +-
src/GPU/pair_beck_gpu.h | 2 +-
src/GPU/pair_born_coul_long_gpu.cpp | 42 +-
src/GPU/pair_born_coul_long_gpu.h | 7 +-
src/GPU/pair_born_coul_wolf_gpu.cpp | 68 +-
src/GPU/pair_born_coul_wolf_gpu.h | 2 +-
src/GPU/pair_born_gpu.cpp | 46 +-
src/GPU/pair_born_gpu.h | 2 +-
src/GPU/pair_buck_coul_cut_gpu.cpp | 8 +-
src/GPU/pair_buck_coul_long_gpu.cpp | 10 +-
src/GPU/pair_buck_coul_long_gpu.h | 5 +-
src/GPU/pair_buck_gpu.cpp | 10 +-
src/GPU/pair_colloid_gpu.cpp | 68 +-
src/GPU/pair_colloid_gpu.h | 2 +-
src/GPU/pair_coul_cut_gpu.cpp | 10 +-
src/GPU/pair_coul_cut_gpu.h | 4 +-
src/GPU/pair_coul_debye_gpu.cpp | 38 +-
src/GPU/pair_coul_debye_gpu.h | 6 +-
src/GPU/pair_coul_dsf_gpu.cpp | 30 +-
src/GPU/pair_coul_long_gpu.cpp | 12 +-
src/GPU/pair_coul_long_gpu.h | 5 +-
src/GPU/pair_dpd_gpu.cpp | 40 +-
src/GPU/pair_dpd_gpu.h | 2 +-
src/GPU/pair_dpd_tstat_gpu.cpp | 42 +-
src/GPU/pair_dpd_tstat_gpu.h | 2 +-
src/GPU/pair_eam_alloy_gpu.cpp | 249 +-
src/GPU/pair_eam_alloy_gpu.h | 20 +-
src/GPU/pair_eam_fs_gpu.cpp | 253 +-
src/GPU/pair_eam_fs_gpu.h | 20 +-
src/GPU/pair_eam_gpu.cpp | 18 +-
src/GPU/pair_eam_gpu.h | 2 +-
src/GPU/pair_gauss_gpu.cpp | 38 +-
src/GPU/pair_gauss_gpu.h | 2 +-
src/GPU/pair_gayberne_gpu.cpp | 8 +-
src/GPU/pair_lj96_cut_gpu.cpp | 8 +-
src/GPU/pair_lj_charmm_coul_long_gpu.cpp | 11 +-
src/GPU/pair_lj_charmm_coul_long_gpu.h | 5 +-
src/GPU/pair_lj_class2_coul_long_gpu.cpp | 10 +-
src/GPU/pair_lj_class2_coul_long_gpu.h | 5 +-
src/GPU/pair_lj_class2_gpu.cpp | 8 +-
src/GPU/pair_lj_cubic_gpu.cpp | 242 +
src/GPU/pair_lj_cubic_gpu.h | 58 +
src/GPU/pair_lj_cut_coul_cut_gpu.cpp | 8 +-
src/GPU/pair_lj_cut_coul_debye_gpu.cpp | 44 +-
src/GPU/pair_lj_cut_coul_debye_gpu.h | 2 +-
src/GPU/pair_lj_cut_coul_dsf_gpu.cpp | 30 +-
src/GPU/pair_lj_cut_coul_long_gpu.cpp | 12 +-
src/GPU/pair_lj_cut_coul_long_gpu.h | 5 +-
src/GPU/pair_lj_cut_coul_msm_gpu.cpp | 34 +-
src/GPU/pair_lj_cut_coul_msm_gpu.h | 2 +-
src/GPU/pair_lj_cut_dipole_cut_gpu.cpp | 66 +-
src/GPU/pair_lj_cut_dipole_cut_gpu.h | 2 +-
src/GPU/pair_lj_cut_gpu.cpp | 12 +-
src/GPU/pair_lj_expand_gpu.cpp | 10 +-
src/GPU/pair_lj_gromacs_gpu.cpp | 32 +-
src/GPU/pair_lj_gromacs_gpu.h | 2 +-
src/GPU/pair_lj_sdk_coul_long_gpu.cpp | 8 +-
src/GPU/pair_lj_sdk_gpu.cpp | 8 +-
src/GPU/pair_lj_sf_dipole_sf_gpu.cpp | 74 +-
src/GPU/pair_lj_sf_dipole_sf_gpu.h | 8 +-
src/GPU/pair_mie_cut_gpu.cpp | 30 +-
src/GPU/pair_mie_cut_gpu.h | 2 +-
src/GPU/pair_morse_gpu.cpp | 8 +-
src/GPU/pair_resquared_gpu.cpp | 8 +-
src/GPU/pair_soft_gpu.cpp | 32 +-
src/GPU/pair_soft_gpu.h | 2 +-
src/GPU/pair_sw_gpu.cpp | 24 +-
src/GPU/pair_table_gpu.cpp | 8 +-
src/GPU/pair_tersoff_gpu.cpp | 263 +
src/GPU/pair_tersoff_gpu.h | 71 +
src/GPU/pair_yukawa_colloid_gpu.cpp | 64 +-
src/GPU/pair_yukawa_colloid_gpu.h | 2 +-
src/GPU/pair_yukawa_gpu.cpp | 8 +-
src/GPU/pair_zbl_gpu.cpp | 242 +
src/GPU/pair_zbl_gpu.h | 58 +
src/GPU/pppm_gpu.cpp | 18 +-
src/GRANULAR/fix_freeze.cpp | 2 +-
src/GRANULAR/fix_pour.cpp | 28 +-
src/GRANULAR/fix_pour.h | 9 +-
src/GRANULAR/fix_wall_gran.cpp | 6 +-
src/GRANULAR/pair_gran_hertz_history.cpp | 8 +-
src/GRANULAR/pair_gran_hooke.cpp | 6 +-
src/GRANULAR/pair_gran_hooke_history.cpp | 14 +-
src/KIM/README | 9 +-
src/KIM/pair_kim.cpp | 115 +-
src/KIM/pair_kim.h | 3 +
src/KIM/pair_kim_version.h | 64 +
src/KOKKOS/Install.sh | 90 +-
src/KOKKOS/angle_charmm_kokkos.cpp | 421 +
src/KOKKOS/angle_charmm_kokkos.h | 95 +
src/KOKKOS/angle_harmonic_kokkos.cpp | 391 +
src/KOKKOS/angle_harmonic_kokkos.h | 92 +
src/KOKKOS/atom_kokkos.cpp | 14 +-
src/KOKKOS/atom_vec_angle_kokkos.cpp | 10 +-
src/KOKKOS/atom_vec_angle_kokkos.h | 9 +
src/KOKKOS/atom_vec_atomic_kokkos.cpp | 43 +-
src/KOKKOS/atom_vec_atomic_kokkos.h | 27 +-
src/KOKKOS/atom_vec_bond_kokkos.cpp | 8 +-
src/KOKKOS/atom_vec_bond_kokkos.h | 9 +
src/KOKKOS/atom_vec_charge_kokkos.cpp | 8 +-
src/KOKKOS/atom_vec_charge_kokkos.h | 9 +
src/KOKKOS/atom_vec_full_kokkos.cpp | 19 +-
src/KOKKOS/atom_vec_full_kokkos.h | 9 +
src/KOKKOS/atom_vec_kokkos.h | 32 +-
src/KOKKOS/atom_vec_molecular_kokkos.cpp | 19 +-
src/KOKKOS/atom_vec_molecular_kokkos.h | 9 +
src/KOKKOS/bond_fene_kokkos.cpp | 385 +
src/KOKKOS/bond_fene_kokkos.h | 113 +
src/KOKKOS/bond_harmonic_kokkos.cpp | 323 +
src/KOKKOS/bond_harmonic_kokkos.h | 91 +
src/KOKKOS/comm_kokkos.cpp | 30 +-
src/KOKKOS/comm_kokkos.h | 15 +-
src/KOKKOS/compute_temp_kokkos.cpp | 153 +
src/KOKKOS/compute_temp_kokkos.h | 107 +
src/KOKKOS/dihedral_charmm_kokkos.cpp | 745 +
src/KOKKOS/dihedral_charmm_kokkos.h | 191 +
src/KOKKOS/dihedral_opls_kokkos.cpp | 521 +
src/KOKKOS/dihedral_opls_kokkos.h | 106 +
src/KOKKOS/domain_kokkos.cpp | 225 +-
src/KOKKOS/domain_kokkos.h | 31 +-
src/KOKKOS/fix_deform_kokkos.cpp | 374 +
src/KOKKOS/fix_deform_kokkos.h | 104 +
src/KOKKOS/fix_langevin_kokkos.cpp | 6 +-
src/KOKKOS/fix_langevin_kokkos.h | 62 +-
src/KOKKOS/fix_nh_kokkos.cpp | 738 +
src/KOKKOS/fix_nh_kokkos.h | 86 +
src/KOKKOS/fix_nph_kokkos.cpp | 74 +
src/KOKKOS/fix_nph_kokkos.h | 43 +
src/KOKKOS/fix_npt_kokkos.cpp | 74 +
src/KOKKOS/fix_npt_kokkos.h | 43 +
src/KOKKOS/fix_nve_kokkos.cpp | 4 +-
src/KOKKOS/fix_nve_kokkos.h | 2 +-
src/KOKKOS/fix_nvt_kokkos.cpp | 55 +
src/KOKKOS/fix_nvt_kokkos.h | 44 +
src/KOKKOS/fix_wall_reflect_kokkos.cpp | 111 +
src/KOKKOS/fix_wall_reflect_kokkos.h | 62 +
src/KOKKOS/improper_harmonic_kokkos.cpp | 472 +
src/KOKKOS/improper_harmonic_kokkos.h | 102 +
src/KOKKOS/kokkos.cpp | 20 +-
src/KOKKOS/kokkos.h | 14 +
src/KOKKOS/kokkos_type.h | 106 +-
src/KOKKOS/memory_kokkos.h | 69 +-
src/KOKKOS/modify_kokkos.cpp | 2 +-
src/KOKKOS/modify_kokkos.h | 2 +-
src/KOKKOS/neigh_bond_kokkos.cpp | 1284 +
src/KOKKOS/neigh_bond_kokkos.h | 256 +
src/KOKKOS/neigh_full_kokkos.h | 159 +-
src/KOKKOS/neigh_list_kokkos.cpp | 14 +-
src/KOKKOS/neigh_list_kokkos.h | 12 +-
src/KOKKOS/neighbor_kokkos.cpp | 355 +-
src/KOKKOS/neighbor_kokkos.h | 112 +-
src/KOKKOS/pair_buck_coul_cut_kokkos.cpp | 373 +
src/KOKKOS/pair_buck_coul_cut_kokkos.h | 134 +
src/KOKKOS/pair_buck_coul_long_kokkos.cpp | 517 +
src/KOKKOS/pair_buck_coul_long_kokkos.h | 150 +
src/KOKKOS/pair_buck_kokkos.cpp | 10 +-
src/KOKKOS/pair_buck_kokkos.h | 12 +-
src/KOKKOS/pair_coul_cut_kokkos.cpp | 8 +-
src/KOKKOS/pair_coul_cut_kokkos.h | 25 +-
src/KOKKOS/pair_coul_debye_kokkos.cpp | 313 +
src/KOKKOS/pair_coul_debye_kokkos.h | 135 +
src/KOKKOS/pair_coul_dsf_kokkos.cpp | 12 +-
src/KOKKOS/pair_coul_dsf_kokkos.h | 8 +-
src/KOKKOS/pair_coul_long_kokkos.cpp | 456 +
src/KOKKOS/pair_coul_long_kokkos.h | 154 +
src/KOKKOS/pair_coul_wolf_kokkos.cpp | 10 +-
src/KOKKOS/pair_coul_wolf_kokkos.h | 8 +-
src/KOKKOS/pair_eam_alloy_kokkos.cpp | 1177 +
src/KOKKOS/pair_eam_alloy_kokkos.h | 183 +
src/KOKKOS/pair_eam_fs_kokkos.cpp | 1186 +
src/KOKKOS/pair_eam_fs_kokkos.h | 183 +
src/KOKKOS/pair_eam_kokkos.cpp | 209 +-
src/KOKKOS/pair_eam_kokkos.h | 26 +-
src/KOKKOS/pair_kokkos.h | 56 +-
.../pair_lj_charmm_coul_charmm_implicit_kokkos.cpp | 516 +
.../pair_lj_charmm_coul_charmm_implicit_kokkos.h | 151 +
src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp | 518 +
src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.h | 151 +
src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp | 537 +
src/KOKKOS/pair_lj_charmm_coul_long_kokkos.h | 151 +
src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp | 354 +
src/KOKKOS/pair_lj_class2_coul_cut_kokkos.h | 130 +
src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp | 503 +
src/KOKKOS/pair_lj_class2_coul_long_kokkos.h | 147 +
src/KOKKOS/pair_lj_class2_kokkos.cpp | 281 +
src/KOKKOS/pair_lj_class2_kokkos.h | 124 +
src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp | 8 +-
src/KOKKOS/pair_lj_cut_coul_cut_kokkos.h | 20 +-
src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp | 375 +
src/KOKKOS/pair_lj_cut_coul_debye_kokkos.h | 131 +
src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp | 366 +
src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.h | 130 +
src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp | 10 +-
src/KOKKOS/pair_lj_cut_coul_long_kokkos.h | 18 +-
src/KOKKOS/pair_lj_cut_kokkos.cpp | 12 +-
src/KOKKOS/pair_lj_cut_kokkos.h | 20 +-
src/KOKKOS/pair_lj_expand_kokkos.cpp | 285 +
src/KOKKOS/pair_lj_expand_kokkos.h | 125 +
src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp | 501 +
src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.h | 151 +
src/KOKKOS/pair_lj_gromacs_kokkos.cpp | 333 +
src/KOKKOS/pair_lj_gromacs_kokkos.h | 153 +
src/KOKKOS/pair_lj_sdk_kokkos.cpp | 314 +
src/KOKKOS/pair_lj_sdk_kokkos.h | 136 +
src/KOKKOS/pair_sw_kokkos.cpp | 908 +
src/KOKKOS/pair_sw_kokkos.h | 150 +
src/KOKKOS/pair_table_kokkos.cpp | 28 +-
src/KOKKOS/pair_table_kokkos.h | 14 +-
src/KOKKOS/pair_tersoff_kokkos.cpp | 1202 +
src/KOKKOS/pair_tersoff_kokkos.h | 220 +
src/KOKKOS/pair_tersoff_mod_kokkos.cpp | 1208 +
src/KOKKOS/pair_tersoff_mod_kokkos.h | 220 +
src/KOKKOS/pair_tersoff_zbl_kokkos.cpp | 1302 +
src/KOKKOS/pair_tersoff_zbl_kokkos.h | 231 +
src/KOKKOS/verlet_kokkos.cpp | 62 +-
src/KOKKOS/verlet_kokkos.h | 2 +-
src/KSPACE/ewald.cpp | 36 +-
src/KSPACE/ewald.h | 13 +-
src/KSPACE/ewald_disp.cpp | 30 +-
src/KSPACE/ewald_disp.h | 9 +-
src/KSPACE/fft3d.cpp | 8 +-
src/KSPACE/fft3d.h | 4 +-
src/KSPACE/fft3d_wrap.cpp | 2 +-
src/KSPACE/fix_tune_kspace.cpp | 17 +-
src/KSPACE/fix_tune_kspace.h | 2 +-
src/KSPACE/gridcomm.cpp | 56 +-
src/KSPACE/msm.cpp | 38 +-
src/KSPACE/msm.h | 32 +-
src/KSPACE/msm_cg.cpp | 10 +-
src/KSPACE/msm_cg.h | 6 +-
src/KSPACE/pair_born_coul_long.cpp | 10 +-
src/KSPACE/pair_born_coul_msm.cpp | 14 +-
src/KSPACE/pair_born_coul_msm.h | 24 -
src/KSPACE/pair_buck_coul_long.cpp | 44 +-
src/KSPACE/pair_buck_coul_long.h | 2 +-
src/KSPACE/pair_buck_coul_msm.cpp | 14 +-
src/KSPACE/pair_buck_coul_msm.h | 24 -
src/KSPACE/pair_buck_long_coul_long.cpp | 22 +-
src/KSPACE/pair_coul_long.cpp | 39 +-
src/KSPACE/pair_coul_long.h | 4 +-
src/KSPACE/pair_coul_msm.cpp | 8 +-
src/KSPACE/pair_coul_msm.h | 24 -
src/KSPACE/pair_lj_charmm_coul_long.cpp | 47 +-
src/KSPACE/pair_lj_charmm_coul_long.h | 8 +-
src/KSPACE/pair_lj_charmm_coul_msm.cpp | 29 +-
src/KSPACE/pair_lj_charmm_coul_msm.h | 36 +-
src/KSPACE/pair_lj_cut_coul_long.cpp | 13 +-
src/KSPACE/pair_lj_cut_coul_msm.cpp | 17 +-
src/KSPACE/pair_lj_cut_coul_msm.h | 24 -
src/KSPACE/pair_lj_cut_tip4p_long.cpp | 8 +-
src/KSPACE/pair_lj_long_coul_long.cpp | 58 +-
src/KSPACE/pair_lj_long_coul_long.h | 2 +-
src/KSPACE/pair_lj_long_tip4p_long.cpp | 100 +-
src/KSPACE/pair_lj_long_tip4p_long.h | 2 +-
src/KSPACE/pair_tip4p_long.cpp | 8 +-
src/KSPACE/pppm.cpp | 52 +-
src/KSPACE/pppm.h | 37 +-
src/KSPACE/pppm_cg.cpp | 10 +-
src/KSPACE/pppm_cg.h | 4 +
src/KSPACE/pppm_disp.cpp | 679 +-
src/KSPACE/pppm_disp.h | 59 +-
src/KSPACE/pppm_disp_tip4p.cpp | 38 +-
src/KSPACE/pppm_disp_tip4p.h | 8 +-
src/KSPACE/pppm_stagger.cpp | 22 +-
src/KSPACE/pppm_stagger.h | 6 +-
src/KSPACE/pppm_tip4p.cpp | 14 +-
src/KSPACE/pppm_tip4p.h | 4 +
src/KSPACE/remap.cpp | 18 +-
src/KSPACE/remap_wrap.cpp | 2 +-
src/MAKE/MACHINES/Makefile.beacon | 14 +-
src/MAKE/MACHINES/Makefile.bgl | 14 +-
src/MAKE/MACHINES/Makefile.bgq | 19 +-
src/MAKE/MACHINES/Makefile.chama | 24 +-
src/MAKE/MACHINES/Makefile.cygwin | 14 +-
src/MAKE/MACHINES/Makefile.glory | 14 +-
src/MAKE/MACHINES/Makefile.jaguar | 14 +-
src/MAKE/MACHINES/Makefile.mac | 14 +-
src/MAKE/MACHINES/Makefile.mac_mpi | 14 +-
src/MAKE/MACHINES/Makefile.mingw32-cross | 24 +-
src/MAKE/MACHINES/Makefile.mingw32-cross-mpi | 28 +-
src/MAKE/MACHINES/Makefile.mingw64-cross | 24 +-
src/MAKE/MACHINES/Makefile.mingw64-cross-mpi | 26 +-
src/MAKE/MACHINES/Makefile.myrinet | 14 +-
src/MAKE/MACHINES/Makefile.power | 14 +-
src/MAKE/MACHINES/Makefile.redsky | 14 +-
src/MAKE/MACHINES/Makefile.serial | 14 +-
src/MAKE/MACHINES/Makefile.stampede | 8 +-
src/MAKE/MACHINES/Makefile.storm | 21 +-
src/MAKE/MACHINES/Makefile.tacc | 14 +-
src/MAKE/MACHINES/Makefile.ubuntu | 14 +-
src/MAKE/MACHINES/Makefile.ubuntu_simple | 14 +-
src/MAKE/MACHINES/Makefile.xe6 | 14 +-
src/MAKE/MACHINES/Makefile.xt3 | 14 +-
src/MAKE/MACHINES/Makefile.xt5 | 14 +-
src/MAKE/Makefile.mpi | 14 +-
src/MAKE/Makefile.serial | 16 +-
src/MAKE/OPTIONS/Makefile.fftw | 14 +-
src/MAKE/OPTIONS/Makefile.intel_cpu | 18 +-
src/MAKE/OPTIONS/Makefile.intel_phi | 14 +-
src/MAKE/OPTIONS/Makefile.jpeg | 14 +-
src/MAKE/OPTIONS/Makefile.kokkos_cuda | 29 +-
src/MAKE/OPTIONS/Makefile.kokkos_omp | 16 +-
src/MAKE/OPTIONS/Makefile.kokkos_phi | 24 +-
src/MAKE/OPTIONS/Makefile.mpi_fastmgpt | 113 +
src/MAKE/OPTIONS/Makefile.mpich_g++ | 14 +-
src/MAKE/OPTIONS/Makefile.mpich_icc | 14 +-
src/MAKE/OPTIONS/Makefile.mpich_native_g++ | 14 +-
src/MAKE/OPTIONS/Makefile.mpich_native_icc | 14 +-
src/MAKE/OPTIONS/Makefile.omp | 14 +-
src/MAKE/OPTIONS/Makefile.ompi_g++ | 14 +-
src/MAKE/OPTIONS/Makefile.ompi_icc | 14 +-
src/MAKE/OPTIONS/Makefile.ompi_native_g++ | 14 +-
src/MAKE/OPTIONS/Makefile.ompi_native_icc | 14 +-
src/MAKE/OPTIONS/Makefile.opt | 16 +-
src/MAKE/OPTIONS/Makefile.pgi | 14 +-
src/MAKE/OPTIONS/Makefile.png | 14 +-
src/MAKE/OPTIONS/Makefile.serial_icc | 14 +-
src/MAKE/README | 2 +-
src/MANYBODY/fix_qeq_comb.cpp | 11 +-
src/MANYBODY/fix_qeq_comb.h | 2 +-
src/MANYBODY/pair_adp.cpp | 11 +-
src/MANYBODY/pair_airebo.cpp | 42 +-
src/MANYBODY/pair_airebo.h | 2 +-
src/MANYBODY/pair_bop.cpp | 11054 +--
src/MANYBODY/pair_bop.h | 64 +-
src/MANYBODY/pair_comb.cpp | 33 +-
src/MANYBODY/pair_comb.h | 6 +-
src/MANYBODY/pair_comb3.cpp | 670 +-
src/MANYBODY/pair_comb3.h | 96 +-
src/MANYBODY/pair_eam.cpp | 107 +-
src/MANYBODY/pair_eam.h | 2 +-
src/MANYBODY/pair_eam_alloy.cpp | 6 +-
src/MANYBODY/pair_eam_fs.cpp | 6 +-
src/MANYBODY/pair_eim.cpp | 11 +-
src/MANYBODY/pair_eim.h | 2 +-
src/MANYBODY/pair_lcbop.cpp | 10 +-
src/MANYBODY/pair_lcbop.h | 2 +-
src/MANYBODY/pair_nb3b_harmonic.cpp | 82 +-
src/MANYBODY/pair_nb3b_harmonic.h | 10 +-
src/MANYBODY/pair_polymorphic.cpp | 796 +
src/MANYBODY/pair_polymorphic.h | 315 +
src/MANYBODY/pair_sw.cpp | 17 +-
src/MANYBODY/pair_sw.h | 12 +-
src/MANYBODY/pair_tersoff.cpp | 15 +-
src/MANYBODY/pair_tersoff.h | 10 +-
src/MANYBODY/pair_tersoff_mod.cpp | 40 +-
src/MANYBODY/pair_tersoff_mod.h | 20 +-
src/MANYBODY/pair_tersoff_zbl.cpp | 8 +-
src/MANYBODY/pair_vashishta.cpp | 618 +
src/MANYBODY/pair_vashishta.h | 121 +
src/MC/fix_atom_swap.cpp | 193 +-
src/MC/fix_atom_swap.h | 38 +-
src/MC/fix_bond_break.cpp | 20 +-
src/MC/fix_bond_break.h | 15 +-
src/MC/fix_bond_create.cpp | 52 +-
src/MC/fix_bond_create.h | 35 +-
src/MC/fix_bond_swap.cpp | 8 +-
src/MC/fix_gcmc.cpp | 961 +-
src/MC/fix_gcmc.h | 113 +-
src/MC/fix_tfmc.cpp | 30 +-
src/MC/fix_tfmc.h | 10 +-
src/MC/pair_dsmc.cpp | 10 +-
src/MEAM/pair_meam.cpp | 10 +-
src/MISC/compute_msd_nongauss.cpp | 2 +-
src/MISC/compute_ti.cpp | 42 +-
src/MISC/compute_ti.h | 2 +-
src/MISC/fix_deposit.cpp | 66 +-
src/MISC/fix_deposit.h | 7 +-
src/MISC/fix_efield.cpp | 22 +-
src/MISC/fix_efield.h | 2 +-
src/MISC/fix_evaporate.cpp | 8 +-
src/MISC/fix_gld.cpp | 52 +-
src/MISC/fix_gld.h | 2 +-
src/MISC/fix_oneway.cpp | 9 +-
src/MISC/fix_oneway.h | 4 +
src/MISC/fix_orient_fcc.cpp | 10 +-
src/MISC/fix_thermal_conductivity.cpp | 8 +-
src/MISC/fix_ttm.cpp | 8 +-
src/MISC/fix_viscosity.cpp | 10 +-
src/MISC/pair_nm_cut.cpp | 36 +-
src/MISC/pair_nm_cut_coul_cut.cpp | 36 +-
src/MISC/pair_nm_cut_coul_long.cpp | 32 +-
src/MOLECULE/angle_charmm.cpp | 6 +-
src/MOLECULE/angle_charmm.h | 6 +-
src/MOLECULE/angle_cosine.cpp | 4 +-
src/MOLECULE/angle_cosine.h | 2 +-
src/MOLECULE/angle_cosine_delta.cpp | 4 +-
src/MOLECULE/angle_cosine_delta.h | 2 +-
src/MOLECULE/angle_cosine_periodic.cpp | 10 +-
src/MOLECULE/angle_cosine_periodic.h | 2 +-
src/MOLECULE/angle_cosine_squared.cpp | 4 +-
src/MOLECULE/angle_cosine_squared.h | 2 +-
src/MOLECULE/angle_harmonic.cpp | 6 +-
src/MOLECULE/angle_harmonic.h | 6 +-
src/MOLECULE/angle_table.cpp | 6 +-
src/MOLECULE/angle_table.h | 2 +-
src/MOLECULE/atom_vec_angle.cpp | 4 +-
src/MOLECULE/atom_vec_bond.cpp | 2 +-
src/MOLECULE/atom_vec_full.cpp | 2 +-
src/MOLECULE/atom_vec_molecular.cpp | 6 +-
src/MOLECULE/atom_vec_template.cpp | 8 +-
src/MOLECULE/bond_fene.cpp | 10 +-
src/MOLECULE/bond_fene.h | 6 +-
src/MOLECULE/bond_fene_expand.cpp | 6 +-
src/MOLECULE/bond_fene_expand.h | 2 +-
src/MOLECULE/bond_harmonic.cpp | 6 +-
src/MOLECULE/bond_harmonic.h | 4 +-
src/MOLECULE/bond_morse.cpp | 4 +-
src/MOLECULE/bond_morse.h | 2 +-
src/MOLECULE/bond_nonlinear.cpp | 4 +-
src/MOLECULE/bond_nonlinear.h | 2 +-
src/MOLECULE/bond_quartic.cpp | 6 +-
src/MOLECULE/bond_quartic.h | 2 +-
src/MOLECULE/bond_table.cpp | 8 +-
src/MOLECULE/bond_table.h | 2 +-
src/MOLECULE/dihedral_charmm.cpp | 12 +-
src/MOLECULE/dihedral_charmm.h | 8 +-
src/MOLECULE/dihedral_harmonic.cpp | 10 +-
src/MOLECULE/dihedral_harmonic.h | 2 +-
src/MOLECULE/dihedral_helix.cpp | 10 +-
src/MOLECULE/dihedral_helix.h | 2 +-
src/MOLECULE/dihedral_multi_harmonic.cpp | 8 +-
src/MOLECULE/dihedral_multi_harmonic.h | 2 +-
src/MOLECULE/dihedral_opls.cpp | 10 +-
src/MOLECULE/dihedral_opls.h | 4 +-
src/MOLECULE/improper_cvff.cpp | 10 +-
src/MOLECULE/improper_cvff.h | 2 +-
src/MOLECULE/improper_harmonic.cpp | 12 +-
src/MOLECULE/improper_harmonic.h | 6 +-
src/MOLECULE/improper_umbrella.cpp | 14 +-
src/MOLECULE/improper_umbrella.h | 2 +-
src/MOLECULE/pair_hbond_dreiding_lj.cpp | 8 +-
src/MOLECULE/pair_hbond_dreiding_morse.cpp | 8 +-
src/MOLECULE/pair_lj_charmm_coul_charmm.cpp | 12 +-
src/MOLECULE/pair_lj_charmm_coul_charmm.h | 8 +-
.../pair_lj_charmm_coul_charmm_implicit.cpp | 4 +-
src/MOLECULE/pair_lj_cut_tip4p_cut.cpp | 20 +-
src/MOLECULE/pair_tip4p_cut.cpp | 8 +-
src/MPIIO/dump_atom_mpiio.cpp | 6 +-
src/MPIIO/dump_atom_mpiio.h | 4 +-
src/MPIIO/dump_cfg_mpiio.cpp | 52 +-
src/MPIIO/dump_cfg_mpiio.h | 15 +-
src/MPIIO/dump_custom_mpiio.cpp | 6 +-
src/MPIIO/dump_custom_mpiio.h | 4 +-
src/MPIIO/dump_xyz_mpiio.cpp | 6 +-
src/MPIIO/dump_xyz_mpiio.h | 4 +-
src/MPIIO/restart_mpiio.cpp | 4 +-
src/Make.py | 346 +-
src/Makefile | 18 +-
src/Makefile.package.empty | 2 +
src/OPT/pair_eam_alloy_opt.h | 1 +
src/OPT/pair_eam_fs_opt.h | 1 +
src/OPT/pair_eam_opt.cpp | 4 +-
src/OPT/pair_lj_charmm_coul_long_opt.cpp | 4 +-
src/OPT/pair_lj_cut_coul_long_opt.cpp | 2 +-
src/OPT/pair_lj_cut_opt.cpp | 2 +-
src/OPT/pair_lj_cut_tip4p_long_opt.cpp | 2 +-
src/OPT/pair_lj_long_coul_long_opt.cpp | 66 +-
src/OPT/pair_morse_opt.cpp | 4 +-
src/PERI/atom_vec_peri.cpp | 10 +-
src/PERI/compute_damage_atom.cpp | 8 +-
src/PERI/compute_dilatation_atom.cpp | 6 +-
src/PERI/compute_dilatation_atom.h | 26 +-
src/PERI/compute_plasticity_atom.cpp | 4 +-
src/PERI/compute_plasticity_atom.h | 22 +
src/PERI/fix_peri_neigh.cpp | 56 +-
src/PERI/fix_peri_neigh.h | 8 +-
src/PERI/pair_peri_eps.cpp | 102 +-
src/PERI/pair_peri_eps.h | 2 +-
src/PERI/pair_peri_lps.cpp | 14 +-
src/PERI/pair_peri_pmb.cpp | 10 +-
src/PERI/pair_peri_ves.cpp | 46 +-
src/PERI/pair_peri_ves.h | 6 +-
src/POEMS/fix_poems.cpp | 17 +-
src/PYTHON/Install.sh | 69 +
src/PYTHON/python.cpp | 401 +
src/PYTHON/python.h | 127 +
src/QEQ/fix_qeq.cpp | 14 +-
src/QEQ/fix_qeq.h | 27 +
src/QEQ/fix_qeq_dynamic.cpp | 16 +-
src/QEQ/fix_qeq_dynamic.h | 26 +
src/QEQ/fix_qeq_point.cpp | 10 +-
src/QEQ/fix_qeq_point.h | 22 +
src/QEQ/fix_qeq_shielded.cpp | 17 +-
src/QEQ/fix_qeq_shielded.h | 38 +
src/QEQ/fix_qeq_slater.cpp | 26 +-
src/QEQ/fix_qeq_slater.h | 40 +
src/REAX/fix_reax_bonds.cpp | 4 +-
src/REAX/fix_reax_bonds.h | 2 +-
src/REAX/pair_reax.cpp | 15 +-
src/REAX/pair_reax.h | 8 +
src/REPLICA/compute_event_displace.cpp | 8 +-
src/REPLICA/fix_event.cpp | 4 +-
src/REPLICA/fix_event_prd.cpp | 4 +-
src/REPLICA/fix_event_tad.cpp | 4 +-
src/REPLICA/fix_neb.cpp | 10 +-
src/REPLICA/neb.cpp | 26 +-
src/REPLICA/neb.h | 2 +-
src/REPLICA/prd.cpp | 101 +-
src/REPLICA/tad.cpp | 106 +-
src/REPLICA/temper.cpp | 12 +-
src/REPLICA/verlet_split.cpp | 47 +-
src/REPLICA/verlet_split.h | 4 +
src/RIGID/compute_erotate_rigid.cpp | 6 +-
src/RIGID/compute_ke_rigid.cpp | 4 +-
src/RIGID/fix_rattle.cpp | 168 +-
src/RIGID/fix_rattle.h | 28 +
src/RIGID/fix_rigid.cpp | 276 +-
src/RIGID/fix_rigid.h | 16 +-
src/RIGID/fix_rigid_nh.cpp | 374 +-
src/RIGID/fix_rigid_nh.h | 22 +-
src/RIGID/fix_rigid_nh_small.cpp | 393 +-
src/RIGID/fix_rigid_nh_small.h | 54 +-
src/RIGID/fix_rigid_nph.cpp | 14 +-
src/RIGID/fix_rigid_nph.h | 2 +-
src/RIGID/fix_rigid_nph_small.cpp | 25 +-
src/RIGID/fix_rigid_nph_small.h | 14 +-
src/RIGID/fix_rigid_npt.cpp | 16 +-
src/RIGID/fix_rigid_npt.h | 2 +-
src/RIGID/fix_rigid_npt_small.cpp | 26 +-
src/RIGID/fix_rigid_npt_small.h | 20 +-
src/RIGID/fix_rigid_nve.cpp | 2 +-
src/RIGID/fix_rigid_nve.h | 2 +-
src/RIGID/fix_rigid_nve_small.cpp | 2 +-
src/RIGID/fix_rigid_nve_small.h | 2 +-
src/RIGID/fix_rigid_nvt.cpp | 10 +-
src/RIGID/fix_rigid_nvt.h | 2 +-
src/RIGID/fix_rigid_nvt_small.cpp | 10 +-
src/RIGID/fix_rigid_nvt_small.h | 20 +-
src/RIGID/fix_rigid_small.cpp | 316 +-
src/RIGID/fix_rigid_small.h | 23 +-
src/RIGID/fix_shake.cpp | 47 +-
src/RIGID/fix_shake.h | 2 +-
src/SHOCK/fix_append_atoms.cpp | 10 +-
src/SHOCK/fix_msst.cpp | 8 +-
src/SHOCK/fix_nphug.cpp | 10 +-
src/SHOCK/fix_wall_piston.cpp | 16 +-
src/SHOCK/fix_wall_piston.h | 1 +
src/SNAP/compute_sna_atom.cpp | 28 +-
src/SNAP/compute_sna_atom.h | 26 +-
src/SNAP/compute_snad_atom.cpp | 28 +-
src/SNAP/compute_snad_atom.h | 26 +-
src/SNAP/compute_snav_atom.cpp | 24 +-
src/SNAP/compute_snav_atom.h | 26 +-
src/SNAP/pair_snap.cpp | 101 +-
src/SNAP/pair_snap.h | 61 +
src/SNAP/sna.cpp | 72 +-
src/SNAP/sna.h | 13 +-
src/SRD/fix_srd.cpp | 69 +-
src/SRD/fix_srd.h | 16 +-
src/SRD/fix_wall_srd.cpp | 6 +-
src/STUBS/mpi.c | 43 +-
src/STUBS/mpi.h | 13 +-
src/USER-ATC/fix_atc.cpp | 122 +-
src/USER-ATC/fix_atc.h | 20 +-
src/USER-AWPMD/atom_vec_wavepacket.cpp | 12 +-
src/USER-AWPMD/fix_nve_awpmd.cpp | 12 +-
src/USER-AWPMD/pair_awpmd_cut.cpp | 13 +-
src/USER-AWPMD/pair_awpmd_cut.h | 2 +-
src/USER-CG-CMM/angle_sdk.cpp | 6 +-
src/USER-CG-CMM/angle_sdk.h | 2 +-
src/USER-CG-CMM/lj_sdk_common.h | 2 +-
src/USER-CG-CMM/pair_lj_sdk.cpp | 8 +-
src/USER-CG-CMM/pair_lj_sdk.h | 8 +-
src/USER-CG-CMM/pair_lj_sdk_coul_long.cpp | 18 +-
src/USER-CG-CMM/pair_lj_sdk_coul_msm.cpp | 10 +-
src/USER-CG-CMM/pair_lj_sdk_coul_msm.h | 2 +-
src/USER-COLVARS/colvarproxy_lammps.cpp | 7 +-
src/USER-COLVARS/colvarproxy_lammps.h | 14 +-
src/USER-CUDA/comm_cuda.cpp | 2 +-
src/USER-CUDA/compute_pe_cuda.cpp | 2 +-
src/USER-CUDA/compute_pressure_cuda.cpp | 2 +-
src/USER-CUDA/compute_temp_cuda.cpp | 2 +-
src/USER-CUDA/compute_temp_partial_cuda.cpp | 2 +-
src/USER-CUDA/cuda.cpp | 12 +-
src/USER-CUDA/domain_cuda.cpp | 10 +-
src/USER-CUDA/fft3d_cuda.cpp | 2 +-
src/USER-CUDA/fft3d_wrap_cuda.cpp | 2 +-
src/USER-CUDA/fix_aveforce_cuda.cpp | 2 +-
src/USER-CUDA/fix_shake_cuda.cpp | 5 +-
src/USER-CUDA/neighbor_cuda.cpp | 2 +-
src/USER-CUDA/pair_eam_cuda.cpp | 2 +-
src/USER-CUDA/pair_eam_cuda.h | 2 +-
src/USER-CUDA/pair_gran_hooke_cuda.cpp | 4 +-
src/USER-CUDA/pair_tersoff_zbl_cuda.cpp | 8 +-
src/USER-CUDA/pppm_cuda.cpp | 10 +-
src/USER-CUDA/pppm_old.cpp | 10 +-
src/USER-CUDA/pppm_old.h | 2 +-
src/USER-CUDA/verlet_cuda.cpp | 61 +-
src/USER-DIFFRACTION/README | 69 +
src/USER-DIFFRACTION/compute_saed.cpp | 538 +
src/USER-DIFFRACTION/compute_saed.h | 63 +
src/USER-DIFFRACTION/compute_saed_consts.h | 458 +
src/USER-DIFFRACTION/compute_xrd.cpp | 541 +
src/USER-DIFFRACTION/compute_xrd.h | 60 +
src/USER-DIFFRACTION/compute_xrd_consts.h | 506 +
src/USER-DIFFRACTION/fix_saed_vtk.cpp | 611 +
src/USER-DIFFRACTION/fix_saed_vtk.h | 188 +
src/USER-DRUDE/README | 21 +
src/USER-DRUDE/compute_temp_drude.cpp | 218 +
src/USER-DRUDE/compute_temp_drude.h | 63 +
src/USER-DRUDE/fix_drude.cpp | 497 +
src/USER-DRUDE/fix_drude.h | 69 +
src/USER-DRUDE/fix_drude_transform.cpp | 319 +
src/USER-DRUDE/fix_drude_transform.h | 52 +
src/USER-DRUDE/fix_langevin_drude.cpp | 420 +
src/USER-DRUDE/fix_langevin_drude.h | 63 +
src/USER-DRUDE/pair_lj_cut_thole_long.cpp | 703 +
src/USER-DRUDE/pair_lj_cut_thole_long.h | 97 +
src/USER-DRUDE/pair_thole.cpp | 421 +
src/USER-DRUDE/pair_thole.h | 75 +
src/USER-EFF/atom_vec_electron.cpp | 12 +-
src/USER-EFF/compute_ke_atom_eff.cpp | 6 +-
src/USER-EFF/compute_ke_eff.cpp | 6 +-
src/USER-EFF/compute_temp_deform_eff.cpp | 17 +-
src/USER-EFF/compute_temp_deform_eff.h | 1 -
src/USER-EFF/compute_temp_eff.cpp | 17 +-
src/USER-EFF/compute_temp_eff.h | 1 -
src/USER-EFF/compute_temp_region_eff.cpp | 12 +-
src/USER-EFF/fix_langevin_eff.cpp | 8 +-
src/USER-EFF/fix_nh_eff.cpp | 4 +-
src/USER-EFF/fix_nph_eff.cpp | 2 +-
src/USER-EFF/fix_npt_eff.cpp | 2 +-
src/USER-EFF/fix_nve_eff.cpp | 10 +-
src/USER-EFF/fix_nvt_eff.cpp | 4 +-
src/USER-EFF/fix_nvt_sllod_eff.cpp | 4 +-
src/USER-EFF/fix_temp_rescale_eff.cpp | 6 +-
src/USER-EFF/pair_eff_cut.cpp | 20 +-
src/USER-FEP/compute_fep.cpp | 70 +-
src/USER-FEP/compute_fep.h | 1 -
src/USER-FEP/fix_adapt_fep.cpp | 18 +-
src/USER-FEP/fix_adapt_fep.h | 2 +-
src/USER-FEP/pair_coul_cut_soft.cpp | 12 +-
src/USER-FEP/pair_coul_long_soft.cpp | 14 +-
src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp | 44 +-
src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp | 20 +-
src/USER-FEP/pair_lj_cut_coul_long_soft.cpp | 44 +-
src/USER-FEP/pair_lj_cut_soft.cpp | 28 +-
src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp | 12 +-
src/USER-FEP/pair_tip4p_long_soft.cpp | 8 +-
src/USER-H5MD/Install.sh | 62 +
src/USER-H5MD/README | 9 +
src/USER-H5MD/dump_h5md.cpp | 555 +
src/USER-H5MD/dump_h5md.h | 106 +
src/USER-INTEL/README | 13 +-
src/USER-INTEL/fix_intel.cpp | 27 +-
src/USER-INTEL/fix_intel.h | 36 +-
src/USER-INTEL/intel_buffers.cpp | 10 +-
src/USER-INTEL/intel_buffers.h | 38 +-
src/USER-INTEL/intel_preprocess.h | 36 +-
src/USER-INTEL/neigh_half_bin_intel.cpp | 642 +-
src/USER-INTEL/pair_gayberne_intel.cpp | 116 +-
src/USER-INTEL/pair_gayberne_intel.h | 6 +-
src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp | 44 +-
src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp | 16 +-
src/USER-INTEL/pair_lj_cut_intel.cpp | 16 +-
src/USER-INTEL/pair_sw_intel.cpp | 32 +-
src/USER-INTEL/pair_sw_intel.h | 2 +-
src/USER-INTEL/verlet_intel.cpp | 53 +-
src/USER-INTEL/verlet_split_intel.cpp | 36 +-
src/USER-LB/README | 4 +-
src/USER-LB/fix_lb_fluid.cpp | 746 +-
src/USER-LB/fix_lb_fluid.h | 38 +-
src/USER-LB/fix_lb_momentum.cpp | 41 +-
src/USER-LB/fix_lb_momentum.h | 2 +-
src/USER-LB/fix_lb_pc.cpp | 80 +-
src/USER-LB/fix_lb_pc.h | 4 +-
src/USER-LB/fix_lb_rigid_pc_sphere.cpp | 222 +-
src/USER-LB/fix_lb_rigid_pc_sphere.h | 6 +-
src/USER-LB/fix_lb_viscous.cpp | 14 +-
src/USER-LB/fix_lb_viscous.h | 4 +-
src/USER-MGPT/README | 33 +
src/USER-MGPT/mgpt_bgmul_7.c.h | 181 +
src/USER-MGPT/mgpt_linalg.cpp | 203 +
src/USER-MGPT/mgpt_linalg.h | 69 +
src/USER-MGPT/mgpt_mmul3_538.c.h | 295 +
src/USER-MGPT/mgpt_mmul3_748.c.h | 508 +
src/USER-MGPT/mgpt_mmul3d_526.c.h | 443 +
src/USER-MGPT/mgpt_mmul3d_744.c.h | 1116 +
src/USER-MGPT/mgpt_mmul_bg_552.c.h | 358 +
src/USER-MGPT/mgpt_mmul_bg_722.c.h | 1075 +
src/USER-MGPT/mgpt_mmul_bgq_n5_lda8_2x8.c.h | 236 +
src/USER-MGPT/mgpt_mmul_bgq_n7_lda8_4x8.c.h | 332 +
src/USER-MGPT/mgpt_readpot.cpp | 566 +
src/USER-MGPT/mgpt_readpot.h | 418 +
src/USER-MGPT/mgpt_splinetab.cpp | 125 +
src/USER-MGPT/mgpt_splinetab.h | 62 +
src/USER-MGPT/mgpt_ttr_5022.c.h | 202 +
src/USER-MGPT/mgpt_ttr_5042.c.h | 150 +
src/USER-MGPT/mgpt_ttr_5123.c.h | 245 +
src/USER-MGPT/mgpt_ttr_5141.c.h | 142 +
src/USER-MGPT/mgpt_ttr_7022.c.h | 345 +
src/USER-MGPT/mgpt_ttr_7042.c.h | 194 +
src/USER-MGPT/mgpt_ttr_7123.c.h | 349 +
src/USER-MGPT/mgpt_ttr_7141.c.h | 174 +
src/USER-MGPT/pair_mgpt.cpp | 2927 +
src/USER-MGPT/pair_mgpt.h | 718 +
src/USER-MISC/README | 1 +
src/USER-MISC/angle_cosine_shift.cpp | 4 +-
src/USER-MISC/angle_cosine_shift.h | 2 +-
src/USER-MISC/angle_cosine_shift_exp.cpp | 4 +-
src/USER-MISC/angle_cosine_shift_exp.h | 2 +-
src/USER-MISC/angle_dipole.cpp | 4 +-
src/USER-MISC/angle_dipole.h | 2 +-
src/USER-MISC/angle_fourier.cpp | 10 +-
src/USER-MISC/angle_fourier.h | 4 +-
src/USER-MISC/angle_fourier_simple.cpp | 8 +-
src/USER-MISC/angle_fourier_simple.h | 4 +-
src/USER-MISC/angle_quartic.cpp | 10 +-
src/USER-MISC/angle_quartic.h | 4 +-
src/USER-MISC/bond_harmonic_shift.cpp | 4 +-
src/USER-MISC/bond_harmonic_shift.h | 2 +-
src/USER-MISC/bond_harmonic_shift_cut.cpp | 4 +-
src/USER-MISC/bond_harmonic_shift_cut.h | 2 +-
src/USER-MISC/compute_ackland_atom.cpp | 87 +-
src/USER-MISC/compute_basal_atom.cpp | 50 +-
src/USER-MISC/compute_temp_rotate.cpp | 16 +-
src/USER-MISC/dihedral_cosine_shift_exp.cpp | 10 +-
src/USER-MISC/dihedral_cosine_shift_exp.h | 2 +-
src/USER-MISC/dihedral_fourier.cpp | 32 +-
src/USER-MISC/dihedral_fourier.h | 4 +-
src/USER-MISC/dihedral_nharmonic.cpp | 20 +-
src/USER-MISC/dihedral_nharmonic.h | 4 +-
src/USER-MISC/dihedral_quadratic.cpp | 20 +-
src/USER-MISC/dihedral_quadratic.h | 4 +-
src/USER-MISC/dihedral_table.cpp | 203 +-
src/USER-MISC/fix_addtorque.cpp | 10 +-
src/USER-MISC/fix_ave_correlate_long.cpp | 786 +
src/USER-MISC/fix_ave_correlate_long.h | 152 +
src/USER-MISC/fix_ave_spatial_sphere.cpp | 122 +-
src/USER-MISC/fix_ave_spatial_sphere.h | 30 +-
src/USER-MISC/fix_gle.cpp | 16 +-
src/USER-MISC/fix_imd.cpp | 20 +-
src/USER-MISC/fix_ipi.cpp | 14 +-
src/USER-MISC/fix_ipi.h | 2 +-
src/USER-MISC/fix_pimd.cpp | 344 +-
src/USER-MISC/fix_pimd.h | 46 +-
src/USER-MISC/fix_smd.cpp | 15 +-
src/USER-MISC/fix_srp.cpp | 90 +-
src/USER-MISC/fix_srp.h | 4 +-
src/USER-MISC/fix_ti_rs.cpp | 56 +-
src/USER-MISC/fix_ti_rs.h | 8 +-
src/USER-MISC/fix_ti_spring.cpp | 57 +-
src/USER-MISC/fix_ti_spring.h | 10 +-
src/USER-MISC/fix_ttm_mod.cpp | 26 +-
src/USER-MISC/improper_cossq.cpp | 10 +-
src/USER-MISC/improper_cossq.h | 2 +-
src/USER-MISC/improper_fourier.cpp | 34 +-
src/USER-MISC/improper_fourier.h | 4 +-
src/USER-MISC/improper_ring.cpp | 6 +-
src/USER-MISC/improper_ring.h | 2 +-
src/USER-MISC/pair_cdeam.cpp | 10 +-
src/USER-MISC/pair_coul_diel.cpp | 8 +-
src/USER-MISC/pair_edip.cpp | 10 +-
src/USER-MISC/pair_gauss_cut.cpp | 8 +-
src/USER-MISC/pair_list.cpp | 12 +-
src/USER-MISC/pair_list.h | 6 +-
src/USER-MISC/pair_lj_sf.cpp | 6 +-
src/USER-MISC/pair_lj_sf_dipole_sf.cpp | 6 +-
src/USER-MISC/pair_meam_spline.cpp | 10 +-
src/USER-MISC/pair_meam_spline.h | 4 +-
src/USER-MISC/pair_meam_sw_spline.cpp | 28 +-
src/USER-MISC/pair_meam_sw_spline.h | 20 +-
src/USER-MISC/pair_srp.cpp | 216 +-
src/USER-MISC/pair_srp.h | 5 +-
src/USER-MISC/pair_tersoff_table.cpp | 25 +-
src/USER-MOLFILE/dump_molfile.cpp | 3 +-
src/USER-MOLFILE/molfile_interface.cpp | 5 +-
src/USER-MOLFILE/reader_molfile.cpp | 6 +-
src/USER-OMP/Install.sh | 13 +-
src/USER-OMP/angle_charmm_omp.cpp | 2 +
src/USER-OMP/angle_class2_omp.cpp | 2 +
src/USER-OMP/angle_cosine_delta_omp.cpp | 2 +
src/USER-OMP/angle_cosine_omp.cpp | 2 +
src/USER-OMP/angle_cosine_periodic_omp.cpp | 8 +-
src/USER-OMP/angle_cosine_shift_exp_omp.cpp | 2 +
src/USER-OMP/angle_cosine_shift_omp.cpp | 2 +
src/USER-OMP/angle_cosine_squared_omp.cpp | 2 +
src/USER-OMP/angle_dipole_omp.cpp | 2 +
src/USER-OMP/angle_fourier_omp.cpp | 2 +
src/USER-OMP/angle_fourier_simple_omp.cpp | 2 +
src/USER-OMP/angle_harmonic_omp.cpp | 2 +
src/USER-OMP/angle_quartic_omp.cpp | 2 +
src/USER-OMP/angle_sdk_omp.cpp | 2 +
src/USER-OMP/angle_table_omp.cpp | 2 +
src/USER-OMP/bond_class2_omp.cpp | 2 +
src/USER-OMP/bond_fene_expand_omp.cpp | 2 +
src/USER-OMP/bond_fene_omp.cpp | 2 +
src/USER-OMP/bond_harmonic_omp.cpp | 2 +
src/USER-OMP/bond_harmonic_shift_cut_omp.cpp | 2 +
src/USER-OMP/bond_harmonic_shift_omp.cpp | 2 +
src/USER-OMP/bond_morse_omp.cpp | 2 +
src/USER-OMP/bond_nonlinear_omp.cpp | 2 +
src/USER-OMP/bond_quartic_omp.cpp | 2 +
src/USER-OMP/bond_table_omp.cpp | 2 +
src/USER-OMP/dihedral_charmm_omp.cpp | 6 +-
src/USER-OMP/dihedral_class2_omp.cpp | 4 +-
src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp | 4 +-
src/USER-OMP/dihedral_fourier_omp.cpp | 4 +-
src/USER-OMP/dihedral_harmonic_omp.cpp | 4 +-
src/USER-OMP/dihedral_helix_omp.cpp | 4 +-
src/USER-OMP/dihedral_multi_harmonic_omp.cpp | 4 +-
src/USER-OMP/dihedral_nharmonic_omp.cpp | 4 +-
src/USER-OMP/dihedral_opls_omp.cpp | 4 +-
src/USER-OMP/dihedral_quadratic_omp.cpp | 4 +-
src/USER-OMP/dihedral_table_omp.cpp | 2 +
src/USER-OMP/ewald_omp.cpp | 4 +-
src/USER-OMP/fix_gravity_omp.cpp | 8 +-
src/USER-OMP/fix_nh_asphere_omp.cpp | 10 +-
src/USER-OMP/fix_nh_sphere_omp.cpp | 4 +-
src/USER-OMP/fix_nph_asphere_omp.cpp | 2 +-
src/USER-OMP/fix_nph_omp.cpp | 2 +-
src/USER-OMP/fix_nph_sphere_omp.cpp | 2 +-
src/USER-OMP/fix_nphug_omp.cpp | 8 +-
src/USER-OMP/fix_npt_asphere_omp.cpp | 2 +-
src/USER-OMP/fix_npt_omp.cpp | 2 +-
src/USER-OMP/fix_npt_sphere_omp.cpp | 2 +-
src/USER-OMP/fix_nve_sphere_omp.cpp | 6 +-
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 | 4 +-
src/USER-OMP/fix_nvt_sphere_omp.cpp | 2 +-
src/USER-OMP/fix_omp.cpp | 80 +-
src/USER-OMP/fix_omp.h | 2 +
src/USER-OMP/fix_qeq_comb_omp.cpp | 6 +-
src/USER-OMP/fix_rigid_nh_omp.cpp | 112 +-
src/USER-OMP/fix_rigid_nh_omp.h | 4 +-
src/USER-OMP/fix_rigid_nph_omp.cpp | 18 +-
src/USER-OMP/fix_rigid_nph_omp.h | 2 +-
src/USER-OMP/fix_rigid_npt_omp.cpp | 18 +-
src/USER-OMP/fix_rigid_npt_omp.h | 2 +-
src/USER-OMP/fix_rigid_nve_omp.cpp | 2 +-
src/USER-OMP/fix_rigid_nve_omp.h | 2 +-
src/USER-OMP/fix_rigid_nvt_omp.cpp | 10 +-
src/USER-OMP/fix_rigid_nvt_omp.h | 2 +-
src/USER-OMP/fix_rigid_omp.cpp | 6 +-
src/USER-OMP/fix_rigid_small_omp.cpp | 10 +-
src/USER-OMP/fix_shear_history_omp.cpp | 4 +-
src/USER-OMP/fix_wall_gran_omp.cpp | 2 +-
src/USER-OMP/improper_class2_omp.cpp | 4 +-
src/USER-OMP/improper_cossq_omp.cpp | 4 +-
src/USER-OMP/improper_cvff_omp.cpp | 4 +-
src/USER-OMP/improper_fourier_omp.cpp | 20 +-
src/USER-OMP/improper_harmonic_omp.cpp | 4 +-
src/USER-OMP/improper_ring_omp.cpp | 4 +-
src/USER-OMP/improper_umbrella_omp.cpp | 8 +-
src/USER-OMP/msm_cg_omp.cpp | 11 +-
src/USER-OMP/msm_omp.cpp | 8 +-
src/USER-OMP/neigh_full_omp.cpp | 1 -
src/USER-OMP/neighbor_omp.h | 22 +-
src/USER-OMP/pair_adp_omp.cpp | 8 +-
src/USER-OMP/pair_airebo_omp.cpp | 37 +-
src/USER-OMP/pair_beck_omp.cpp | 4 +-
src/USER-OMP/pair_born_coul_long_omp.cpp | 4 +-
src/USER-OMP/pair_born_coul_msm_omp.cpp | 4 +-
src/USER-OMP/pair_born_coul_wolf_omp.cpp | 6 +-
src/USER-OMP/pair_born_omp.cpp | 4 +-
src/USER-OMP/pair_brownian_omp.cpp | 34 +-
src/USER-OMP/pair_brownian_omp.h | 1 +
src/USER-OMP/pair_brownian_poly_omp.cpp | 35 +-
src/USER-OMP/pair_brownian_poly_omp.h | 1 +
src/USER-OMP/pair_buck_coul_cut_omp.cpp | 4 +-
src/USER-OMP/pair_buck_coul_long_omp.cpp | 4 +-
src/USER-OMP/pair_buck_coul_msm_omp.cpp | 4 +-
src/USER-OMP/pair_buck_long_coul_long_omp.cpp | 14 +-
src/USER-OMP/pair_buck_omp.cpp | 4 +-
src/USER-OMP/pair_cdeam_omp.cpp | 28 +-
src/USER-OMP/pair_colloid_omp.cpp | 4 +-
src/USER-OMP/pair_comb_omp.cpp | 4 +-
src/USER-OMP/pair_coul_cut_omp.cpp | 4 +-
src/USER-OMP/pair_coul_cut_soft_omp.cpp | 4 +-
src/USER-OMP/pair_coul_debye_omp.cpp | 4 +-
src/USER-OMP/pair_coul_diel_omp.cpp | 4 +-
src/USER-OMP/pair_coul_dsf_omp.cpp | 13 +-
src/USER-OMP/pair_coul_long_omp.cpp | 4 +-
src/USER-OMP/pair_coul_long_soft_omp.cpp | 4 +-
src/USER-OMP/pair_coul_msm_omp.cpp | 4 +-
src/USER-OMP/pair_coul_wolf_omp.cpp | 4 +-
src/USER-OMP/pair_dpd_omp.cpp | 30 +-
src/USER-OMP/pair_dpd_omp.h | 1 +
src/USER-OMP/pair_dpd_tstat_omp.cpp | 31 +-
src/USER-OMP/pair_dpd_tstat_omp.h | 1 +
src/USER-OMP/pair_eam_alloy_omp.cpp | 6 +-
src/USER-OMP/pair_eam_fs_omp.cpp | 6 +-
src/USER-OMP/pair_eam_omp.cpp | 8 +-
src/USER-OMP/pair_edip_omp.cpp | 4 +-
src/USER-OMP/pair_eim_omp.cpp | 10 +-
src/USER-OMP/pair_gauss_cut_omp.cpp | 4 +-
src/USER-OMP/pair_gauss_omp.cpp | 4 +-
src/USER-OMP/pair_gayberne_omp.cpp | 4 +-
src/USER-OMP/pair_gran_hertz_history_omp.cpp | 4 +-
src/USER-OMP/pair_gran_hooke_history_omp.cpp | 8 +-
src/USER-OMP/pair_gran_hooke_omp.cpp | 6 +-
src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp | 4 +-
src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp | 4 +-
src/USER-OMP/pair_line_lj_omp.cpp | 4 +-
src/USER-OMP/pair_lj96_cut_omp.cpp | 4 +-
.../pair_lj_charmm_coul_charmm_implicit_omp.cpp | 4 +-
src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp | 4 +-
src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp | 4 +-
src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp | 5 +-
src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp | 10 +-
src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp | 4 +-
src/USER-OMP/pair_lj_class2_coul_long_omp.cpp | 4 +-
src/USER-OMP/pair_lj_class2_omp.cpp | 4 +-
src/USER-OMP/pair_lj_cubic_omp.cpp | 4 +-
src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp | 4 +-
src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp | 8 +-
src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp | 4 +-
src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp | 22 +-
src/USER-OMP/pair_lj_cut_coul_long_omp.cpp | 4 +-
src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp | 12 +-
src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp | 4 +-
src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp | 4 +-
src/USER-OMP/pair_lj_cut_omp.cpp | 5 +-
src/USER-OMP/pair_lj_cut_soft_omp.cpp | 8 +-
src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp | 6 +-
src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp | 6 +-
src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp | 8 +-
src/USER-OMP/pair_lj_expand_omp.cpp | 4 +-
src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp | 4 +-
src/USER-OMP/pair_lj_gromacs_omp.cpp | 4 +-
src/USER-OMP/pair_lj_long_coul_long_omp.cpp | 44 +-
src/USER-OMP/pair_lj_long_coul_long_omp.h | 2 +-
src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp | 18 +-
src/USER-OMP/pair_lj_long_tip4p_long_omp.h | 2 +-
src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp | 4 +-
src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp | 4 +-
src/USER-OMP/pair_lj_sdk_omp.cpp | 4 +-
src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp | 4 +-
src/USER-OMP/pair_lj_sf_omp.cpp | 4 +-
src/USER-OMP/pair_lj_smooth_linear_omp.cpp | 4 +-
src/USER-OMP/pair_lj_smooth_omp.cpp | 4 +-
src/USER-OMP/pair_lubricate_omp.cpp | 4 +-
src/USER-OMP/pair_lubricate_poly_omp.cpp | 4 +-
src/USER-OMP/pair_meam_spline_omp.cpp | 7 +-
src/USER-OMP/pair_morse_omp.cpp | 4 +-
src/USER-OMP/pair_nb3b_harmonic_omp.cpp | 39 +-
src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp | 4 +-
src/USER-OMP/pair_nm_cut_coul_long_omp.cpp | 4 +-
src/USER-OMP/pair_nm_cut_omp.cpp | 4 +-
src/USER-OMP/pair_peri_lps_omp.cpp | 6 +-
src/USER-OMP/pair_peri_pmb_omp.cpp | 6 +-
src/USER-OMP/pair_resquared_omp.cpp | 4 +-
src/USER-OMP/pair_soft_omp.cpp | 4 +-
src/USER-OMP/pair_sw_omp.cpp | 10 +-
src/USER-OMP/pair_table_omp.cpp | 4 +-
src/USER-OMP/pair_tersoff_mod_omp.cpp | 4 +-
src/USER-OMP/pair_tersoff_omp.cpp | 4 +-
src/USER-OMP/pair_tersoff_table_omp.cpp | 15 +-
src/USER-OMP/pair_tersoff_zbl_omp.cpp | 8 +-
src/USER-OMP/pair_tip4p_cut_omp.cpp | 6 +-
src/USER-OMP/pair_tip4p_long_omp.cpp | 6 +-
src/USER-OMP/pair_tip4p_long_soft_omp.cpp | 6 +-
src/USER-OMP/pair_tri_lj_omp.cpp | 4 +-
src/USER-OMP/pair_vashishta_omp.cpp | 213 +
src/USER-OMP/pair_vashishta_omp.h | 48 +
src/USER-OMP/pair_yukawa_colloid_omp.cpp | 4 +-
src/USER-OMP/pair_yukawa_omp.cpp | 4 +-
src/USER-OMP/pair_zbl_omp.cpp | 4 +-
src/USER-OMP/pppm_cg_omp.cpp | 19 +-
src/USER-OMP/pppm_disp_omp.cpp | 91 +-
src/USER-OMP/pppm_disp_omp.h | 2 +-
src/USER-OMP/pppm_omp.cpp | 19 +-
src/USER-OMP/pppm_tip4p_omp.cpp | 17 +-
src/USER-OMP/respa_omp.cpp | 145 +-
src/USER-OMP/thr_data.cpp | 78 +-
src/USER-OMP/thr_data.h | 19 +-
src/USER-OMP/thr_omp.cpp | 21 +-
src/USER-PHONON/fix_phonon.cpp | 48 +-
src/USER-PHONON/fix_phonon.h | 23 +-
src/USER-QMMM/fix_qmmm.cpp | 14 +-
src/USER-QTB/README | 56 +
src/USER-QTB/fix_qbmsst.cpp | 1194 +
src/USER-QTB/fix_qbmsst.h | 124 +
src/USER-QTB/fix_qtb.cpp | 429 +
src/USER-QTB/fix_qtb.h | 71 +
src/USER-QUIP/pair_quip.cpp | 26 +-
src/USER-QUIP/pair_quip.h | 8 +-
src/USER-REAXC/compute_spec_atom.cpp | 20 +-
src/USER-REAXC/compute_spec_atom.h | 6 +-
src/USER-REAXC/fix_qeq_reax.cpp | 16 +-
src/USER-REAXC/fix_reaxc_bonds.cpp | 6 +-
src/USER-REAXC/fix_reaxc_bonds.h | 2 +-
src/USER-REAXC/fix_reaxc_species.cpp | 88 +-
src/USER-REAXC/fix_reaxc_species.h | 2 +-
src/USER-REAXC/pair_reax_c.cpp | 34 +-
src/USER-REAXC/pair_reax_c.h | 6 +-
src/USER-REAXC/reaxc_allocate.cpp | 86 +-
src/USER-REAXC/reaxc_bond_orders.cpp | 30 +-
src/USER-REAXC/reaxc_bond_orders.h | 27 +-
src/USER-REAXC/reaxc_bonds.cpp | 32 +-
src/USER-REAXC/reaxc_control.cpp | 2 +-
src/USER-REAXC/reaxc_ffield.cpp | 20 +-
src/USER-REAXC/reaxc_ffield.h | 2 +-
src/USER-REAXC/reaxc_forces.cpp | 229 +-
src/USER-REAXC/reaxc_hydrogen_bonds.cpp | 6 +-
src/USER-REAXC/reaxc_init_md.cpp | 6 +-
src/USER-REAXC/reaxc_io_tools.cpp | 428 -
src/USER-REAXC/reaxc_io_tools.h | 74 -
src/USER-REAXC/reaxc_lookup.cpp | 88 +-
src/USER-REAXC/reaxc_multi_body.cpp | 22 +-
src/USER-REAXC/reaxc_nonbonded.cpp | 46 +-
src/USER-REAXC/reaxc_nonbonded.h | 2 +-
src/USER-REAXC/reaxc_reset_tools.cpp | 27 +-
src/USER-REAXC/reaxc_reset_tools.h | 5 -
src/USER-REAXC/reaxc_system_props.cpp | 217 +-
src/USER-REAXC/reaxc_system_props.h | 12 -
src/USER-REAXC/reaxc_tool_box.cpp | 196 +-
src/USER-REAXC/reaxc_tool_box.h | 27 +-
src/USER-REAXC/reaxc_torsion_angles.cpp | 70 +-
src/USER-REAXC/reaxc_types.h | 345 +-
src/USER-REAXC/reaxc_valence_angles.cpp | 58 +-
src/USER-REAXC/reaxc_valence_angles.h | 4 +-
src/USER-REAXC/reaxc_vector.cpp | 90 +-
src/USER-REAXC/reaxc_vector.h | 23 +-
src/USER-SMD/Install.sh | 61 +
src/USER-SMD/README | 7 +
src/USER-SMD/atom_vec_smd.cpp | 1287 +
src/USER-SMD/atom_vec_smd.h | 125 +
src/USER-SMD/compute_smd_contact_radius.cpp | 109 +
src/USER-SMD/compute_smd_contact_radius.h | 55 +
src/USER-SMD/compute_smd_damage.cpp | 109 +
src/USER-SMD/compute_smd_damage.h | 55 +
src/USER-SMD/compute_smd_hourglass_error.cpp | 112 +
src/USER-SMD/compute_smd_hourglass_error.h | 55 +
src/USER-SMD/compute_smd_internal_energy.cpp | 109 +
src/USER-SMD/compute_smd_internal_energy.h | 55 +
src/USER-SMD/compute_smd_plastic_strain.cpp | 109 +
src/USER-SMD/compute_smd_plastic_strain.h | 55 +
src/USER-SMD/compute_smd_plastic_strain_rate.cpp | 109 +
src/USER-SMD/compute_smd_plastic_strain_rate.h | 55 +
src/USER-SMD/compute_smd_rho.cpp | 107 +
src/USER-SMD/compute_smd_rho.h | 55 +
src/USER-SMD/compute_smd_tlsph_defgrad.cpp | 138 +
src/USER-SMD/compute_smd_tlsph_defgrad.h | 55 +
src/USER-SMD/compute_smd_tlsph_dt.cpp | 115 +
src/USER-SMD/compute_smd_tlsph_dt.h | 55 +
src/USER-SMD/compute_smd_tlsph_num_neighs.cpp | 107 +
src/USER-SMD/compute_smd_tlsph_num_neighs.h | 69 +
src/USER-SMD/compute_smd_tlsph_shape.cpp | 137 +
src/USER-SMD/compute_smd_tlsph_shape.h | 55 +
src/USER-SMD/compute_smd_tlsph_strain.cpp | 145 +
src/USER-SMD/compute_smd_tlsph_strain.h | 55 +
src/USER-SMD/compute_smd_tlsph_strain_rate.cpp | 114 +
src/USER-SMD/compute_smd_tlsph_strain_rate.h | 55 +
src/USER-SMD/compute_smd_tlsph_stress.cpp | 132 +
src/USER-SMD/compute_smd_tlsph_stress.h | 55 +
.../compute_smd_triangle_mesh_vertices.cpp | 130 +
src/USER-SMD/compute_smd_triangle_mesh_vertices.h | 55 +
src/USER-SMD/compute_smd_ulsph_effm.cpp | 115 +
src/USER-SMD/compute_smd_ulsph_effm.h | 55 +
src/USER-SMD/compute_smd_ulsph_num_neighs.cpp | 107 +
src/USER-SMD/compute_smd_ulsph_num_neighs.h | 69 +
src/USER-SMD/compute_smd_ulsph_strain.cpp | 120 +
src/USER-SMD/compute_smd_ulsph_strain.h | 55 +
src/USER-SMD/compute_smd_ulsph_strain_rate.cpp | 123 +
src/USER-SMD/compute_smd_ulsph_strain_rate.h | 55 +
src/USER-SMD/compute_smd_ulsph_stress.cpp | 134 +
src/USER-SMD/compute_smd_ulsph_stress.h | 55 +
src/USER-SMD/compute_smd_vol.cpp | 130 +
src/USER-SMD/compute_smd_vol.h | 56 +
src/USER-SMD/fix_smd_adjust_dt.cpp | 233 +
src/USER-SMD/fix_smd_adjust_dt.h | 80 +
src/USER-SMD/fix_smd_integrate_tlsph.cpp | 254 +
src/USER-SMD/fix_smd_integrate_tlsph.h | 73 +
src/USER-SMD/fix_smd_integrate_ulsph.cpp | 325 +
src/USER-SMD/fix_smd_integrate_ulsph.h | 64 +
src/USER-SMD/fix_smd_move_triangulated_surface.cpp | 517 +
src/USER-SMD/fix_smd_move_triangulated_surface.h | 63 +
src/USER-SMD/fix_smd_setvel.cpp | 375 +
src/USER-SMD/fix_smd_setvel.h | 95 +
.../fix_smd_tlsph_reference_configuration.cpp | 608 +
.../fix_smd_tlsph_reference_configuration.h | 86 +
src/USER-SMD/fix_smd_wall_surface.cpp | 509 +
src/USER-SMD/fix_smd_wall_surface.h | 51 +
src/USER-SMD/pair_smd_hertz.cpp | 385 +
src/USER-SMD/pair_smd_hertz.h | 69 +
src/USER-SMD/pair_smd_tlsph.cpp | 2161 +
src/USER-SMD/pair_smd_tlsph.h | 224 +
src/USER-SMD/pair_smd_triangulated_surface.cpp | 846 +
src/USER-SMD/pair_smd_triangulated_surface.h | 74 +
src/USER-SMD/pair_smd_ulsph.cpp | 1651 +
src/USER-SMD/pair_smd_ulsph.h | 136 +
src/USER-SMD/smd_kernels.h | 146 +
src/USER-SMD/smd_material_models.cpp | 474 +
src/USER-SMD/smd_material_models.h | 65 +
src/USER-SMD/smd_math.h | 287 +
src/USER-SMTBQ/README | 14 +
src/USER-SMTBQ/pair_smtbq.cpp | 4241 +
src/USER-SMTBQ/pair_smtbq.h | 197 +
src/USER-SPH/atom_vec_meso.cpp | 34 +-
src/USER-SPH/compute_meso_e_atom.cpp | 2 +-
src/USER-SPH/compute_meso_rho_atom.cpp | 2 +-
src/USER-SPH/compute_meso_t_atom.cpp | 2 +-
src/USER-SPH/fix_meso.cpp | 12 +-
src/USER-SPH/fix_meso_stationary.cpp | 10 +-
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 | 6 +-
src/USER-SPH/pair_sph_taitwater.cpp | 4 +-
src/USER-SPH/pair_sph_taitwater_morris.cpp | 4 +-
src/USER-TALLY/README | 27 +
src/USER-TALLY/compute_force_tally.cpp | 223 +
src/USER-TALLY/compute_force_tally.h | 66 +
src/USER-TALLY/compute_heat_flux_tally.cpp | 286 +
src/USER-TALLY/compute_heat_flux_tally.h | 65 +
src/USER-TALLY/compute_pe_tally.cpp | 204 +
src/USER-TALLY/compute_pe_tally.h | 66 +
src/USER-TALLY/compute_stress_tally.cpp | 249 +
src/USER-TALLY/compute_stress_tally.h | 66 +
src/VORONOI/compute_voronoi_atom.cpp | 28 +-
src/VORONOI/compute_voronoi_atom.h | 20 +-
src/WINDOWS/LAMMPS.sln | 36 -
src/WINDOWS/LAMMPS.vcproj | 2957 -
src/WINDOWS/LAMMPS.vsmacros | Bin 182784 -> 0 bytes
src/WINDOWS/README.txt | 78 -
src/WINDOWS/STUBS.vcproj | 156 -
src/WINDOWS/extra/dirent.h | 372 -
src/WINDOWS/extra/erf.h | 19 -
src/WINDOWS/extra/erf_namd.c | 345 -
src/WINDOWS/extra/fftw2/FFTW2dll.dll | Bin 263168 -> 0 bytes
src/WINDOWS/extra/fftw2/FFTW2dll.lib | Bin 22998 -> 0 bytes
src/WINDOWS/extra/fftw2/FFTW2st.lib | Bin 404572 -> 0 bytes
src/WINDOWS/extra/fftw2/RFFTW2dll.dll | Bin 481792 -> 0 bytes
src/WINDOWS/extra/fftw2/RFFTW2dll.lib | Bin 35830 -> 0 bytes
src/WINDOWS/extra/fftw2/RFFTW2st.lib | Bin 337962 -> 0 bytes
src/WINDOWS/extra/fftw2/fftw.h | 421 -
src/WINDOWS/extra/inttypes.h | 305 -
src/WINDOWS/extra/sleep.cpp | 10 -
src/WINDOWS/extra/sleep.h | 1 -
src/WINDOWS/extra/stdint.h | 247 -
src/WINDOWS/extra/sys/time.h | 28 -
src/WINDOWS/extra/unistd.h | 1 -
src/WINDOWS/settings/style_angle.h | 9 -
src/WINDOWS/settings/style_atom.h | 12 -
src/WINDOWS/settings/style_bond.h | 9 -
src/WINDOWS/settings/style_command.h | 16 -
src/WINDOWS/settings/style_compute.h | 44 -
src/WINDOWS/settings/style_dihedral.h | 7 -
src/WINDOWS/settings/style_dump.h | 8 -
src/WINDOWS/settings/style_fix.h | 69 -
src/WINDOWS/settings/style_improper.h | 5 -
src/WINDOWS/settings/style_integrate.h | 3 -
src/WINDOWS/settings/style_kspace.h | 5 -
src/WINDOWS/settings/style_minimize.h | 6 -
src/WINDOWS/settings/style_pair.h | 49 -
src/WINDOWS/settings/style_region.h | 9 -
src/XTC/dump_xtc.cpp | 24 +-
src/XTC/dump_xtc.h | 14 +-
src/accelerator_intel.h | 8 +-
src/accelerator_kokkos.h | 1 +
src/angle.cpp | 8 +-
src/angle.h | 3 +-
src/angle_hybrid.cpp | 6 +-
src/angle_hybrid.h | 10 +-
src/atom.cpp | 201 +-
src/atom.h | 46 +-
src/atom_map.cpp | 12 +-
src/atom_vec.cpp | 10 +-
src/atom_vec.h | 8 +-
src/atom_vec_atomic.cpp | 4 +-
src/atom_vec_body.cpp | 20 +-
src/atom_vec_body.h | 2 +-
src/atom_vec_charge.cpp | 4 +-
src/atom_vec_ellipsoid.cpp | 14 +-
src/atom_vec_hybrid.cpp | 10 +-
src/atom_vec_hybrid.h | 2 +-
src/atom_vec_line.cpp | 14 +-
src/atom_vec_sphere.cpp | 16 +-
src/atom_vec_tri.cpp | 20 +-
src/balance.cpp | 33 +-
src/balance.h | 8 +-
src/body.cpp | 6 +-
src/body.h | 2 +-
src/bond.cpp | 8 +-
src/bond.h | 3 +-
src/bond_hybrid.cpp | 6 +-
src/bond_hybrid.h | 2 +-
src/change_box.cpp | 8 +-
src/citeme.cpp | 4 +-
src/citeme.h | 2 +-
src/comm.cpp | 63 +-
src/comm.h | 77 +-
src/comm_brick.cpp | 45 +-
src/comm_brick.h | 65 +-
src/comm_tiled.cpp | 85 +-
src/comm_tiled.h | 33 +-
src/compute.cpp | 25 +-
src/compute.h | 33 +-
src/compute_angle_local.cpp | 6 +-
src/compute_angmom_chunk.cpp | 255 +
src/compute_angmom_chunk.h | 75 +
src/compute_bond_local.cpp | 12 +-
src/compute_centro_atom.cpp | 4 +-
src/compute_chunk_atom.cpp | 92 +-
src/compute_chunk_atom.h | 97 +-
src/compute_cluster_atom.cpp | 6 +-
src/compute_cna_atom.cpp | 8 +-
src/compute_com_chunk.cpp | 4 +-
src/compute_com_chunk.h | 6 +-
src/compute_contact_atom.cpp | 6 +-
src/compute_coord_atom.cpp | 12 +-
src/compute_dihedral_local.cpp | 6 +-
src/compute_displace_atom.cpp | 4 +-
src/compute_erotate_sphere.cpp | 2 +-
src/compute_erotate_sphere_atom.cpp | 4 +-
src/compute_group_group.cpp | 8 +-
src/compute_gyration.cpp | 2 +-
src/compute_gyration_chunk.cpp | 6 +-
src/compute_gyration_chunk.h | 6 +-
src/compute_heat_flux.cpp | 4 +-
src/compute_hexorder_atom.cpp | 346 +
src/compute_hexorder_atom.h | 71 +
src/compute_improper_local.cpp | 6 +-
src/compute_inertia_chunk.cpp | 6 +-
src/compute_inertia_chunk.h | 6 +-
src/compute_ke.cpp | 2 +-
src/compute_ke_atom.cpp | 2 +-
src/compute_msd.cpp | 4 +-
src/compute_msd_chunk.cpp | 5 +-
src/compute_msd_chunk.h | 12 +-
src/compute_omega_chunk.cpp | 333 +
src/compute_omega_chunk.h | 77 +
src/compute_orientorder_atom.cpp | 505 +
src/compute_orientorder_atom.h | 80 +
src/compute_pair.cpp | 4 +-
src/compute_pair_local.cpp | 7 +-
src/compute_pe.cpp | 4 +-
src/compute_pe_atom.cpp | 2 +-
src/compute_pressure.cpp | 16 +-
src/compute_pressure.h | 10 +-
src/compute_property_atom.cpp | 12 +-
src/compute_property_atom.h | 4 +-
src/compute_property_chunk.cpp | 4 +-
src/compute_property_chunk.h | 24 +-
src/compute_property_local.cpp | 2 +-
src/compute_rdf.cpp | 47 +-
src/compute_rdf.h | 3 +-
src/compute_reduce.cpp | 31 +-
src/compute_reduce_region.cpp | 4 +-
src/compute_slice.cpp | 4 +-
src/compute_stress_atom.cpp | 6 +-
src/compute_stress_atom.h | 8 +
src/compute_temp.cpp | 17 +-
src/compute_temp.h | 4 +-
src/compute_temp_chunk.cpp | 16 +-
src/compute_temp_chunk.h | 22 +-
src/compute_temp_com.cpp | 16 +-
src/compute_temp_deform.cpp | 13 +-
src/compute_temp_partial.cpp | 13 +-
src/compute_temp_profile.cpp | 25 +-
src/compute_temp_ramp.cpp | 17 +-
src/compute_temp_region.cpp | 6 +-
src/compute_temp_sphere.cpp | 16 +-
src/compute_torque_chunk.cpp | 16 +-
src/compute_torque_chunk.h | 6 +-
src/compute_vacf.cpp | 2 +-
src/compute_vcm_chunk.cpp | 8 +-
src/compute_vcm_chunk.h | 6 +-
src/create_atoms.cpp | 14 +-
src/create_atoms.h | 20 +
src/create_bonds.cpp | 12 +-
src/create_bonds.h | 52 +-
src/create_box.cpp | 20 +-
src/delete_atoms.cpp | 32 +-
src/delete_atoms.h | 22 +-
src/delete_bonds.cpp | 10 +-
src/dihedral.cpp | 8 +-
src/dihedral.h | 3 +-
src/dihedral_hybrid.cpp | 6 +-
src/dihedral_hybrid.h | 2 +-
src/displace_atoms.cpp | 83 +-
src/displace_atoms.h | 5 +
src/domain.cpp | 114 +-
src/domain.h | 21 +-
src/dump.cpp | 36 +-
src/dump.h | 6 +-
src/dump_atom.cpp | 6 +-
src/dump_cfg.cpp | 50 +-
src/dump_cfg.h | 4 +-
src/dump_custom.cpp | 38 +-
src/dump_custom.h | 30 +-
src/dump_dcd.cpp | 12 +-
src/dump_image.cpp | 20 +-
src/dump_local.cpp | 10 +-
src/dump_local.h | 5 +
src/dump_movie.cpp | 6 +-
src/dump_xyz.cpp | 2 +-
src/error.cpp | 8 +-
src/error.h | 2 +-
src/finish.cpp | 467 +-
src/fix.cpp | 21 +-
src/fix.h | 11 +-
src/fix_adapt.cpp | 51 +-
src/fix_adapt.h | 11 +-
src/fix_addforce.cpp | 8 +-
src/fix_ave_atom.cpp | 20 +-
src/fix_ave_atom.h | 11 +-
src/fix_ave_chunk.cpp | 109 +-
src/fix_ave_chunk.h | 78 +-
src/fix_ave_correlate.cpp | 30 +-
src/fix_ave_correlate.h | 11 +-
src/fix_ave_histo.cpp | 37 +-
src/fix_ave_histo.h | 21 +-
src/fix_ave_histo_weight.cpp | 571 +
src/fix_ave_histo_weight.h | 193 +
src/fix_ave_spatial.cpp | 41 +-
src/fix_ave_spatial.h | 23 +-
src/fix_ave_time.cpp | 123 +-
src/fix_ave_time.h | 33 +-
src/fix_aveforce.cpp | 6 +-
src/fix_balance.cpp | 7 +-
src/fix_balance.h | 10 +-
src/fix_box_relax.cpp | 6 +-
src/fix_deform.cpp | 6 +-
src/fix_deform.h | 8 +-
src/fix_drag.cpp | 6 +-
src/fix_dt_reset.cpp | 6 +-
src/fix_enforce2d.cpp | 2 +-
src/fix_external.cpp | 8 +-
src/fix_gravity.cpp | 8 +-
src/fix_group.cpp | 12 +-
src/fix_group.h | 30 +
src/fix_heat.cpp | 20 +-
src/fix_indent.cpp | 6 +-
src/fix_langevin.cpp | 22 +-
src/fix_langevin.h | 12 +-
src/fix_lineforce.cpp | 6 +-
src/fix_minimize.cpp | 2 +-
src/fix_momentum.cpp | 76 +-
src/fix_momentum.h | 2 +-
src/fix_move.cpp | 19 +-
src/fix_move.h | 2 +-
src/fix_nh.cpp | 46 +-
src/fix_nh.h | 4 +-
src/fix_nh_sphere.cpp | 2 +-
src/fix_nph.cpp | 2 +-
src/fix_nph_sphere.cpp | 2 +-
src/fix_npt.cpp | 2 +-
src/fix_npt_sphere.cpp | 2 +-
src/fix_nve.cpp | 4 +-
src/fix_nve_limit.cpp | 13 +-
src/fix_nve_noforce.cpp | 4 +-
src/fix_nve_sphere.cpp | 6 +-
src/fix_nvt.cpp | 2 +-
src/fix_nvt_sllod.cpp | 4 +-
src/fix_nvt_sphere.cpp | 2 +-
src/fix_planeforce.cpp | 6 +-
src/fix_press_berendsen.cpp | 6 +-
src/fix_print.cpp | 4 +-
src/fix_print.h | 2 +-
src/fix_property_atom.cpp | 46 +-
src/fix_property_atom.h | 2 +-
src/fix_read_restart.cpp | 2 +-
src/fix_recenter.cpp | 4 +-
src/fix_respa.cpp | 35 +-
src/fix_respa.h | 4 +-
src/fix_restrain.cpp | 10 +-
src/fix_setforce.cpp | 8 +-
src/fix_shear_history.cpp | 8 +-
src/fix_spring.cpp | 6 +-
src/fix_spring_rg.cpp | 6 +-
src/fix_spring_self.cpp | 4 +-
src/fix_store.cpp | 10 +-
src/fix_store_force.cpp | 2 +-
src/fix_store_state.cpp | 13 +-
src/fix_store_state.h | 10 +
src/fix_temp_berendsen.cpp | 10 +-
src/fix_temp_csld.cpp | 311 +
src/fix_temp_csld.h | 101 +
src/fix_temp_csvr.cpp | 179 +-
src/fix_temp_csvr.h | 14 +-
src/fix_temp_rescale.cpp | 13 +-
src/fix_tmd.cpp | 8 +-
src/fix_tmd.h | 2 +-
src/fix_vector.cpp | 10 +-
src/fix_vector.h | 61 +
src/fix_viscous.cpp | 6 +-
src/fix_wall.cpp | 10 +-
src/fix_wall_harmonic.cpp | 2 +-
src/fix_wall_lj1043.cpp | 12 +-
src/fix_wall_lj1043.h | 2 +-
src/fix_wall_lj126.cpp | 2 +-
src/fix_wall_lj93.cpp | 2 +-
src/fix_wall_reflect.cpp | 8 +-
src/fix_wall_region.cpp | 16 +-
src/force.cpp | 72 +-
src/force.h | 20 +-
src/group.cpp | 93 +-
src/group.h | 35 +-
src/image.cpp | 22 +-
src/image.h | 4 +-
src/improper.cpp | 8 +-
src/improper.h | 3 +-
src/improper_hybrid.cpp | 6 +-
src/improper_hybrid.h | 2 +-
src/info.cpp | 676 +
src/info.h | 55 +
src/input.cpp | 424 +-
src/input.h | 37 +-
src/integrate.cpp | 2 +-
src/irregular.cpp | 10 +-
src/irregular.h | 2 +-
src/kspace.cpp | 10 +-
src/kspace.h | 32 +-
src/lammps.cpp | 162 +-
src/lammps.h | 44 +-
src/lattice.cpp | 6 +-
src/library.cpp | 33 +-
src/library.h | 4 +-
src/lmptype.h | 6 +-
src/lmpwindows.h | 4 +-
src/main.cpp | 4 +-
src/math_extra.cpp | 8 +-
src/math_extra.h | 6 +-
src/math_vector.h | 4 +-
src/memory.cpp | 6 +-
src/memory.h | 108 +-
src/min.cpp | 47 +-
src/min_cg.cpp | 9 +-
src/min_fire.cpp | 5 +-
src/min_hftn.cpp | 6 +-
src/min_linesearch.cpp | 2 +-
src/min_quickmin.cpp | 7 +-
src/min_sd.cpp | 7 +-
src/minimize.cpp | 8 +-
src/modify.cpp | 33 +-
src/modify.h | 25 +-
src/molecule.cpp | 345 +-
src/molecule.h | 22 +-
src/my_page.h | 8 +-
src/my_pool_chunk.h | 2 +-
src/neigh_bond.cpp | 44 +-
src/neigh_list.cpp | 4 +-
src/neigh_request.cpp | 2 +-
src/neigh_request.h | 4 +-
src/neighbor.cpp | 75 +-
src/neighbor.h | 11 +-
src/output.cpp | 27 +-
src/output.h | 6 +-
src/pair.cpp | 146 +-
src/pair.h | 20 +-
src/pair_beck.cpp | 6 +-
src/pair_born.cpp | 10 +-
src/pair_born_coul_wolf.cpp | 10 +-
src/pair_buck.cpp | 12 +-
src/pair_buck_coul_cut.cpp | 10 +-
src/pair_buck_coul_cut.h | 2 +-
src/pair_coul_cut.cpp | 10 +-
src/pair_coul_debye.cpp | 8 +-
src/pair_coul_dsf.cpp | 52 +-
src/pair_coul_dsf.h | 4 +-
src/pair_coul_streitz.cpp | 62 +-
src/pair_coul_streitz.h | 53 +-
src/pair_coul_wolf.cpp | 20 +-
src/pair_dpd.cpp | 8 +-
src/pair_dpd_tstat.cpp | 4 +-
src/pair_gauss.cpp | 14 +-
src/pair_hybrid.cpp | 233 +-
src/pair_hybrid.h | 31 +-
src/pair_hybrid_overlay.cpp | 6 +-
src/pair_lj96_cut.cpp | 8 +-
src/pair_lj_cubic.cpp | 8 +-
src/pair_lj_cut.cpp | 8 +-
src/pair_lj_cut_coul_cut.cpp | 10 +-
src/pair_lj_cut_coul_debye.cpp | 4 +-
src/pair_lj_cut_coul_dsf.cpp | 109 +-
src/pair_lj_cut_coul_dsf.h | 12 +-
src/pair_lj_expand.cpp | 48 +-
src/pair_lj_expand.h | 6 +-
src/pair_lj_gromacs.cpp | 12 +-
src/pair_lj_gromacs.h | 4 +-
src/pair_lj_gromacs_coul_gromacs.cpp | 12 +-
src/pair_lj_gromacs_coul_gromacs.h | 6 +-
src/pair_lj_smooth.cpp | 6 +-
src/pair_lj_smooth_linear.cpp | 6 +-
src/pair_mie_cut.cpp | 20 +-
src/pair_morse.cpp | 18 +-
src/pair_morse.h | 1 +
src/pair_soft.cpp | 10 +-
src/pair_table.cpp | 8 +-
src/pair_yukawa.cpp | 4 +-
src/pair_zbl.cpp | 174 +-
src/pair_zbl.h | 1 +
src/pointers.h | 7 +-
src/python_wrapper.h | 47 +
src/random_mars.cpp | 2 +-
src/random_park.cpp | 2 +-
src/rcb.cpp | 83 +-
src/rcb.h | 10 +-
src/read_data.cpp | 646 +-
src/read_data.h | 108 +-
src/read_dump.cpp | 17 +-
src/read_dump.h | 6 +-
src/read_restart.cpp | 144 +-
src/read_restart.h | 14 +-
src/reader.cpp | 4 +-
src/reader_native.cpp | 20 +-
src/reader_xyz.cpp | 18 +-
src/region.cpp | 6 +-
src/region_block.cpp | 4 +-
src/region_cone.cpp | 8 +-
src/region_cylinder.cpp | 10 +-
src/region_intersect.cpp | 8 +-
src/region_plane.cpp | 6 +-
src/region_prism.cpp | 6 +-
src/region_sphere.cpp | 6 +-
src/region_union.cpp | 8 +-
src/replicate.cpp | 11 +-
src/rerun.cpp | 8 +-
src/rerun.h | 4 +
src/respa.cpp | 208 +-
src/respa.h | 13 +
src/run.cpp | 20 +-
src/set.cpp | 78 +-
src/special.cpp | 44 +-
src/special.h | 1 +
src/thermo.cpp | 45 +-
src/thermo.h | 2 +-
src/timer.cpp | 180 +-
src/timer.h | 54 +-
src/universe.cpp | 56 +-
src/universe.h | 6 +-
src/update.cpp | 24 +-
src/variable.cpp | 510 +-
src/variable.h | 57 +-
src/velocity.cpp | 17 +-
src/velocity.h | 8 +
src/verlet.cpp | 54 +-
src/version.h | 2 +-
src/write_data.cpp | 40 +-
src/write_data.h | 3 +-
src/write_dump.cpp | 9 +-
src/write_dump.h | 10 +-
src/write_restart.cpp | 52 +-
src/write_restart.h | 4 +-
tools/README | 1 +
tools/chain.f | 4 +-
tools/drude/drude.dff | 29 +
tools/drude/polarizer.py | 726 +
tools/drude/schwerdtfeger.dff | 70 +
tools/moltemplate/common/gaff.lt | 2 +-
tools/moltemplate/common/graphene.lt | 3 +
tools/moltemplate/common/spce.lt | 6 +-
tools/moltemplate/common/watmw.lt | 25 +-
.../force_field_AMBER/benzene/README_run.sh | 10 +-
.../force_field_AMBER/benzene/README_setup.sh | 13 +-
.../README_remove_irrelevant_info.sh | 17 +-
.../ethylene+benzene/README_run.sh | 10 +-
.../ethylene+benzene/README_setup.sh | 12 +-
.../README_remove_irrelevant_info.sh | 17 +-
.../force_field_AMBER/hexadecane/README_run.sh | 10 +-
.../force_field_AMBER/hexadecane/README_setup.sh | 12 +-
.../README_remove_irrelevant_info.sh | 17 +-
.../waterTIP3P+isobutane/README_run.sh | 10 +-
.../waterTIP3P+isobutane/README_setup.sh | 9 +-
.../README_remove_irrelevant_info.sh | 17 +-
.../alkane_chain_single/README.TXT | 8 +-
.../alkane_chain_single/README_run.sh | 10 +-
.../alkane_chain_single/README_setup.sh | 2 +-
.../oplsaa_lt_generator/README.TXT | 2 +-
.../oplsaa_lt_generator/oplsaa_moltemplate.py | 408 -
.../oplsaa_lt_generator/oplsaa_subset.prm | 9 +-
.../alkane_chain_single/run.in.min | 5 +-
.../ethylene+benzene/README_run.sh | 10 +-
.../ethylene+benzene/README_setup.sh | 2 +-
.../oplsaa_lt_generator/README.TXT | 2 +-
.../oplsaa_lt_generator/oplsaa_moltemplate.py | 408 -
.../oplsaa_lt_generator/oplsaa_subset.prm | 2 +
.../ethylene+benzene_PACKMOL/README_run.sh | 10 +-
.../ethylene+benzene_PACKMOL/README_setup.sh | 2 +-
.../oplsaa_lt_generator/README.TXT | 2 +-
.../oplsaa_lt_generator/oplsaa_moltemplate.py | 408 -
.../oplsaa_lt_generator/oplsaa_subset.prm | 2 +
.../moltemplate_files/system.xyz | 12002 +++
.../ethylene+benzene_PACKMOL/run.in.npt | 2 +-
.../force_field_OPLSAA/hexadecane/README_run.sh | 10 +-
.../force_field_OPLSAA/hexadecane/README_setup.sh | 2 +-
.../oplsaa_lt_generator/README.TXT | 2 +-
.../oplsaa_lt_generator/oplsaa_moltemplate.py | 408 -
.../oplsaa_lt_generator/oplsaa_subset.prm | 9 +-
.../force_field_OPLSAA/hexadecane/run.in.npt | 1 +
.../force_field_OPLSAA/hexadecane/run.in.nvt | 1 +
.../force_field_OPLSAA/methane/README_run.sh | 10 +-
.../force_field_OPLSAA/methane/README_setup.sh | 2 +-
.../oplsaa_lt_generator/README.TXT | 2 +-
.../oplsaa_lt_generator/oplsaa_moltemplate.py | 408 -
.../oplsaa_lt_generator/oplsaa_subset.prm | 5025 +-
.../waterSPCE+methane/README_run.sh | 10 +-
.../waterSPCE+methane/README_setup.sh | 2 +-
.../oplsaa_lt_generator/README.TXT | 2 +-
.../oplsaa_lt_generator/oplsaa_moltemplate.py | 408 -
.../oplsaa_lt_generator/oplsaa_subset.prm | 5018 +-
.../waterSPCE+methane/moltemplate_files/spce.lt | 23 +-
.../waterSPC_using_OPLSAA/README_run.sh | 10 +-
.../waterSPC_using_OPLSAA/README_setup.sh | 2 +-
.../oplsaa_lt_generator/README.TXT | 12 +-
.../oplsaa_lt_generator/oplsaa_moltemplate.py | 408 -
.../oplsaa_lt_generator/oplsaa_subset.prm | 5019 +-
.../aluminum_crystal_strain/README.TXT | 4 +-
.../force_field_explicit/ice_crystal/README_run.sh | 10 +-
.../nanotube+water/README_realistic_junctions.txt | 22 +
.../nanotube+water/README_run.sh | 10 +-
.../nanotube+water/moltemplate_files/graphene.lt | 3 +
.../moltemplate_files/graphene_walls.lt | 36 +-
.../nanotube+water/moltemplate_files/spce.lt | 13 +-
.../nanotube+water/moltemplate_files}/watmw.lt | 0
.../force_field_explicit/nanotube+water/run.in.npt | 2 +
.../force_field_explicit/nanotube+water/run.in.nvt | 6 +-
.../waterSPCE+Na+Cl/README_run.sh | 10 +-
.../README_run.sh | 10 +-
.../DPPC_bilayer_formation_PACKMOL/README_run.sh | 12 +-
.../moltemplate_files/lipid.lt | 1 -
.../DPPC_bilayer_preformed/README_run.sh | 12 +-
.../moltemplate_files/lipid.lt | 1 -
.../abstract_2bead_heteropolymer/README_run.sh | 6 +-
.../abstract_random_heteropolymer/README_run.sh | 4 +-
.../abstract_translocation/README_run.sh | 10 +-
.../chromosome_metaphase_Naumova2013/README_run.sh | 8 +-
.../README.TXT | 0
.../membrane+protein/README_WARNING.TXT | 10 +
.../membrane+protein/README_run.sh | 33 +
.../README_setup.sh | 0
.../README_visualize.txt | 0
.../images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg | Bin
.../images/membrane+protein_t=0ps_LR.jpg | Bin
.../images/membrane+protein_t=0ps_no_pbc_LR.jpg | Bin
.../images/membrane+protein_t=0ps_top_LR.jpg | Bin
.../images/membrane+protein_t=5000ps_LR.jpg | Bin
.../moltemplate_files/1beadProtSci2010.lt | 233 +
.../1beadProtSci2010_variations.lt | 225 +
.../moltemplate_files/CGLipidBr2005.lt | 196 +
.../calc_table/calc_CGLipidTableINTvsINT.py | 0
.../calc_table/version_charmm_cutoff/calc_table.py | 0
.../membrane+protein/moltemplate_files/system.lt | 178 +
.../moltemplate_files/table_int.dat | 0
.../run.in.min | 0
.../membrane+protein/run.in.npt | 66 +
.../membrane+protein/run.in.nvt | 71 +
.../README_run.sh | 33 -
.../moltemplate_files/1beadProtSci2010.lt | 254 -
.../1beadProtSci2010_variations.lt | 225 -
.../moltemplate_files/CGLipidBr2005.lt | 198 -
.../moltemplate_files/system.lt | 219 -
.../run.in.npt | 65 -
.../run.in.nvt | 71 -
.../membrane_BranniganPRE2005/README_run.sh | 10 +-
.../moltemplate_files/CGLipidBr2005Orig.lt | 55 +-
.../frustrated+chaperonin/README_run.sh | 4 +-
.../frustrated+minichaperone/README_run.sh | 4 +-
.../1bead+chaperone/frustrated/README_run.sh | 4 +-
.../1bead+chaperone/unfrustrated/README_run.sh | 4 +-
.../1beadProtSci2010/README_run.sh | 4 +-
.../README_WARNING.TXT | 20 +
.../README_run.sh | 10 +-
.../README_setup.sh | 30 +-
.../moltemplate_files/1beadProtSci2010.lt | 14 +-
.../1beadProtSci2010_variations.lt | 12 +-
.../moltemplate_files/CGLipidBr2005.lt | 28 +-
.../moltemplate_files/README.sh | 2 +-
.../moltemplate_files/system.lt | 134 +-
.../packmol_files/DLPC.xyz | 6 -
.../packmol_files/DPPC.xyz | 7 -
.../packmol_files/README.sh | 33 +-
.../packmol_files/protein.xyz | 75 -
.../packmol_files/step2_innerlayer.inp | 6 +-
.../packmol_files/step3_outerlayer.inp | 9 +-
.../vesicle_Brannigan2005+Bellesia2010/run.in.min | 6 +-
.../cnad-cnt/README_step2_run_moltemplate.sh | 6 +-
.../cnad-cnt/README_step3_run_lammps.sh | 4 +-
.../cnad-cnt/cnad-cnt.in | 2 +-
.../convert_LAMMPS_to_LT_examples/cnad-cnt/junk.in | 1 -
.../waterSPCE_from_PDBfile/README_run.sh | 10 +-
.../misc_examples/menger_sponge/README.TXT | 4 +-
.../misc_examples/pyramids_vs_gravity/README.TXT | 11 +-
.../misc_examples/pyramids_vs_gravity/run.in | 10 +-
tools/moltemplate/moltemplate_manual.pdf | Bin 716180 -> 720204 bytes
tools/moltemplate/src/dump2data.py | 15 +-
tools/moltemplate/src/ltemplify.py | 541 +-
tools/moltemplate/src/moltemplate.sh | 96 +-
tools/moltemplate/src/nbody_by_type_backup.py | 651 -
tools/moltemplate/src/oplsaa_moltemplate.py | 261 +-
tools/moltemplate/src/raw2data.py | 5 +
tools/moltemplate/src/ttree.py | 86 +-
tools/msi2lmp/README | 8 +
tools/msi2lmp/frc_files/oplsaa.frc | 1 +
tools/msi2lmp/src/Forcefield.h | 2 +-
tools/msi2lmp/src/GetParameters.c | 9 +-
tools/msi2lmp/src/Makefile | 3 +-
tools/msi2lmp/src/ReadFrcFile.c | 29 +-
tools/msi2lmp/src/SearchAndFill.c | 38 +-
tools/msi2lmp/src/msi2lmp.c | 4 +
tools/msi2lmp/src/msi2lmp.h | 3 +-
tools/msi2lmp/test/cnt-hexagonal-class1.car | 611 +
tools/msi2lmp/test/cnt-hexagonal-class1.mdf | 632 +
tools/msi2lmp/test/cnt-hexagonal-class2a.car | 611 +
tools/msi2lmp/test/cnt-hexagonal-class2a.mdf | 632 +
tools/msi2lmp/test/cnt-hexagonal-class2b.car | 611 +
tools/msi2lmp/test/cnt-hexagonal-class2b.mdf | 632 +
tools/msi2lmp/test/decane-oplsaa.car | 3206 +
tools/msi2lmp/test/decane-oplsaa.mdf | 3223 +
tools/msi2lmp/test/in.cnt-hexagonal-class1 | 15 +
tools/msi2lmp/test/in.cnt-hexagonal-class2a | 15 +
tools/msi2lmp/test/in.cnt-hexagonal-class2b | 15 +
tools/msi2lmp/test/in.decane-oplsaa | 14 +
tools/msi2lmp/test/in.solv-poly-class2c | 15 +
tools/msi2lmp/test/reference/PyAC_bulk-clayff.data | 2590 +-
.../msi2lmp/test/reference/PyAC_bulk-clayff.data2 | 2568 +-
tools/msi2lmp/test/reference/benzene-class1.data | 62 +-
tools/msi2lmp/test/reference/benzene-class1.data2 | 40 +-
.../test/reference/cnt-hexagonal-class1.data | 7608 ++
.../test/reference/cnt-hexagonal-class1.data2 | 8213 ++
.../test/reference/cnt-hexagonal-class2a.data | 7640 ++
.../test/reference/cnt-hexagonal-class2a.data2 | 8245 ++
.../test/reference/cnt-hexagonal-class2b.data | 7640 ++
.../test/reference/cnt-hexagonal-class2b.data2 | 8245 ++
tools/msi2lmp/test/reference/crambin-class1.data | 1972 +-
tools/msi2lmp/test/reference/crambin-class1.data2 | 1298 +-
tools/msi2lmp/test/reference/decane-oplsaa.data | 20456 ++++
tools/msi2lmp/test/reference/decane-oplsaa.data2 | 23656 +++++
tools/msi2lmp/test/reference/ethane-class1.data | 46 +-
tools/msi2lmp/test/reference/ethane-class1.data2 | 28 +-
tools/msi2lmp/test/reference/ethane-class2a.data | 48 +-
tools/msi2lmp/test/reference/ethane-class2a.data2 | 30 +-
tools/msi2lmp/test/reference/ethane-class2b.data | 48 +-
tools/msi2lmp/test/reference/ethane-class2b.data2 | 30 +-
tools/msi2lmp/test/reference/ethane-oplsaa.data | 46 +-
tools/msi2lmp/test/reference/ethane-oplsaa.data2 | 28 +-
tools/msi2lmp/test/reference/h2-h2o-class1.data | 38 +-
tools/msi2lmp/test/reference/h2-h2o-class1.data2 | 20 +-
tools/msi2lmp/test/reference/h2-h2o-class2b.data | 38 +-
tools/msi2lmp/test/reference/h2-h2o-class2b.data2 | 20 +-
.../msi2lmp/test/reference/hap_crystal-class1.data | 208 +-
.../test/reference/hap_crystal-class1.data2 | 186 +-
.../test/reference/hap_crystal-class2b.data | 210 +-
.../test/reference/hap_crystal-class2b.data2 | 188 +-
.../msi2lmp/test/reference/naphthalene-class1.data | 76 +-
.../test/reference/naphthalene-class1.data2 | 52 +-
.../test/reference/naphthalene-class2a.data | 78 +-
.../test/reference/naphthalene-class2a.data2 | 52 +-
.../test/reference/naphthalene-class2b.data | 78 +-
.../test/reference/naphthalene-class2b.data2 | 52 +-
tools/msi2lmp/test/reference/nylon-class1.data | 394 +-
tools/msi2lmp/test/reference/nylon-class1.data2 | 248 +-
.../msi2lmp/test/reference/phen3_cff97-class1.data | 182 +-
.../test/reference/phen3_cff97-class1.data2 | 60 +-
tools/msi2lmp/test/reference/water-class1.data | 28 +-
tools/msi2lmp/test/reference/water-class1.data2 | 16 +-
tools/msi2lmp/test/reference/water-class2b.data | 28 +-
tools/msi2lmp/test/reference/water-class2b.data2 | 16 +-
tools/msi2lmp/test/runtests.sh | 5 +-
tools/msi2lmp/test/test.input | 27 -
tools/python/pizza/dump.py | 412 +-
tools/python/pizza/gnu.py | 2 +-
tools/python/pizza/log.py | 10 +-
tools/smd/Makefile | 7 +
tools/smd/dump2vtk_tris.cpp | 235 +
4859 files changed, 1032121 insertions(+), 205212 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