From a979c6eeec5d8feef355c70d0df5210921382b07 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Wed, 10 Oct 2018 08:50:34 -0600 Subject: [PATCH 01/12] updating files that have lists of command styles --- doc/src/Commands_bond.txt | 11 +- doc/src/Commands_compute.txt | 6 +- doc/src/Commands_fix.txt | 27 +++-- doc/src/Commands_pair.txt | 48 ++++---- doc/src/angle_style.txt | 22 ++-- doc/src/bond_style.txt | 22 ++-- doc/src/compute.txt | 4 + doc/src/dihedral_style.txt | 18 +-- doc/src/improper_style.txt | 14 +-- doc/src/pair_born.txt | 8 +- doc/src/pair_coul.txt | 19 +-- doc/src/pair_cs.txt | 11 ++ doc/src/pair_lj.txt | 10 +- doc/src/pair_style.txt | 228 ++++++++++++++++++----------------- 14 files changed, 230 insertions(+), 218 deletions(-) diff --git a/doc/src/Commands_bond.txt b/doc/src/Commands_bond.txt index 773202f126..d4d48924a7 100644 --- a/doc/src/Commands_bond.txt +++ b/doc/src/Commands_bond.txt @@ -34,7 +34,7 @@ OPT. "fene (iko)"_bond_fene.html, "fene/expand (o)"_bond_fene_expand.html, "gromos (o)"_bond_gromos.html, -"harmonic (ko)"_bond_harmonic.html, +"harmonic (iko)"_bond_harmonic.html, "harmonic/shift (o)"_bond_harmonic_shift.html, "harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html, "morse (o)"_bond_morse.html, @@ -57,9 +57,11 @@ OPT. "zero"_angle_zero.html, "hybrid"_angle_hybrid.html :tb(c=3,ea=c) -"charmm (ko)"_angle_charmm.html, +"charmm (iko)"_angle_charmm.html, "class2 (ko)"_angle_class2.html, +"class2/p6"_angle_class2.html, "cosine (o)"_angle_cosine.html, +"cosine/buck6d"_angle_cosine_buck6d.html, "cosine/delta (o)"_angle_cosine_delta.html, "cosine/periodic (o)"_angle_cosine_periodic.html, "cosine/shift (o)"_angle_cosine_shift.html, @@ -97,7 +99,7 @@ OPT. "nharmonic (o)"_dihedral_nharmonic.html, "opls (iko)"_dihedral_opls.html, "quadratic (o)"_dihedral_quadratic.html, -"spherical (o)"_dihedral_spherical.html, +"spherical"_dihedral_spherical.html, "table (o)"_dihedral_table.html, "table/cut"_dihedral_table_cut.html :tb(c=4,ea=c) @@ -112,7 +114,7 @@ OPT. "none"_improper_none.html, "zero"_improper_zero.html, -"hybrid"_improper_hybrid.html :tb(c=3,ea=c) +"hybrid"_improper_hybrid.html :tb(c=3,ea=c) "class2 (ko)"_improper_class2.html, "cossq (o)"_improper_cossq.html, @@ -120,5 +122,6 @@ OPT. "distance"_improper_distance.html, "fourier (o)"_improper_fourier.html, "harmonic (iko)"_improper_harmonic.html, +"inversion/harmonic"_improper_inversion_harmonic.html, "ring (o)"_improper_ring.html, "umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c) diff --git a/doc/src/Commands_compute.txt b/doc/src/Commands_compute.txt index 81b618a6e2..62629db91e 100644 --- a/doc/src/Commands_compute.txt +++ b/doc/src/Commands_compute.txt @@ -92,6 +92,7 @@ KOKKOS, o = USER-OMP, t = OPT. "pe/tally"_compute_tally.html, "plasticity/atom"_compute_plasticity_atom.html, "pressure"_compute_pressure.html, +"pressure/cylinder"_compute_pressure_cylinder.html, "pressure/uef"_compute_pressure_uef.html, "property/atom"_compute_property_atom.html, "property/chunk"_compute_property_chunk.html, @@ -118,7 +119,7 @@ KOKKOS, o = USER-OMP, t = OPT. "smd/tlsph/strain"_compute_smd_tlsph_strain.html, "smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html, "smd/tlsph/stress"_compute_smd_tlsph_stress.html, -"smd/triangle/mesh/vertices"_compute_smd_triangle_vertices.html, +"smd/triangle/vertices"_compute_smd_triangle_vertices.html, "smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html, "smd/ulsph/strain"_compute_smd_ulsph_strain.html, "smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html, @@ -129,6 +130,8 @@ KOKKOS, o = USER-OMP, t = OPT. "snav/atom"_compute_sna_atom.html, "spin"_compute_spin.html, "stress/atom"_compute_stress_atom.html, +"stress/mop"_compute_stress_mop.html, +"stress/mop/profile"_compute_stress_mop.html, "stress/tally"_compute_tally.html, "tdpd/cc/atom"_compute_tdpd_cc_atom.html, "temp (k)"_compute_temp.html, @@ -136,6 +139,7 @@ KOKKOS, o = USER-OMP, t = OPT. "temp/body"_compute_temp_body.html, "temp/chunk"_compute_temp_chunk.html, "temp/com"_compute_temp_com.html, +"temp/cs"_compute_temp_cs.html, "temp/deform"_compute_temp_deform.html, "temp/deform/eff"_compute_temp_deform_eff.html, "temp/drude"_compute_temp_drude.html, diff --git a/doc/src/Commands_fix.txt b/doc/src/Commands_fix.txt index 58828d5c9e..4144c7eb90 100644 --- a/doc/src/Commands_fix.txt +++ b/doc/src/Commands_fix.txt @@ -40,11 +40,13 @@ OPT. "ave/time"_fix_ave_time.html, "aveforce"_fix_aveforce.html, "balance"_fix_balance.html, +"bocs"_fix_bocs.html, "bond/break"_fix_bond_break.html, "bond/create"_fix_bond_create.html, "bond/react"_fix_bond_react.html, "bond/swap"_fix_bond_swap.html, "box/relax"_fix_box_relax.html, +"client/md"_fix_client_md.html, "cmap"_fix_cmap.html, "colvars"_fix_colvars.html, "controller"_fix_controller.html, @@ -54,7 +56,7 @@ OPT. "drag"_fix_drag.html, "drude"_fix_drude.html, "drude/transform/direct"_fix_drude_transform.html, -"drude/transform/reverse"_fix_drude_transform.html, +"drude/transform/inverse"_fix_drude_transform.html, "dt/reset"_fix_dt_reset.html, "edpd/source"_fix_dpd_source.html, "efield"_fix_efield.html, @@ -107,15 +109,16 @@ OPT. "nph/eff"_fix_nh_eff.html, "nph/sphere (ko)"_fix_nph_sphere.html, "nphug (o)"_fix_nphug.html, -"npt (kio)"_fix_nh.html, +"npt (iko)"_fix_nh.html, "npt/asphere (o)"_fix_npt_asphere.html, "npt/body"_fix_npt_body.html, "npt/eff"_fix_nh_eff.html, "npt/sphere (o)"_fix_npt_sphere.html, "npt/uef"_fix_nh_uef.html, -"nve (kio)"_fix_nve.html, +"nve (iko)"_fix_nve.html, "nve/asphere (i)"_fix_nve_asphere.html, "nve/asphere/noforce"_fix_nve_asphere_noforce.html, +"nve/awpmd"_fix_nve_awpmd.html, "nve/body"_fix_nve_body.html, "nve/dot"_fix_nve_dot.html, "nve/dotc/langevin"_fix_nve_dotc_langevin.html, @@ -170,26 +173,26 @@ OPT. "rhok"_fix_rhok.html, "rigid (o)"_fix_rigid.html, "rigid/nph (o)"_fix_rigid.html, +"rigid/nph/small"_fix_rigid.html, "rigid/npt (o)"_fix_rigid.html, +"rigid/npt/small"_fix_rigid.html, "rigid/nve (o)"_fix_rigid.html, +"rigid/nve/small"_fix_rigid.html, "rigid/nvt (o)"_fix_rigid.html, +"rigid/nvt/small"_fix_rigid.html, "rigid/small (o)"_fix_rigid.html, -"rigid/small/nph"_fix_rigid.html, -"rigid/small/npt"_fix_rigid.html, -"rigid/small/nve"_fix_rigid.html, -"rigid/small/nvt"_fix_rigid.html, "rx (k)"_fix_rx.html, "saed/vtk"_fix_saed_vtk.html, "setforce (k)"_fix_setforce.html, "shake"_fix_shake.html, "shardlow (k)"_fix_shardlow.html, "smd"_fix_smd.html, -"smd/adjust/dt"_fix_smd_adjust_dt.html, -"smd/integrate/tlsph"_fix_smd_integrate_tlsph.html, -"smd/integrate/ulsph"_fix_smd_integrate_ulsph.html, -"smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html, +"smd/adjust_dt"_fix_smd_adjust_dt.html, +"smd/integrate_tlsph"_fix_smd_integrate_tlsph.html, +"smd/integrate_ulsph"_fix_smd_integrate_ulsph.html, +"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html, "smd/setvel"_fix_smd_setvel.html, -"smd/wall/surface"_fix_smd_wall_surface.html, +"smd/wall_surface"_fix_smd_wall_surface.html, "spring"_fix_spring.html, "spring/chunk"_fix_spring_chunk.html, "spring/rg"_fix_spring_rg.html, diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt index 090101d5ea..85ebcdda10 100644 --- a/doc/src/Commands_pair.txt +++ b/doc/src/Commands_pair.txt @@ -31,8 +31,8 @@ OPT. "adp (o)"_pair_adp.html, "agni (o)"_pair_agni.html, -"airebo (oi)"_pair_airebo.html, -"airebo/morse (oi)"_pair_airebo.html, +"airebo (io)"_pair_airebo.html, +"airebo/morse (io)"_pair_airebo.html, "atm"_pair_atm.html, "awpmd/cut"_pair_awpmd.html, "beck (go)"_pair_beck.html, @@ -42,21 +42,23 @@ OPT. "bop"_pair_bop.html, "born (go)"_pair_born.html, "born/coul/dsf"_pair_born.html, -"born/coul/dsf/cs"_pair_born.html, +"born/coul/dsf/cs"_pair_cs.html, "born/coul/long (go)"_pair_born.html, -"born/coul/long/cs"_pair_born.html, +"born/coul/long/cs (g)"_pair_cs.html, "born/coul/msm (o)"_pair_born.html, "born/coul/wolf (go)"_pair_born.html, -"born/coul/wolf/cs"_pair_born.html, +"born/coul/wolf/cs (g)"_pair_cs.html, "brownian (o)"_pair_brownian.html, "brownian/poly (o)"_pair_brownian.html, "buck (giko)"_pair_buck.html, "buck/coul/cut (giko)"_pair_buck.html, "buck/coul/long (giko)"_pair_buck.html, -"buck/coul/long/cs"_pair_buck.html, +"buck/coul/long/cs"_pair_cs.html, "buck/coul/msm (o)"_pair_buck.html, "buck/long/coul/long (o)"_pair_buck_long.html, "buck/mdf"_pair_mdf.html, +"buck6d/coul/gauss/dsf"_pair_buck6d_coul_gauss.html, +"buck6d/coul/gauss/long"_pair_buck6d_coul_gauss.html, "colloid (go)"_pair_colloid.html, "comb (o)"_pair_comb.html, "comb3"_pair_comb.html, @@ -68,7 +70,7 @@ OPT. "coul/long (gko)"_pair_coul.html, "coul/long/cs"_pair_coul.html, "coul/long/soft (o)"_pair_lj_soft.html, -"coul/msm"_pair_coul.html, +"coul/msm (o)"_pair_coul.html, "coul/shield"_pair_coul_shield.html, "coul/streitz"_pair_coul.html, "coul/wolf (ko)"_pair_coul.html, @@ -91,7 +93,7 @@ OPT. "exp6/rx (k)"_pair_exp6_rx.html, "extep"_pair_extep.html, "gauss (go)"_pair_gauss.html, -"gauss/cut"_pair_gauss.html, +"gauss/cut (o)"_pair_gauss.html, "gayberne (gio)"_pair_gayberne.html, "gran/hertz/history (o)"_pair_gran.html, "gran/hooke (o)"_pair_gran.html, @@ -110,9 +112,9 @@ OPT. "list"_pair_list.html, "lj/charmm/coul/charmm (iko)"_pair_charmm.html, "lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html, -"lj/charmm/coul/long (giko)"_pair_charmm.html, -"lj/charmm/coul/long/soft (o)"_pair_charmm.html, -"lj/charmm/coul/msm"_pair_charmm.html, +"lj/charmm/coul/long (gikot)"_pair_charmm.html, +"lj/charmm/coul/long/soft (o)"_pair_lj_soft.html, +"lj/charmm/coul/msm (o)"_pair_charmm.html, "lj/charmmfsw/coul/charmmfsh"_pair_charmm.html, "lj/charmmfsw/coul/long"_pair_charmm.html, "lj/class2 (gko)"_pair_class2.html, @@ -130,7 +132,7 @@ OPT. "lj/cut/coul/msm (go)"_pair_lj.html, "lj/cut/coul/wolf (o)"_pair_lj.html, "lj/cut/dipole/cut (go)"_pair_dipole.html, -"lj/cut/dipole/long"_pair_dipole.html, +"lj/cut/dipole/long (g)"_pair_dipole.html, "lj/cut/dipole/sf (go)"_pair_dipole.html, "lj/cut/soft (o)"_pair_lj_soft.html, "lj/cut/thole/long (o)"_pair_thole.html, @@ -138,15 +140,17 @@ OPT. "lj/cut/tip4p/long (ot)"_pair_lj.html, "lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html, "lj/expand (gko)"_pair_lj_expand.html, +"lj/expand/coul/long (g)"_pair_lj_expand.html, "lj/gromacs (gko)"_pair_gromacs.html, "lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html, -"lj/long/coul/long (io)"_pair_lj_long.html, +"lj/long/coul/long (iot)"_pair_lj_long.html, "lj/long/dipole/long"_pair_dipole.html, -"lj/long/tip4p/long"_pair_lj_long.html, +"lj/long/tip4p/long (o)"_pair_lj_long.html, "lj/mdf"_pair_mdf.html, "lj/sdk (gko)"_pair_sdk.html, "lj/sdk/coul/long (go)"_pair_sdk.html, "lj/sdk/coul/msm (o)"_pair_sdk.html, +"lj/sf/dipole/sf (go)"_pair_dipole.html, "lj/smooth (o)"_pair_lj_smooth.html, "lj/smooth/linear (o)"_pair_lj_smooth_linear.html, "lj96/cut (go)"_pair_lj96.html, @@ -161,10 +165,10 @@ OPT. "meam/spline (o)"_pair_meam_spline.html, "meam/sw/spline"_pair_meam_sw_spline.html, "mgpt"_pair_mgpt.html, -"mie/cut (o)"_pair_mie.html, +"mie/cut (g)"_pair_mie.html, "momb"_pair_momb.html, "morse (gkot)"_pair_morse.html, -"morse/smooth/linear"_pair_morse.html, +"morse/smooth/linear (o)"_pair_morse.html, "morse/soft"_pair_morse.html, "multi/lucy"_pair_multi_lucy.html, "multi/lucy/rx (k)"_pair_multi_lucy_rx.html, @@ -180,7 +184,9 @@ OPT. "oxdna2/coaxstk"_pair_oxdna2.html, "oxdna2/dh"_pair_oxdna2.html, "oxdna2/excv"_pair_oxdna2.html, +"oxdna2/hbond"_pair_oxdna2.html, "oxdna2/stk"_pair_oxdna2.html, +"oxdna2/xstk"_pair_oxdna2.html, "peri/eps"_pair_peri.html, "peri/lps (o)"_pair_peri.html, "peri/pmb (o)"_pair_peri.html, @@ -190,11 +196,11 @@ OPT. "quip"_pair_quip.html, "reax"_pair_reax.html, "reax/c (ko)"_pair_reaxc.html, -"rebo (oi)"_pair_airebo.html, +"rebo (io)"_pair_airebo.html, "resquared (go)"_pair_resquared.html, "smd/hertz"_pair_smd_hertz.html, "smd/tlsph"_pair_smd_tlsph.html, -"smd/triangulated/surface"_pair_smd_triangulated_surface.html, +"smd/tri_surface"_pair_smd_triangulated_surface.html, "smd/ulsph"_pair_smd_ulsph.html, "smtbq"_pair_smtbq.html, "snap (k)"_pair_snap.html, @@ -226,8 +232,8 @@ OPT. "tip4p/long/soft (o)"_pair_lj_soft.html, "tri/lj"_pair_tri_lj.html, "ufm (got)"_pair_ufm.html, -"vashishta (ko)"_pair_vashishta.html, +"vashishta (gko)"_pair_vashishta.html, "vashishta/table (o)"_pair_vashishta.html, -"yukawa (gok)"_pair_yukawa.html, +"yukawa (gko)"_pair_yukawa.html, "yukawa/colloid (go)"_pair_yukawa_colloid.html, -"zbl (gok)"_pair_zbl.html :tb(c=4,ea=c) +"zbl (gko)"_pair_zbl.html :tb(c=4,ea=c) diff --git a/doc/src/angle_style.txt b/doc/src/angle_style.txt index 756cfc0c60..817179eacf 100644 --- a/doc/src/angle_style.txt +++ b/doc/src/angle_style.txt @@ -62,18 +62,18 @@ which are included in the LAMMPS distribution. The full list of all angle styles are is on the "Commands bond"_Commands_bond.html#angle doc page. -"angle_style none"_angle_none.html - turn off angle interactions -"angle_style zero"_angle_zero.html - topology but no interactions -"angle_style hybrid"_angle_hybrid.html - define multiple styles of angle interactions :ul +"none"_angle_none.html - turn off angle interactions +"zero"_angle_zero.html - topology but no interactions +"hybrid"_angle_hybrid.html - define multiple styles of angle interactions :ul -"angle_style charmm"_angle_charmm.html - CHARMM angle -"angle_style class2"_angle_class2.html - COMPASS (class 2) angle -"angle_style cosine"_angle_cosine.html - cosine angle potential -"angle_style cosine/delta"_angle_cosine_delta.html - difference of cosines angle potential -"angle_style cosine/periodic"_angle_cosine_periodic.html - DREIDING angle -"angle_style cosine/squared"_angle_cosine_squared.html - cosine squared angle potential -"angle_style harmonic"_angle_harmonic.html - harmonic angle -"angle_style table"_angle_table.html - tabulated by angle :ul +"charmm"_angle_charmm.html - CHARMM angle +"class2"_angle_class2.html - COMPASS (class 2) angle +"cosine"_angle_cosine.html - cosine angle potential +"cosine/delta"_angle_cosine_delta.html - difference of cosines angle potential +"cosine/periodic"_angle_cosine_periodic.html - DREIDING angle +"cosine/squared"_angle_cosine_squared.html - cosine squared angle potential +"harmonic"_angle_harmonic.html - harmonic angle +"table"_angle_table.html - tabulated by angle :ul :line diff --git a/doc/src/bond_style.txt b/doc/src/bond_style.txt index 22fae3e346..dd406c7da0 100644 --- a/doc/src/bond_style.txt +++ b/doc/src/bond_style.txt @@ -69,18 +69,18 @@ Note that there are also additional bond styles submitted by users which are included in the LAMMPS distribution. The full list of all bond styles is on the "Commands bond"_Commands_bond.html doc page. -"bond_style none"_bond_none.html - turn off bonded interactions -"bond_style zero"_bond_zero.html - topology but no interactions -"bond_style hybrid"_bond_hybrid.html - define multiple styles of bond interactions :ul +"none"_bond_none.html - turn off bonded interactions +"zero"_bond_zero.html - topology but no interactions +"hybrid"_bond_hybrid.html - define multiple styles of bond interactions :ul -"bond_style class2"_bond_class2.html - COMPASS (class 2) bond -"bond_style fene"_bond_fene.html - FENE (finite-extensible non-linear elastic) bond -"bond_style fene/expand"_bond_fene_expand.html - FENE bonds with variable size particles -"bond_style harmonic"_bond_harmonic.html - harmonic bond -"bond_style morse"_bond_morse.html - Morse bond -"bond_style nonlinear"_bond_nonlinear.html - nonlinear bond -"bond_style quartic"_bond_quartic.html - breakable quartic bond -"bond_style table"_bond_table.html - tabulated by bond length :ul +"class2"_bond_class2.html - COMPASS (class 2) bond +"fene"_bond_fene.html - FENE (finite-extensible non-linear elastic) bond +"fene/expand"_bond_fene_expand.html - FENE bonds with variable size particles +"harmonic"_bond_harmonic.html - harmonic bond +"morse"_bond_morse.html - Morse bond +"nonlinear"_bond_nonlinear.html - nonlinear bond +"quartic"_bond_quartic.html - breakable quartic bond +"table"_bond_table.html - tabulated by bond length :ul :line diff --git a/doc/src/compute.txt b/doc/src/compute.txt index 72ea1c1930..14ab84b436 100644 --- a/doc/src/compute.txt +++ b/doc/src/compute.txt @@ -230,15 +230,19 @@ compute"_Commands_compute.html doc page are followed by one or more of "reduce/region"_compute_reduce.html - same as compute reduce, within a region "rigid/local"_compute_rigid_local.html - extract rigid body attributes "slice"_compute_slice.html - extract values from global vector or array +"smd/triangle/vertices"_compute_smd_triangle_vertices.html - "sna/atom"_compute_sna_atom.html - calculate bispectrum coefficients for each atom "snad/atom"_compute_sna_atom.html - derivative of bispectrum coefficients for each atom "snav/atom"_compute_sna_atom.html - virial contribution from bispectrum coefficients for each atom "stress/atom"_compute_stress_atom.html - stress tensor for each atom +"stress/mop"_compute_stress_mop.html - +"stress/mop/profile"_compute_stress_mop.html - "temp"_compute_temp.html - temperature of group of atoms "temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles "temp/body"_compute_temp_body.html - temperature of body particles "temp/chunk"_compute_temp_chunk.html - temperature of each chunk "temp/com"_compute_temp_com.html - temperature after subtracting center-of-mass velocity +"temp/cs"_compute_temp_cs.html - "temp/deform"_compute_temp_deform.html - temperature excluding box deformation velocity "temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity "temp/profile"_compute_temp_profile.html - temperature excluding a binned velocity profile diff --git a/doc/src/dihedral_style.txt b/doc/src/dihedral_style.txt index 749f74e399..9744f1b71f 100644 --- a/doc/src/dihedral_style.txt +++ b/doc/src/dihedral_style.txt @@ -85,16 +85,16 @@ which are included in the LAMMPS distribution. The full list of all dihedral styles is on the "Commands bond"_Commands_bond.html#dihedral doc page. -"dihedral_style none"_dihedral_none.html - turn off dihedral interactions -"dihedral_style zero"_dihedral_zero.html - topology but no interactions -"dihedral_style hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions :ul +"none"_dihedral_none.html - turn off dihedral interactions +"zero"_dihedral_zero.html - topology but no interactions +"hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions :ul -"dihedral_style charmm"_dihedral_charmm.html - CHARMM dihedral -"dihedral_style class2"_dihedral_class2.html - COMPASS (class 2) dihedral -"dihedral_style harmonic"_dihedral_harmonic.html - harmonic dihedral -"dihedral_style helix"_dihedral_helix.html - helix dihedral -"dihedral_style multi/harmonic"_dihedral_multi_harmonic.html - multi-harmonic dihedral -"dihedral_style opls"_dihedral_opls.html - OPLS dihedral :ul +"charmm"_dihedral_charmm.html - CHARMM dihedral +"class2"_dihedral_class2.html - COMPASS (class 2) dihedral +"harmonic"_dihedral_harmonic.html - harmonic dihedral +"helix"_dihedral_helix.html - helix dihedral +"multi/harmonic"_dihedral_multi_harmonic.html - multi-harmonic dihedral +"opls"_dihedral_opls.html - OPLS dihedral :ul :line diff --git a/doc/src/improper_style.txt b/doc/src/improper_style.txt index ef0c524d14..c9db7678a9 100644 --- a/doc/src/improper_style.txt +++ b/doc/src/improper_style.txt @@ -64,14 +64,14 @@ which are included in the LAMMPS distribution. The full list of all improper styles is on the "Commands bond"_Commands_bond.html#improper doc page. -"improper_style none"_improper_none.html - turn off improper interactions -"improper_style zero"_improper_zero.html - topology but no interactions -"improper_style hybrid"_improper_hybrid.html - define multiple styles of improper interactions :ul +"none"_improper_none.html - turn off improper interactions +"zero"_improper_zero.html - topology but no interactions +"hybrid"_improper_hybrid.html - define multiple styles of improper interactions :ul -"improper_style class2"_improper_class2.html - COMPASS (class 2) improper -"improper_style cvff"_improper_cvff.html - CVFF improper -"improper_style harmonic"_improper_harmonic.html - harmonic improper -"improper_style umbrella"_improper_umbrella.html - DREIDING improper :ul +"class2"_improper_class2.html - COMPASS (class 2) improper +"cvff"_improper_cvff.html - CVFF improper +"harmonic"_improper_harmonic.html - harmonic improper +"umbrella"_improper_umbrella.html - DREIDING improper :ul :line diff --git a/doc/src/pair_born.txt b/doc/src/pair_born.txt index 9cbfcffea0..d12cea79a6 100644 --- a/doc/src/pair_born.txt +++ b/doc/src/pair_born.txt @@ -24,21 +24,21 @@ pair_style born/coul/dsf command :h3 pair_style style args :pre -style = {born} or {born/coul/long} or {born/coul/long/cs} or {born/coul/msm} or {born/coul/wolf} +style = {born} or {born/coul/long} or {born/coul/msm} or {born/coul/wolf} args = list of arguments for a particular style :ul {born} args = cutoff cutoff = global cutoff for non-Coulombic interactions (distance units) - {born/coul/long} or {born/coul/long/cs} args = cutoff (cutoff2) + {born/coul/long} args = cutoff (cutoff2) cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units) cutoff2 = global cutoff for Coulombic (optional) (distance units) {born/coul/msm} args = cutoff (cutoff2) cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units) cutoff2 = global cutoff for Coulombic (optional) (distance units) - {born/coul/wolf} or {born/coul/wolf/cs} args = alpha cutoff (cutoff2) + {born/coul/wolf} args = alpha cutoff (cutoff2) alpha = damping parameter (inverse distance units) cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units) cutoff2 = global cutoff for Coulombic (optional) (distance units) - {born/coul/dsf} or {born/coul/dsf/cs} args = alpha cutoff (cutoff2) + {born/coul/dsf} args = alpha cutoff (cutoff2) alpha = damping parameter (inverse distance units) cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units) cutoff2 = global cutoff for Coulombic (distance units) :pre diff --git a/doc/src/pair_coul.txt b/doc/src/pair_coul.txt index bc0d76a071..cf66c711c8 100644 --- a/doc/src/pair_coul.txt +++ b/doc/src/pair_coul.txt @@ -19,8 +19,6 @@ pair_style coul/dsf/gpu command :h3 pair_style coul/dsf/kk command :h3 pair_style coul/dsf/omp command :h3 pair_style coul/long command :h3 -pair_style coul/long/cs command :h3 -pair_style coul/long/cs/gpu command :h3 pair_style coul/long/omp command :h3 pair_style coul/long/gpu command :h3 pair_style coul/long/kk command :h3 @@ -30,7 +28,6 @@ pair_style coul/streitz command :h3 pair_style coul/wolf command :h3 pair_style coul/wolf/kk command :h3 pair_style coul/wolf/omp command :h3 -pair_style coul/wolf/cs command :h3 pair_style tip4p/cut command :h3 pair_style tip4p/long command :h3 pair_style tip4p/cut/omp command :h3 @@ -42,10 +39,8 @@ pair_style coul/cut cutoff pair_style coul/debye kappa cutoff pair_style coul/dsf alpha cutoff pair_style coul/long cutoff -pair_style coul/long/cs cutoff pair_style coul/long/gpu cutoff pair_style coul/wolf alpha cutoff -pair_style coul/wolf/cs alpha cutoff pair_style coul/streitz cutoff keyword alpha pair_style tip4p/cut otype htype btype atype qdist cutoff pair_style tip4p/long otype htype btype atype qdist cutoff :pre @@ -68,14 +63,12 @@ pair_style coul/dsf 0.05 10.0 pair_coeff * * :pre pair_style coul/long 10.0 -pair_style coul/long/cs 10.0 pair_coeff * * :pre pair_style coul/msm 10.0 pair_coeff * * :pre pair_style coul/wolf 0.2 9.0 -pair_style coul/wolf/cs 0.2 9.0 pair_coeff * * :pre pair_style coul/streitz 12.0 ewald @@ -204,12 +197,6 @@ option. The Coulombic cutoff specified for this style means that pairwise interactions within this distance are computed directly; interactions outside that distance are computed in reciprocal space. -Style {coul/long/cs} is identical to {coul/long} except that a term is -added for the "core/shell model"_Howto_coreshell.html to allow charges -on core and shell particles to be separated by r = 0.0. The same -correction is introduced for the {coul/wolf/cs} style which is -identical to {coul/wolf}. - Styles {tip4p/cut} and {tip4p/long} implement the coulomb part of the TIP4P water model of "(Jorgensen)"_#Jorgensen3, which introduces a massless site located a short distance away from the oxygen atom @@ -317,9 +304,9 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] The {coul/long}, {coul/msm} and {tip4p/long} styles are part of the -KSPACE package. The {coul/long/cs} style is part of the CORESHELL -package. They are only enabled if LAMMPS was built with that package. -See the "Build package"_Build_package.html doc page for more info. +KSPACE package. They are only enabled if LAMMPS was built with that +package. See the "Build package"_Build_package.html doc page for more +info. [Related commands:] diff --git a/doc/src/pair_cs.txt b/doc/src/pair_cs.txt index faaea42f15..80b971e393 100644 --- a/doc/src/pair_cs.txt +++ b/doc/src/pair_cs.txt @@ -12,6 +12,7 @@ pair_style buck/coul/long/cs command :h3 pair_style born/coul/dsf/cs command :h3 pair_style born/coul/wolf/cs command :h3 pair_style born/coul/wolf/cs/gpu command :h3 +pair_style lj/cut/coul/long/cs command :h3 [Syntax:] @@ -52,6 +53,11 @@ pair_style born/coul/wolf/cs 0.25 10.0 12.0 pair_coeff * * 0.0 1.00 0.00 0.00 0.00 pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre +pair_style lj/cut/coul/long/cs 10.0 +pair_style lj/cut/coul/long/cs 10.0 8.0 +pair_coeff * * 100.0 3.0 +pair_coeff 1 1 100.0 3.5 9.0 :pre + [Description:] These pair styles are designed to be used with the adiabatic @@ -99,6 +105,11 @@ a long-range solver, thus the only correction is the addition of a minimal distance to avoid the possible r = 0.0 case for a core/shell pair. +Style {lj/cut/coul/long/cs} is identical to {lj/cut/coul/long} except +that a term is added for the "core/shell model"_Howto_coreshell.html +to allow charges on core and shell particles to be separated by r = +0.0. + :line Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are diff --git a/doc/src/pair_lj.txt b/doc/src/pair_lj.txt index 4939f505bb..9c61e0bf25 100644 --- a/doc/src/pair_lj.txt +++ b/doc/src/pair_lj.txt @@ -25,7 +25,6 @@ pair_style lj/cut/coul/dsf/gpu command :h3 pair_style lj/cut/coul/dsf/kk command :h3 pair_style lj/cut/coul/dsf/omp command :h3 pair_style lj/cut/coul/long command :h3 -pair_style lj/cut/coul/long/cs command :h3 pair_style lj/cut/coul/long/gpu command :h3 pair_style lj/cut/coul/long/kk command :h3 pair_style lj/cut/coul/long/intel command :h3 @@ -46,7 +45,7 @@ pair_style lj/cut/tip4p/long/opt command :h3 pair_style style args :pre -style = {lj/cut} or {lj/cut/coul/cut} or {lj/cut/coul/debye} or {lj/cut/coul/dsf} or {lj/cut/coul/long} or {lj/cut/coul/long/cs} or {lj/cut/coul/msm} or {lj/cut/tip4p/long} +style = {lj/cut} or {lj/cut/coul/cut} or {lj/cut/coul/debye} or {lj/cut/coul/dsf} or {lj/cut/coul/long} {lj/cut/coul/msm} or {lj/cut/tip4p/long} args = list of arguments for a particular style :ul {lj/cut} args = cutoff cutoff = global cutoff for Lennard Jones interactions (distance units) @@ -107,9 +106,7 @@ pair_coeff * * 1.0 1.0 pair_coeff 1 1 1.0 1.0 2.5 :pre pair_style lj/cut/coul/long 10.0 -pair_style lj/cut/coul/long/cs 10.0 pair_style lj/cut/coul/long 10.0 8.0 -pair_style lj/cut/coul/long/cs 10.0 8.0 pair_coeff * * 100.0 3.0 pair_coeff 1 1 100.0 3.5 9.0 :pre @@ -186,11 +183,6 @@ specified for this style means that pairwise interactions within this distance are computed directly; interactions outside that distance are computed in reciprocal space. -Style {lj/cut/coul/long/cs} is identical to {lj/cut/coul/long} except -that a term is added for the "core/shell model"_Howto_coreshell.html -to allow charges on core and shell particles to be separated by r = -0.0. - Style {coul/wolf} adds a Coulombic pairwise interaction via the Wolf summation method, described in "Wolf"_#Wolf1, given by: diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt index 9dfead300e..86ac61c752 100644 --- a/doc/src/pair_style.txt +++ b/doc/src/pair_style.txt @@ -95,120 +95,122 @@ GPUs, and KNLs. The individual style names on the "Commands pair"_Commands_pair.html doc page are followed by one or more of (g,i,k,o,t) to indicate which accelerated styles exist. -"pair_style none"_pair_none.html - turn off pairwise interactions -"pair_style hybrid"_pair_hybrid.html - multiple styles of pairwise interactions -"pair_style hybrid/overlay"_pair_hybrid.html - multiple styles of superposed pairwise interactions -"pair_style zero"_pair_zero.html - neighbor list but no interactions :ul +"none"_pair_none.html - turn off pairwise interactions +"hybrid"_pair_hybrid.html - multiple styles of pairwise interactions +"hybrid/overlay"_pair_hybrid.html - multiple styles of superposed pairwise interactions +"zero"_pair_zero.html - neighbor list but no interactions :ul -"pair_style adp"_pair_adp.html - angular dependent potential (ADP) of Mishin -"pair_style airebo"_pair_airebo.html - AIREBO potential of Stuart -"pair_style airebo/morse"_pair_airebo.html - AIREBO with Morse instead of LJ -"pair_style atm"_pair_atm.html - Axilrod-Teller-Muto potential -"pair_style beck"_pair_beck.html - Beck potential -"pair_style body/nparticle"_pair_body_nparticle.html - interactions between body particles -"pair_style bop"_pair_bop.html - BOP potential of Pettifor -"pair_style born"_pair_born.html - Born-Mayer-Huggins potential -"pair_style born/coul/long"_pair_born.html - Born-Mayer-Huggins with long-range Coulombics -"pair_style born/coul/long/cs"_pair_born.html - Born-Mayer-Huggins with long-range Coulombics and core/shell -"pair_style born/coul/msm"_pair_born.html - Born-Mayer-Huggins with long-range MSM Coulombics -"pair_style born/coul/wolf"_pair_born.html - Born-Mayer-Huggins with Coulombics via Wolf potential -"pair_style brownian"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics -"pair_style brownian/poly"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics with polydispersity -"pair_style buck"_pair_buck.html - Buckingham potential -"pair_style buck/coul/cut"_pair_buck.html - Buckingham with cutoff Coulomb -"pair_style buck/coul/long"_pair_buck.html - Buckingham with long-range Coulombics -"pair_style buck/coul/long/cs"_pair_buck.html - Buckingham with long-range Coulombics and core/shell -"pair_style buck/coul/msm"_pair_buck.html - Buckingham long-range MSM Coulombics -"pair_style buck/long/coul/long"_pair_buck_long.html - long-range Buckingham with long-range Coulombics -"pair_style colloid"_pair_colloid.html - integrated colloidal potential -"pair_style comb"_pair_comb.html - charge-optimized many-body (COMB) potential -"pair_style comb3"_pair_comb.html - charge-optimized many-body (COMB3) potential -"pair_style coul/cut"_pair_coul.html - cutoff Coulombic potential -"pair_style coul/debye"_pair_coul.html - cutoff Coulombic potential with Debye screening -"pair_style coul/dsf"_pair_coul.html - Coulombics via damped shifted forces -"pair_style coul/long"_pair_coul.html - long-range Coulombic potential -"pair_style coul/long/cs"_pair_coul.html - long-range Coulombic potential and core/shell -"pair_style coul/msm"_pair_coul.html - long-range MSM Coulombics -"pair_style coul/streitz"_pair_coul.html - Coulombics via Streitz/Mintmire Slater orbitals -"pair_style coul/wolf"_pair_coul.html - Coulombics via Wolf potential -"pair_style dpd"_pair_dpd.html - dissipative particle dynamics (DPD) -"pair_style dpd/tstat"_pair_dpd.html - DPD thermostatting -"pair_style dsmc"_pair_dsmc.html - Direct Simulation Monte Carlo (DSMC) -"pair_style eam"_pair_eam.html - embedded atom method (EAM) -"pair_style eam/alloy"_pair_eam.html - alloy EAM -"pair_style eam/fs"_pair_eam.html - Finnis-Sinclair EAM -"pair_style eim"_pair_eim.html - embedded ion method (EIM) -"pair_style gauss"_pair_gauss.html - Gaussian potential -"pair_style gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential -"pair_style gran/hertz/history"_pair_gran.html - granular potential with Hertzian interactions -"pair_style gran/hooke"_pair_gran.html - granular potential with history effects -"pair_style gran/hooke/history"_pair_gran.html - granular potential without history effects -"pair_style hbond/dreiding/lj"_pair_hbond_dreiding.html - DREIDING hydrogen bonding LJ potential -"pair_style hbond/dreiding/morse"_pair_hbond_dreiding.html - DREIDING hydrogen bonding Morse potential -"pair_style kim"_pair_kim.html - interface to potentials provided by KIM project -"pair_style lcbop"_pair_lcbop.html - long-range bond-order potential (LCBOP) -"pair_style line/lj"_pair_line_lj.html - LJ potential between line segments -"pair_style lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb -"pair_style lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent -"pair_style lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb -"pair_style lj/charmm/coul/msm"_pair_charmm.html - CHARMM with long-range MSM Coulombics -"pair_style lj/class2"_pair_class2.html - COMPASS (class 2) force field with no Coulomb -"pair_style lj/class2/coul/cut"_pair_class2.html - COMPASS with cutoff Coulomb -"pair_style lj/class2/coul/long"_pair_class2.html - COMPASS with long-range Coulomb -"pair_style lj/cubic"_pair_lj_cubic.html - LJ with cubic after inflection point -"pair_style lj/cut"_pair_lj.html - cutoff Lennard-Jones potential with no Coulomb -"pair_style lj/cut/coul/cut"_pair_lj.html - LJ with cutoff Coulomb -"pair_style lj/cut/coul/debye"_pair_lj.html - LJ with Debye screening added to Coulomb -"pair_style lj/cut/coul/dsf"_pair_lj.html - LJ with Coulombics via damped shifted forces -"pair_style lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulombics -"pair_style lj/cut/coul/long/cs"_pair_lj.html - LJ with long-range Coulombics and core/shell -"pair_style lj/cut/coul/msm"_pair_lj.html - LJ with long-range MSM Coulombics -"pair_style lj/cut/dipole/cut"_pair_dipole.html - point dipoles with cutoff -"pair_style lj/cut/dipole/long"_pair_dipole.html - point dipoles with long-range Ewald -"pair_style lj/cut/tip4p/cut"_pair_lj.html - LJ with cutoff Coulomb for TIP4P water -"pair_style lj/cut/tip4p/long"_pair_lj.html - LJ with long-range Coulomb for TIP4P water -"pair_style lj/expand"_pair_lj_expand.html - Lennard-Jones for variable size particles -"pair_style lj/gromacs"_pair_gromacs.html - GROMACS-style Lennard-Jones potential -"pair_style lj/gromacs/coul/gromacs"_pair_gromacs.html - GROMACS-style LJ and Coulombic potential -"pair_style lj/long/coul/long"_pair_lj_long.html - long-range LJ and long-range Coulombics -"pair_style lj/long/dipole/long"_pair_dipole.html - long-range LJ and long-range point dipoles -"pair_style lj/long/tip4p/long"_pair_lj_long.html - long-range LJ and long-range Coulomb for TIP4P water -"pair_style lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential -"pair_style lj/smooth/linear"_pair_lj_smooth_linear.html - linear smoothed Lennard-Jones potential -"pair_style lj96/cut"_pair_lj96.html - Lennard-Jones 9/6 potential -"pair_style lubricate"_pair_lubricate.html - hydrodynamic lubrication forces -"pair_style lubricate/poly"_pair_lubricate.html - hydrodynamic lubrication forces with polydispersity -"pair_style lubricateU"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication Dynamics -"pair_style lubricateU/poly"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication with polydispersity -"pair_style meam"_pair_meam.html - modified embedded atom method (MEAM) -"pair_style mie/cut"_pair_mie.html - Mie potential -"pair_style morse"_pair_morse.html - Morse potential -"pair_style nb3b/harmonic"_pair_nb3b_harmonic.html - nonbonded 3-body harmonic potential -"pair_style nm/cut"_pair_nm.html - N-M potential -"pair_style nm/cut/coul/cut"_pair_nm.html - N-M potential with cutoff Coulomb -"pair_style nm/cut/coul/long"_pair_nm.html - N-M potential with long-range Coulombics -"pair_style peri/eps"_pair_peri.html - peridynamic EPS potential -"pair_style peri/lps"_pair_peri.html - peridynamic LPS potential -"pair_style peri/pmb"_pair_peri.html - peridynamic PMB potential -"pair_style peri/ves"_pair_peri.html - peridynamic VES potential -"pair_style polymorphic"_pair_polymorphic.html - polymorphic 3-body potential -"pair_style reax"_pair_reax.html - ReaxFF potential -"pair_style rebo"_pair_airebo.html - 2nd generation REBO potential of Brenner -"pair_style resquared"_pair_resquared.html - Everaers RE-Squared ellipsoidal potential -"pair_style snap"_pair_snap.html - SNAP quantum-accurate potential -"pair_style soft"_pair_soft.html - Soft (cosine) potential -"pair_style sw"_pair_sw.html - Stillinger-Weber 3-body potential -"pair_style table"_pair_table.html - tabulated pair potential -"pair_style tersoff"_pair_tersoff.html - Tersoff 3-body potential -"pair_style tersoff/mod"_pair_tersoff_mod.html - modified Tersoff 3-body potential -"pair_style tersoff/zbl"_pair_tersoff_zbl.html - Tersoff/ZBL 3-body potential -"pair_style tip4p/cut"_pair_coul.html - Coulomb for TIP4P water w/out LJ -"pair_style tip4p/long"_pair_coul.html - long-range Coulombics for TIP4P water w/out LJ -"pair_style tri/lj"_pair_tri_lj.html - LJ potential between triangles -"pair_style vashishta"_pair_vashishta.html - Vashishta 2-body and 3-body potential -"pair_style yukawa"_pair_yukawa.html - Yukawa potential -"pair_style yukawa/colloid"_pair_yukawa_colloid.html - screened Yukawa potential for finite-size particles -"pair_style zbl"_pair_zbl.html - Ziegler-Biersack-Littmark potential :ul +"adp"_pair_adp.html - angular dependent potential (ADP) of Mishin +"airebo"_pair_airebo.html - AIREBO potential of Stuart +"airebo/morse"_pair_airebo.html - AIREBO with Morse instead of LJ +"atm"_pair_atm.html - Axilrod-Teller-Muto potential +"beck"_pair_beck.html - Beck potential +"body/nparticle"_pair_body_nparticle.html - interactions between body particles +"bop"_pair_bop.html - BOP potential of Pettifor +"born"_pair_born.html - Born-Mayer-Huggins potential +"born/coul/long"_pair_born.html - Born-Mayer-Huggins with long-range Coulombics +"born/coul/long/cs"_pair_cs.html - Born-Mayer-Huggins with long-range Coulombics and core/shell +"born/coul/msm"_pair_born.html - Born-Mayer-Huggins with long-range MSM Coulombics +"born/coul/wolf"_pair_born.html - Born-Mayer-Huggins with Coulombics via Wolf potential +"brownian"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics +"brownian/poly"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics with polydispersity +"buck"_pair_buck.html - Buckingham potential +"buck/coul/cut"_pair_buck.html - Buckingham with cutoff Coulomb +"buck/coul/long"_pair_buck.html - Buckingham with long-range Coulombics +"buck/coul/long/cs"_pair_cs.html - Buckingham with long-range Coulombics and core/shell +"buck/coul/msm"_pair_buck.html - Buckingham long-range MSM Coulombics +"buck/long/coul/long"_pair_buck_long.html - long-range Buckingham with long-range Coulombics +"buck6d/coul/gauss/dsf"_pair_buck6d_coul_gauss.html - +"buck6d/coul/gauss/long"_pair_buck6d_coul_gauss.html - +"colloid"_pair_colloid.html - integrated colloidal potential +"comb"_pair_comb.html - charge-optimized many-body (COMB) potential +"comb3"_pair_comb.html - charge-optimized many-body (COMB3) potential +"coul/cut"_pair_coul.html - cutoff Coulombic potential +"coul/debye"_pair_coul.html - cutoff Coulombic potential with Debye screening +"coul/dsf"_pair_coul.html - Coulombics via damped shifted forces +"coul/long"_pair_coul.html - long-range Coulombic potential +"coul/long/cs"_pair_cs.html - long-range Coulombic potential and core/shell +"coul/msm"_pair_coul.html - long-range MSM Coulombics +"coul/streitz"_pair_coul.html - Coulombics via Streitz/Mintmire Slater orbitals +"coul/wolf"_pair_coul.html - Coulombics via Wolf potential +"dpd"_pair_dpd.html - dissipative particle dynamics (DPD) +"dpd/tstat"_pair_dpd.html - DPD thermostatting +"dsmc"_pair_dsmc.html - Direct Simulation Monte Carlo (DSMC) +"eam"_pair_eam.html - embedded atom method (EAM) +"eam/alloy"_pair_eam.html - alloy EAM +"eam/fs"_pair_eam.html - Finnis-Sinclair EAM +"eim"_pair_eim.html - embedded ion method (EIM) +"gauss"_pair_gauss.html - Gaussian potential +"gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential +"gran/hertz/history"_pair_gran.html - granular potential with Hertzian interactions +"gran/hooke"_pair_gran.html - granular potential with history effects +"gran/hooke/history"_pair_gran.html - granular potential without history effects +"hbond/dreiding/lj"_pair_hbond_dreiding.html - DREIDING hydrogen bonding LJ potential +"hbond/dreiding/morse"_pair_hbond_dreiding.html - DREIDING hydrogen bonding Morse potential +"kim"_pair_kim.html - interface to potentials provided by KIM project +"lcbop"_pair_lcbop.html - long-range bond-order potential (LCBOP) +"line/lj"_pair_line_lj.html - LJ potential between line segments +"lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb +"lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent +"lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb +"lj/charmm/coul/msm"_pair_charmm.html - CHARMM with long-range MSM Coulombics +"lj/class2"_pair_class2.html - COMPASS (class 2) force field with no Coulomb +"lj/class2/coul/cut"_pair_class2.html - COMPASS with cutoff Coulomb +"lj/class2/coul/long"_pair_class2.html - COMPASS with long-range Coulomb +"lj/cubic"_pair_lj_cubic.html - LJ with cubic after inflection point +"lj/cut"_pair_lj.html - cutoff Lennard-Jones potential with no Coulomb +"lj/cut/coul/cut"_pair_lj.html - LJ with cutoff Coulomb +"lj/cut/coul/debye"_pair_lj.html - LJ with Debye screening added to Coulomb +"lj/cut/coul/dsf"_pair_lj.html - LJ with Coulombics via damped shifted forces +"lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulombics +"lj/cut/coul/long/cs"_pair_lj.html - LJ with long-range Coulombics and core/shell +"lj/cut/coul/msm"_pair_lj.html - LJ with long-range MSM Coulombics +"lj/cut/dipole/cut"_pair_dipole.html - point dipoles with cutoff +"lj/cut/dipole/long"_pair_dipole.html - point dipoles with long-range Ewald +"lj/cut/tip4p/cut"_pair_lj.html - LJ with cutoff Coulomb for TIP4P water +"lj/cut/tip4p/long"_pair_lj.html - LJ with long-range Coulomb for TIP4P water +"lj/expand"_pair_lj_expand.html - Lennard-Jones for variable size particles +"lj/gromacs"_pair_gromacs.html - GROMACS-style Lennard-Jones potential +"lj/gromacs/coul/gromacs"_pair_gromacs.html - GROMACS-style LJ and Coulombic potential +"lj/long/coul/long"_pair_lj_long.html - long-range LJ and long-range Coulombics +"lj/long/dipole/long"_pair_dipole.html - long-range LJ and long-range point dipoles +"lj/long/tip4p/long"_pair_lj_long.html - long-range LJ and long-range Coulomb for TIP4P water +"lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential +"lj/smooth/linear"_pair_lj_smooth_linear.html - linear smoothed Lennard-Jones potential +"lj96/cut"_pair_lj96.html - Lennard-Jones 9/6 potential +"lubricate"_pair_lubricate.html - hydrodynamic lubrication forces +"lubricate/poly"_pair_lubricate.html - hydrodynamic lubrication forces with polydispersity +"lubricateU"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication Dynamics +"lubricateU/poly"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication with polydispersity +"meam"_pair_meam.html - modified embedded atom method (MEAM) +"mie/cut"_pair_mie.html - Mie potential +"morse"_pair_morse.html - Morse potential +"nb3b/harmonic"_pair_nb3b_harmonic.html - nonbonded 3-body harmonic potential +"nm/cut"_pair_nm.html - N-M potential +"nm/cut/coul/cut"_pair_nm.html - N-M potential with cutoff Coulomb +"nm/cut/coul/long"_pair_nm.html - N-M potential with long-range Coulombics +"peri/eps"_pair_peri.html - peridynamic EPS potential +"peri/lps"_pair_peri.html - peridynamic LPS potential +"peri/pmb"_pair_peri.html - peridynamic PMB potential +"peri/ves"_pair_peri.html - peridynamic VES potential +"polymorphic"_pair_polymorphic.html - polymorphic 3-body potential +"reax"_pair_reax.html - ReaxFF potential +"rebo"_pair_airebo.html - 2nd generation REBO potential of Brenner +"resquared"_pair_resquared.html - Everaers RE-Squared ellipsoidal potential +"snap"_pair_snap.html - SNAP quantum-accurate potential +"soft"_pair_soft.html - Soft (cosine) potential +"sw"_pair_sw.html - Stillinger-Weber 3-body potential +"table"_pair_table.html - tabulated pair potential +"tersoff"_pair_tersoff.html - Tersoff 3-body potential +"tersoff/mod"_pair_tersoff_mod.html - modified Tersoff 3-body potential +"tersoff/zbl"_pair_tersoff_zbl.html - Tersoff/ZBL 3-body potential +"tip4p/cut"_pair_coul.html - Coulomb for TIP4P water w/out LJ +"tip4p/long"_pair_coul.html - long-range Coulombics for TIP4P water w/out LJ +"tri/lj"_pair_tri_lj.html - LJ potential between triangles +"vashishta"_pair_vashishta.html - Vashishta 2-body and 3-body potential +"yukawa"_pair_yukawa.html - Yukawa potential +"yukawa/colloid"_pair_yukawa_colloid.html - screened Yukawa potential for finite-size particles +"zbl"_pair_zbl.html - Ziegler-Biersack-Littmark potential :ul :line From dc89bdd9248a8ab040eb956b43e14eba59c4c20f Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Wed, 10 Oct 2018 09:42:20 -0600 Subject: [PATCH 02/12] more changes augmenting lists with USER styles and to core/shell doc pages --- doc/src/Commands_pair.txt | 6 +- doc/src/angle_style.txt | 9 ++ doc/src/bond_style.txt | 5 ++ doc/src/compute.txt | 68 +++++++++++++-- doc/src/dihedral_style.txt | 10 ++- doc/src/fix.txt | 168 +++++++++++++++++++++++++++---------- doc/src/improper_style.txt | 5 ++ doc/src/pair_cs.txt | 103 +++++++++++++---------- doc/src/pair_style.txt | 100 +++++++++++++++++++++- 9 files changed, 373 insertions(+), 101 deletions(-) diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt index 85ebcdda10..a74574367c 100644 --- a/doc/src/Commands_pair.txt +++ b/doc/src/Commands_pair.txt @@ -68,13 +68,13 @@ OPT. "coul/diel (o)"_pair_coul_diel.html, "coul/dsf (gko)"_pair_coul.html, "coul/long (gko)"_pair_coul.html, -"coul/long/cs"_pair_coul.html, +"coul/long/cs (g)"_pair_cs.html, "coul/long/soft (o)"_pair_lj_soft.html, "coul/msm (o)"_pair_coul.html, "coul/shield"_pair_coul_shield.html, "coul/streitz"_pair_coul.html, "coul/wolf (ko)"_pair_coul.html, -"coul/wolf/cs"_pair_coul.html, +"coul/wolf/cs"_pair_cs.html, "dpd (gio)"_pair_dpd.html, "dpd/fdt"_pair_dpd_fdt.html, "dpd/fdt/energy (k)"_pair_dpd_fdt.html, @@ -127,7 +127,7 @@ OPT. "lj/cut/coul/debye (gko)"_pair_lj.html, "lj/cut/coul/dsf (gko)"_pair_lj.html, "lj/cut/coul/long (gikot)"_pair_lj.html, -"lj/cut/coul/long/cs"_pair_lj.html, +"lj/cut/coul/long/cs"_pair_cs.html, "lj/cut/coul/long/soft (o)"_pair_lj_soft.html, "lj/cut/coul/msm (go)"_pair_lj.html, "lj/cut/coul/wolf (o)"_pair_lj.html, diff --git a/doc/src/angle_style.txt b/doc/src/angle_style.txt index 817179eacf..68d69d488d 100644 --- a/doc/src/angle_style.txt +++ b/doc/src/angle_style.txt @@ -68,11 +68,20 @@ doc page. "charmm"_angle_charmm.html - CHARMM angle "class2"_angle_class2.html - COMPASS (class 2) angle +"class2/p6"_angle_class2.html - "cosine"_angle_cosine.html - cosine angle potential +"cosine/buck6d"_angle_cosine_buck6d.html - "cosine/delta"_angle_cosine_delta.html - difference of cosines angle potential "cosine/periodic"_angle_cosine_periodic.html - DREIDING angle +"cosine/shift"_angle_cosine_shift.html - +"cosine/shift/exp"_angle_cosine_shift_exp.html - "cosine/squared"_angle_cosine_squared.html - cosine squared angle potential +"dipole"_angle_dipole.html - +"fourier"_angle_fourier.html - +"fourier/simple"_angle_fourier_simple.html - "harmonic"_angle_harmonic.html - harmonic angle +"quartic"_angle_quartic.html - +"sdk"_angle_sdk.html - "table"_angle_table.html - tabulated by angle :ul :line diff --git a/doc/src/bond_style.txt b/doc/src/bond_style.txt index dd406c7da0..c9252a8eb3 100644 --- a/doc/src/bond_style.txt +++ b/doc/src/bond_style.txt @@ -76,9 +76,14 @@ bond styles is on the "Commands bond"_Commands_bond.html doc page. "class2"_bond_class2.html - COMPASS (class 2) bond "fene"_bond_fene.html - FENE (finite-extensible non-linear elastic) bond "fene/expand"_bond_fene_expand.html - FENE bonds with variable size particles +"gromos"_bond_gromos.html - "harmonic"_bond_harmonic.html - harmonic bond +"harmonic/shift"_bond_harmonic_shift.html - +"harmonic/shift/cut"_bond_harmonic_shift_cut.html - "morse"_bond_morse.html - Morse bond "nonlinear"_bond_nonlinear.html - nonlinear bond +"oxdna/fene"_bond_oxdna.html - +"oxdna2/fene"_bond_oxdna.html - "quartic"_bond_quartic.html - breakable quartic bond "table"_bond_table.html - tabulated by bond length :ul diff --git a/doc/src/compute.txt b/doc/src/compute.txt index 14ab84b436..857795ffe5 100644 --- a/doc/src/compute.txt +++ b/doc/src/compute.txt @@ -175,9 +175,13 @@ The individual style names on the "Commands compute"_Commands_compute.html doc page are followed by one or more of (g,i,k,o,t) to indicate which accelerated styles exist. +"ackland/atom"_compute_ackland_atom.html - "aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom +"angle"_compute_angle.html - +"angle/local"_compute_angle_local.html - "angle/local"_compute_bond_local.html - theta and energy of each angle "angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk +"basal/atom"_compute_basal_atom.html - "body/local"_compute_body_local.html - attributes of body sub-particles "bond"_compute_bond.html - values computed by a bond style "bond/local"_compute_bond_local.html - distance and energy of each bond @@ -186,30 +190,48 @@ compute"_Commands_compute.html doc page are followed by one or more of "chunk/spread/atom"_compute_chunk_spread_atom.html - spreads chunk values to each atom in chunk "cluster/atom"_compute_cluster_atom.html - cluster ID for each atom "cna/atom"_compute_cna_atom.html - common neighbor analysis (CNA) for each atom +"cnp/atom"_compute_cnp_atom.html - "com"_compute_com.html - center-of-mass of group of atoms "com/chunk"_compute_com_chunk.html - center-of-mass for each chunk "contact/atom"_compute_contact_atom.html - contact count for each spherical particle "coord/atom"_compute_coord_atom.html - coordination number for each atom "damage/atom"_compute_damage_atom.html - Peridynamic damage for each atom +"dihedral"_compute_dihedral.html - "dihedral/local"_compute_dihedral_local.html - angle of each dihedral "dilatation/atom"_compute_dilatation_atom.html - Peridynamic dilatation for each atom +"dipole/chunk"_compute_dipole_chunk.html - "displace/atom"_compute_displace_atom.html - displacement of each atom +"dpd"_compute_dpd.html - +"dpd/atom"_compute_dpd_atom.html - +"edpd/temp/atom"_compute_edpd_temp_atom.html - +"entropy/atom"_compute_entropy_atom.html - "erotate/asphere"_compute_erotate_asphere.html - rotational energy of aspherical particles "erotate/rigid"_compute_erotate_rigid.html - rotational energy of rigid bodies "erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles "erotate/sphere/atom"_compute_erotate_sphere.html - rotational energy for each spherical particle +"erotate/sphere/atom"_compute_erotate_sphere_atom.html - "event/displace"_compute_event_displace.html - detect event on atom displacement +"fep"_compute_fep.html - +"force/tally"_compute_tally.html - "fragment/atom"_compute_cluster_atom.html - fragment ID for each atom +"global/atom"_compute_global_atom.html - "group/group"_compute_group_group.html - energy/force between two groups of atoms "gyration"_compute_gyration.html - radius of gyration of group of atoms "gyration/chunk"_compute_gyration_chunk.html - radius of gyration for each chunk "heat/flux"_compute_heat_flux.html - heat flux through a group of atoms +"heat/flux/tally"_compute_tally.html - "hexorder/atom"_compute_hexorder_atom.html - bond orientational order parameter q6 +"improper"_compute_improper.html - "improper/local"_compute_improper_local.html - angle of each improper "inertia/chunk"_compute_inertia_chunk.html - inertia tensor for each chunk "ke"_compute_ke.html - translational kinetic energy "ke/atom"_compute_ke_atom.html - kinetic energy for each atom +"ke/atom/eff"_compute_ke_atom_eff.html - +"ke/eff"_compute_ke_eff.html - "ke/rigid"_compute_ke_rigid.html - translational kinetic energy of rigid bodies +"meso/e/atom"_compute_meso_e_atom.html - +"meso/rho/atom"_compute_meso_rho_atom.html - +"meso/t/atom"_compute_meso_t_atom.html - "msd"_compute_msd.html - mean-squared displacement of group of atoms "msd/chunk"_compute_msd_chunk.html - mean-squared displacement for each chunk "msd/nongauss"_compute_msd_nongauss.html - MSD and non-Gaussian parameter of group of atoms @@ -219,41 +241,77 @@ compute"_Commands_compute.html doc page are followed by one or more of "pair/local"_compute_pair_local.html - distance/energy/force of each pairwise interaction "pe"_compute_pe.html - potential energy "pe/atom"_compute_pe_atom.html - potential energy for each atom +"pe/mol/tally"_compute_tally.html - +"pe/tally"_compute_tally.html - "plasticity/atom"_compute_plasticity_atom.html - Peridynamic plasticity for each atom "pressure"_compute_pressure.html - total pressure and pressure tensor +"pressure/cylinder"_compute_pressure_cylinder.html - +"pressure/uef"_compute_pressure_uef.html - "property/atom"_compute_property_atom.html - convert atom attributes to per-atom vectors/arrays -"property/local"_compute_property_local.html - convert local attributes to localvectors/arrays "property/chunk"_compute_property_chunk.html - extract various per-chunk attributes +"property/local"_compute_property_local.html - convert local attributes to localvectors/arrays +"ptm/atom"_compute_ptm_atom.html - "rdf"_compute_rdf.html - radial distribution function g(r) histogram of group of atoms "reduce"_compute_reduce.html - combine per-atom quantities into a single global value "reduce/chunk"_compute_reduce_chunk.html - reduce per-atom quantities within each chunk "reduce/region"_compute_reduce.html - same as compute reduce, within a region "rigid/local"_compute_rigid_local.html - extract rigid body attributes +"saed"_compute_saed.html - "slice"_compute_slice.html - extract values from global vector or array +"smd/contact/radius"_compute_smd_contact_radius.html - +"smd/damage"_compute_smd_damage.html - +"smd/hourglass/error"_compute_smd_hourglass_error.html - +"smd/internal/energy"_compute_smd_internal_energy.html - +"smd/plastic/strain"_compute_smd_plastic_strain.html - +"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html - +"smd/rho"_compute_smd_rho.html - +"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html - +"smd/tlsph/dt"_compute_smd_tlsph_dt.html - +"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html - +"smd/tlsph/shape"_compute_smd_tlsph_shape.html - +"smd/tlsph/strain"_compute_smd_tlsph_strain.html - +"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html - +"smd/tlsph/stress"_compute_smd_tlsph_stress.html - "smd/triangle/vertices"_compute_smd_triangle_vertices.html - +"smd/triangle/vertices"_compute_smd_triangle_vertices.html - +"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html - +"smd/ulsph/strain"_compute_smd_ulsph_strain.html - +"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html - +"smd/ulsph/stress"_compute_smd_ulsph_stress.html - +"smd/vol"_compute_smd_vol.html - "sna/atom"_compute_sna_atom.html - calculate bispectrum coefficients for each atom "snad/atom"_compute_sna_atom.html - derivative of bispectrum coefficients for each atom "snav/atom"_compute_sna_atom.html - virial contribution from bispectrum coefficients for each atom +"spin"_compute_spin.html - "stress/atom"_compute_stress_atom.html - stress tensor for each atom -"stress/mop"_compute_stress_mop.html - -"stress/mop/profile"_compute_stress_mop.html - +"stress/mop"_compute_stress_mop.html - +"stress/mop/profile"_compute_stress_mop.html - +"stress/tally"_compute_tally.html - +"tdpd/cc/atom"_compute_tdpd_cc_atom.html - "temp"_compute_temp.html - temperature of group of atoms "temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles "temp/body"_compute_temp_body.html - temperature of body particles "temp/chunk"_compute_temp_chunk.html - temperature of each chunk "temp/com"_compute_temp_com.html - temperature after subtracting center-of-mass velocity -"temp/cs"_compute_temp_cs.html - +"temp/cs"_compute_temp_cs.html - "temp/deform"_compute_temp_deform.html - temperature excluding box deformation velocity +"temp/deform/eff"_compute_temp_deform_eff.html - +"temp/drude"_compute_temp_drude.html - +"temp/eff"_compute_temp_eff.html - "temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity "temp/profile"_compute_temp_profile.html - temperature excluding a binned velocity profile "temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component "temp/region"_compute_temp_region.html - temperature of a region of atoms +"temp/region/eff"_compute_temp_region_eff.html - +"temp/rotate"_compute_temp_rotate.html - "temp/sphere"_compute_temp_sphere.html - temperature of spherical particles +"temp/uef"_compute_temp_uef.html - "ti"_compute_ti.html - thermodynamic integration free energy values "torque/chunk"_compute_torque_chunk.html - torque applied on each chunk "vacf"_compute_vacf.html - velocity-autocorrelation function of group of atoms "vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk -"voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom :ul +"voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom +"xrd"_compute_xrd.html - :ul [Restrictions:] none diff --git a/doc/src/dihedral_style.txt b/doc/src/dihedral_style.txt index 9744f1b71f..02634c6073 100644 --- a/doc/src/dihedral_style.txt +++ b/doc/src/dihedral_style.txt @@ -90,11 +90,19 @@ doc page. "hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions :ul "charmm"_dihedral_charmm.html - CHARMM dihedral +"charmmfsw"_dihedral_charmm.html - "class2"_dihedral_class2.html - COMPASS (class 2) dihedral +"cosine/shift/exp"_dihedral_cosine_shift_exp.html - +"fourier"_dihedral_fourier.html - "harmonic"_dihedral_harmonic.html - harmonic dihedral "helix"_dihedral_helix.html - helix dihedral "multi/harmonic"_dihedral_multi_harmonic.html - multi-harmonic dihedral -"opls"_dihedral_opls.html - OPLS dihedral :ul +"nharmonic"_dihedral_nharmonic.html - +"opls"_dihedral_opls.html - OPLS dihedral +"quadratic"_dihedral_quadratic.html - +"spherical"_dihedral_spherical.html - +"table"_dihedral_table.html - +"table/cut"_dihedral_table_cut.html - :ul :line diff --git a/doc/src/fix.txt b/doc/src/fix.txt index ee0d006fe8..27cc0467e2 100644 --- a/doc/src/fix.txt +++ b/doc/src/fix.txt @@ -167,136 +167,211 @@ page are followed by one or more of (g,i,k,o,t) to indicate which accelerated styles exist. "adapt"_fix_adapt.html - change a simulation parameter over time +"adapt/fep"_fix_adapt_fep.html - "addforce"_fix_addforce.html - add a force to each atom +"addtorque"_fix_addtorque.html - "append/atoms"_fix_append_atoms.html - append atoms to a running simulation +"atc"_fix_atc.html - "atom/swap"_fix_atom_swap.html - Monte Carlo atom type swapping -"aveforce"_fix_aveforce.html - add an averaged force to each atom "ave/atom"_fix_ave_atom.html - compute per-atom time-averaged quantities "ave/chunk"_fix_ave_chunk.html - compute per-chunk time-averaged quantities "ave/correlate"_fix_ave_correlate.html - compute/output time correlations +"ave/correlate/long"_fix_ave_correlate_long.html - "ave/histo"_fix_ave_histo.html - compute/output time-averaged histograms +"ave/histo/weight"_fix_ave_histo.html - "ave/time"_fix_ave_time.html - compute/output global time-averaged quantities +"aveforce"_fix_aveforce.html - add an averaged force to each atom "balance"_fix_balance.html - perform dynamic load-balancing +"bocs"_fix_bocs.html - "bond/break"_fix_bond_break.html - break bonds on the fly "bond/create"_fix_bond_create.html - create bonds on the fly +"bond/react"_fix_bond_react.html - "bond/swap"_fix_bond_swap.html - Monte Carlo bond swapping "box/relax"_fix_box_relax.html - relax box size during energy minimization +"client/md"_fix_client_md.html - +"cmap"_fix_cmap.html - +"colvars"_fix_colvars.html - +"controller"_fix_controller.html - "deform"_fix_deform.html - change the simulation box size/shape "deposit"_fix_deposit.html - add new atoms above a surface +"dpd/energy"_fix_dpd_energy.html - "drag"_fix_drag.html - drag atoms towards a defined coordinate +"drude"_fix_drude.html - +"drude/transform/direct"_fix_drude_transform.html - +"drude/transform/inverse"_fix_drude_transform.html - "dt/reset"_fix_dt_reset.html - reset the timestep based on velocity, forces +"edpd/source"_fix_dpd_source.html - "efield"_fix_efield.html - impose electric field on system "ehex"_fix_ehex.html - ehanced heat exchange algorithm "enforce2d"_fix_enforce2d.html - zero out z-dimension velocity and force +"eos/cv"_fix_eos_cv.html - +"eos/table"_fix_eos_table.html - +"eos/table/rx"_fix_eos_table_rx.html - "evaporate"_fix_evaporate.html - remove atoms from simulation periodically "external"_fix_external.html - callback to an external driver program +"ffl"_fix_ffl.html - +"filter/corotate"_fix_filter_corotate.html - +"flow/gauss"_fix_flow_gauss.html - "freeze"_fix_freeze.html - freeze atoms in a granular simulation "gcmc"_fix_gcmc.html - grand canonical insertions/deletions "gld"_fix_gcmc.html - generalized Langevin dynamics integrator +"gld"_fix_gld.html - +"gle"_fix_gle.html - "gravity"_fix_gravity.html - add gravity to atoms in a granular simulation +"grem"_fix_grem.html - "halt"_fix_halt.html - terminate a dynamics run or minimization "heat"_fix_heat.html - add/subtract momentum-conserving heat +"imd"_fix_imd.html - "indent"_fix_indent.html - impose force due to an indenter -"latte"_fix_latte.html - wrapper on LATTE density-functional tight-binding code +"ipi"_fix_ipi.html - "langevin"_fix_langevin.html - Langevin temperature control +"langevin/drude"_fix_langevin_drude.html - +"langevin/eff"_fix_langevin_eff.html - +"langevin/spin"_fix_langevin_spin.html - +"latte"_fix_latte.html - wrapper on LATTE density-functional tight-binding code +"lb/fluid"_fix_lb_fluid.html - +"lb/momentum"_fix_lb_momentum.html - +"lb/pc"_fix_lb_pc.html - +"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html - +"lb/viscous"_fix_lb_viscous.html - "lineforce"_fix_lineforce.html - constrain atoms to move in a line +"manifoldforce"_fix_manifoldforce.html - +"meso"_fix_meso.html - +"meso/stationary"_fix_meso_stationary.html - "momentum"_fix_momentum.html - zero the linear and/or angular momentum of a group of atoms "move"_fix_move.html - move atoms in a prescribed fashion +"mscg"_fix_mscg.html - "msst"_fix_msst.html - multi-scale shock technique (MSST) integration +"mvv/dpd"_fix_mvv_dpd.html - +"mvv/edpd"_fix_mvv_dpd.html - +"mvv/tdpd"_fix_mvv_dpd.html - "neb"_fix_neb.html - nudged elastic band (NEB) spring forces "nph"_fix_nh.html - constant NPH time integration via Nose/Hoover -"nphug"_fix_nphug.html - constant-stress Hugoniostat integration "nph/asphere"_fix_nph_asphere.html - NPH for aspherical particles +"nph/body"_fix_nph_body.html - "nph/body"_fix_nve_body.html - NPH for body particles +"nph/eff"_fix_nh_eff.html - "nph/sphere"_fix_nph_sphere.html - NPH for spherical particles +"nphug"_fix_nphug.html - constant-stress Hugoniostat integration "npt"_fix_nh.html - constant NPT time integration via Nose/Hoover "npt/asphere"_fix_npt_asphere.html - NPT for aspherical particles +"npt/body"_fix_npt_body.html - "npt/body"_fix_nve_body.html - NPT for body particles +"npt/eff"_fix_nh_eff.html - "npt/sphere"_fix_npt_sphere.html - NPT for spherical particles +"npt/uef"_fix_nh_uef.html - "nve"_fix_nve.html - constant NVE time integration "nve/asphere"_fix_nve_asphere.html - NVE for aspherical particles "nve/asphere/noforce"_fix_nve_asphere_noforce.html - NVE for aspherical particles without forces" +"nve/awpmd"_fix_nve_awpmd.html - "nve/body"_fix_nve_body.html - NVE for body particles +"nve/dot"_fix_nve_dot.html - +"nve/dotc/langevin"_fix_nve_dotc_langevin.html - +"nve/eff"_fix_nve_eff.html - "nve/limit"_fix_nve_limit.html - NVE with limited step length "nve/line"_fix_nve_line.html - NVE for line segments +"nve/manifold/rattle"_fix_nve_manifold_rattle.html - "nve/noforce"_fix_nve_noforce.html - NVE without forces (v only) "nve/sphere"_fix_nve_sphere.html - NVE for spherical particles +"nve/spin"_fix_nve_spin.html - "nve/tri"_fix_nve_tri.html - NVE for triangles +"nvk"_fix_nvk.html - "nvt"_fix_nh.html - constant NVT time integration via Nose/Hoover "nvt/asphere"_fix_nvt_asphere.html - NVT for aspherical particles "nvt/body"_fix_nve_body.html - NVT for body particles +"nvt/body"_fix_nvt_body.html - +"nvt/eff"_fix_nh_eff.html - +"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html - "nvt/sllod"_fix_nvt_sllod.html - NVT for NEMD with SLLOD equations +"nvt/sllod/eff"_fix_nvt_sllod_eff.html - "nvt/sphere"_fix_nvt_sphere.html - NVT for spherical particles +"nvt/uef"_fix_nh_uef.html - "oneway"_fix_oneway.html - constrain particles on move in one direction "orient/bcc"_fix_orient.html - add grain boundary migration force for BCC "orient/fcc"_fix_orient.html - add grain boundary migration force for FCC +"phonon"_fix_phonon.html - +"pimd"_fix_pimd.html - "planeforce"_fix_planeforce.html - constrain atoms to move in a plane -"poems"_fix_poems.html - constrain clusters of atoms to move \ - as coupled rigid bodies +"poems"_fix_poems.html - constrain clusters of atoms to move as coupled rigid bodies "pour"_fix_pour.html - pour new atoms/molecules into a granular simulation domain -"press/berendsen"_fix_press_berendsen.html - pressure control by \ - Berendsen barostat +"precession/spin"_fix_precession_spin.html - +"press/berendsen"_fix_press_berendsen.html - pressure control by Berendsen barostat "print"_fix_print.html - print text and variables during a simulation "property/atom"_fix_property_atom.html - add customized per-atom values -"qeq/comb"_fix_qeq_comb.html - charge equilibration for COMB potential \ -"qeq/dynamic"_fix_qeq.html - charge equilibration via dynamic method \ -"qeq/fire"_fix_qeq.html - charge equilibration via FIRE minimizer \ -"qeq/point"_fix_qeq.html - charge equilibration via point method \ -"qeq/shielded"_fix_qeq.html - charge equilibration via shielded method \ -"qeq/slater"_fix_qeq.html - charge equilibration via Slater method \ +"python/invoke"_fix_python_invoke.html - +"python/move"_fix_python_move.html - +"qbmsst"_fix_qbmsst.html - +"qeq/comb"_fix_qeq_comb.html - charge equilibration for COMB potential +"qeq/dynamic"_fix_qeq.html - charge equilibration via dynamic method +"qeq/fire"_fix_qeq.html - charge equilibration via FIRE minimizer +"qeq/point"_fix_qeq.html - charge equilibration via point method +"qeq/reax"_fix_qeq_reax.html - +"qeq/shielded"_fix_qeq.html - charge equilibration via shielded method +"qeq/slater"_fix_qeq.html - charge equilibration via Slater method +"qmmm"_fix_qmmm.html - +"qtb"_fix_qtb.html - "rattle"_fix_shake.html - RATTLE constraints on bonds and/or angles -"reax/bonds"_fix_reax_bonds.html - write out ReaxFF bond information \ -"recenter"_fix_recenter.html - constrain the center-of-mass position \ - of a group of atoms +"reax/bonds"_fix_reax_bonds.html - write out ReaxFF bond information +"reax/c/bonds"_fix_reax_bonds.html - +"reax/c/species"_fix_reaxc_species.html - +"recenter"_fix_recenter.html - constrain the center-of-mass position of a group of atoms "restrain"_fix_restrain.html - constrain a bond, angle, dihedral -"rigid"_fix_rigid.html - constrain one or more clusters of atoms to \ - move as a rigid body with NVE integration -"rigid/nph"_fix_rigid.html - constrain one or more clusters of atoms to \ - move as a rigid body with NPH integration -"rigid/npt"_fix_rigid.html - constrain one or more clusters of atoms to \ - move as a rigid body with NPT integration -"rigid/nve"_fix_rigid.html - constrain one or more clusters of atoms to \ - move as a rigid body with alternate NVE integration -"rigid/nvt"_fix_rigid.html - constrain one or more clusters of atoms to \ - move as a rigid body with NVT integration -"rigid/small"_fix_rigid.html - constrain many small clusters of atoms to \ - move as a rigid body with NVE integration -"rigid/small/nph"_fix_rigid.html - constrain many small clusters of atoms to \ - move as a rigid body with NPH integration -"rigid/small/npt"_fix_rigid.html - constrain many small clusters of atoms to \ - move as a rigid body with NPT integration -"rigid/small/nve"_fix_rigid.html - constrain many small clusters of atoms to \ - move as a rigid body with alternate NVE integration -"rigid/small/nvt"_fix_rigid.html - constrain many small clusters of atoms to \ - move as a rigid body with NVT integration +"rhok"_fix_rhok.html - +"rigid"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVE integration +"rigid/nph"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPH integration +"rigid/nph/small"_fix_rigid.html - +"rigid/npt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPT integration +"rigid/npt/small"_fix_rigid.html - +"rigid/nve"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with alternate NVE integration +"rigid/nve/small"_fix_rigid.html - +"rigid/nvt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVT integration +"rigid/nvt/small"_fix_rigid.html - +"rigid/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVE integration +"rigid/small/nph"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPH integration +"rigid/small/npt"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPT integration +"rigid/small/nve"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with alternate NVE integration +"rigid/small/nvt"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVT integration +"rx"_fix_rx.html - +"saed/vtk"_fix_saed_vtk.html - "setforce"_fix_setforce.html - set the force on each atom "shake"_fix_shake.html - SHAKE constraints on bonds and/or angles +"shardlow"_fix_shardlow.html - +"smd"_fix_smd.html - +"smd/adjust_dt"_fix_smd_adjust_dt.html - +"smd/integrate_tlsph"_fix_smd_integrate_tlsph.html - +"smd/integrate_ulsph"_fix_smd_integrate_ulsph.html - +"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html - +"smd/setvel"_fix_smd_setvel.html - +"smd/wall_surface"_fix_smd_wall_surface.html - "spring"_fix_spring.html - apply harmonic spring force to group of atoms "spring/chunk"_fix_spring_chunk.html - apply harmonic spring force to each chunk of atoms -"spring/rg"_fix_spring_rg.html - spring on radius of gyration of \ - group of atoms +"spring/rg"_fix_spring_rg.html - spring on radius of gyration of group of atoms "spring/self"_fix_spring_self.html - spring from each atom to its origin "srd"_fix_srd.html - stochastic rotation dynamics (SRD) "store/force"_fix_store_force.html - store force on each atom "store/state"_fix_store_state.html - store attributes for each atom -"temp/berendsen"_fix_temp_berendsen.html - temperature control by \ - Berendsen thermostat +"tdpd/source"_fix_dpd_source.html - +"temp/berendsen"_fix_temp_berendsen.html - temperature control by Berendsen thermostat "temp/csld"_fix_temp_csvr.html - canonical sampling thermostat with Langevin dynamics "temp/csvr"_fix_temp_csvr.html - canonical sampling thermostat with Hamiltonian dynamics -"temp/rescale"_fix_temp_rescale.html - temperature control by \ - velocity rescaling +"temp/rescale"_fix_temp_rescale.html - temperature control by velocity rescaling +"temp/rescale/eff"_fix_temp_rescale_eff.html - "tfmc"_fix_tfmc.html - perform force-bias Monte Carlo with time-stamped method -"thermal/conductivity"_fix_thermal_conductivity.html - Muller-Plathe kinetic energy exchange for \ - thermal conductivity calculation +"thermal/conductivity"_fix_thermal_conductivity.html - Muller-Plathe kinetic energy exchange for thermal conductivity calculation +"ti/spring"_fix_ti_spring.html - "tmd"_fix_tmd.html - guide a group of atoms to a new configuration "ttm"_fix_ttm.html - two-temperature model for electronic/atomic coupling +"ttm/mod"_fix_ttm.html - "tune/kspace"_fix_tune_kspace.html - auto-tune KSpace parameters "vector"_fix_vector.html - accumulate a global vector every N timesteps -"viscosity"_fix_viscosity.html - Muller-Plathe momentum exchange for \ - viscosity calculation +"viscosity"_fix_viscosity.html - Muller-Plathe momentum exchange for viscosity calculation "viscous"_fix_viscous.html - viscous damping for granular simulations +"wall/body/polygon"_fix_wall_body_polygon.html - +"wall/body/polyhedron"_fix_wall_body_polyhedron.html - "wall/colloid"_fix_wall.html - Lennard-Jones wall interacting with finite-size particles +"wall/ees"_fix_wall_ees.html - "wall/gran"_fix_wall_gran.html - frictional wall(s) for granular simulations +"wall/gran/region"_fix_wall_gran_region.html - "wall/harmonic"_fix_wall.html - harmonic spring wall "wall/lj1043"_fix_wall.html - Lennard-Jones 10-4-3 wall "wall/lj126"_fix_wall.html - Lennard-Jones 12-6 wall @@ -304,6 +379,7 @@ accelerated styles exist. "wall/piston"_fix_wall_piston.html - moving reflective piston wall "wall/reflect"_fix_wall_reflect.html - reflecting wall(s) "wall/region"_fix_wall_region.html - use region surface as wall +"wall/region/ees"_fix_wall_ees.html - "wall/srd"_fix_wall_srd.html - slip/no-slip wall for SRD particles :ul [Restrictions:] diff --git a/doc/src/improper_style.txt b/doc/src/improper_style.txt index c9db7678a9..28b3b440b2 100644 --- a/doc/src/improper_style.txt +++ b/doc/src/improper_style.txt @@ -69,8 +69,13 @@ doc page. "hybrid"_improper_hybrid.html - define multiple styles of improper interactions :ul "class2"_improper_class2.html - COMPASS (class 2) improper +"cossq"_improper_cossq.html - "cvff"_improper_cvff.html - CVFF improper +"distance"_improper_distance.html - +"fourier"_improper_fourier.html - "harmonic"_improper_harmonic.html - harmonic improper +"inversion/harmonic"_improper_inversion_harmonic.html - +"ring"_improper_ring.html - "umbrella"_improper_umbrella.html - DREIDING improper :ul :line diff --git a/doc/src/pair_cs.txt b/doc/src/pair_cs.txt index 80b971e393..830e0586d2 100644 --- a/doc/src/pair_cs.txt +++ b/doc/src/pair_cs.txt @@ -6,52 +6,69 @@ :line +pair_style born/coul/dsf/cs command :h3 pair_style born/coul/long/cs command :h3 pair_style born/coul/long/cs/gpu command :h3 -pair_style buck/coul/long/cs command :h3 -pair_style born/coul/dsf/cs command :h3 pair_style born/coul/wolf/cs command :h3 pair_style born/coul/wolf/cs/gpu command :h3 +pair_style buck/coul/long/cs command :h3 +pair_style coul/long/cs command :h3 +pair_style coul/long/cs/gpu command :h3 +pair_style coul/wolf/cs command :h3 pair_style lj/cut/coul/long/cs command :h3 [Syntax:] pair_style style args :pre -style = {born/coul/long/cs} or {buck/coul/long/cs} or {born/coul/dsf/cs} or {born/coul/wolf/cs} +style = {born/coul/dsf/cs} or {born/coul/long/cs} or {born/coul/wolf/cs} or {buck/coul/long/cs} or {coul/long/cs} or {coul/wolf/cs} or {lj/cut/coul/long/cs} args = list of arguments for a particular style :ul - {born/coul/long/cs} args = cutoff (cutoff2) - cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) - {buck/coul/long/cs} args = cutoff (cutoff2) - cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (optional) (distance units) {born/coul/dsf/cs} args = alpha cutoff (cutoff2) alpha = damping parameter (inverse distance units) cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units) - cutoff2 = global cutoff for Coulombic (distance units) :pre + cutoff2 = global cutoff for Coulombic (distance units) + {born/coul/long/cs} args = cutoff (cutoff2) + cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) {born/coul/wolf/cs} args = alpha cutoff (cutoff2) alpha = damping parameter (inverse distance units) cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units) cutoff2 = global cutoff for Coulombic (optional) (distance units) + {buck/coul/long/cs} args = cutoff (cutoff2) + cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) + {coul/long} args = cutoff + cutoff = global cutoff for Coulombic (distance units) + {coul/wolf} args = alpha cutoff + alpha = damping parameter (inverse distance units) + cutoff = global cutoff for Coulombic (distance units) + {lj/cut/coul/long/cs} args = cutoff (cutoff2) + cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre [Examples:] +pair_style born/coul/dsf/cs 0.1 10.0 12.0 +pair_coeff * * 0.0 1.00 0.00 0.00 0.00 +pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre + pair_style born/coul/long/cs 10.0 8.0 pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre +pair_style born/coul/wolf/cs 0.25 10.0 12.0 +pair_coeff * * 0.0 1.00 0.00 0.00 0.00 +pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre + pair_style buck/coul/long/cs 10.0 pair_style buck/coul/long/cs 10.0 8.0 pair_coeff * * 100.0 1.5 200.0 pair_coeff 1 1 100.0 1.5 200.0 9.0 :pre -pair_style born/coul/dsf/cs 0.1 10.0 12.0 -pair_coeff * * 0.0 1.00 0.00 0.00 0.00 -pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre +pair_style coul/long/cs 10.0 +pair_coeff * * :pre -pair_style born/coul/wolf/cs 0.25 10.0 12.0 -pair_coeff * * 0.0 1.00 0.00 0.00 0.00 -pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre +pair_style coul/wolf/cs 0.2 9.0 +pair_coeff * * :pre pair_style lj/cut/coul/long/cs 10.0 pair_style lj/cut/coul/long/cs 10.0 8.0 @@ -65,16 +82,28 @@ core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham2. See the "Howto coreshell"_Howto_coreshell.html doc page for an overview of the model as implemented in LAMMPS. -The styles with a {coul/long} term are identical to the "pair_style -born/coul/long"_pair_born.html and "pair_style -buck/coul/long"_pair_buck.html styles, except they correctly treat the -special case where the distance between two charged core and shell -atoms in the same core/shell pair approach r = 0.0. This needs -special treatment when a long-range solver for Coulombic interactions -is also used, i.e. via the "kspace_style"_kspace_style.html command. +All the styles are identical to the corresponding pair style without +the "/cs" in the name: -More specifically, the short-range Coulomb interaction between a core -and its shell should be turned off using the +"pair_style born/coul/dsf"_pair_born.html +"pair_style born/coul/long"_pair_born.html +"pair_style born/coul/wolf"_pair_born.html +"pair_style buck/coul/long"_pair_buck.html +"pair_style coul/long"_pair_coul.html +"pair_style coul/wolf"_pair_coul.html +"pair_style lj/cut/coul/long"_pair_lj.html :ul + +except that they correctly treat the special case where the distance +between two charged core and shell atoms in the same core/shell pair +approach r = 0.0. + +Styles with a "/long" in the name are used with a long-range solver +for Coulombic interactions via the "kspace_style"_kspace_style.html +command. They require special treatment of the short-range Coulombic +interactions within the cor/shell model. + +Specifically, the short-range Coulomb interaction between a core and +its shell should be turned off using the "special_bonds"_special_bonds.html command by setting the 1-2 weight to 0.0, which works because the core and shell atoms are bonded to each other. This induces a long-range correction approximation which @@ -89,26 +118,10 @@ where C is an energy-conversion constant, Qi and Qj are the charges on the core and shell, epsilon is the dielectric constant and r_min is the minimal distance. -The pair style {born/coul/dsf/cs} is identical to the -"pair_style born/coul/dsf"_pair_born.html style, which uses -the damped shifted force model as in "coul/dsf"_pair_coul.html -to compute the Coulomb contribution. This approach does not require -a long-range solver, thus the only correction is the addition of a -minimal distance to avoid the possible r = 0.0 case for a -core/shell pair. - -The pair style {born/coul/wolf/cs} is identical to the -"pair_style born/coul/wolf"_pair_born.html style, which uses -the Wolf summation as in "coul/wolf"_pair_coul.html to compute -the Coulomb contribution. This approach does not require -a long-range solver, thus the only correction is the addition of a -minimal distance to avoid the possible r = 0.0 case for a -core/shell pair. - -Style {lj/cut/coul/long/cs} is identical to {lj/cut/coul/long} except -that a term is added for the "core/shell model"_Howto_coreshell.html -to allow charges on core and shell particles to be separated by r = -0.0. +For styles that are not used with a long-range solver, i.e. those with +"/dsf" or "/wolf" in the name, the only correction is the addition of +a minimal distance to avoid the possible r = 0.0 case for a core/shell +pair. :line diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt index 86ac61c752..c728445952 100644 --- a/doc/src/pair_style.txt +++ b/doc/src/pair_style.txt @@ -101,17 +101,25 @@ pair"_Commands_pair.html doc page are followed by one or more of "zero"_pair_zero.html - neighbor list but no interactions :ul "adp"_pair_adp.html - angular dependent potential (ADP) of Mishin +"agni"_pair_agni.html - "airebo"_pair_airebo.html - AIREBO potential of Stuart "airebo/morse"_pair_airebo.html - AIREBO with Morse instead of LJ "atm"_pair_atm.html - Axilrod-Teller-Muto potential +"awpmd/cut"_pair_awpmd.html - "beck"_pair_beck.html - Beck potential "body/nparticle"_pair_body_nparticle.html - interactions between body particles +"body/rounded/polygon"_pair_body_rounded_polygon.html - +"body/rounded/polyhedron"_pair_body_rounded_polyhedron.html - "bop"_pair_bop.html - BOP potential of Pettifor "born"_pair_born.html - Born-Mayer-Huggins potential +"born/coul/dsf"_pair_born.html - +"born/coul/dsf/cs"_pair_cs.html - "born/coul/long"_pair_born.html - Born-Mayer-Huggins with long-range Coulombics +"born/coul/long/cs"_pair_cs.html - "born/coul/long/cs"_pair_cs.html - Born-Mayer-Huggins with long-range Coulombics and core/shell "born/coul/msm"_pair_born.html - Born-Mayer-Huggins with long-range MSM Coulombics "born/coul/wolf"_pair_born.html - Born-Mayer-Huggins with Coulombics via Wolf potential +"born/coul/wolf/cs"_pair_cs.html - "brownian"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics "brownian/poly"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics with polydispersity "buck"_pair_buck.html - Buckingham potential @@ -120,61 +128,102 @@ pair"_Commands_pair.html doc page are followed by one or more of "buck/coul/long/cs"_pair_cs.html - Buckingham with long-range Coulombics and core/shell "buck/coul/msm"_pair_buck.html - Buckingham long-range MSM Coulombics "buck/long/coul/long"_pair_buck_long.html - long-range Buckingham with long-range Coulombics +"buck/mdf"_pair_mdf.html - "buck6d/coul/gauss/dsf"_pair_buck6d_coul_gauss.html - +"buck6d/coul/gauss/dsf"_pair_buck6d_coul_gauss.html - "buck6d/coul/gauss/long"_pair_buck6d_coul_gauss.html - +"buck6d/coul/gauss/long"_pair_buck6d_coul_gauss.html - "colloid"_pair_colloid.html - integrated colloidal potential "comb"_pair_comb.html - charge-optimized many-body (COMB) potential "comb3"_pair_comb.html - charge-optimized many-body (COMB3) potential "coul/cut"_pair_coul.html - cutoff Coulombic potential +"coul/cut/soft"_pair_lj_soft.html - "coul/debye"_pair_coul.html - cutoff Coulombic potential with Debye screening +"coul/diel"_pair_coul_diel.html - "coul/dsf"_pair_coul.html - Coulombics via damped shifted forces "coul/long"_pair_coul.html - long-range Coulombic potential "coul/long/cs"_pair_cs.html - long-range Coulombic potential and core/shell +"coul/long/soft"_pair_lj_soft.html - "coul/msm"_pair_coul.html - long-range MSM Coulombics +"coul/shield"_pair_coul_shield.html - "coul/streitz"_pair_coul.html - Coulombics via Streitz/Mintmire Slater orbitals "coul/wolf"_pair_coul.html - Coulombics via Wolf potential +"coul/wolf/cs"_pair_cs.html - ditto with core/shell adjustments "dpd"_pair_dpd.html - dissipative particle dynamics (DPD) +"dpd/fdt"_pair_dpd_fdt.html - +"dpd/fdt/energy"_pair_dpd_fdt.html - "dpd/tstat"_pair_dpd.html - DPD thermostatting "dsmc"_pair_dsmc.html - Direct Simulation Monte Carlo (DSMC) "eam"_pair_eam.html - embedded atom method (EAM) "eam/alloy"_pair_eam.html - alloy EAM +"eam/cd"_pair_eam.html - +"eam/cd/old"_pair_eam.html - "eam/fs"_pair_eam.html - Finnis-Sinclair EAM +"edip"_pair_edip.html - +"edip/multi"_pair_edip.html - +"edpd"_pair_meso.html - +"eff/cut"_pair_eff.html - "eim"_pair_eim.html - embedded ion method (EIM) +"exp6/rx"_pair_exp6_rx.html - +"extep"_pair_extep.html - "gauss"_pair_gauss.html - Gaussian potential +"gauss/cut"_pair_gauss.html - "gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential "gran/hertz/history"_pair_gran.html - granular potential with Hertzian interactions "gran/hooke"_pair_gran.html - granular potential with history effects "gran/hooke/history"_pair_gran.html - granular potential without history effects +"gw"_pair_gw.html - +"gw/zbl"_pair_gw.html - "hbond/dreiding/lj"_pair_hbond_dreiding.html - DREIDING hydrogen bonding LJ potential "hbond/dreiding/morse"_pair_hbond_dreiding.html - DREIDING hydrogen bonding Morse potential +"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html - "kim"_pair_kim.html - interface to potentials provided by KIM project +"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html - +"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html - "lcbop"_pair_lcbop.html - long-range bond-order potential (LCBOP) +"lennard/mdf"_pair_mdf.html - "line/lj"_pair_line_lj.html - LJ potential between line segments +"list"_pair_list.html - "lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb "lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent "lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb +"lj/charmm/coul/long/soft"_pair_lj_soft.html - "lj/charmm/coul/msm"_pair_charmm.html - CHARMM with long-range MSM Coulombics +"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html - +"lj/charmmfsw/coul/long"_pair_charmm.html - "lj/class2"_pair_class2.html - COMPASS (class 2) force field with no Coulomb "lj/class2/coul/cut"_pair_class2.html - COMPASS with cutoff Coulomb "lj/class2/coul/long"_pair_class2.html - COMPASS with long-range Coulomb "lj/cubic"_pair_lj_cubic.html - LJ with cubic after inflection point "lj/cut"_pair_lj.html - cutoff Lennard-Jones potential with no Coulomb "lj/cut/coul/cut"_pair_lj.html - LJ with cutoff Coulomb +"lj/cut/coul/cut/soft"_pair_lj_soft.html - "lj/cut/coul/debye"_pair_lj.html - LJ with Debye screening added to Coulomb "lj/cut/coul/dsf"_pair_lj.html - LJ with Coulombics via damped shifted forces "lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulombics -"lj/cut/coul/long/cs"_pair_lj.html - LJ with long-range Coulombics and core/shell +"lj/cut/coul/long/cs"_pair_cs.html - ditto with core/shell adjustments +"lj/cut/coul/long/soft"_pair_lj_soft.html - "lj/cut/coul/msm"_pair_lj.html - LJ with long-range MSM Coulombics +"lj/cut/coul/wolf"_pair_lj.html - "lj/cut/dipole/cut"_pair_dipole.html - point dipoles with cutoff "lj/cut/dipole/long"_pair_dipole.html - point dipoles with long-range Ewald +"lj/cut/soft"_pair_lj_soft.html - +"lj/cut/thole/long"_pair_thole.html - "lj/cut/tip4p/cut"_pair_lj.html - LJ with cutoff Coulomb for TIP4P water "lj/cut/tip4p/long"_pair_lj.html - LJ with long-range Coulomb for TIP4P water +"lj/cut/tip4p/long/soft"_pair_lj_soft.html - "lj/expand"_pair_lj_expand.html - Lennard-Jones for variable size particles +"lj/expand/coul/long"_pair_lj_expand.html - "lj/gromacs"_pair_gromacs.html - GROMACS-style Lennard-Jones potential "lj/gromacs/coul/gromacs"_pair_gromacs.html - GROMACS-style LJ and Coulombic potential "lj/long/coul/long"_pair_lj_long.html - long-range LJ and long-range Coulombics "lj/long/dipole/long"_pair_dipole.html - long-range LJ and long-range point dipoles "lj/long/tip4p/long"_pair_lj_long.html - long-range LJ and long-range Coulomb for TIP4P water +"lj/mdf"_pair_mdf.html - +"lj/sdk"_pair_sdk.html - +"lj/sdk/coul/long"_pair_sdk.html - +"lj/sdk/coul/msm"_pair_sdk.html - +"lj/sf/dipole/sf"_pair_dipole.html - "lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential "lj/smooth/linear"_pair_lj_smooth_linear.html - linear smoothed Lennard-Jones potential "lj96/cut"_pair_lj96.html - Lennard-Jones 9/6 potential @@ -182,32 +231,81 @@ pair"_Commands_pair.html doc page are followed by one or more of "lubricate/poly"_pair_lubricate.html - hydrodynamic lubrication forces with polydispersity "lubricateU"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication Dynamics "lubricateU/poly"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication with polydispersity +"mdpd"_pair_meso.html - +"mdpd/rhosum"_pair_meso.html - "meam"_pair_meam.html - modified embedded atom method (MEAM) +"meam/c"_pair_meam.html - +"meam/spline"_pair_meam_spline.html - +"meam/sw/spline"_pair_meam_sw_spline.html - +"mgpt"_pair_mgpt.html - "mie/cut"_pair_mie.html - Mie potential +"momb"_pair_momb.html - "morse"_pair_morse.html - Morse potential +"morse/smooth/linear"_pair_morse.html - +"morse/soft"_pair_morse.html - +"multi/lucy"_pair_multi_lucy.html - +"multi/lucy/rx"_pair_multi_lucy_rx.html - "nb3b/harmonic"_pair_nb3b_harmonic.html - nonbonded 3-body harmonic potential "nm/cut"_pair_nm.html - N-M potential "nm/cut/coul/cut"_pair_nm.html - N-M potential with cutoff Coulomb "nm/cut/coul/long"_pair_nm.html - N-M potential with long-range Coulombics +"oxdna/coaxstk"_pair_oxdna.html - +"oxdna/excv"_pair_oxdna.html - +"oxdna/hbond"_pair_oxdna.html - +"oxdna/stk"_pair_oxdna.html - +"oxdna/xstk"_pair_oxdna.html - +"oxdna2/coaxstk"_pair_oxdna2.html - +"oxdna2/dh"_pair_oxdna2.html - +"oxdna2/excv"_pair_oxdna2.html - +"oxdna2/hbond"_pair_oxdna2.html - +"oxdna2/stk"_pair_oxdna2.html - +"oxdna2/xstk"_pair_oxdna2.html - "peri/eps"_pair_peri.html - peridynamic EPS potential "peri/lps"_pair_peri.html - peridynamic LPS potential "peri/pmb"_pair_peri.html - peridynamic PMB potential "peri/ves"_pair_peri.html - peridynamic VES potential "polymorphic"_pair_polymorphic.html - polymorphic 3-body potential +"python"_pair_python.html - +"quip"_pair_quip.html - "reax"_pair_reax.html - ReaxFF potential +"reax/c"_pair_reaxc.html - "rebo"_pair_airebo.html - 2nd generation REBO potential of Brenner "resquared"_pair_resquared.html - Everaers RE-Squared ellipsoidal potential +"smd/hertz"_pair_smd_hertz.html - +"smd/tlsph"_pair_smd_tlsph.html - +"smd/tri_surface"_pair_smd_triangulated_surface.html - +"smd/ulsph"_pair_smd_ulsph.html - +"smtbq"_pair_smtbq.html - "snap"_pair_snap.html - SNAP quantum-accurate potential "soft"_pair_soft.html - Soft (cosine) potential +"sph/heatconduction"_pair_sph_heatconduction.html - +"sph/idealgas"_pair_sph_idealgas.html - +"sph/lj"_pair_sph_lj.html - +"sph/rhosum"_pair_sph_rhosum.html - +"sph/taitwater"_pair_sph_taitwater.html - +"sph/taitwater/morris"_pair_sph_taitwater_morris.html - +"spin/dmi"_pair_spin_dmi.html - +"spin/exchange"_pair_spin_exchange.html - +"spin/magelec"_pair_spin_magelec.html - +"spin/neel"_pair_spin_neel.html - +"srp"_pair_srp.html - "sw"_pair_sw.html - Stillinger-Weber 3-body potential "table"_pair_table.html - tabulated pair potential +"table/rx"_pair_table_rx.html - +"tdpd"_pair_meso.html - "tersoff"_pair_tersoff.html - Tersoff 3-body potential "tersoff/mod"_pair_tersoff_mod.html - modified Tersoff 3-body potential +"tersoff/mod/c"_pair_tersoff_mod.html - +"tersoff/table"_pair_tersoff.html - "tersoff/zbl"_pair_tersoff_zbl.html - Tersoff/ZBL 3-body potential +"thole"_pair_thole.html - "tip4p/cut"_pair_coul.html - Coulomb for TIP4P water w/out LJ "tip4p/long"_pair_coul.html - long-range Coulombics for TIP4P water w/out LJ +"tip4p/long/soft"_pair_lj_soft.html - "tri/lj"_pair_tri_lj.html - LJ potential between triangles +"ufm"_pair_ufm.html - "vashishta"_pair_vashishta.html - Vashishta 2-body and 3-body potential +"vashishta/table"_pair_vashishta.html - "yukawa"_pair_yukawa.html - Yukawa potential "yukawa/colloid"_pair_yukawa_colloid.html - screened Yukawa potential for finite-size particles "zbl"_pair_zbl.html - Ziegler-Biersack-Littmark potential :ul From 5f1c77ced256b6097e4e6079d849d88a3f9fab50 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Wed, 10 Oct 2018 10:20:03 -0600 Subject: [PATCH 03/12] tweaks to USER-PTM package doc --- doc/src/Packages_details.txt | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 6efcfd5f62..58145926b9 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -1757,7 +1757,8 @@ Matching methodology. [Supporting info:] -src/USER-PTM: filename starting with ptm_ -> supporting code, other filenames -> commands +src/USER-PTM: filenames not starting with ptm_ -> commands +src/USER-PTM: filenames starting with ptm_ -> supporting code src/USER-PTM/LICENSE "compute ptm/atom"_compute_ptm_atom.html :ul From 36a1ca7e72dfda3883db3f0b545925f9d110df19 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Thu, 11 Oct 2018 08:26:37 -0600 Subject: [PATCH 04/12] updates some one-line style defs --- doc/src/angle_class2.txt | 2 +- doc/src/angle_style.txt | 24 +++++++++--------- doc/src/bond_style.txt | 10 ++++---- doc/src/dihedral_style.txt | 18 +++++++------- doc/src/improper_style.txt | 10 ++++---- doc/src/prd.txt | 50 ++++++++++++++++++++++++-------------- 6 files changed, 64 insertions(+), 50 deletions(-) diff --git a/doc/src/angle_class2.txt b/doc/src/angle_class2.txt index fa5e29582c..5a772f8fa9 100644 --- a/doc/src/angle_class2.txt +++ b/doc/src/angle_class2.txt @@ -7,8 +7,8 @@ :line angle_style class2 command :h3 -angle_style class2/omp command :h3 angle_style class2/kk command :h3 +angle_style class2/omp command :h3 angle_style class2/p6 command :h3 [Syntax:] diff --git a/doc/src/angle_style.txt b/doc/src/angle_style.txt index 68d69d488d..a0bc47ba4c 100644 --- a/doc/src/angle_style.txt +++ b/doc/src/angle_style.txt @@ -68,20 +68,20 @@ doc page. "charmm"_angle_charmm.html - CHARMM angle "class2"_angle_class2.html - COMPASS (class 2) angle -"class2/p6"_angle_class2.html - -"cosine"_angle_cosine.html - cosine angle potential -"cosine/buck6d"_angle_cosine_buck6d.html - -"cosine/delta"_angle_cosine_delta.html - difference of cosines angle potential +"class2/p6"_angle_class2.html - COMPASS (class 2) angle expanded to 6th order +"cosine"_angle_cosine.html - angle with cosine term +"cosine/buck6d"_angle_cosine_buck6d.html - same as cosine with Buckingham term between 1-3 atoms +"cosine/delta"_angle_cosine_delta.html - angle with difference of cosines "cosine/periodic"_angle_cosine_periodic.html - DREIDING angle -"cosine/shift"_angle_cosine_shift.html - -"cosine/shift/exp"_angle_cosine_shift_exp.html - -"cosine/squared"_angle_cosine_squared.html - cosine squared angle potential -"dipole"_angle_dipole.html - -"fourier"_angle_fourier.html - -"fourier/simple"_angle_fourier_simple.html - +"cosine/shift"_angle_cosine_shift.html - angle cosine with a shift +"cosine/shift/exp"_angle_cosine_shift_exp.html - cosine with shift and exponential term in spring constant +"cosine/squared"_angle_cosine_squared.html - angle with cosine squared term +"dipole"_angle_dipole.html - angle that controls orientation of a point dipole +"fourier"_angle_fourier.html - angle with multiple cosine terms +"fourier/simple"_angle_fourier_simple.html - angle with a single cosine term "harmonic"_angle_harmonic.html - harmonic angle -"quartic"_angle_quartic.html - -"sdk"_angle_sdk.html - +"quartic"_angle_quartic.html - angle with cubic and quartic terms +"sdk"_angle_sdk.html - harmonic angle with repulsive SDK pair style between 1-3 atoms "table"_angle_table.html - tabulated by angle :ul :line diff --git a/doc/src/bond_style.txt b/doc/src/bond_style.txt index c9252a8eb3..197a4fb1b6 100644 --- a/doc/src/bond_style.txt +++ b/doc/src/bond_style.txt @@ -76,14 +76,14 @@ bond styles is on the "Commands bond"_Commands_bond.html doc page. "class2"_bond_class2.html - COMPASS (class 2) bond "fene"_bond_fene.html - FENE (finite-extensible non-linear elastic) bond "fene/expand"_bond_fene_expand.html - FENE bonds with variable size particles -"gromos"_bond_gromos.html - +"gromos"_bond_gromos.html - GROMOS force field bond "harmonic"_bond_harmonic.html - harmonic bond -"harmonic/shift"_bond_harmonic_shift.html - -"harmonic/shift/cut"_bond_harmonic_shift_cut.html - +"harmonic/shift"_bond_harmonic_shift.html - shifted harmonic bond +"harmonic/shift/cut"_bond_harmonic_shift_cut.html - shifted harmonic bond with a cutoff "morse"_bond_morse.html - Morse bond "nonlinear"_bond_nonlinear.html - nonlinear bond -"oxdna/fene"_bond_oxdna.html - -"oxdna2/fene"_bond_oxdna.html - +"oxdna/fene"_bond_oxdna.html - modified FENE bond suitable for DNA modeling +"oxdna2/fene"_bond_oxdna.html - same as oxdna but used with different pair styles "quartic"_bond_quartic.html - breakable quartic bond "table"_bond_table.html - tabulated by bond length :ul diff --git a/doc/src/dihedral_style.txt b/doc/src/dihedral_style.txt index 02634c6073..d45d9b488d 100644 --- a/doc/src/dihedral_style.txt +++ b/doc/src/dihedral_style.txt @@ -90,19 +90,19 @@ doc page. "hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions :ul "charmm"_dihedral_charmm.html - CHARMM dihedral -"charmmfsw"_dihedral_charmm.html - +"charmmfsw"_dihedral_charmm.html - CHARMM dihedral with force switching "class2"_dihedral_class2.html - COMPASS (class 2) dihedral -"cosine/shift/exp"_dihedral_cosine_shift_exp.html - -"fourier"_dihedral_fourier.html - +"cosine/shift/exp"_dihedral_cosine_shift_exp.html - dihedral with exponential in spring constant +"fourier"_dihedral_fourier.html - dihedral with multiple cosine terms "harmonic"_dihedral_harmonic.html - harmonic dihedral "helix"_dihedral_helix.html - helix dihedral -"multi/harmonic"_dihedral_multi_harmonic.html - multi-harmonic dihedral -"nharmonic"_dihedral_nharmonic.html - +"multi/harmonic"_dihedral_multi_harmonic.html - dihedral with 5 harmonic terms +"nharmonic"_dihedral_nharmonic.html - same as multi-harmonic with N terms "opls"_dihedral_opls.html - OPLS dihedral -"quadratic"_dihedral_quadratic.html - -"spherical"_dihedral_spherical.html - -"table"_dihedral_table.html - -"table/cut"_dihedral_table_cut.html - :ul +"quadratic"_dihedral_quadratic.html - dihedral with quadratic term in angle +"spherical"_dihedral_spherical.html - dihedral which includes angle terms to avoid singularities +"table"_dihedral_table.html - tabulated dihedral +"table/cut"_dihedral_table_cut.html - tabulated dihedral with analytic cutoff :ul :line diff --git a/doc/src/improper_style.txt b/doc/src/improper_style.txt index 28b3b440b2..f315509fe4 100644 --- a/doc/src/improper_style.txt +++ b/doc/src/improper_style.txt @@ -69,13 +69,13 @@ doc page. "hybrid"_improper_hybrid.html - define multiple styles of improper interactions :ul "class2"_improper_class2.html - COMPASS (class 2) improper -"cossq"_improper_cossq.html - +"cossq"_improper_cossq.html - improper with a cosine squared term "cvff"_improper_cvff.html - CVFF improper -"distance"_improper_distance.html - -"fourier"_improper_fourier.html - +"distance"_improper_distance.html - improper based on distance between atom planes +"fourier"_improper_fourier.html - improper with multiple cosine terms "harmonic"_improper_harmonic.html - harmonic improper -"inversion/harmonic"_improper_inversion_harmonic.html - -"ring"_improper_ring.html - +"inversion/harmonic"_improper_inversion_harmonic.html - harmonic improper with Wilson-Decius out-of-plane definition +"ring"_improper_ring.html - improper which prevents planar conformations "umbrella"_improper_umbrella.html - DREIDING improper :ul :line diff --git a/doc/src/prd.txt b/doc/src/prd.txt index f71f285336..43c0d309c8 100644 --- a/doc/src/prd.txt +++ b/doc/src/prd.txt @@ -48,11 +48,12 @@ replicas of a system. One or more replicas can be used. The total number of steps {N} to run can be interpreted in one of two ways; see discussion of the {time} keyword below. -PRD is described in "this paper"_#Voter1998 by Art Voter. It is a method -for performing accelerated dynamics that is suitable for -infrequent-event systems that obey first-order kinetics. A good -overview of accelerated dynamics methods for such systems in given in -"this review paper"_#Voter2002prd from the same group. To quote from the +PRD is described in "(Voter1998)"_#Voter1998 by Art Voter. Similar to +global or local hyperdynamics (HD), PRD is a method for performing +accelerated dynamics that is suitable for infrequent-event systems +that obey first-order kinetics. A good overview of accelerated +dynamics methods for such systems in given in this review paper +"(Voter2002)"_#Voter2002prd from Art's group. To quote from the paper: "The dynamical evolution is characterized by vibrational excursions within a potential basin, punctuated by occasional transitions between basins." The transition probability is @@ -61,15 +62,27 @@ Running multiple replicas gives an effective enhancement in the timescale spanned by the multiple simulations, while waiting for an event to occur. -Each replica runs on a partition of one or more processors. Processor -partitions are defined at run-time using the "-partition command-line -switch"_Run_options.html. Note that if you have MPI installed, you -can run a multi-replica simulation with more replicas (partitions) -than you have physical processors, e.g you can run a 10-replica -simulation on one or two processors. However for PRD, this makes -little sense, since running a replica on virtual instead of physical -processors,offers no effective parallel speed-up in searching for -infrequent events. See the "Howto replica"_Howto_replica.html doc +Both PRD and HD produce a time-accurate trajectory that effectively +extends the timescale over which a system can be simulated, but they +do it differently. PRD creates Nr replicas of the system and runs +dynamics on each independently with a normal unbiased potential until +an event occurs in one of the replicas. The time between events is +reduced by a factor of Nr replicas. HD uses a single replica of the +system and accelerates time by biasing the interaction potential in a +manner such that each timestep is effectively longer. For both +methods, per wall-clock second, more physical time elapses and more +events occur. See the "hyper"_hyper.html doc page for more info about +HD. + +In PRD, each replica runs on a partition of one or more processors. +Processor partitions are defined at run-time using the "-partition +command-line switch"_Run_options.html. Note that if you have MPI +installed, you can run a multi-replica simulation with more replicas +(partitions) than you have physical processors, e.g you can run a +10-replica simulation on one or two processors. However for PRD, this +makes little sense, since running a replica on virtual instead of +physical processors,offers no effective parallel speed-up in searching +for infrequent events. See the "Howto replica"_Howto_replica.html doc page for further discussion. When a PRD simulation is performed, it is assumed that each replica is @@ -78,8 +91,8 @@ I.e. the simulation domain, the number of atoms, the interaction potentials, etc should be the same for every replica. A PRD run has several stages, which are repeated each time an "event" -occurs in one of the replicas, as defined below. The logic for a PRD -run is as follows: +occurs in one of the replicas, as explained below. The logic for a +PRD run is as follows: while (time remains): dephase for n_dephase*t_dephase steps @@ -129,7 +142,8 @@ Minimization parameters may be set via the PRD command. The latter are the settings that would be used with the "minimize"_minimize.html command. Note that typically, you do not need to perform a highly-converged minimization to detect a transition -event. +event, though you may need to in order to prevent a set of atoms in +the system from relaxing to a saddle point. The event check is performed by a compute with the specified {compute-ID}. Currently there is only one compute that works with the @@ -307,7 +321,7 @@ deposit"_fix_deposit.html. "min_modify"_min_modify.html, "min_style"_min_style.html, "run_style"_run_style.html, "minimize"_minimize.html, "velocity"_velocity.html, "temper"_temper.html, "neb"_neb.html, -"tad"_tad.html +"tad"_tad.html, "hyper"_hyper.html [Default:] From d1f260a76552760583ce74142c8773863cc31450 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Thu, 11 Oct 2018 08:28:10 -0600 Subject: [PATCH 05/12] undo changes to PRD doc from another branch --- doc/src/prd.txt | 50 ++++++++++++++++++------------------------------- 1 file changed, 18 insertions(+), 32 deletions(-) diff --git a/doc/src/prd.txt b/doc/src/prd.txt index 43c0d309c8..f71f285336 100644 --- a/doc/src/prd.txt +++ b/doc/src/prd.txt @@ -48,12 +48,11 @@ replicas of a system. One or more replicas can be used. The total number of steps {N} to run can be interpreted in one of two ways; see discussion of the {time} keyword below. -PRD is described in "(Voter1998)"_#Voter1998 by Art Voter. Similar to -global or local hyperdynamics (HD), PRD is a method for performing -accelerated dynamics that is suitable for infrequent-event systems -that obey first-order kinetics. A good overview of accelerated -dynamics methods for such systems in given in this review paper -"(Voter2002)"_#Voter2002prd from Art's group. To quote from the +PRD is described in "this paper"_#Voter1998 by Art Voter. It is a method +for performing accelerated dynamics that is suitable for +infrequent-event systems that obey first-order kinetics. A good +overview of accelerated dynamics methods for such systems in given in +"this review paper"_#Voter2002prd from the same group. To quote from the paper: "The dynamical evolution is characterized by vibrational excursions within a potential basin, punctuated by occasional transitions between basins." The transition probability is @@ -62,27 +61,15 @@ Running multiple replicas gives an effective enhancement in the timescale spanned by the multiple simulations, while waiting for an event to occur. -Both PRD and HD produce a time-accurate trajectory that effectively -extends the timescale over which a system can be simulated, but they -do it differently. PRD creates Nr replicas of the system and runs -dynamics on each independently with a normal unbiased potential until -an event occurs in one of the replicas. The time between events is -reduced by a factor of Nr replicas. HD uses a single replica of the -system and accelerates time by biasing the interaction potential in a -manner such that each timestep is effectively longer. For both -methods, per wall-clock second, more physical time elapses and more -events occur. See the "hyper"_hyper.html doc page for more info about -HD. - -In PRD, each replica runs on a partition of one or more processors. -Processor partitions are defined at run-time using the "-partition -command-line switch"_Run_options.html. Note that if you have MPI -installed, you can run a multi-replica simulation with more replicas -(partitions) than you have physical processors, e.g you can run a -10-replica simulation on one or two processors. However for PRD, this -makes little sense, since running a replica on virtual instead of -physical processors,offers no effective parallel speed-up in searching -for infrequent events. See the "Howto replica"_Howto_replica.html doc +Each replica runs on a partition of one or more processors. Processor +partitions are defined at run-time using the "-partition command-line +switch"_Run_options.html. Note that if you have MPI installed, you +can run a multi-replica simulation with more replicas (partitions) +than you have physical processors, e.g you can run a 10-replica +simulation on one or two processors. However for PRD, this makes +little sense, since running a replica on virtual instead of physical +processors,offers no effective parallel speed-up in searching for +infrequent events. See the "Howto replica"_Howto_replica.html doc page for further discussion. When a PRD simulation is performed, it is assumed that each replica is @@ -91,8 +78,8 @@ I.e. the simulation domain, the number of atoms, the interaction potentials, etc should be the same for every replica. A PRD run has several stages, which are repeated each time an "event" -occurs in one of the replicas, as explained below. The logic for a -PRD run is as follows: +occurs in one of the replicas, as defined below. The logic for a PRD +run is as follows: while (time remains): dephase for n_dephase*t_dephase steps @@ -142,8 +129,7 @@ Minimization parameters may be set via the PRD command. The latter are the settings that would be used with the "minimize"_minimize.html command. Note that typically, you do not need to perform a highly-converged minimization to detect a transition -event, though you may need to in order to prevent a set of atoms in -the system from relaxing to a saddle point. +event. The event check is performed by a compute with the specified {compute-ID}. Currently there is only one compute that works with the @@ -321,7 +307,7 @@ deposit"_fix_deposit.html. "min_modify"_min_modify.html, "min_style"_min_style.html, "run_style"_run_style.html, "minimize"_minimize.html, "velocity"_velocity.html, "temper"_temper.html, "neb"_neb.html, -"tad"_tad.html, "hyper"_hyper.html +"tad"_tad.html [Default:] From 9bca5ae6071297d653f6cc0f89a82eb15dca106d Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Thu, 11 Oct 2018 10:29:51 -0600 Subject: [PATCH 06/12] added one-line pair descriptions --- doc/src/angle_cosine_buck6d.txt | 8 +-- doc/src/bond_oxdna.txt | 63 +++++++++++++++--------- doc/src/pair_style.txt | 87 ++++++++++++++++----------------- 3 files changed, 85 insertions(+), 73 deletions(-) diff --git a/doc/src/angle_cosine_buck6d.txt b/doc/src/angle_cosine_buck6d.txt index 54709c1370..686e123ca0 100644 --- a/doc/src/angle_cosine_buck6d.txt +++ b/doc/src/angle_cosine_buck6d.txt @@ -38,10 +38,10 @@ Theta0 (degrees) :ul Theta0 is specified in degrees, but LAMMPS converts it to radians internally. -Additional to the cosine term the {cosine/buck6d} angle style computes -the short range (vdW) interaction belonging to the -"pair_buck6d"_pair_buck6d_coul_gauss.html between the end atoms of -the angle. For this reason this angle style only works in combination +Additional to the cosine term the {cosine/buck6d} angle style computes +the short range (vdW) interaction belonging to the +"pair_buck6d"_pair_buck6d_coul_gauss.html between the end atoms of the +angle. For this reason this angle style only works in combination with the "pair_buck6d"_pair_buck6d_coul_gauss.html styles and needs the "special_bonds"_special_bonds.html 1-3 interactions to be weighted 0.0 to prevent double counting. diff --git a/doc/src/bond_oxdna.txt b/doc/src/bond_oxdna.txt index 1944f7027a..724951f961 100644 --- a/doc/src/bond_oxdna.txt +++ b/doc/src/bond_oxdna.txt @@ -28,34 +28,44 @@ The {oxdna/fene} and {oxdna2/fene} bond styles use the potential :c,image(Eqs/bond_oxdna_fene.jpg) -to define a modified finite extensible nonlinear elastic (FENE) potential -"(Ouldridge)"_#oxdna_fene to model the connectivity of the phosphate backbone -in the oxDNA force field for coarse-grained modelling of DNA. +to define a modified finite extensible nonlinear elastic (FENE) +potential "(Ouldridge)"_#oxdna_fene to model the connectivity of the +phosphate backbone in the oxDNA force field for coarse-grained +modelling of DNA. The following coefficients must be defined for the bond type via the -"bond_coeff"_bond_coeff.html command as given in the above example, or in -the data file or restart files read by the "read_data"_read_data.html -or "read_restart"_read_restart.html commands: +"bond_coeff"_bond_coeff.html command as given in the above example, or +in the data file or restart files read by the +"read_data"_read_data.html or "read_restart"_read_restart.html +commands: epsilon (energy) Delta (distance) r0 (distance) :ul -NOTE: The oxDNA bond style has to be used together with the corresponding oxDNA pair styles -for excluded volume interaction {oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk} -and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of -"pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2 "(Snodin)"_#oxdna2 bond style the analogous pair styles and an additional Debye-Hueckel pair -style {oxdna2/dh} have to be defined. -The coefficients in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model. +NOTE: The oxDNA bond style has to be used together with the +corresponding oxDNA pair styles for excluded volume interaction +{oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk} and +coaxial stacking interaction {oxdna/coaxstk} as well as +hydrogen-bonding interaction {oxdna/hbond} (see also documentation of +"pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2 +"(Snodin)"_#oxdna2 bond style the analogous pair styles and an +additional Debye-Hueckel pair style {oxdna2/dh} have to be defined. +The coefficients in the above example have to be kept fixed and cannot +be changed without reparametrizing the entire model. -Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. -A simple python setup tool which creates single straight or helical DNA strands, -DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/. +Example input and data files for DNA duplexes can be found in +examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. A simple python +setup tool which creates single straight or helical DNA strands, DNA +duplexes or arrays of DNA duplexes can be found in +examples/USER/cgdna/util/. -Please cite "(Henrich)"_#Henrich2 and the relevant oxDNA articles in any publication that uses this implementation. -The article contains more information on the model, the structure of the input file, the setup tool -and the performance of the LAMMPS-implementation of oxDNA. -The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf. +Please cite "(Henrich)"_#Henrich2 and the relevant oxDNA articles in +any publication that uses this implementation. The article contains +more information on the model, the structure of the input file, the +setup tool and the performance of the LAMMPS-implementation of oxDNA. +The preprint version of the article can be found +"here"_PDF/USER-CGDNA.pdf. :line @@ -65,20 +75,25 @@ This bond style can only be used if LAMMPS was built with the USER-CGDNA package and the MOLECULE and ASPHERE package. See the "Build package"_Build_package.html doc page for more info. - [Related commands:] -"pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html +"pair_style oxdna/excv"_pair_oxdna.html, "pair_style +oxdna2/excv"_pair_oxdna2.html, "fix +nve/dotc/langevin"_fix_nve_dotc_langevin.html, +"bond_coeff"_bond_coeff.html [Default:] none :line :link(Henrich2) -[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018). +[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, +T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018). :link(oxdna_fene) -[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011). +[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, +J. Chem. Phys. 134, 085101 (2011). :link(oxdna2) -[(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015). +[(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al., +J. Chem. Phys. 142, 234901 (2015). diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt index c728445952..f1713f5270 100644 --- a/doc/src/pair_style.txt +++ b/doc/src/pair_style.txt @@ -101,89 +101,86 @@ pair"_Commands_pair.html doc page are followed by one or more of "zero"_pair_zero.html - neighbor list but no interactions :ul "adp"_pair_adp.html - angular dependent potential (ADP) of Mishin -"agni"_pair_agni.html - +"agni"_pair_agni.html - machine learned potential mapping atomic environment to forces "airebo"_pair_airebo.html - AIREBO potential of Stuart "airebo/morse"_pair_airebo.html - AIREBO with Morse instead of LJ "atm"_pair_atm.html - Axilrod-Teller-Muto potential -"awpmd/cut"_pair_awpmd.html - +"awpmd/cut"_pair_awpmd.html - Antisymmetrized Wave Packet MD potential for atoms and electrons "beck"_pair_beck.html - Beck potential "body/nparticle"_pair_body_nparticle.html - interactions between body particles -"body/rounded/polygon"_pair_body_rounded_polygon.html - -"body/rounded/polyhedron"_pair_body_rounded_polyhedron.html - +"body/rounded/polygon"_pair_body_rounded_polygon.html - granular-style 2d polygon potential +"body/rounded/polyhedron"_pair_body_rounded_polyhedron.html - granular-style 3d polyhedron potential "bop"_pair_bop.html - BOP potential of Pettifor "born"_pair_born.html - Born-Mayer-Huggins potential -"born/coul/dsf"_pair_born.html - -"born/coul/dsf/cs"_pair_cs.html - -"born/coul/long"_pair_born.html - Born-Mayer-Huggins with long-range Coulombics -"born/coul/long/cs"_pair_cs.html - -"born/coul/long/cs"_pair_cs.html - Born-Mayer-Huggins with long-range Coulombics and core/shell -"born/coul/msm"_pair_born.html - Born-Mayer-Huggins with long-range MSM Coulombics -"born/coul/wolf"_pair_born.html - Born-Mayer-Huggins with Coulombics via Wolf potential -"born/coul/wolf/cs"_pair_cs.html - +"born/coul/dsf"_pair_born.html - Born with damped-shifted-force model +"born/coul/dsf/cs"_pair_cs.html - Born with damped-shifted-force and core/shell model +"born/coul/long"_pair_born.html - Born with long-range Coulombics +"born/coul/long/cs"_pair_cs.html - Born with long-range Coulombics and core/shell +"born/coul/msm"_pair_born.html - Born with long-range MSM Coulombics +"born/coul/wolf"_pair_born.html - Born with Wolf potential for Coulombics +"born/coul/wolf/cs"_pair_cs.html - Born with Wolf potential for Coulombics and core/shell model "brownian"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics "brownian/poly"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics with polydispersity "buck"_pair_buck.html - Buckingham potential "buck/coul/cut"_pair_buck.html - Buckingham with cutoff Coulomb "buck/coul/long"_pair_buck.html - Buckingham with long-range Coulombics "buck/coul/long/cs"_pair_cs.html - Buckingham with long-range Coulombics and core/shell -"buck/coul/msm"_pair_buck.html - Buckingham long-range MSM Coulombics +"buck/coul/msm"_pair_buck.html - Buckingham with long-range MSM Coulombics "buck/long/coul/long"_pair_buck_long.html - long-range Buckingham with long-range Coulombics -"buck/mdf"_pair_mdf.html - -"buck6d/coul/gauss/dsf"_pair_buck6d_coul_gauss.html - -"buck6d/coul/gauss/dsf"_pair_buck6d_coul_gauss.html - -"buck6d/coul/gauss/long"_pair_buck6d_coul_gauss.html - -"buck6d/coul/gauss/long"_pair_buck6d_coul_gauss.html - +"buck/mdf"_pair_mdf.html - Buckingham with a taper function +"buck6d/coul/gauss/dsf"_pair_buck6d_coul_gauss.html - dispersion-damped Buckingham with damped-shift-force model +"buck6d/coul/gauss/long"_pair_buck6d_coul_gauss.html - dispersion-damped Buckingham with long-range Coulombics "colloid"_pair_colloid.html - integrated colloidal potential "comb"_pair_comb.html - charge-optimized many-body (COMB) potential "comb3"_pair_comb.html - charge-optimized many-body (COMB3) potential "coul/cut"_pair_coul.html - cutoff Coulombic potential -"coul/cut/soft"_pair_lj_soft.html - +"coul/cut/soft"_pair_lj_soft.html - Coulombic potential with a soft core "coul/debye"_pair_coul.html - cutoff Coulombic potential with Debye screening -"coul/diel"_pair_coul_diel.html - -"coul/dsf"_pair_coul.html - Coulombics via damped shifted forces +"coul/diel"_pair_coul_diel.html - Coulomb potential with dielectric permittivity +"coul/dsf"_pair_coul.html - Coulombics with damped-shifted-force model "coul/long"_pair_coul.html - long-range Coulombic potential "coul/long/cs"_pair_cs.html - long-range Coulombic potential and core/shell -"coul/long/soft"_pair_lj_soft.html - +"coul/long/soft"_pair_lj_soft.html - long-range Coulombic potential with a soft core "coul/msm"_pair_coul.html - long-range MSM Coulombics -"coul/shield"_pair_coul_shield.html - +"coul/shield"_pair_coul_shield.html - Coulombics for boron nitride for use with "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html potential "coul/streitz"_pair_coul.html - Coulombics via Streitz/Mintmire Slater orbitals "coul/wolf"_pair_coul.html - Coulombics via Wolf potential "coul/wolf/cs"_pair_cs.html - ditto with core/shell adjustments "dpd"_pair_dpd.html - dissipative particle dynamics (DPD) -"dpd/fdt"_pair_dpd_fdt.html - -"dpd/fdt/energy"_pair_dpd_fdt.html - -"dpd/tstat"_pair_dpd.html - DPD thermostatting +"dpd/fdt"_pair_dpd_fdt.html - DPD for constant temperature and pressure +"dpd/fdt/energy"_pair_dpd_fdt.html - DPD for constant energy and enthalpy +"dpd/tstat"_pair_dpd.html - pair-wise DPD thermostatting "dsmc"_pair_dsmc.html - Direct Simulation Monte Carlo (DSMC) "eam"_pair_eam.html - embedded atom method (EAM) "eam/alloy"_pair_eam.html - alloy EAM -"eam/cd"_pair_eam.html - -"eam/cd/old"_pair_eam.html - +"eam/cd"_pair_eam.html - concentration-dependent EAM +"eam/cd/old"_pair_eam.html - older two-site model for concentration-dependent EAM "eam/fs"_pair_eam.html - Finnis-Sinclair EAM -"edip"_pair_edip.html - -"edip/multi"_pair_edip.html - -"edpd"_pair_meso.html - -"eff/cut"_pair_eff.html - +"edip"_pair_edip.html - three-body EDIP potential +"edip/multi"_pair_edip.html - multi-element EDIP potential +"edpd"_pair_meso.html - eDPD particle interactions +"eff/cut"_pair_eff.html - electron force field with a cutoff "eim"_pair_eim.html - embedded ion method (EIM) -"exp6/rx"_pair_exp6_rx.html - -"extep"_pair_extep.html - +"exp6/rx"_pair_exp6_rx.html - reactive DPD potential +"extep"_pair_extep.html - extended Tersoff potential "gauss"_pair_gauss.html - Gaussian potential -"gauss/cut"_pair_gauss.html - +"gauss/cut"_pair_gauss.html - generalized Gaussian potential "gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential "gran/hertz/history"_pair_gran.html - granular potential with Hertzian interactions "gran/hooke"_pair_gran.html - granular potential with history effects "gran/hooke/history"_pair_gran.html - granular potential without history effects -"gw"_pair_gw.html - -"gw/zbl"_pair_gw.html - +"gw"_pair_gw.html - Gao-Weber potential +"gw/zbl"_pair_gw.html - Gao-Weber potential with a repulsive ZBL core "hbond/dreiding/lj"_pair_hbond_dreiding.html - DREIDING hydrogen bonding LJ potential "hbond/dreiding/morse"_pair_hbond_dreiding.html - DREIDING hydrogen bonding Morse potential -"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html - +"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html - registry-dependent interlayer potential (ILP) "kim"_pair_kim.html - interface to potentials provided by KIM project -"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html - -"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html - +"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html - Kolmogorov-Crespi (KC) potential with no simplifications +"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html - Kolmogorov-Crespi (KC) potential with normals along z-axis "lcbop"_pair_lcbop.html - long-range bond-order potential (LCBOP) -"lennard/mdf"_pair_mdf.html - +"lennard/mdf"_pair_mdf.html - LJ potential in A/B form with a taper function "line/lj"_pair_line_lj.html - LJ potential between line segments -"list"_pair_list.html - +"list"_pair_list.html - potential between pairs of atoms explicitly listed in an input file "lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb "lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent "lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb @@ -219,7 +216,7 @@ pair"_Commands_pair.html doc page are followed by one or more of "lj/long/coul/long"_pair_lj_long.html - long-range LJ and long-range Coulombics "lj/long/dipole/long"_pair_dipole.html - long-range LJ and long-range point dipoles "lj/long/tip4p/long"_pair_lj_long.html - long-range LJ and long-range Coulomb for TIP4P water -"lj/mdf"_pair_mdf.html - +"lj/mdf"_pair_mdf.html - LJ potential with a taper function "lj/sdk"_pair_sdk.html - "lj/sdk/coul/long"_pair_sdk.html - "lj/sdk/coul/msm"_pair_sdk.html - @@ -231,7 +228,7 @@ pair"_Commands_pair.html doc page are followed by one or more of "lubricate/poly"_pair_lubricate.html - hydrodynamic lubrication forces with polydispersity "lubricateU"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication Dynamics "lubricateU/poly"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication with polydispersity -"mdpd"_pair_meso.html - +"mdpd"_pair_meso.html - mDPD particle interactions "mdpd/rhosum"_pair_meso.html - "meam"_pair_meam.html - modified embedded atom method (MEAM) "meam/c"_pair_meam.html - @@ -292,7 +289,7 @@ pair"_Commands_pair.html doc page are followed by one or more of "sw"_pair_sw.html - Stillinger-Weber 3-body potential "table"_pair_table.html - tabulated pair potential "table/rx"_pair_table_rx.html - -"tdpd"_pair_meso.html - +"tdpd"_pair_meso.html - tDPD particle interactions "tersoff"_pair_tersoff.html - Tersoff 3-body potential "tersoff/mod"_pair_tersoff_mod.html - modified Tersoff 3-body potential "tersoff/mod/c"_pair_tersoff_mod.html - From f5206d2f7bd780cc1470951dff3fdc43d4c98da8 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Tue, 16 Oct 2018 13:35:44 -0600 Subject: [PATCH 07/12] more one-liner in pair_style doc page --- doc/src/pair_style.txt | 60 +++++++++++++++++++++--------------------- 1 file changed, 30 insertions(+), 30 deletions(-) diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt index f1713f5270..14e3f79215 100644 --- a/doc/src/pair_style.txt +++ b/doc/src/pair_style.txt @@ -184,64 +184,64 @@ pair"_Commands_pair.html doc page are followed by one or more of "lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb "lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent "lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb -"lj/charmm/coul/long/soft"_pair_lj_soft.html - +"lj/charmm/coul/long/soft"_pair_lj_soft.html - CHARMM with long-range Coulomb and a soft core "lj/charmm/coul/msm"_pair_charmm.html - CHARMM with long-range MSM Coulombics -"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html - -"lj/charmmfsw/coul/long"_pair_charmm.html - +"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html - CHARMM with force switching and shifting +"lj/charmmfsw/coul/long"_pair_charmm.html - CHARMM with force switching and long-rnage Coulombics "lj/class2"_pair_class2.html - COMPASS (class 2) force field with no Coulomb "lj/class2/coul/cut"_pair_class2.html - COMPASS with cutoff Coulomb "lj/class2/coul/long"_pair_class2.html - COMPASS with long-range Coulomb "lj/cubic"_pair_lj_cubic.html - LJ with cubic after inflection point "lj/cut"_pair_lj.html - cutoff Lennard-Jones potential with no Coulomb "lj/cut/coul/cut"_pair_lj.html - LJ with cutoff Coulomb -"lj/cut/coul/cut/soft"_pair_lj_soft.html - +"lj/cut/coul/cut/soft"_pair_lj_soft.html - LJ with cutoff Coulomb with a soft core "lj/cut/coul/debye"_pair_lj.html - LJ with Debye screening added to Coulomb "lj/cut/coul/dsf"_pair_lj.html - LJ with Coulombics via damped shifted forces "lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulombics "lj/cut/coul/long/cs"_pair_cs.html - ditto with core/shell adjustments -"lj/cut/coul/long/soft"_pair_lj_soft.html - +"lj/cut/coul/long/soft"_pair_lj_soft.html - LJ with long-range Coulombics with a soft core "lj/cut/coul/msm"_pair_lj.html - LJ with long-range MSM Coulombics -"lj/cut/coul/wolf"_pair_lj.html - +"lj/cut/coul/wolf"_pair_lj.html - LJ with Coulombics via Wolf potential "lj/cut/dipole/cut"_pair_dipole.html - point dipoles with cutoff "lj/cut/dipole/long"_pair_dipole.html - point dipoles with long-range Ewald -"lj/cut/soft"_pair_lj_soft.html - -"lj/cut/thole/long"_pair_thole.html - +"lj/cut/soft"_pair_lj_soft.html - LJ with a soft core +"lj/cut/thole/long"_pair_thole.html - LJ with Coulomibics with thole damping "lj/cut/tip4p/cut"_pair_lj.html - LJ with cutoff Coulomb for TIP4P water "lj/cut/tip4p/long"_pair_lj.html - LJ with long-range Coulomb for TIP4P water -"lj/cut/tip4p/long/soft"_pair_lj_soft.html - +"lj/cut/tip4p/long/soft"_pair_lj_soft.html - LJ with cutoff Coulomb for TIP4P water with a soft core "lj/expand"_pair_lj_expand.html - Lennard-Jones for variable size particles -"lj/expand/coul/long"_pair_lj_expand.html - +"lj/expand/coul/long"_pair_lj_expand.html - Lennard-Jones for variable size particles with long-range Coulombics "lj/gromacs"_pair_gromacs.html - GROMACS-style Lennard-Jones potential "lj/gromacs/coul/gromacs"_pair_gromacs.html - GROMACS-style LJ and Coulombic potential "lj/long/coul/long"_pair_lj_long.html - long-range LJ and long-range Coulombics "lj/long/dipole/long"_pair_dipole.html - long-range LJ and long-range point dipoles -"lj/long/tip4p/long"_pair_lj_long.html - long-range LJ and long-range Coulomb for TIP4P water +"lj/long/tip4p/long"_pair_lj_long.html - long-range LJ and long-range Coulombics for TIP4P water "lj/mdf"_pair_mdf.html - LJ potential with a taper function -"lj/sdk"_pair_sdk.html - -"lj/sdk/coul/long"_pair_sdk.html - -"lj/sdk/coul/msm"_pair_sdk.html - -"lj/sf/dipole/sf"_pair_dipole.html - +"lj/sdk"_pair_sdk.html - LJ for SDK coarse-graining +"lj/sdk/coul/long"_pair_sdk.html - LJ for SDK coarse-graining with long-range Coulombics +"lj/sdk/coul/msm"_pair_sdk.html - LJ for SDK coarse-graining with long-range Coulombics via MSM +"lj/sf/dipole/sf"_pair_dipole.html - LJ with dipole interaction with shifted forces "lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential -"lj/smooth/linear"_pair_lj_smooth_linear.html - linear smoothed Lennard-Jones potential +"lj/smooth/linear"_pair_lj_smooth_linear.html - linear smoothed LJ potential "lj96/cut"_pair_lj96.html - Lennard-Jones 9/6 potential "lubricate"_pair_lubricate.html - hydrodynamic lubrication forces "lubricate/poly"_pair_lubricate.html - hydrodynamic lubrication forces with polydispersity "lubricateU"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication Dynamics "lubricateU/poly"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication with polydispersity "mdpd"_pair_meso.html - mDPD particle interactions -"mdpd/rhosum"_pair_meso.html - -"meam"_pair_meam.html - modified embedded atom method (MEAM) -"meam/c"_pair_meam.html - -"meam/spline"_pair_meam_spline.html - -"meam/sw/spline"_pair_meam_sw_spline.html - -"mgpt"_pair_mgpt.html - +"mdpd/rhosum"_pair_meso.html - mDPD particle interactions for mass density +"meam"_pair_meam.html - modified embedded atom method (MEAM) in Fortran +"meam/c"_pair_meam.html - modified embedded atom method (MEAM) in C +"meam/spline"_pair_meam_spline.html - splined version of MEAM +"meam/sw/spline"_pair_meam_sw_spline.html - splined version of MEAM with a Stillinger-Weber term +"mgpt"_pair_mgpt.html - simplified model generalized pseudopotential theory (MGPT) potential "mie/cut"_pair_mie.html - Mie potential -"momb"_pair_momb.html - +"momb"_pair_momb.html - Many-Body Metal-Organic (MOMB) force field "morse"_pair_morse.html - Morse potential -"morse/smooth/linear"_pair_morse.html - -"morse/soft"_pair_morse.html - -"multi/lucy"_pair_multi_lucy.html - -"multi/lucy/rx"_pair_multi_lucy_rx.html - +"morse/smooth/linear"_pair_morse.html - linear smoothed Morse potential +"morse/soft"_pair_morse.html - Morse potential with a soft core +"multi/lucy"_pair_multi_lucy.html - DPD potential with density-dependent force +"multi/lucy/rx"_pair_multi_lucy_rx.html - reactive DPD potential with density-dependent force "nb3b/harmonic"_pair_nb3b_harmonic.html - nonbonded 3-body harmonic potential "nm/cut"_pair_nm.html - N-M potential "nm/cut/coul/cut"_pair_nm.html - N-M potential with cutoff Coulomb @@ -264,8 +264,8 @@ pair"_Commands_pair.html doc page are followed by one or more of "polymorphic"_pair_polymorphic.html - polymorphic 3-body potential "python"_pair_python.html - "quip"_pair_quip.html - -"reax"_pair_reax.html - ReaxFF potential -"reax/c"_pair_reaxc.html - +"reax"_pair_reax.html - ReaxFF potential in Fortran +"reax/c"_pair_reaxc.html - ReaxFF potential in C "rebo"_pair_airebo.html - 2nd generation REBO potential of Brenner "resquared"_pair_resquared.html - Everaers RE-Squared ellipsoidal potential "smd/hertz"_pair_smd_hertz.html - @@ -295,7 +295,7 @@ pair"_Commands_pair.html doc page are followed by one or more of "tersoff/mod/c"_pair_tersoff_mod.html - "tersoff/table"_pair_tersoff.html - "tersoff/zbl"_pair_tersoff_zbl.html - Tersoff/ZBL 3-body potential -"thole"_pair_thole.html - +"thole"_pair_thole.html - Coulomb interactions with thole damping "tip4p/cut"_pair_coul.html - Coulomb for TIP4P water w/out LJ "tip4p/long"_pair_coul.html - long-range Coulombics for TIP4P water w/out LJ "tip4p/long/soft"_pair_lj_soft.html - From 1c994bda469704101abc907e89ad033e30c1f32d Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Tue, 16 Oct 2018 17:35:38 -0600 Subject: [PATCH 08/12] corrections to fix neb doc page --- doc/src/fix_neb.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/src/fix_neb.txt b/doc/src/fix_neb.txt index 521dfff12b..410ab3d4d1 100644 --- a/doc/src/fix_neb.txt +++ b/doc/src/fix_neb.txt @@ -35,7 +35,7 @@ keyword = {parallel} or {perp} or {end} :l fix 1 active neb 10.0 fix 2 all neb 1.0 perp 1.0 end last fix 2 all neb 1.0 perp 1.0 end first 1.0 end last 1.0 -fix 1 all neb 1.0 nudge ideal end last/efirst 1 :pre +fix 1 all neb 1.0 parallel ideal end last/efirst 1 :pre [Description:] @@ -212,7 +212,7 @@ page for more info. [Default:] -The option defaults are nudge = neigh, perp = 0.0, ends is not +The option defaults are parallel = neigh, perp = 0.0, ends is not specified (no inter-replica force on the end replicas). :line From 07a499fcc18784765b86a71dfb405ddafd722d19 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 20 Oct 2018 10:01:55 -0400 Subject: [PATCH 09/12] improve check for missing styles in lammps.book --- doc/Makefile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/Makefile b/doc/Makefile index e4ba2fe6a1..6ab89cd5af 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -123,9 +123,9 @@ pdf: utils/txt2html/txt2html.exe cd ..; \ ../utils/txt2html/txt2html.exe -b *.txt; \ htmldoc --batch lammps.book; \ - for s in `echo *.txt | sed -e 's,\.txt,\.html,g'` ; \ - do grep -q $$s lammps.book || \ - echo doc file $$s missing in src/lammps.book; done; \ + for s in `echo *.txt | sed -e 's/ \(pairs\|bonds\|angles\|dihedrals\|impropers\|commands_list\|fixes\|computes\).txt/ /g' | sed -e 's,\.txt,\.html,g'` ; \ + do grep -q ^$$s lammps.book || \ + echo WARNING: doc file $$s missing in src/lammps.book; done; \ rm *.html; \ ) From c0dd1878027878ecc544708ca8c4cf10b7ff2e91 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 21 Oct 2018 18:38:46 -0400 Subject: [PATCH 10/12] make sure all pictures are includes in epub/mobi files --- doc/Makefile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/doc/Makefile b/doc/Makefile index 6ab89cd5af..cf649eb37b 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -95,9 +95,10 @@ spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt @echo "Spell check finished." epub: $(OBJECTS) - @mkdir -p epub + @mkdir -p epub/JPG @rm -f LAMMPS.epub @cp src/JPG/lammps-logo.png epub/ + @cp src/JPG/*.* epub/JPG @(\ . $(VENV)/bin/activate ;\ cp -r src/* $(RSTDIR)/ ;\ From 86490819040184506b1453988934f023213373ff Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 21 Oct 2018 18:39:25 -0400 Subject: [PATCH 11/12] fix broken links in manual --- doc/src/Build_extras.txt | 8 ++++---- doc/src/Install_mac.txt | 3 ++- doc/src/Packages_details.txt | 20 ++++++++++---------- doc/src/Packages_user.txt | 1 + doc/src/balance.txt | 1 + doc/src/dump_h5md.txt | 6 +++--- doc/src/fix_balance.txt | 1 + doc/src/message.txt | 4 ++-- 8 files changed, 24 insertions(+), 20 deletions(-) diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt index fb96699743..d256a1afc8 100644 --- a/doc/src/Build_extras.txt +++ b/doc/src/Build_extras.txt @@ -563,9 +563,9 @@ file. VORONOI package :h4,link(voronoi) To build with this package, you must download and build the "Voro++ -library"_voro_home. +library"_voro-home. -:link(voro_home,http://math.lbl.gov/voro++) +:link(voro-home,http://math.lbl.gov/voro++) [CMake build]: @@ -932,9 +932,9 @@ successfully build on your system. USER-SCAFACOS package :h4,link(user-scafacos) To build with this package, you must download and build the "ScaFaCoS -Coulomb solver library"_scafacos_home +Coulomb solver library"_scafacos-home -:link(scafacos_home,http://www.scafacos.de) +:link(scafacos-home,http://www.scafacos.de) [CMake build]: diff --git a/doc/src/Install_mac.txt b/doc/src/Install_mac.txt index 3fcc55b8ab..3ab119522c 100644 --- a/doc/src/Install_mac.txt +++ b/doc/src/Install_mac.txt @@ -49,7 +49,8 @@ Lennard-Jones benchmark file: % brew test lammps -v :pre If you have problems with the installation you can post issues to -"this link"_https://github.com/Homebrew/homebrew-science/issues. +"this link"_homebrew. Thanks to Derek Thomas (derekt at cello.t.u-tokyo.ac.jp) for setting up the Homebrew capability. +:link(homebrew,https://github.com/Homebrew/homebrew-science/issues) diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 58145926b9..031858e846 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -462,10 +462,10 @@ dynamics can be run with LAMMPS using density-functional tight-binding quantum forces calculated by LATTE. More information on LATTE can be found at this web site: -"https://github.com/lanl/LATTE"_latte_home. A brief technical +"https://github.com/lanl/LATTE"_latte-home. A brief technical description is given with the "fix latte"_fix_latte.html command. -:link(latte_home,https://github.com/lanl/LATTE) +:link(latte-home,https://github.com/lanl/LATTE) [Authors:] Christian Negre (LANL) and Steve Plimpton (Sandia). LATTE itself is developed at Los Alamos National Laboratory by Marc @@ -668,9 +668,9 @@ MSCG package :link(PKG-mscg),h4 A "fix mscg"_fix_mscg.html command which can parameterize a Multi-Scale Coarse-Graining (MSCG) model using the open-source "MS-CG -library"_mscg_home. +library"_mscg-home. -:link(mscg_home,https://github.com/uchicago-voth/MSCG-release) +:link(mscg-home,https://github.com/uchicago-voth/MSCG-release) To use this package you must have the MS-CG library available on your system. @@ -1008,11 +1008,11 @@ VORONOI package :link(PKG-VORONOI),h4 [Contents:] A compute command which calculates the Voronoi tesselation of a -collection of atoms by wrapping the "Voro++ library"_voro_home. This +collection of atoms by wrapping the "Voro++ library"_voro-home. This can be used to calculate the local volume or each atoms or its near neighbors. -:link(voro_home,http://math.lbl.gov/voro++) +:link(voro-home,http://math.lbl.gov/voro++) To use this package you must have the Voro++ library available on your system. @@ -1520,7 +1520,7 @@ USER-MEAMC package :link(PKG-USER-MEAMC),h4 [Contents:] A pair style for the modified embedded atom (MEAM) potential -translated from the Fortran version in the "MEAM"_MEAM package +translated from the Fortran version in the "MEAM"_#PKG-MEAM package to plain C++. In contrast to the MEAM package, no library needs to be compiled and the pair style can be instantiated multiple times. @@ -1601,7 +1601,7 @@ USER-MOLFILE package :link(PKG-USER-MOLFILE),h4 [Contents:] A "dump molfile"_dump_molfile.html command which uses molfile plugins -that are bundled with the "VMD"_vmd_home +that are bundled with the "VMD"_vmd-home molecular visualization and analysis program, to enable LAMMPS to dump snapshots in formats compatible with various molecular simulation tools. @@ -1653,11 +1653,11 @@ Note that NetCDF files can be directly visualized with the following tools: "Ovito"_ovito (Ovito supports the AMBER convention and the extensions mentioned above) -"VMD"_vmd_home +"VMD"_vmd-home "AtomEye"_atomeye (the libAtoms version of AtomEye contains a NetCDF reader not present in the standard distribution) :ul :link(ovito,http://www.ovito.org) -:link(vmd_home,https://www.ks.uiuc.edu/Research/vmd/) +:link(vmd-home,https://www.ks.uiuc.edu/Research/vmd/) :link(atomeye,http://www.libatoms.org) [Author:] Lars Pastewka (Karlsruhe Institute of Technology). diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt index 6e363b28f7..9bb3fbd18c 100644 --- a/doc/src/Packages_user.txt +++ b/doc/src/Packages_user.txt @@ -74,3 +74,4 @@ Package, Description, Doc page, Example, Library "USER-TALLY"_Packages_details.html#PKG-USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, no "USER-UEF"_Packages_details.html#PKG-USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, no "USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, n/a, ext :tb(ea=c,ca1=l) +:link(MOFplus,https://www.mofplus.org/content/show/MOF-FF) diff --git a/doc/src/balance.txt b/doc/src/balance.txt index 26e146d89b..49202b0149 100644 --- a/doc/src/balance.txt +++ b/doc/src/balance.txt @@ -516,3 +516,4 @@ appear in {dimstr} for the {shift} style. "fix balance"_fix_balance.html [Default:] none +:link(pizza,http://pizza.sandia.gov) diff --git a/doc/src/dump_h5md.txt b/doc/src/dump_h5md.txt index 9065e8a648..a3849f103c 100644 --- a/doc/src/dump_h5md.txt +++ b/doc/src/dump_h5md.txt @@ -50,7 +50,7 @@ dump h5md1 all h5md 100 dump_h5md.h5 velocity author "John Doe" :pre [Description:] Dump a snapshot of atom coordinates every N timesteps in the -"HDF5"_HDF5_ws based "H5MD"_h5md file format "(de Buyl)"_#h5md_cpc. +"HDF5"_HDF5-ws based "H5MD"_h5md file format "(de Buyl)"_#h5md_cpc. HDF5 files are binary, portable and self-describing. This dump style will write only one file, on the root node. @@ -102,11 +102,11 @@ enabled if LAMMPS was built with that package. See the "Build package"_Build_package.html doc page for more info. It also requires (i) building the ch5md library provided with LAMMPS (See the "Build package"_Build_package.html doc page for more info.) and (ii) having -the "HDF5"_HDF5_ws library installed (C bindings are sufficient) on +the "HDF5"_HDF5-ws library installed (C bindings are sufficient) on your system. The library ch5md is compiled with the h5cc wrapper provided by the HDF5 library. -:link(HDF5_ws,http://www.hdfgroup.org/HDF5/) +:link(HDF5-ws,http://www.hdfgroup.org/HDF5/) :line diff --git a/doc/src/fix_balance.txt b/doc/src/fix_balance.txt index 2de17cdd2a..77ad13033e 100644 --- a/doc/src/fix_balance.txt +++ b/doc/src/fix_balance.txt @@ -376,3 +376,4 @@ appear in {dimstr} for the {shift} style. "group"_group.html, "processors"_processors.html, "balance"_balance.html [Default:] none +:link(pizza,http://pizza.sandia.gov) diff --git a/doc/src/message.txt b/doc/src/message.txt index cca1a5b369..6ceb62a3e6 100644 --- a/doc/src/message.txt +++ b/doc/src/message.txt @@ -137,8 +137,8 @@ If LAMMPS is the server code, it will begin receiving messages when the "server"_server.html command is invoked. A fix client command will terminate its messaging with the server when -LAMMPS ends, or the fix is deleted via the "unfix"_unfix command. The -server command will terminate its messaging with the client when the +LAMMPS ends, or the fix is deleted via the "unfix"_unfix.html command. +The server command will terminate its messaging with the client when the client signals it. Then the remainder of the LAMMPS input script will be processed. From aa27c8f733dd41117a477d1b352a67951a89717c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 23 Oct 2018 09:17:00 -0400 Subject: [PATCH 12/12] convert double quotes to latex style --- doc/src/Developer/developer.tex | 36 ++++++++++++++++----------------- 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/doc/src/Developer/developer.tex b/doc/src/Developer/developer.tex index 8852f44168..15fd3a4ce5 100644 --- a/doc/src/Developer/developer.tex +++ b/doc/src/Developer/developer.tex @@ -22,10 +22,10 @@ users. LAMMPS source files are in two directories of the distribution tarball. The src directory has the majority of them, all of which are C++ files (*.cpp and *.h). Many of these files are in the src -directory itself. There are also dozens of "packages", which can be +directory itself. There are also dozens of ``packages'', which can be included or excluded when LAMMPS is built. See the doc/Section\_build.html section of the manual for more information -about packages, or type "make" from within the src directory, which +about packages, or type ``make'' from within the src directory, which lists package-related commands, such as ``make package-status''. The source files for each package are in an all-uppercase sub-directory of src, like src/MOLECULE or src/USER-CUDA. If the package is currently @@ -38,17 +38,17 @@ The lib directory also contains source code for external libraries, used by a few of the packages. Each sub-directory, like meam or gpu, contains the source files, some of which are in different languages such as Fortran. The files are compiled into libraries from within -each sub-directory, e.g. performing a "make" in the lib/meam directory +each sub-directory, e.g. performing a ``make'' in the lib/meam directory creates a libmeam.a file. These libraries are linked to during a LAMMPS build, if the corresponding package is installed. LAMMPS C++ source files almost always come in pairs, such as run.cpp and run.h. The pair of files defines a C++ class, the Run class in -this case, which contains the code invoked by the "run" command in a +this case, which contains the code invoked by the ``run'' command in a LAMMPS input script. As this example illustrates, source file and class names often have a one-to-one correspondence with a command used in a LAMMPS input script. Some source files and classes do not have a -corresponding input script command, e.g. force.cpp and the Force +corresponding input script command, e.g. ``force.cpp'' and the Force class. They are discussed in the next section. \pagebreak @@ -57,12 +57,12 @@ class. They are discussed in the next section. Though LAMMPS has a lot of source files and classes, its class hierarchy is quite simple, as outlined in Fig \ref{fig:classes}. Each boxed name refers to a class and has a pair of associated source files -in lammps/src, e.g. memory.cpp and memory.h. More details on the +in lammps/src, e.g. ``memory.cpp'' and ``memory.h''. More details on the class and its methods and data structures can be found by examining its *.h file. LAMMPS (lammps.cpp/h) is the top-level class for the entire code. It -holds an "instance" of LAMMPS and can be instantiated one or more +holds an ``instance'' of LAMMPS and can be instantiated one or more times by a calling code. For example, the file src/main.cpp simply instantiates one instance of LAMMPS and passes it the input script. @@ -81,7 +81,7 @@ enabled by a bit of cleverness in the Pointers class (see src/pointers.h) which every class inherits from. There are a handful of virtual parent classes in LAMMPS that define -what LAMMPS calls "styles". They are shaded red in Fig +what LAMMPS calls ``styles''. They are shaded red in Fig \ref{fig:classes}. Each of these are parents of a number of child classes that implement the interface defined by the parent class. For example, the fix style has around 100 child classes. They are the @@ -89,17 +89,17 @@ possible fixes that can be specified by the fix command in an input script, e.g. fix nve, fix shake, fix ave/time, etc. The corresponding classes are Fix (for the parent class), FixNVE, FixShake, FixAveTime, etc. The source files for these classes are easy to identify in the -src directory, since they begin with the word "fix", e,g, +src directory, since they begin with the word ``fix'', e,g, fix\_nve.cpp, fix\_shake,cpp, fix\_ave\_time.cpp, etc. -The one exception is child class files for the "command" style. These +The one exception is child class files for the ``command'' style. These implement specific commands in the input script that can be invoked before/after/between runs or which launch a simulation. Examples are the create\_box, minimize, run, and velocity commands which encode the CreateBox, Minimize, Run, and Velocity classes. The corresponding files are create\_box,cpp, minimize.cpp, run.cpp, and velocity.cpp. -The list of command style files can be found by typing "grep -COMMAND\_CLASS *.h" from within the src directory, since that word in +The list of command style files can be found by typing ``grep +COMMAND\_CLASS *.h'' from within the src directory, since that word in the header file identifies the class as an input script command. Similar words can be grepped to list files for the other LAMMPS styles. E.g. ATOM\_CLASS, PAIR\_CLASS, BOND\_CLASS, REGION\_CLASS, @@ -471,13 +471,13 @@ FixStyle(your/fix/name,FixMine) \end{verbatim} \end{center} -Where "your/fix/name" is a name of your fix in the script and FixMine +Where ``your/fix/name'' is a name of your fix in the script and FixMine is the name of the class. This code allows LAMMPS to find your fix when it parses input script. In addition, your fix header must be -included in the file "style\_fix.h". In case if you use LAMMPS make, +included in the file ``style\_fix.h''. In case if you use LAMMPS make, this file is generated automatically - all files starting with prefix fix\_ are included, so call your header the same way. Otherwise, don't -forget to add your include into "style\_fix.h". +forget to add your include into ``style\_fix.h''. Let's write a simple fix which will print average velocity at the end of each timestep. First of all, implement a constructor: @@ -567,11 +567,11 @@ void FixPrintVel::end_of_step() \end{center} In the code above, we use MathExtra routines defined in -"math\_extra.h". There are bunch of math functions to work with +``math\_extra.h''. There are bunch of math functions to work with arrays of doubles as with math vectors. In this code we use an instance of Atom class. This object is stored -in the Pointers class (see "pointers.h"). This object contains all +in the Pointers class (see ``pointers.h''). This object contains all global information about the simulation system. Data from Pointers class available to all classes inherited from it using protected inheritance. Hence when you write you own class, which is going to use @@ -689,7 +689,7 @@ int FixSavePos::unpack_exchange(int nlocal, double *buf) Now, a little bit about memory allocation. We used Memory class which is just a bunch of template functions for allocating 1D and 2D -arrays. So you need to add include "memory.h" to have access to them. +arrays. So you need to add include ``memory.h'' to have access to them. Finally, if you need to write/read some global information used in your fix to the restart file, you might do it by setting flag