Merge pull request #1152 from lammps/doc-adjust2
More Documentation consistency improvements
This commit is contained in:
Axel Kohlmeyer
@ -95,9 +95,10 @@ spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt
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@echo "Spell check finished."
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epub: $(OBJECTS)
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@mkdir -p epub
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@mkdir -p epub/JPG
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@rm -f LAMMPS.epub
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@cp src/JPG/lammps-logo.png epub/
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@cp src/JPG/*.* epub/JPG
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@(\
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. $(VENV)/bin/activate ;\
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cp -r src/* $(RSTDIR)/ ;\
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@ -123,9 +124,9 @@ pdf: utils/txt2html/txt2html.exe
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cd ..; \
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../utils/txt2html/txt2html.exe -b *.txt; \
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htmldoc --batch lammps.book; \
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for s in `echo *.txt | sed -e 's,\.txt,\.html,g'` ; \
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do grep -q $$s lammps.book || \
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echo doc file $$s missing in src/lammps.book; done; \
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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'` ; \
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do grep -q ^$$s lammps.book || \
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echo WARNING: doc file $$s missing in src/lammps.book; done; \
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rm *.html; \
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)
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@ -563,9 +563,9 @@ file.
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VORONOI package :h4,link(voronoi)
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To build with this package, you must download and build the "Voro++
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library"_voro_home.
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library"_voro-home.
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:link(voro_home,http://math.lbl.gov/voro++)
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:link(voro-home,http://math.lbl.gov/voro++)
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[CMake build]:
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@ -932,9 +932,9 @@ successfully build on your system.
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USER-SCAFACOS package :h4,link(user-scafacos)
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To build with this package, you must download and build the "ScaFaCoS
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Coulomb solver library"_scafacos_home
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Coulomb solver library"_scafacos-home
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:link(scafacos_home,http://www.scafacos.de)
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:link(scafacos-home,http://www.scafacos.de)
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[CMake build]:
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@ -34,7 +34,7 @@ OPT.
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"fene (iko)"_bond_fene.html,
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"fene/expand (o)"_bond_fene_expand.html,
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"gromos (o)"_bond_gromos.html,
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"harmonic (ko)"_bond_harmonic.html,
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"harmonic (iko)"_bond_harmonic.html,
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"harmonic/shift (o)"_bond_harmonic_shift.html,
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"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
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"morse (o)"_bond_morse.html,
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@ -57,9 +57,11 @@ OPT.
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"zero"_angle_zero.html,
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"hybrid"_angle_hybrid.html :tb(c=3,ea=c)
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"charmm (ko)"_angle_charmm.html,
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"charmm (iko)"_angle_charmm.html,
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"class2 (ko)"_angle_class2.html,
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"class2/p6"_angle_class2.html,
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"cosine (o)"_angle_cosine.html,
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"cosine/buck6d"_angle_cosine_buck6d.html,
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"cosine/delta (o)"_angle_cosine_delta.html,
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"cosine/periodic (o)"_angle_cosine_periodic.html,
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"cosine/shift (o)"_angle_cosine_shift.html,
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@ -97,7 +99,7 @@ OPT.
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"nharmonic (o)"_dihedral_nharmonic.html,
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"opls (iko)"_dihedral_opls.html,
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"quadratic (o)"_dihedral_quadratic.html,
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"spherical (o)"_dihedral_spherical.html,
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"spherical"_dihedral_spherical.html,
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"table (o)"_dihedral_table.html,
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"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c)
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@ -112,7 +114,7 @@ OPT.
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"none"_improper_none.html,
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"zero"_improper_zero.html,
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"hybrid"_improper_hybrid.html :tb(c=3,ea=c)
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"hybrid"_improper_hybrid.html :tb(c=3,ea=c)
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"class2 (ko)"_improper_class2.html,
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"cossq (o)"_improper_cossq.html,
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@ -120,5 +122,6 @@ OPT.
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"distance"_improper_distance.html,
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"fourier (o)"_improper_fourier.html,
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"harmonic (iko)"_improper_harmonic.html,
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"inversion/harmonic"_improper_inversion_harmonic.html,
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"ring (o)"_improper_ring.html,
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"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)
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@ -93,6 +93,7 @@ KOKKOS, o = USER-OMP, t = OPT.
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"pe/tally"_compute_tally.html,
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"plasticity/atom"_compute_plasticity_atom.html,
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"pressure"_compute_pressure.html,
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"pressure/cylinder"_compute_pressure_cylinder.html,
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"pressure/uef"_compute_pressure_uef.html,
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"property/atom"_compute_property_atom.html,
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"property/chunk"_compute_property_chunk.html,
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@ -119,7 +120,7 @@ KOKKOS, o = USER-OMP, t = OPT.
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"smd/tlsph/strain"_compute_smd_tlsph_strain.html,
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"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html,
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"smd/tlsph/stress"_compute_smd_tlsph_stress.html,
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"smd/triangle/mesh/vertices"_compute_smd_triangle_vertices.html,
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"smd/triangle/vertices"_compute_smd_triangle_vertices.html,
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"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html,
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"smd/ulsph/strain"_compute_smd_ulsph_strain.html,
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"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html,
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@ -130,6 +131,8 @@ KOKKOS, o = USER-OMP, t = OPT.
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"snav/atom"_compute_sna_atom.html,
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"spin"_compute_spin.html,
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"stress/atom"_compute_stress_atom.html,
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"stress/mop"_compute_stress_mop.html,
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"stress/mop/profile"_compute_stress_mop.html,
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"stress/tally"_compute_tally.html,
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"tdpd/cc/atom"_compute_tdpd_cc_atom.html,
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"temp (k)"_compute_temp.html,
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@ -137,6 +140,7 @@ KOKKOS, o = USER-OMP, t = OPT.
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"temp/body"_compute_temp_body.html,
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"temp/chunk"_compute_temp_chunk.html,
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"temp/com"_compute_temp_com.html,
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"temp/cs"_compute_temp_cs.html,
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"temp/deform"_compute_temp_deform.html,
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"temp/deform/eff"_compute_temp_deform_eff.html,
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"temp/drude"_compute_temp_drude.html,
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@ -40,11 +40,13 @@ OPT.
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"ave/time"_fix_ave_time.html,
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"aveforce"_fix_aveforce.html,
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"balance"_fix_balance.html,
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"bocs"_fix_bocs.html,
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"bond/break"_fix_bond_break.html,
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"bond/create"_fix_bond_create.html,
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"bond/react"_fix_bond_react.html,
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"bond/swap"_fix_bond_swap.html,
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"box/relax"_fix_box_relax.html,
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"client/md"_fix_client_md.html,
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"cmap"_fix_cmap.html,
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"colvars"_fix_colvars.html,
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"controller"_fix_controller.html,
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@ -54,7 +56,7 @@ OPT.
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"drag"_fix_drag.html,
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"drude"_fix_drude.html,
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"drude/transform/direct"_fix_drude_transform.html,
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"drude/transform/reverse"_fix_drude_transform.html,
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"drude/transform/inverse"_fix_drude_transform.html,
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"dt/reset"_fix_dt_reset.html,
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"edpd/source"_fix_dpd_source.html,
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"efield"_fix_efield.html,
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@ -107,15 +109,16 @@ OPT.
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"nph/eff"_fix_nh_eff.html,
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"nph/sphere (ko)"_fix_nph_sphere.html,
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"nphug (o)"_fix_nphug.html,
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"npt (kio)"_fix_nh.html,
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"npt (iko)"_fix_nh.html,
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"npt/asphere (o)"_fix_npt_asphere.html,
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"npt/body"_fix_npt_body.html,
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"npt/eff"_fix_nh_eff.html,
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"npt/sphere (o)"_fix_npt_sphere.html,
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"npt/uef"_fix_nh_uef.html,
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"nve (kio)"_fix_nve.html,
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"nve (iko)"_fix_nve.html,
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"nve/asphere (i)"_fix_nve_asphere.html,
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"nve/asphere/noforce"_fix_nve_asphere_noforce.html,
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"nve/awpmd"_fix_nve_awpmd.html,
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"nve/body"_fix_nve_body.html,
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"nve/dot"_fix_nve_dot.html,
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"nve/dotc/langevin"_fix_nve_dotc_langevin.html,
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@ -170,26 +173,26 @@ OPT.
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"rhok"_fix_rhok.html,
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"rigid (o)"_fix_rigid.html,
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"rigid/nph (o)"_fix_rigid.html,
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"rigid/nph/small"_fix_rigid.html,
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"rigid/npt (o)"_fix_rigid.html,
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"rigid/npt/small"_fix_rigid.html,
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"rigid/nve (o)"_fix_rigid.html,
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"rigid/nve/small"_fix_rigid.html,
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"rigid/nvt (o)"_fix_rigid.html,
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"rigid/nvt/small"_fix_rigid.html,
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"rigid/small (o)"_fix_rigid.html,
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"rigid/small/nph"_fix_rigid.html,
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"rigid/small/npt"_fix_rigid.html,
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"rigid/small/nve"_fix_rigid.html,
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"rigid/small/nvt"_fix_rigid.html,
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"rx (k)"_fix_rx.html,
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"saed/vtk"_fix_saed_vtk.html,
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"setforce (k)"_fix_setforce.html,
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"shake"_fix_shake.html,
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"shardlow (k)"_fix_shardlow.html,
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"smd"_fix_smd.html,
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"smd/adjust/dt"_fix_smd_adjust_dt.html,
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"smd/integrate/tlsph"_fix_smd_integrate_tlsph.html,
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"smd/integrate/ulsph"_fix_smd_integrate_ulsph.html,
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"smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html,
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"smd/adjust_dt"_fix_smd_adjust_dt.html,
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"smd/integrate_tlsph"_fix_smd_integrate_tlsph.html,
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"smd/integrate_ulsph"_fix_smd_integrate_ulsph.html,
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"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html,
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"smd/setvel"_fix_smd_setvel.html,
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"smd/wall/surface"_fix_smd_wall_surface.html,
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"smd/wall_surface"_fix_smd_wall_surface.html,
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"spring"_fix_spring.html,
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"spring/chunk"_fix_spring_chunk.html,
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"spring/rg"_fix_spring_rg.html,
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@ -31,8 +31,8 @@ OPT.
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"adp (o)"_pair_adp.html,
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"agni (o)"_pair_agni.html,
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"airebo (oi)"_pair_airebo.html,
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"airebo/morse (oi)"_pair_airebo.html,
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"airebo (io)"_pair_airebo.html,
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"airebo/morse (io)"_pair_airebo.html,
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"atm"_pair_atm.html,
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"awpmd/cut"_pair_awpmd.html,
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"beck (go)"_pair_beck.html,
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@ -42,21 +42,23 @@ OPT.
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"bop"_pair_bop.html,
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"born (go)"_pair_born.html,
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"born/coul/dsf"_pair_born.html,
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"born/coul/dsf/cs"_pair_born.html,
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||||
"born/coul/dsf/cs"_pair_cs.html,
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"born/coul/long (go)"_pair_born.html,
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"born/coul/long/cs"_pair_born.html,
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||||
"born/coul/long/cs (g)"_pair_cs.html,
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"born/coul/msm (o)"_pair_born.html,
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"born/coul/wolf (go)"_pair_born.html,
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||||
"born/coul/wolf/cs"_pair_born.html,
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||||
"born/coul/wolf/cs (g)"_pair_cs.html,
|
||||
"brownian (o)"_pair_brownian.html,
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||||
"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,
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||||
"buck/coul/msm (o)"_pair_buck.html,
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||||
"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,
|
||||
@ -66,13 +68,13 @@ OPT.
|
||||
"coul/diel (o)"_pair_coul_diel.html,
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||||
"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"_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,
|
||||
"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,
|
||||
@ -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,
|
||||
@ -125,12 +127,12 @@ 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,
|
||||
"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)
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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)
|
||||
|
||||
@ -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).
|
||||
@ -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
|
||||
|
||||
|
||||
@ -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)
|
||||
|
||||
@ -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:]
|
||||
|
||||
@ -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.
|
||||
|
||||
@ -62,18 +62,27 @@ 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
|
||||
"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 - 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 - 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
|
||||
|
||||
|
||||
@ -516,3 +516,4 @@ appear in {dimstr} for the {shift} style.
|
||||
"fix balance"_fix_balance.html
|
||||
|
||||
[Default:] none
|
||||
:link(pizza,http://pizza.sandia.gov)
|
||||
|
||||
@ -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).
|
||||
|
||||
@ -69,18 +69,23 @@ 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
|
||||
"gromos"_bond_gromos.html - GROMOS force field bond
|
||||
"harmonic"_bond_harmonic.html - harmonic bond
|
||||
"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 - 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
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -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
|
||||
@ -219,37 +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/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/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
|
||||
|
||||
|
||||
@ -85,16 +85,24 @@ 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
|
||||
"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 - 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 - 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 - 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
|
||||
|
||||
|
||||
@ -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
|
||||
|
||||
|
||||
168
doc/src/fix.txt
168
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:]
|
||||
|
||||
@ -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)
|
||||
|
||||
@ -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
|
||||
|
||||
@ -64,14 +64,19 @@ 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
|
||||
"cossq"_improper_cossq.html - improper with a cosine squared term
|
||||
"cvff"_improper_cvff.html - CVFF improper
|
||||
"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 - 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
|
||||
|
||||
|
||||
@ -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.
|
||||
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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:]
|
||||
|
||||
|
||||
@ -6,51 +6,74 @@
|
||||
|
||||
: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
|
||||
pair_coeff * * 100.0 3.0
|
||||
pair_coeff 1 1 100.0 3.5 9.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
@ -59,16 +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
|
||||
@ -83,21 +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.
|
||||
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
|
||||
|
||||
|
||||
@ -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:
|
||||
|
||||
|
||||
@ -95,120 +95,217 @@ 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
|
||||
"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 - 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 - 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 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 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 - 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 - Coulombic potential with a soft core
|
||||
"coul/debye"_pair_coul.html - cutoff Coulombic potential with Debye screening
|
||||
"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 - long-range Coulombic potential with a soft core
|
||||
"coul/msm"_pair_coul.html - long-range MSM Coulombics
|
||||
"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 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 - 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 - 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 - reactive DPD potential
|
||||
"extep"_pair_extep.html - extended Tersoff potential
|
||||
"gauss"_pair_gauss.html - Gaussian potential
|
||||
"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 - 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 - 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 (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 - 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 - 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
|
||||
"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 - 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 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 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 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 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 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 - 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 Coulombics for TIP4P water
|
||||
"lj/mdf"_pair_mdf.html - LJ potential with a taper function
|
||||
"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 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 - 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 - Many-Body Metal-Organic (MOMB) force field
|
||||
"morse"_pair_morse.html - Morse potential
|
||||
"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
|
||||
"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 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 -
|
||||
"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 - 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 -
|
||||
"tersoff/table"_pair_tersoff.html -
|
||||
"tersoff/zbl"_pair_tersoff_zbl.html - Tersoff/ZBL 3-body potential
|
||||
"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 -
|
||||
"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
|
||||
|
||||
:line
|
||||
|
||||
|
||||
Reference in New Issue
Block a user