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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@617 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2007-06-20 12:56:17 +00:00
parent c323fdae33
commit a7ab72af62
80 changed files with 1099 additions and 621 deletions
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96
doc/Eqs/Script.create
View File

@ -1,48 +1,52 @@
# create dvi files for every LaTex eq
latex angle_charmm.tex
latex angle_class2.tex
latex angle_cosine.tex
latex angle_cosine_squared.tex
latex angle_harmonic.tex
latex bond_class2.tex
latex bond_fene.tex
latex bond_fene_expand.tex
latex bond_harmonic.tex
latex bond_morse.tex
latex bond_nonlinear.tex
latex bond_quartic.tex
latex centro_symmetry.tex
latex dihedral_charmm.tex
latex dihedral_class2.tex
latex dihedral_harmonic.tex
latex dihedral_helix.tex
latex dihedral_multiharmonic.tex
latex dihedral_opls.tex
latex fix_gyration.tex
latex fix_orient_fcc.tex
latex fix_spring_rg.tex
latex fix_wall_lj93.tex
latex improper_class2.tex
latex improper_cvff.tex
latex improper_harmonic.tex
latex pair_buck.tex
latex pair_charmm.tex
latex pair_class2.tex
latex pair_coulomb.tex
latex pair_debye.tex
latex pair_dpd.tex
latex pair_eam.tex
latex pair_eam_fs.tex
latex pair_granular.tex
latex pair_lj.tex
latex pair_lj_expand.tex
latex pair_lj_smooth.tex
latex pair_meam.tex
latex pair_morse.tex
latex pair_soft.tex
latex pair_sw.tex
latex pair_tersoff.tex
latex pair_yukawa.tex
latex pressure.tex
latex stress_tensor.tex
latex angle_charmm
latex angle_class2
latex angle_cosine
latex angle_cosine_squared
latex angle_harmonic
latex bond_class2
latex bond_fene
latex bond_fene_expand
latex bond_harmonic
latex bond_morse
latex bond_nonlinear
latex bond_quartic
latex centro_symmetry
latex dihedral_charmm
latex dihedral_class2
latex dihedral_harmonic
latex dihedral_helix
latex dihedral_multiharmonic
latex dihedral_opls
latex fix_gyration
latex fix_orient_fcc
latex fix_spring_rg
latex fix_wall_lj93
latex improper_class2
latex improper_cvff
latex improper_harmonic
latex pair_buck
latex pair_charmm
latex pair_class2
latex pair_colloid_cc
latex pair_colloid_cs
latex pair_colloid_ss
latex pair_coulomb
latex pair_debye
latex pair_dipole
latex pair_dpd
latex pair_eam
latex pair_eam_fs
latex pair_granular
latex pair_lj
latex pair_lj_expand
latex pair_lj_smooth
latex pair_meam
latex pair_morse
latex pair_soft
latex pair_sw
latex pair_tersoff
latex pair_yukawa
latex pressure
latex stress_tensor

45
doc/Section_commands.html
View File

@ -249,8 +249,8 @@ in the command's documentation.
<A HREF = "group.html">group</A>, <A HREF = "mass.html">mass</A>, <A HREF = "min_modify.html">min_modify</A>,
<A HREF = "min_style.html">min_style</A>, <A HREF = "neigh_modify.html">neigh_modify</A>,
<A HREF = "neighbor.html">neighbor</A>, <A HREF = "reset_timestep.html">reset_timestep</A>,
<A HREF = "run_style.html">run_style</A>, <A HREF = "set.html">set</A>, <A HREF = "timestep.html">timestep</A>,
<A HREF = "velocity.html">velocity</A>
<A HREF = "run_style.html">run_style</A>, <A HREF = "set.html">set</A>, <A HREF = "shape.html">shape</A>,
<A HREF = "timestep.html">timestep</A>, <A HREF = "velocity.html">velocity</A>
</P>
<P>Fixes:
</P>
@ -305,9 +305,9 @@ in the command's documentation.
<TR ALIGN="center"><TD ><A HREF = "neighbor.html">neighbor</A></TD><TD ><A HREF = "newton.html">newton</A></TD><TD ><A HREF = "next.html">next</A></TD><TD ><A HREF = "pair_coeff.html">pair_coeff</A></TD><TD ><A HREF = "pair_modify.html">pair_modify</A></TD><TD ><A HREF = "pair_style.html">pair_style</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_write.html">pair_write</A></TD><TD ><A HREF = "print.html">print</A></TD><TD ><A HREF = "processors.html">processors</A></TD><TD ><A HREF = "read_data.html">read_data</A></TD><TD ><A HREF = "read_restart.html">read_restart</A></TD><TD ><A HREF = "region.html">region</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "replicate.html">replicate</A></TD><TD ><A HREF = "reset_timestep.html">reset_timestep</A></TD><TD ><A HREF = "restart.html">restart</A></TD><TD ><A HREF = "run.html">run</A></TD><TD ><A HREF = "run_style.html">run_style</A></TD><TD ><A HREF = "set.html">set</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "shell.html">shell</A></TD><TD ><A HREF = "special_bonds.html">special_bonds</A></TD><TD ><A HREF = "temper.html">temper</A></TD><TD ><A HREF = "thermo.html">thermo</A></TD><TD ><A HREF = "thermo_modify.html">thermo_modify</A></TD><TD ><A HREF = "thermo_style.html">thermo_style</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "timestep.html">timestep</A></TD><TD ><A HREF = "uncompute.html">uncompute</A></TD><TD ><A HREF = "undump.html">undump</A></TD><TD ><A HREF = "unfix.html">unfix</A></TD><TD ><A HREF = "units.html">units</A></TD><TD ><A HREF = "variable.html">variable</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "velocity.html">velocity</A></TD><TD ><A HREF = "write_restart.html">write_restart</A>
<TR ALIGN="center"><TD ><A HREF = "shape.html">shape</A></TD><TD ><A HREF = "shell.html">shell</A></TD><TD ><A HREF = "special_bonds.html">special_bonds</A></TD><TD ><A HREF = "temper.html">temper</A></TD><TD ><A HREF = "thermo.html">thermo</A></TD><TD ><A HREF = "thermo_modify.html">thermo_modify</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "thermo_style.html">thermo_style</A></TD><TD ><A HREF = "timestep.html">timestep</A></TD><TD ><A HREF = "uncompute.html">uncompute</A></TD><TD ><A HREF = "undump.html">undump</A></TD><TD ><A HREF = "unfix.html">unfix</A></TD><TD ><A HREF = "units.html">units</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "variable.html">variable</A></TD><TD ><A HREF = "velocity.html">velocity</A></TD><TD ><A HREF = "write_restart.html">write_restart</A>
</TD></TR></TABLE></DIV>
<HR>
@ -318,12 +318,12 @@ description:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "fix_addforce.html">addforce</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce</A></TD><TD ><A HREF = "fix_ave_spatial.html">ave/spatial</A></TD><TD ><A HREF = "fix_ave_time.html">ave/time</A></TD><TD ><A HREF = "fix_box_relax.html">box/relax</A></TD><TD ><A HREF = "fix_com.html">com</A></TD><TD ><A HREF = "fix_deform.html">deform</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_ellipsoid.html">ellipsoid</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gran_diag.html">gran/diag</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_gyration.html">gyration</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_heat.html">heat</A></TD><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_msd.html">msd</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_nph.html">nph</A></TD><TD ><A HREF = "fix_npt.html">npt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_gran.html">nve/gran</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nvt.html">nvt</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_uniaxial.html">uniaxial</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_volume_rescale.html">volume/rescale</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A>
<TR ALIGN="center"><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gran_diag.html">gran/diag</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_gyration.html">gyration</A></TD><TD ><A HREF = "fix_heat.html">heat</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_msd.html">msd</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_nph.html">nph</A></TD><TD ><A HREF = "fix_npt.html">npt</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_dipole.html">nve/dipole</A></TD><TD ><A HREF = "fix_nve_gran.html">nve/gran</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nvt.html">nvt</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_uniaxial.html">uniaxial</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_volume_rescale.html">volume/rescale</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A>
</TD></TR></TABLE></DIV>
<HR>
@ -334,8 +334,8 @@ description:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_epair_atom.html">epair/atom</A></TD><TD ><A HREF = "compute_etotal_atom.html">etotal/atom</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_rotate_dipole.html">rotate/dipole</A></TD><TD ><A HREF = "compute_rotate_gran.html">rotate/gran</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_variable.html">variable</A></TD><TD ><A HREF = "compute_variable_atom.html">variable/atom</A>
<TR ALIGN="center"><TD ><A HREF = "compute_rotate_dipole.html">rotate/dipole</A></TD><TD ><A HREF = "compute_rotate_gran.html">rotate/gran</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_dipole.html">temp/dipole</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_variable.html">variable</A></TD><TD ><A HREF = "compute_variable_atom.html">variable/atom</A>
</TD></TR></TABLE></DIV>
<HR>
@ -346,15 +346,16 @@ full description:
</P>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "pair_none.html">none</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid</A></TD><TD ><A HREF = "pair_airebo.html">airebo</A></TD><TD ><A HREF = "pair_buck.html">buck</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/coul/cut</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long</A></TD><TD ><A HREF = "pair_dpd.html">dpd</A></TD><TD ><A HREF = "pair_eam.html">eam</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/fs</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/fs/opt</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne</A></TD><TD ><A HREF = "pair_gran.html">gran/hertzian</A></TD><TD ><A HREF = "pair_gran.html">gran/history</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gran.html">gran/no_history</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/opt</A></TD><TD ><A HREF = "pair_class2.html">lj/class2</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/tip4p</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_meam.html">meam</A></TD><TD ><A HREF = "pair_morse.html">morse</A></TD><TD ><A HREF = "pair_morse.html">morse/opt</A></TD><TD ><A HREF = "pair_soft.html">soft</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_sw.html">sw</A></TD><TD ><A HREF = "pair_table.html">table</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A>
<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/coul/cut</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long</A></TD><TD ><A HREF = "pair_dipole/cut.html">dipole/cut</A></TD><TD ><A HREF = "pair_dpd.html">dpd</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam</A></TD><TD ><A HREF = "pair_eam.html">eam/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/fs</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/opt</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne</A></TD><TD ><A HREF = "pair_gran.html">gran/hertzian</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gran.html">gran/history</A></TD><TD ><A HREF = "pair_gran.html">gran/no_history</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/opt</A></TD><TD ><A HREF = "pair_class2.html">lj/class2</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/tip4p</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD><TD ><A HREF = "pair_meam.html">meam</A></TD><TD ><A HREF = "pair_morse.html">morse</A></TD><TD ><A HREF = "pair_morse.html">morse/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_soft.html">soft</A></TD><TD ><A HREF = "pair_sw.html">sw</A></TD><TD ><A HREF = "pair_table.html">table</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_yukawa.html">yukawa</A>
</TD></TR></TABLE></DIV>
<HR>

13
doc/Section_commands.txt
View File

@ -246,8 +246,8 @@ Settings:
"group"_group.html, "mass"_mass.html, "min_modify"_min_modify.html,
"min_style"_min_style.html, "neigh_modify"_neigh_modify.html,
"neighbor"_neighbor.html, "reset_timestep"_reset_timestep.html,
"run_style"_run_style.html, "set"_set.html, "timestep"_timestep.html,
"velocity"_velocity.html
"run_style"_run_style.html, "set"_set.html, "shape"_shape.html,
"timestep"_timestep.html, "velocity"_velocity.html
Fixes:
@ -351,6 +351,7 @@ in the command's documentation.
"run"_run.html,
"run_style"_run_style.html,
"set"_set.html,
"shape"_shape.html,
"shell"_shell.html,
"special_bonds"_special_bonds.html,
"temper"_temper.html,
@ -382,7 +383,6 @@ description:
"deposit"_fix_deposit.html,
"drag"_fix_drag.html,
"efield"_fix_efield.html,
"ellipsoid"_fix_ellipsoid.html,
"enforce2d"_fix_enforce2d.html,
"freeze"_fix_freeze.html,
"gran/diag"_fix_gran_diag.html,
@ -399,9 +399,11 @@ description:
"npt/asphere"_fix_npt_asphere.html,
"nve"_fix_nve.html,
"nve/asphere"_fix_nve_asphere.html,
"nve/dipole"_fix_nve_dipole.html,
"nve/gran"_fix_nve_gran.html,
"nve/noforce"_fix_nve_noforce.html,
"nvt"_fix_nvt.html,
"nvt/sllod"_fix_nvt_sllod.html,
"nvt/asphere"_fix_nvt_asphere.html,
"orient/fcc"_fix_orient_fcc.html,
"planeforce"_fix_planeforce.html,
@ -418,9 +420,7 @@ description:
"spring/self"_fix_spring_self.html,
"temp/rescale"_fix_temp_rescale.html,
"tmd"_fix_tmd.html,
"uniaxial"_fix_uniaxial.html,
"viscous"_fix_viscous.html,
"volume/rescale"_fix_volume_rescale.html,
"wall/gran"_fix_wall_gran.html,
"wall/lj93"_fix_wall_lj93.html,
"wall/lj126"_fix_wall_lj126.html,
@ -443,7 +443,9 @@ description:
"rotate/gran"_compute_rotate_gran.html,
"stress/atom"_compute_stress_atom.html,
"temp"_compute_temp.html,
"temp/deform"_compute_temp_deform.html,
"temp/asphere"_compute_temp_asphere.html,
"temp/dipole"_compute_temp_dipole.html,
"temp/partial"_compute_temp_partial.html,
"temp/ramp"_compute_temp_ramp.html,
"temp/region"_compute_temp_region.html,
@ -462,6 +464,7 @@ full description:
"buck"_pair_buck.html,
"buck/coul/cut"_pair_buck.html,
"buck/coul/long"_pair_buck.html,
"dipole/cut"_pair_dipole/cut.html,
"dpd"_pair_dpd.html,
"eam"_pair_eam.html,
"eam/opt"_pair_eam.html,

2
doc/Section_modify.html
View File

@ -488,7 +488,7 @@ other variables = v_a, v_myvar, ...
math functions = div(x,y), mult(x,y), add(x,y), ...
group functions = mass(group), xcm(group,x), ...
atom values = x<B>123</B>, y<B>3</B>, vx<B>34</B>, ...
compute values = c_mytemp<B>0</B>, c_thermo_press<B>3</B>, ...
compute values = c_mytemp<B>0</B>, c_thermo_pressure<B>3</B>, ...
</P>
<P>Adding keywords for the <A HREF = "themo_style.html">thermo_style custom</A> command
(which can then be accessed by variables) was discussed

2
doc/Section_modify.txt
View File

@ -465,7 +465,7 @@ other variables = v_a, v_myvar, ...
math functions = div(x,y), mult(x,y), add(x,y), ...
group functions = mass(group), xcm(group,x), ...
atom values = x[123], y[3], vx[34], ...
compute values = c_mytemp[0], c_thermo_press[3], ...
compute values = c_mytemp[0], c_thermo_pressure[3], ...
Adding keywords for the "thermo_style custom"_themo_style.html command
(which can then be accessed by variables) was discussed

1
doc/Section_start.html
View File

@ -276,6 +276,7 @@ list of packages is as follows:
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR><TD >asphere </TD><TD > aspherical particles</TD></TR>
<TR><TD >class2 </TD><TD > class 2 force fields</TD></TR>
<TR><TD >colloid </TD><TD > colloidal particle force fields</TD></TR>
<TR><TD >dpd </TD><TD > dissipative particle dynamics (DPD) force field</TD></TR>
<TR><TD >granular </TD><TD > force fields and boundary conditions for granular systems</TD></TR>
<TR><TD >kspace </TD><TD > long-range Ewald and particle-mesh (PPPM) solvers</TD></TR>

1
doc/Section_start.txt
View File

@ -270,6 +270,7 @@ list of packages is as follows:
asphere : aspherical particles
class2 : class 2 force fields
colloid : colloidal particle force fields
dpd : dissipative particle dynamics (DPD) force field
granular : force fields and boundary conditions for granular systems
kspace : long-range Ewald and particle-mesh (PPPM) solvers

15
doc/atom_style.html
View File

@ -15,7 +15,7 @@
</P>
<PRE>atom_style style args
</PRE>
<UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>bond</I> or <I>charge</I> or <I>dpd</I> or <I>ellipsoid</I> or <I>full</I> or <I>granular</I> or <I>molecular</I> or <I>hybrid</I>
<UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>bond</I> or <I>charge</I> or <I>dipole</I> or <I>dpd</I> or <I>ellipsoid</I> or <I>full</I> or <I>granular</I> or <I>molecular</I> or <I>hybrid</I>
</UL>
<PRE> args = none for any style except <I>hybrid</I>
<I>hybrid</I> args = list of one or more sub-styles
@ -52,11 +52,12 @@ velocities, atom IDs and types.
<LI><I>atomic</I> = only the default values
<LI><I>bond</I> = bonds - e.g. bead-spring polymers
<LI><I>charge</I> = charge
<LI><I>dipole</I> = charge and dipole moment
<LI><I>dpd</I> = default values, also communicates velocities
<LI><I>ellipsoid</I> = quaternion for particle orientation, angular velocity/momentum
<LI><I>molecular</I> = bonds, angles, dihedrals, impropers - e.g. all-atom polymers
<LI><I>full</I> = molecular + charge - e.g. biomolecules, charged polymers
<LI><I>granular</I> = granular atoms with rotational properties
<LI><I>granular</I> = granular atoms with rotational properties
<LI><I>molecular</I> = bonds, angles, dihedrals, impropers - e.g. all-atom polymers
</UL>
<P>Typically, simulations require only a single (non-hybrid) atom style.
If some atoms in the simulation do not have all the properties defined
@ -81,9 +82,11 @@ section</A>.
</P>
<P>The <I>angle</I>, <I>bond</I>, <I>full</I>, and <I>molecular</I> styles are part of the
"molecular" package. The <I>granular</I> style is part of the "granular"
package. The <I>dpd</I> style is part of the "dpd" package. They are only
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
package. The <I>dpd</I> style is part of the "dpd" package. The <I>dipole</I>
style is part of the "dipole" package. The <I>ellipsoid</I> style is part
of the "ellipsoid" package. They are only enabled if LAMMPS was built
with that package. See the <A HREF = "Section_start.html#2_3">Making LAMMPS</A>
section for more info.
</P>
<P><B>Related commands:</B>
</P>

18
doc/atom_style.txt
View File

@ -12,8 +12,9 @@ atom_style command :h3
atom_style style args :pre
style = {angle} or {atomic} or {bond} or {charge} or {dpd} or {ellipsoid} or \
{full} or {granular} or {molecular} or {hybrid} :ul
style = {angle} or {atomic} or {bond} or {charge} or {dipole} or \
{dpd} or {ellipsoid} or {full} or {granular} or {molecular} or \
{hybrid} :ul
args = none for any style except {hybrid}
{hybrid} args = list of one or more sub-styles :pre
@ -49,11 +50,12 @@ velocities, atom IDs and types.
{atomic} = only the default values
{bond} = bonds - e.g. bead-spring polymers
{charge} = charge
{dipole} = charge and dipole moment
{dpd} = default values, also communicates velocities
{ellipsoid} = quaternion for particle orientation, angular velocity/momentum
{molecular} = bonds, angles, dihedrals, impropers - e.g. all-atom polymers
{full} = molecular + charge - e.g. biomolecules, charged polymers
{granular} = granular atoms with rotational properties :ul
{granular} = granular atoms with rotational properties
{molecular} = bonds, angles, dihedrals, impropers - e.g. all-atom polymers :ul
Typically, simulations require only a single (non-hybrid) atom style.
If some atoms in the simulation do not have all the properties defined
@ -78,9 +80,11 @@ This command cannot be used after the simulation box is defined by a
The {angle}, {bond}, {full}, and {molecular} styles are part of the
"molecular" package. The {granular} style is part of the "granular"
package. The {dpd} style is part of the "dpd" package. They are only
enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
package. The {dpd} style is part of the "dpd" package. The {dipole}
style is part of the "dipole" package. The {ellipsoid} style is part
of the "ellipsoid" package. They are only enabled if LAMMPS was built
with that package. See the "Making LAMMPS"_Section_start.html#2_3
section for more info.
[Related commands:]

7
doc/boundary.txt
View File

@ -38,10 +38,9 @@ commands.
The style {p} means the box is periodic, so that particles interact
across the boundary, and they can exit one end of the box and re-enter
the other end. A periodic dimension can change in size due to
constant pressure boundary conditions or volume rescaling (see the
"fix npt"_fix_npt.html and "fix volume/rescale"_fix_volume_rescale.html
commands). The {p} style must be applied to both faces of a
dimension.
constant pressure boundary conditions or box deformation (see the "fix
npt"_fix_npt.html and "fix deform"_fix_deform.html commands). The {p}
style must be applied to both faces of a dimension.
The styles {f}, {s}, and {m} mean the box is non-periodic, so that
particles do not interact across the boundary and do not move from one

35
doc/compute.html
View File

@ -41,24 +41,35 @@ calculate one or more values for each atom in the group can output
those values via the <A HREF = "dump.html">dump custom</A> command or the <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A> command.
</P>
<P>LAMMPS creates its own computes for thermodynamic output and dumping
atom snapshots. Likewise fixes that compute temperature or pressure
create their own computes. These are discussed in the documentation
for <A HREF = "thermo_style.html">thermo_style</A>, <A HREF = "dump.html">dump custom</A>, and
specific <A HREF = "fix.html">fix</A> commands.
<P>LAMMPS creates its own computes for thermodynamic output. Two
computes are always created, named "thermo_temp" and
"thermo_pressure", as if these commands had been invoked:
</P>
<PRE>compute thermo_temp all temp
compute thermo_pressure all pressure thermo_temp
</PRE>
<P>Additional computes are created if the thermo style requires it. See
the documentation for the <A HREF = "thermo_style.html">thermo_style</A> command.
</P>
<P>The dumping of atom snapshots and fixes that compute temperature or
pressure also create computes as required. These are discussed in the
documentation for the <A HREF = "dump.html">dump custom</A> and specific
<A HREF = "fix.html">fix</A> commands.
</P>
<P>In all these cases, the default computes can be replaced by computes
defined in the input script, as described by the
<A HREF = "thermo_modify.html">thermo_modify</A> and <A HREF = "fix_modify.html">fix modify</A>
commands. Code for new computes can also be added to LAMMPS (see
<A HREF = "Section_modify.html">this section</A> of the manaul) and their
commands.
</P>
<P>Properties of either a default of user-defined compute can be modified
via the <A HREF = "compute_modify.html">compute_modify</A> command.
</P>
<P>Computes can be deleted with the <A HREF = "uncompute.html">uncompute</A> command.
</P>
<P>Code for new computes can be added to LAMMPS (see <A HREF = "Section_modify.html">this
section</A> of the manaul) and the results of their
calculations accessed in the various ways described above.
</P>
<P>Properties of a compute can be modified via the
<A HREF = "compute_modify.html">compute_modify</A> command.
</P>
<P>Compute can be deleted with the <A HREF = "uncompute.html">uncompute</A> command.
</P>
<P>Each compute style has its own doc page which describes its arguments
and what it does. Here is an alphabetic list of compute styles
defined in LAMMPS:

35
doc/compute.txt
View File

@ -38,24 +38,35 @@ calculate one or more values for each atom in the group can output
those values via the "dump custom"_dump.html command or the "fix
ave/spatial"_fix_ave_spatial.html command.
LAMMPS creates its own computes for thermodynamic output and dumping
atom snapshots. Likewise fixes that compute temperature or pressure
create their own computes. These are discussed in the documentation
for "thermo_style"_thermo_style.html, "dump custom"_dump.html, and
specific "fix"_fix.html commands.
LAMMPS creates its own computes for thermodynamic output. Two
computes are always created, named "thermo_temp" and
"thermo_pressure", as if these commands had been invoked:
compute thermo_temp all temp
compute thermo_pressure all pressure thermo_temp :pre
Additional computes are created if the thermo style requires it. See
the documentation for the "thermo_style"_thermo_style.html command.
The dumping of atom snapshots and fixes that compute temperature or
pressure also create computes as required. These are discussed in the
documentation for the "dump custom"_dump.html and specific
"fix"_fix.html commands.
In all these cases, the default computes can be replaced by computes
defined in the input script, as described by the
"thermo_modify"_thermo_modify.html and "fix modify"_fix_modify.html
commands. Code for new computes can also be added to LAMMPS (see
"this section"_Section_modify.html of the manaul) and their
commands.
Properties of either a default of user-defined compute can be modified
via the "compute_modify"_compute_modify.html command.
Computes can be deleted with the "uncompute"_uncompute.html command.
Code for new computes can be added to LAMMPS (see "this
section"_Section_modify.html of the manaul) and the results of their
calculations accessed in the various ways described above.
Properties of a compute can be modified via the
"compute_modify"_compute_modify.html command.
Compute can be deleted with the "uncompute"_uncompute.html command.
Each compute style has its own doc page which describes its arguments
and what it does. Here is an alphabetic list of compute styles
defined in LAMMPS:

2
doc/compute_rotate_dipole.html
View File

@ -25,7 +25,7 @@
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the total rotational energy of a
group of dipolar atoms.
group of atoms with point dipole moments.
</P>
<P>The rotational energy is calculated as the sum of 1/2 I w^2 over all
the atoms in the group, where I is the moment of inertia of a

2
doc/compute_rotate_dipole.txt
View File

@ -22,7 +22,7 @@ compute 1 all rotate/dipole :pre
[Description:]
Define a computation that calculates the total rotational energy of a
group of dipolar atoms.
group of atoms with point dipole moments.
The rotational energy is calculated as the sum of 1/2 I w^2 over all
the atoms in the group, where I is the moment of inertia of a

3
doc/compute_temp_asphere.html
View File

@ -35,8 +35,7 @@ moment of inertia and w is the angular velocity.
</P>
<P><B>Restrictions:</B>
</P>
<P>Can only be used if LAMMPS was built with the "asphere" package. Can
only be used with atom_style ellipsoid.
<P>Can only be used if LAMMPS was built with the "asphere" package.
</P>
<P><B>Related commands:</B>
</P>

3
doc/compute_temp_asphere.txt
View File

@ -32,8 +32,7 @@ moment of inertia and w is the angular velocity.
[Restrictions:]
Can only be used if LAMMPS was built with the "asphere" package. Can
only be used with atom_style ellipsoid.
Can only be used if LAMMPS was built with the "asphere" package.
[Related commands:]

9
doc/compute_temp_ramp.html
View File

@ -33,15 +33,15 @@
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the temperature of a group of
atoms, while subtracting out an imposed velocity on the system before
atoms, after subtracting out an imposed velocity on the system before
computing the kinetic energy. A compute of this style can be used by
any command that computes a temperature,
e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A>, <A HREF = "fix_npt.html">fix npt</A>, etc.
</P>
<P>The meaning of the arguments for this command is the same as for the
<A HREF = "velocity.html">velocity</A> command which was presumably used to impose
the velocity.
<A HREF = "velocity.html">velocity ramp</A> command which was presumably used to
impose the velocity.
</P>
<P>The <I>units</I> keyword determines the meaning of the distance units used
for coordinates (c1,c2) and velocities (vlo,vhi). A <I>box</I> value
@ -72,7 +72,8 @@ needed, the subtracted degrees-of-freedom can be altered using the
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_temp_region.html">compute
temp/region</A>, <A HREF = "compute_pressure.html">compute
temp/region</A>, <A HREF = "compute_temp_deform.html">compute
temp/deform</A>, <A HREF = "compute_pressure.html">compute
pressure</A>
</P>
<P><B>Default:</B>

7
doc/compute_temp_ramp.txt
View File

@ -29,15 +29,15 @@ temperature 2nd middle ramp vx 0 8 y 2 12 units lattice :pre
[Description:]
Define a computation that calculates the temperature of a group of
atoms, while subtracting out an imposed velocity on the system before
atoms, after subtracting out an imposed velocity on the system before
computing the kinetic energy. A compute of this style can be used by
any command that computes a temperature,
e.g. "thermo_modify"_thermo_modify.html, "fix
temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_npt.html, etc.
The meaning of the arguments for this command is the same as for the
"velocity"_velocity.html command which was presumably used to impose
the velocity.
"velocity ramp"_velocity.html command which was presumably used to
impose the velocity.
The {units} keyword determines the meaning of the distance units used
for coordinates (c1,c2) and velocities (vlo,vhi). A {box} value
@ -69,6 +69,7 @@ needed, the subtracted degrees-of-freedom can be altered using the
"compute temp"_compute_temp.html, "compute
temp/region"_compute_temp_region.html, "compute
temp/deform"_compute_temp_deform.html, "compute
pressure"_compute_pressure.html
[Default:]

122
doc/create_atoms.html
View File

@ -13,67 +13,107 @@
</H3>
<P><B>Syntax:</B>
</P>
<PRE>create_atoms type keyword values ...
<PRE>create_atoms type style args keyword values ...
</PRE>
<UL><LI>type = atom type (1-N) of atoms to create on a lattice
<UL><LI>type = atom type (1-Ntypes) of atoms to create
<LI>zero or more keyword/value pairs may be appended
<LI>style = <I>box</I> or <I>region</I> or <I>single</I>
<LI>keyword = <I>region</I> or <I>basis</I>
<PRE> <I>region</I> value = region-ID
<PRE> <I>box</I> args = none
<I>region</I> args = region-ID
region-ID = atoms will only be created if contained in the region
<I>basis</I> values = M itype
<I>single</I> args = x y z
x,y,z = coordinates of a single atom (distance units)
</PRE>
<LI>zero or more keyword/value pairs may be appended to the args
<LI>keyword = <I>basis</I> or <I>units</I>
<PRE> <I>basis</I> values = M itype
M = which basis atom
itype = atom type (1-N) to assign to the basis atom
itype = atom type (1-N) to assign to this basis atom
<I>units</I> value = <I>lattice</I> or <I>box</I>
<I>lattice</I> = the geometry is defined in lattice units
<I>box</I> = the geometry is defined in simulation box units
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>create_atoms 1
create_atoms 3 region regsphere
create_atoms 1 basis 2 5
<PRE>create_atoms 1 box
create_atoms 3 region regsphere basis 2 3
create_atoms 3 single 0 0 5
</PRE>
<P><B>Description:</B>
</P>
<P>This command creates atoms on a lattice as an alternative to reading
in their coordinates via a <A HREF = "read_data.html">read_data</A> or
<A HREF = "read_restart.html">read_restart</A> command. A simulation box must
already exist, which is typically created via the
<A HREF = "create_box.html">create_box</A> command.
<P>This command creates atoms on a lattice or a single atom as an
alternative to reading in their coordinates via a
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
command. A simulation box must already exist, which is typically
created via the <A HREF = "create_box.html">create_box</A> command. Before using
this command, a lattice must also be defined using the
<A HREF = "lattice.html">lattice</A> command. The only exception is for the
<I>single</I> style with units = box.
</P>
<P>Before using this command, a lattice must be defined using the
<A HREF = "lattice.html">lattice</A> command. If a region is not specified, the
create_atoms command fills the entire simulation box with atoms on the
lattice. If a region is specified (see the <A HREF = "region.html">region</A>
command), then the geometric volume is filled that is inside the
simulation box and is also consistent with the region volume. Note
that a region can be specified so that its "volume" is either inside
or outside a geometric boundary.
<P>For the <I>box</I> style, the create_atoms command fills the entire
simulation box with atoms on the lattice. If your box is periodic,
you should insure its size is a multiple of the lattice spacings, to
avoid unwanted atom overlap at the box boundaries.
</P>
<P>The <A HREF = "lattice.html">lattice</A> command specifies one or more basis atoms
in each unit cell. By default, when created, all basis atoms are
assigned the argument <I>type</I> as their atom type. The keyword <I>basis</I>
can be used to override the default for one or more basis atoms and
assign them a different atom type.
<P>For the <I>region</I> style, the geometric volume is filled that is inside
the simulation box and is also consistent with the region volume. See
the <A HREF = "region.html">region</A> command for details. Note that a region can
be specified so that its "volume" is either inside or outside a
geometric boundary.
</P>
<P>By using the create_atoms command multiple times (interleaved with
<A HREF = "lattice.html">lattice</A> commands specifying different orientations),
grain boundaries can be created. Using the create_atoms command in
conjunction with the <A HREF = "delete_atoms.html">delete_atoms</A> command,
reasonably complex geometries can be created. The create_atoms
command can also be used to add atoms to a system previously read in
from a data or restart file. In all these cases, care should be taken
to insure that new atoms do not overlap existing atoms
inappropriately.
<P>For the <I>single</I> style, a single atom is added to the system at the
specified coordinates. This can be useful for debugging purposes or
to create a tiny system with a handful of atoms at specified
positions.
</P>
<P>Created atoms are assigned a velocity of 0.0.
<P>The <I>basis</I> keyword specifies an atom type that will be assigned to
specific basis atoms as they are created. See the
<A HREF = "lattice.html">lattice</A> command for specifics on how basis atoms are
defined for the unit cell of the lattice. By default, all created
atoms are assigned the argument <I>type</I> as their atom type.
</P>
<P>The <I>units</I> keyword determines the meaning of the distance units used
to specify the coordinates of the one atom created by the <I>single</I>
style. A <I>box</I> value selects standard distance units as defined by
the <A HREF = "units.html">units</A> command, e.g. Angstroms for units = real or
metal. A <I>lattice</I> value means the distance units are in lattice
spacings.
</P>
<P>Note that this command adds atoms to those that already exist. By
using the create_atoms command multiple times, multiple sets of atoms
can be added to the simulation. For example, interleaving
create_atoms with <A HREF = "lattice.html">lattice</A> commands specifying different
orientations, grain boundaries can be created. By using the
create_atoms command in conjunction with the
<A HREF = "delete_atoms.html">delete_atoms</A> command, reasonably complex
geometries can be created. The create_atoms command can also be used
to add atoms to a system previously read in from a data or restart
file. In all these cases, care should be taken to insure that new
atoms do not overlap existing atoms inappropriately. The
<A HREF = "delete_atoms.html">delete_atoms</A> command can be used to handle
overlaps.
</P>
<P>Aside from their position and atom type, other properties of created
atoms are set to 0.0, e.g velocity, charge, etc. These properties can
be changed via the <A HREF = "velocity.html">velocity</A> or <A HREF = "set.html">set</A>
commands.
</P>
<P>Atom IDs are assigned to created atoms in the following way. The
collection of created atoms are assigned consecutive IDs that start
immediately following the largest atom ID existing before the
create_atoms command was invoked. When a simulation is performed on
different numbers of processors, there is no guarantee a particular
created atom will be assigned the same ID.
</P>
<P><B>Restrictions:</B>
</P>
<P>An <A HREF = "atom_style.html">atom_style</A> and <A HREF = "lattice.html">lattice</A> must be
previously defined to use this command.
<P>An <A HREF = "atom_style.html">atom_style</A> must be previously defined to use this
command.
</P>
<P><B>Related commands:</B>
</P>

116
doc/create_atoms.txt
View File

@ -10,63 +10,101 @@ create_atoms command :h3
[Syntax:]
create_atoms type keyword values ... :pre
create_atoms type style args keyword values ... :pre
type = atom type (1-N) of atoms to create on a lattice :ulb,l
zero or more keyword/value pairs may be appended :l
keyword = {region} or {basis} :l
{region} value = region-ID
type = atom type (1-Ntypes) of atoms to create :ulb,l
style = {box} or {region} or {single} :l
{box} args = none
{region} args = region-ID
region-ID = atoms will only be created if contained in the region
{single} args = x y z
x,y,z = coordinates of a single atom (distance units) :pre
zero or more keyword/value pairs may be appended to the args :l
keyword = {basis} or {units} :l
{basis} values = M itype
M = which basis atom
itype = atom type (1-N) to assign to the basis atom :pre
itype = atom type (1-N) to assign to this basis atom
{units} value = {lattice} or {box}
{lattice} = the geometry is defined in lattice units
{box} = the geometry is defined in simulation box units :pre
:ule
[Examples:]
create_atoms 1
create_atoms 3 region regsphere
create_atoms 1 basis 2 5 :pre
create_atoms 1 box
create_atoms 3 region regsphere basis 2 3
create_atoms 3 single 0 0 5 :pre
[Description:]
This command creates atoms on a lattice as an alternative to reading
in their coordinates via a "read_data"_read_data.html or
"read_restart"_read_restart.html command. A simulation box must
already exist, which is typically created via the
"create_box"_create_box.html command.
This command creates atoms on a lattice or a single atom as an
alternative to reading in their coordinates via a
"read_data"_read_data.html or "read_restart"_read_restart.html
command. A simulation box must already exist, which is typically
created via the "create_box"_create_box.html command. Before using
this command, a lattice must also be defined using the
"lattice"_lattice.html command. The only exception is for the
{single} style with units = box.
Before using this command, a lattice must be defined using the
"lattice"_lattice.html command. If a region is not specified, the
create_atoms command fills the entire simulation box with atoms on the
lattice. If a region is specified (see the "region"_region.html
command), then the geometric volume is filled that is inside the
simulation box and is also consistent with the region volume. Note
that a region can be specified so that its "volume" is either inside
or outside a geometric boundary.
For the {box} style, the create_atoms command fills the entire
simulation box with atoms on the lattice. If your box is periodic,
you should insure its size is a multiple of the lattice spacings, to
avoid unwanted atom overlap at the box boundaries.
The "lattice"_lattice.html command specifies one or more basis atoms
in each unit cell. By default, when created, all basis atoms are
assigned the argument {type} as their atom type. The keyword {basis}
can be used to override the default for one or more basis atoms and
assign them a different atom type.
For the {region} style, the geometric volume is filled that is inside
the simulation box and is also consistent with the region volume. See
the "region"_region.html command for details. Note that a region can
be specified so that its "volume" is either inside or outside a
geometric boundary.
By using the create_atoms command multiple times (interleaved with
"lattice"_lattice.html commands specifying different orientations),
grain boundaries can be created. Using the create_atoms command in
conjunction with the "delete_atoms"_delete_atoms.html command,
reasonably complex geometries can be created. The create_atoms
command can also be used to add atoms to a system previously read in
from a data or restart file. In all these cases, care should be taken
to insure that new atoms do not overlap existing atoms
inappropriately.
For the {single} style, a single atom is added to the system at the
specified coordinates. This can be useful for debugging purposes or
to create a tiny system with a handful of atoms at specified
positions.
Created atoms are assigned a velocity of 0.0.
The {basis} keyword specifies an atom type that will be assigned to
specific basis atoms as they are created. See the
"lattice"_lattice.html command for specifics on how basis atoms are
defined for the unit cell of the lattice. By default, all created
atoms are assigned the argument {type} as their atom type.
The {units} keyword determines the meaning of the distance units used
to specify the coordinates of the one atom created by the {single}
style. A {box} value selects standard distance units as defined by
the "units"_units.html command, e.g. Angstroms for units = real or
metal. A {lattice} value means the distance units are in lattice
spacings.
Note that this command adds atoms to those that already exist. By
using the create_atoms command multiple times, multiple sets of atoms
can be added to the simulation. For example, interleaving
create_atoms with "lattice"_lattice.html commands specifying different
orientations, grain boundaries can be created. By using the
create_atoms command in conjunction with the
"delete_atoms"_delete_atoms.html command, reasonably complex
geometries can be created. The create_atoms command can also be used
to add atoms to a system previously read in from a data or restart
file. In all these cases, care should be taken to insure that new
atoms do not overlap existing atoms inappropriately. The
"delete_atoms"_delete_atoms.html command can be used to handle
overlaps.
Aside from their position and atom type, other properties of created
atoms are set to 0.0, e.g velocity, charge, etc. These properties can
be changed via the "velocity"_velocity.html or "set"_set.html
commands.
Atom IDs are assigned to created atoms in the following way. The
collection of created atoms are assigned consecutive IDs that start
immediately following the largest atom ID existing before the
create_atoms command was invoked. When a simulation is performed on
different numbers of processors, there is no guarantee a particular
created atom will be assigned the same ID.
[Restrictions:]
An "atom_style"_atom_style.html and "lattice"_lattice.html must be
previously defined to use this command.
An "atom_style"_atom_style.html must be previously defined to use this
command.
[Related commands:]

12
doc/create_box.html
View File

@ -45,12 +45,12 @@ origin given by a = (xhi-xlo,0,0); b = (xy,yhi-ylo,0); c =
</P>
<P>A prism region used with the create_box command must have tilt factors
(xy,xz,yz) that do not skew the box more than half the distance of the
perpendicular box length. For example, if ylo = 2 and yhi = 12, then
the y box length is 10 and the xy tilt factor must be between -5 and
5. Similarly, both xz and yz must be between -(zhi-zlo)/2 and
+(zhi-zlo)/2. From a mechanics persepctive this is equivalent to
saying the shear strain of the system (sideways displacement divided
by perpendicular box length) must be between -0.5 and 0.5.
parallel box length. For example, if xlo = 2 and xhi = 12, then the x
box length is 10 and the xy tilt factor must be between -5 and 5.
Similarly, both xz and yz must be between -(xhi-xlo)/2 and
+(yhi-ylo)/2. Note that this is not a limitation, since if the
maximum tilt factor is 5 (as in this example), then configurations
with tilt = ..., -15, -5, 5, 15, 25, ... are all equivalent.
</P>
<P>When a prism region is used, the simulation domain must be periodic in
any dimensions with a non-zero tilt factor, as defined by the

12
doc/create_box.txt
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@ -42,12 +42,12 @@ origin given by a = (xhi-xlo,0,0); b = (xy,yhi-ylo,0); c =
A prism region used with the create_box command must have tilt factors
(xy,xz,yz) that do not skew the box more than half the distance of the
perpendicular box length. For example, if ylo = 2 and yhi = 12, then
the y box length is 10 and the xy tilt factor must be between -5 and
5. Similarly, both xz and yz must be between -(zhi-zlo)/2 and
+(zhi-zlo)/2. From a mechanics persepctive this is equivalent to
saying the shear strain of the system (sideways displacement divided
by perpendicular box length) must be between -0.5 and 0.5.
parallel box length. For example, if xlo = 2 and xhi = 12, then the x
box length is 10 and the xy tilt factor must be between -5 and 5.
Similarly, both xz and yz must be between -(xhi-xlo)/2 and
+(yhi-ylo)/2. Note that this is not a limitation, since if the
maximum tilt factor is 5 (as in this example), then configurations
with tilt = ..., -15, -5, 5, 15, 25, ... are all equivalent.
When a prism region is used, the simulation domain must be periodic in
any dimensions with a non-zero tilt factor, as defined by the

13
doc/dipole.html
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@ -16,7 +16,7 @@
<PRE>dipole I value
</PRE>
<UL><LI>I = atom type (see asterisk form below)
<LI>value = dipole
<LI>value = dipole moment (dipole units)
</UL>
<P><B>Examples:</B>
</P>
@ -33,6 +33,9 @@ if the atom type has no dipole moment. Dipole values can also be set
in the <A HREF = "read_data.html">read_data</A> data file. See the
<A HREF = "units.html">units</A> command for a discussion of dipole units.
</P>
<P>Currently, only <A HREF = "atom_style.html">atom_style dipole</A> requires dipole
moments be set.
</P>
<P>I can be specified in one of two ways. An explicit numeric value can
be used, as in the 1st example above. Or a wild-card asterisk can be
used to set the dipole moment for multiple atom types. This takes the
@ -42,8 +45,8 @@ leading asterisk means all types from 1 to n (inclusive). A trailing
asterisk means all types from n to N (inclusive). A middle asterisk
means all types from m to n (inclusive).
</P>
<P>A line in a data file that specifies a dipole moment uses the exact
same format as the arguments of the dipole command in an input script,
<P>A line in a data file that specifies a dipole moment uses the same
format as the arguments of the dipole command in an input script,
except that no wild-card asterisk can be used. For example, under the
"Dipoles" section of a data file, the line that corresponds to the 1st
example above would be listed as
@ -57,7 +60,9 @@ example above would be listed as
<A HREF = "create_box.html">create_box</A> command.
</P>
<P>All dipoles moments must be defined before a simulation is run (if the
atom style requires dipoles be set).
atom style requires dipoles be set). They must also all be defined
before a <A HREF = "set.html">set dipole</A> or <A HREF = "set.html">set dipole/random</A> command
is used.
</P>
<P><B>Related commands:</B> none
</P>

13
doc/dipole.txt
View File

@ -13,7 +13,7 @@ dipole command :h3
dipole I value :pre
I = atom type (see asterisk form below)
value = dipole :ul
value = dipole moment (dipole units) :ul
[Examples:]
@ -30,6 +30,9 @@ if the atom type has no dipole moment. Dipole values can also be set
in the "read_data"_read_data.html data file. See the
"units"_units.html command for a discussion of dipole units.
Currently, only "atom_style dipole"_atom_style.html requires dipole
moments be set.
I can be specified in one of two ways. An explicit numeric value can
be used, as in the 1st example above. Or a wild-card asterisk can be
used to set the dipole moment for multiple atom types. This takes the
@ -39,8 +42,8 @@ leading asterisk means all types from 1 to n (inclusive). A trailing
asterisk means all types from n to N (inclusive). A middle asterisk
means all types from m to n (inclusive).
A line in a data file that specifies a dipole moment uses the exact
same format as the arguments of the dipole command in an input script,
A line in a data file that specifies a dipole moment uses the same
format as the arguments of the dipole command in an input script,
except that no wild-card asterisk can be used. For example, under the
"Dipoles" section of a data file, the line that corresponds to the 1st
example above would be listed as
@ -54,7 +57,9 @@ This command must come after the simulation box is defined by a
"create_box"_create_box.html command.
All dipoles moments must be defined before a simulation is run (if the
atom style requires dipoles be set).
atom style requires dipoles be set). They must also all be defined
before a "set dipole"_set.html or "set dipole/random"_set.html command
is used.
[Related commands:] none

38
doc/displace_atoms.html
View File

@ -17,7 +17,7 @@
</PRE>
<UL><LI>group-ID = ID of group of atoms to displace
<LI>style = <I>move</I> or <I>ramp</I>
<LI>style = <I>move</I> or <I>ramp</I> or <I>random</I>
<PRE> <I>move</I> args = delx dely delz
delx,dely,delz = distance to displace in each dimension (distance units)
@ -25,7 +25,10 @@
ddim = <I>x</I> or <I>y</I> or <I>z</I>
dlo,dhi = displacement distance between dlo and dhi (distance units)
dim = <I>x</I> or <I>y</I> or <I>z</I>
clo,chi = lower and upper bound of domain to displace (distance units)
clo,chi = lower and upper bound of domain to displace (distance units)
<I>random</I> args = dx dy dz seed
dx,dy,dz = random displacement magnitude in each dimension (distance units)
seed = random # seed (8 digits or less)
</PRE>
<LI>zero or more keyword/value pairs may be appended to the args
@ -42,25 +45,34 @@ displace_atoms flow ramp x 0.0 5.0 y 2.0 20.5
<P><B>Description:</B>
</P>
<P>Displace a group of atoms. This can be used to move atoms a large
distance before beginning a simulation. For example, in a shear
simulation, an initial strain can be imposed on the system. Or two
groups of atoms can be brought into closer proximity.
distance before beginning a simulation or to randomize atoms initially
on a lattice. For example, in a shear simulation, an initial strain
can be imposed on the system. Or two groups of atoms can be brought
into closer proximity.
</P>
<P>The <I>move</I> style displaces the group of atoms by the specified 3d
distance. The <I>ramp</I> style displaces atoms a variable amount in one
dimension depending on the atom's coordinate in a (possibly) different
distance.
</P>
<P>The <I>ramp</I> style displaces atoms a variable amount in one dimension
depending on the atom's coordinate in a (possibly) different
dimension. For example, the second example command displaces atoms in
the x-direction an amount between 0.0 and 5.0 distance units. Each
atom's displacement depends on the fractional distance its y
coordinate is between 2.0 and 20.5. Atoms with y-coordinates outside
those bounds will be moved the minimum (0.0) or maximum (5.0) amount.
</P>
<P>Distance units for the displacement are determined by the setting of
<I>box</I> or <I>lattice</I> for the <I>units</I> keyword. <I>Box</I> means distance
units as defined by the <A HREF = "units.html">units</A> command - e.g. Angstroms
for <I>real</I> units. <I>Lattice</I> means distance units are in lattice
spacings. The <A HREF = "lattice.html">lattice</A> command must have been
previously used to define the lattice spacing.
<P>The <I>random</I> style independently moves each atom in the group by a
random displacement, uniformly sampled from a value between -dx and
+dx in the x dimension, and similarly for y and z. Random numbers are
used in such a way that the displacement of a particular atom is the
same, regardless of how many processors are being used.
</P>
<P>Distance units for displacement are determined by the setting of <I>box</I>
or <I>lattice</I> for the <I>units</I> keyword. <I>Box</I> means distance units as
defined by the <A HREF = "units.html">units</A> command - e.g. Angstroms for <I>real</I>
units. <I>Lattice</I> means distance units are in lattice spacings. The
<A HREF = "lattice.html">lattice</A> command must have been previously used to
define the lattice spacing.
</P>
<P>Care should be taken not to move atoms on top of other atoms. After
the move, atoms are remapped into the periodic simulation box if

38
doc/displace_atoms.txt
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@ -13,14 +13,17 @@ displace_atoms command :h3
displace_atoms group-ID style args keyword value ... :pre
group-ID = ID of group of atoms to displace :ulb,l
style = {move} or {ramp} :l
style = {move} or {ramp} or {random} :l
{move} args = delx dely delz
delx,dely,delz = distance to displace in each dimension (distance units)
{ramp} args = ddim dlo dhi dim clo chi
ddim = {x} or {y} or {z}
dlo,dhi = displacement distance between dlo and dhi (distance units)
dim = {x} or {y} or {z}
clo,chi = lower and upper bound of domain to displace (distance units) :pre
clo,chi = lower and upper bound of domain to displace (distance units)
{random} args = dx dy dz seed
dx,dy,dz = random displacement magnitude in each dimension (distance units)
seed = random # seed (8 digits or less) :pre
zero or more keyword/value pairs may be appended to the args :l
keyword = {units}
value = {box} or {lattice} :pre
@ -34,25 +37,34 @@ displace_atoms flow ramp x 0.0 5.0 y 2.0 20.5 :pre
[Description:]
Displace a group of atoms. This can be used to move atoms a large
distance before beginning a simulation. For example, in a shear
simulation, an initial strain can be imposed on the system. Or two
groups of atoms can be brought into closer proximity.
distance before beginning a simulation or to randomize atoms initially
on a lattice. For example, in a shear simulation, an initial strain
can be imposed on the system. Or two groups of atoms can be brought
into closer proximity.
The {move} style displaces the group of atoms by the specified 3d
distance. The {ramp} style displaces atoms a variable amount in one
dimension depending on the atom's coordinate in a (possibly) different
distance.
The {ramp} style displaces atoms a variable amount in one dimension
depending on the atom's coordinate in a (possibly) different
dimension. For example, the second example command displaces atoms in
the x-direction an amount between 0.0 and 5.0 distance units. Each
atom's displacement depends on the fractional distance its y
coordinate is between 2.0 and 20.5. Atoms with y-coordinates outside
those bounds will be moved the minimum (0.0) or maximum (5.0) amount.
Distance units for the displacement are determined by the setting of
{box} or {lattice} for the {units} keyword. {Box} means distance
units as defined by the "units"_units.html command - e.g. Angstroms
for {real} units. {Lattice} means distance units are in lattice
spacings. The "lattice"_lattice.html command must have been
previously used to define the lattice spacing.
The {random} style independently moves each atom in the group by a
random displacement, uniformly sampled from a value between -dx and
+dx in the x dimension, and similarly for y and z. Random numbers are
used in such a way that the displacement of a particular atom is the
same, regardless of how many processors are being used.
Distance units for displacement are determined by the setting of {box}
or {lattice} for the {units} keyword. {Box} means distance units as
defined by the "units"_units.html command - e.g. Angstroms for {real}
units. {Lattice} means distance units are in lattice spacings. The
"lattice"_lattice.html command must have been previously used to
define the lattice spacing.
Care should be taken not to move atoms on top of other atoms. After
the move, atoms are remapped into the periodic simulation box if

2
doc/dump_modify.html
View File

@ -30,7 +30,7 @@
<I>region</I> arg = region-ID or "none"
<I>thresh</I> args = attribute operation value
attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
operation = < or <= or > or >= or = or <>
operation = "<" or "<=" or ">" or ">=" or "==" or "!="
value = numeric value to compare to
these 3 args can be replaced by the word "none" to turn off threshholding

2
doc/dump_modify.txt
View File

@ -24,7 +24,7 @@ keyword = {format} or {scale} or {image} or {header} or {flush} or {region} or {
{region} arg = region-ID or "none"
{thresh} args = attribute operation value
attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
operation = < or <= or > or >= or = or <>
operation = "<" or "<=" or ">" or ">=" or "==" or "!="
value = numeric value to compare to
these 3 args can be replaced by the word "none" to turn off threshholding
:pre

4
doc/fix.txt
View File

@ -108,11 +108,7 @@ Here is an alphabetic list of fix styles defined in LAMMPS:
"fix temp/rescale"_fix_temp_rescale.html - temperature control by \
velocity rescaling
"fix tmd"_fix_tmd.html - guide a group of atoms to a new configuration
"fix uniaxial"_fix_uniaxial.html - uniaxial straining of system while \
preserving total volume
"fix viscous"_fix_viscous.html - viscous damping for granular simulations
"fix volume/rescale"_fix_volume_rescale.html - density control by \
volume rescaling
"fix wall/gran"_fix_wall_gran.html - frictional wall(s) for \
granular simulations
"fix wall/lj93"_fix_wall_lj93.html - Lennard-Jones 9-3 wall

3
doc/fix_freeze.html
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@ -29,8 +29,7 @@ for preventing certain particles from moving in a simulation.
</P>
<P><B>Restrictions:</B>
</P>
<P>Can only be used if LAMMPS was built with the "granular" package. Can
only be used with atom_style granular.
<P>Can only be used if LAMMPS was built with the "granular" package.
</P>
<P>There can only be a single freeze fix defined. This is because other
parts of the code (pair potentials, thermodynamics, etc) treat frozen

3
doc/fix_freeze.txt
View File

@ -26,8 +26,7 @@ for preventing certain particles from moving in a simulation.
[Restrictions:]
Can only be used if LAMMPS was built with the "granular" package. Can
only be used with atom_style granular.
Can only be used if LAMMPS was built with the "granular" package.
There can only be a single freeze fix defined. This is because other
parts of the code (pair potentials, thermodynamics, etc) treat frozen

3
doc/fix_gran_diag.html
View File

@ -36,8 +36,7 @@ written to the file are averaged over all atoms in the bin.
</P>
<P><B>Restrictions:</B>
</P>
<P>Can only be used if LAMMPS was built with the "granular" package. Can
only be used with atom_style granular.
<P>Can only be used if LAMMPS was built with the "granular" package.
</P>
<P><B>Related commands:</B>
</P>

3
doc/fix_gran_diag.txt
View File

@ -33,8 +33,7 @@ written to the file are averaged over all atoms in the bin.
[Restrictions:]
Can only be used if LAMMPS was built with the "granular" package. Can
only be used with atom_style granular.
Can only be used if LAMMPS was built with the "granular" package.
[Related commands:]

2
doc/fix_langevin.html
View File

@ -23,7 +23,7 @@
<LI>damp = damping parameter (time units)
<LI>seed = random # seed to use for white noise (integer > 0 and < 900000000)
<LI>seed = random # seed to use for white noise (8 digits or less)
<LI>zero or more keyword/value pairs may be appended to the args

2
doc/fix_langevin.txt
View File

@ -16,7 +16,7 @@ ID, group-ID are documented in "fix"_fix.html command :ulb,l
langevin = style name of this fix command :l
Tstart,Tstop = desired temperature at start/end of run (temperature units) :l
damp = damping parameter (time units) :l
seed = random # seed to use for white noise (integer > 0 and < 900000000) :l
seed = random # seed to use for white noise (8 digits or less) :l
zero or more keyword/value pairs may be appended to the args :l
keyword = {axes} or {scale} or {region}
{axes} values = xflag yflag zflag

6
doc/fix_nph.html
View File

@ -136,13 +136,13 @@ fix group.
</P>
<P>Note that these are NOT the computes used by thermodynamic output (see
the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>
and <I>thermo_press</I>. This means you can change the attributes of this
fix's temperature or pressure via the
and <I>thermo_pressure</I>. This means you can change the attributes of
this fix's temperature or pressure via the
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
or pressure during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> or
<I>thermo_press</I> will have no effect on this fix. Alternatively, you
<I>thermo_pressure</I> will have no effect on this fix. Alternatively, you
can directly assign a new compute (for calculating temeperature or
pressure) that you have defined to this fix via the
<A HREF = "fix_modify.html">fix_modify</A> command. If you do this, note that the

6
doc/fix_nph.txt
View File

@ -126,13 +126,13 @@ fix group.
Note that these are NOT the computes used by thermodynamic output (see
the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}
and {thermo_press}. This means you can change the attributes of this
fix's temperature or pressure via the
and {thermo_pressure}. This means you can change the attributes of
this fix's temperature or pressure via the
"compute_modify"_compute_modify.html command or print this temperature
or pressure during thermodyanmic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} or
{thermo_press} will have no effect on this fix. Alternatively, you
{thermo_pressure} will have no effect on this fix. Alternatively, you
can directly assign a new compute (for calculating temeperature or
pressure) that you have defined to this fix via the
"fix_modify"_fix_modify.html command. If you do this, note that the

6
doc/fix_npt.html
View File

@ -140,13 +140,13 @@ fix group.
</P>
<P>Note that these are NOT the computes used by thermodynamic output (see
the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>
and <I>thermo_press</I>. This means you can change the attributes of this
fix's temperature or pressure via the
and <I>thermo_pressure</I>. This means you can change the attributes of
this fix's temperature or pressure via the
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
or pressure during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> or
<I>thermo_press</I> will have no effect on this fix. Alternatively, you
<I>thermo_pressure</I> will have no effect on this fix. Alternatively, you
can directly assign a new compute (for calculating temeperature or
pressure) that you have defined to this fix via the
<A HREF = "fix_modify.html">fix_modify</A> command. If you do this, note that the

6
doc/fix_npt.txt
View File

@ -129,13 +129,13 @@ fix group.
Note that these are NOT the computes used by thermodynamic output (see
the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}
and {thermo_press}. This means you can change the attributes of this
fix's temperature or pressure via the
and {thermo_pressure}. This means you can change the attributes of
this fix's temperature or pressure via the
"compute_modify"_compute_modify.html command or print this temperature
or pressure during thermodyanmic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} or
{thermo_press} will have no effect on this fix. Alternatively, you
{thermo_pressure} will have no effect on this fix. Alternatively, you
can directly assign a new compute (for calculating temeperature or
pressure) that you have defined to this fix via the
"fix_modify"_fix_modify.html command. If you do this, note that the

11
doc/fix_nve_asphere.html
View File

@ -24,15 +24,14 @@
</PRE>
<P><B>Description:</B>
</P>
<P>Perform constant NVE updates of position, velocity, and angular
velocity for aspherical or ellipsoidal particles in the group each
timestep. V is volume; E is energy. This creates a system trajectory
consistent with the microcanonical ensemble.
<P>Perform constant NVE updates of position, velocity, orientation, and
angular velocity for aspherical or ellipsoidal particles in the group
each timestep. V is volume; E is energy. This creates a system
trajectory consistent with the microcanonical ensemble.
</P>
<P><B>Restrictions:</B>
</P>
<P>Can only be used if LAMMPS was built with the "asphere" package. Can
only be used with atom_style ellipsoid.
<P>Can only be used if LAMMPS was built with the "asphere" package.
</P>
<P><B>Related commands:</B>
</P>

11
doc/fix_nve_asphere.txt
View File

@ -21,15 +21,14 @@ fix 1 all nve/asphere :pre
[Description:]
Perform constant NVE updates of position, velocity, and angular
velocity for aspherical or ellipsoidal particles in the group each
timestep. V is volume; E is energy. This creates a system trajectory
consistent with the microcanonical ensemble.
Perform constant NVE updates of position, velocity, orientation, and
angular velocity for aspherical or ellipsoidal particles in the group
each timestep. V is volume; E is energy. This creates a system
trajectory consistent with the microcanonical ensemble.
[Restrictions:]
Can only be used if LAMMPS was built with the "asphere" package. Can
only be used with atom_style ellipsoid.
Can only be used if LAMMPS was built with the "asphere" package.
[Related commands:]

3
doc/fix_nve_gran.html
View File

@ -32,8 +32,7 @@ to forces and torques.
</P>
<P><B>Restrictions:</B> none
</P>
<P>Can only be used if LAMMPS was built with the "granular" package. Can
only be used with atom_style granular.
<P>Can only be used if LAMMPS was built with the "granular" package.
</P>
<P><B>Related commands:</B>
</P>

3
doc/fix_nve_gran.txt
View File

@ -29,8 +29,7 @@ to forces and torques.
[Restrictions:] none
Can only be used if LAMMPS was built with the "granular" package. Can
only be used with atom_style granular.
Can only be used if LAMMPS was built with the "granular" package.
[Related commands:]

3
doc/fix_pour.html
View File

@ -103,8 +103,7 @@ successively higher height over time.
</P>
<P><B>Restrictions:</B>
</P>
<P>Can only be used if LAMMPS was built with the "granular" package. Can
only be used with atom_style granular.
<P>Can only be used if LAMMPS was built with the "granular" package.
</P>
<P>For 3d simulations, a gravity fix in the -z direction must be defined
for use in conjunction with this fix. For 2d simulations, gravity

3
doc/fix_pour.txt
View File

@ -92,8 +92,7 @@ successively higher height over time.
[Restrictions:]
Can only be used if LAMMPS was built with the "granular" package. Can
only be used with atom_style granular.
Can only be used if LAMMPS was built with the "granular" package.
For 3d simulations, a gravity fix in the -z direction must be defined
for use in conjunction with this fix. For 2d simulations, gravity

4
doc/group.html
View File

@ -23,7 +23,7 @@
<I>type</I> or <I>id</I> or <I>molecule</I>
args = one or more atom types, atom IDs, or molecule IDs
args = logical value
logical = "<" or "<=" or ">" or ">="
logical = "<" or "<=" or ">" or ">=" or "==" or "!="
value = an atom type or atom ID or molecule ID (depending on <I>style</I>)
args = logical value1 value2
logical = "<>"
@ -65,7 +65,7 @@ specified atom types, atom IDs, or molecule IDs into the group. These
The 1st format is a list of values (types or IDs). For example, the
2nd command in the examples above puts all atoms of type 3 or 4 into
the group named <I>water</I>. The 2nd format is a <I>logical</I> followed by
one or two values (type or ID). The 5 valid logicals are listed
one or two values (type or ID). The 7 valid logicals are listed
above. All the logicals except <> take a single argument. The 3rd
example above adds all atoms with IDs from 1 to 150 to the group named
<I>sub</I>. The logical <> means "between" and takes 2 arguments. The 4th

4
doc/group.txt
View File

@ -19,7 +19,7 @@ style = {region} or {type} or {id} or {molecule} or {subtract} or \
{type} or {id} or {molecule}
args = one or more atom types, atom IDs, or molecule IDs
args = logical value
logical = "<" or "<=" or ">" or ">="
logical = "<" or "<=" or ">" or ">=" or "==" or "!="
value = an atom type or atom ID or molecule ID (depending on {style})
args = logical value1 value2
logical = "<>"
@ -60,7 +60,7 @@ specified atom types, atom IDs, or molecule IDs into the group. These
The 1st format is a list of values (types or IDs). For example, the
2nd command in the examples above puts all atoms of type 3 or 4 into
the group named {water}. The 2nd format is a {logical} followed by
one or two values (type or ID). The 5 valid logicals are listed
one or two values (type or ID). The 7 valid logicals are listed
above. All the logicals except <> take a single argument. The 3rd
example above adds all atoms with IDs from 1 to 150 to the group named
{sub}. The logical <> means "between" and takes 2 arguments. The 4th

4
doc/if.html
View File

@ -16,11 +16,11 @@
<PRE>if value1 operator value2 then command1 else command2
</PRE>
<UL><LI>value1 = 1st value
<LI>operator = "==" or "!=" or "<" or "<=" or ">" or ">="
<LI>operator = "<" or "<=" or ">" or ">=" or "==" or "!="
<LI>value2 = 2nd value
<LI>then = required word
<LI>command1 = command to execute if condition is met
<LI>else = required word (optional argument)
<LI>else = optional word
<LI>command2 = command to execute if condition is not met (optional argument)
</UL>
<P><B>Examples:</B>

4
doc/if.txt
View File

@ -13,11 +13,11 @@ if command :h3
if value1 operator value2 then command1 else command2 :pre
value1 = 1st value
operator = "==" or "!=" or "<" or "<=" or ">" or ">="
operator = "<" or "<=" or ">" or ">=" or "==" or "!="
value2 = 2nd value
then = required word
command1 = command to execute if condition is met
else = required word (optional argument)
else = optional word
command2 = command to execute if condition is not met (optional argument) :ul
[Examples:]

23
doc/next.html
View File

@ -26,15 +26,24 @@ next a t x myTemp
</P>
<P>This command is used with variables defined by the
<A HREF = "variable.html">variable</A> command. It assigns the next value to the
variable from the variable's list, so that when a variable is
variable from the list of values defined for that variable by the
<A HREF = "variable.html">variable</A> command. Thus when that variable is
subsequently substituted for in an input script command, the new value
is used. If a variable name is a single lower-case character from "a"
to "z", it can be used in an input script command as $a or $z. If it
is multiple letters, it can be used as $<I>myTemp</I>.
is used.
</P>
<P>All variables in a single next command must be the same style:
<I>index</I>, <I>loop</I>, <I>universe</I>, or <I>uloop</I>. <I>Equal</I>- or <I>world</I>-style
variables cannot be incremented by a next command.
<P>See the <A HREF = "variable.html">variable</A> command for info on how to define and
use different kinds of variables in LAMMPS input scripts. If a
variable name is a single lower-case character from "a" to "z", it can
be used in an input script command as $a or $z. If it is multiple
letters, it can be used as ${myTemp}.
</P>
<P>If multiple variables are used as arguments to the <I>next</I> command,
then all must be of the same variable style: <I>index</I>, <I>loop</I>,
<I>universe</I>, or <I>uloop</I>. An exception is that <I>universe</I>- and
<I>uloop</I>-style variables can be mixed in the same <I>next</I> command.
<I>Atom</I>- or <I>equal</I>- or <I>world</I>-style variables cannot be incremented
by a next command. All the variables specified are incremented by one
value from their respective lists.
</P>
<P>When any of the variables in the next command has no more values, a
flag is set that causes the input script to skip the next

23
doc/next.txt
View File

@ -23,15 +23,24 @@ next a t x myTemp :pre
This command is used with variables defined by the
"variable"_variable.html command. It assigns the next value to the
variable from the variable's list, so that when a variable is
variable from the list of values defined for that variable by the
"variable"_variable.html command. Thus when that variable is
subsequently substituted for in an input script command, the new value
is used. If a variable name is a single lower-case character from "a"
to "z", it can be used in an input script command as $a or $z. If it
is multiple letters, it can be used as ${myTemp}.
is used.
All variables in a single next command must be the same style:
{index}, {loop}, {universe}, or {uloop}. {Equal}- or {world}-style
variables cannot be incremented by a next command.
See the "variable"_variable.html command for info on how to define and
use different kinds of variables in LAMMPS input scripts. If a
variable name is a single lower-case character from "a" to "z", it can
be used in an input script command as $a or $z. If it is multiple
letters, it can be used as $\{myTemp\}.
If multiple variables are used as arguments to the {next} command,
then all must be of the same variable style: {index}, {loop},
{universe}, or {uloop}. An exception is that {universe}- and
{uloop}-style variables can be mixed in the same {next} command.
{Atom}- or {equal}- or {world}-style variables cannot be incremented
by a next command. All the variables specified are incremented by one
value from their respective lists.
When any of the variables in the next command has no more values, a
flag is set that causes the input script to skip the next

14
doc/pair_coeff.html
View File

@ -70,11 +70,11 @@ as
</P>
<PRE>2 1.0 1.0 2.5
</PRE>
<P>If coefficients for type pairs with I not equal J are not set
explicity by a pair_coeff command, they are inferred from the I,I and
J,J settings by mixing rules; see the <A HREF = "pair_modify.html">pair_modify</A>
command for a discussion. Exceptions to the mixing rules of the
pair_modify command are discussed with the individual pair styles.
<P>For many potentials, if coefficients for type pairs with I != J are
not set explicity by a pair_coeff command, the values are inferred
from the I,I and J,J settings by mixing rules; see the
<A HREF = "pair_modify.html">pair_modify</A> command for a discussion. Exceptions
to the mixing rules are discussed with the individual pair styles.
</P>
<HR>
@ -86,9 +86,11 @@ the pair_style command, and coefficients specified by the associated
<UL><LI><A HREF = "pair_none.html">pair_style none</A> - turn off pairwise interactions
<LI><A HREF = "pair_hybrid.html">pair_style hybrid</A> - define multiple styles of pairwise interactions
</UL>
<UL><LI><A HREF = "pair_buck.html">pair_style buck</A> - Buckingham potential
<UL><LI><A HREF = "pair_airebo.html">pair_style airebo</A> - AI-REBO potential
<LI><A HREF = "pair_buck.html">pair_style buck</A> - Buckingham potential
<LI><A HREF = "pair_buck.html">pair_style buck/coul/cut</A> - Buckinhham with cutoff Coulomb
<LI><A HREF = "pair_buck.html">pair_style buck/coul/long</A> - Buckingham with long-range Coulomb
<LI><A HREF = "pair_colloid.html">pair_style colloid</A> - integrated colloidal potential
<LI><A HREF = "pair_dpd.html">pair_style dpd</A> - dissipative particle dynamics (DPD)
<LI><A HREF = "pair_eam.html">pair_style eam</A> - embedded atom method (EAM)
<LI><A HREF = "pair_eam.html">pair_style eam/alloy</A> - alloy EAM

12
doc/pair_coeff.txt
View File

@ -67,11 +67,11 @@ as
2 1.0 1.0 2.5 :pre
If coefficients for type pairs with I not equal J are not set
explicity by a pair_coeff command, they are inferred from the I,I and
J,J settings by mixing rules; see the "pair_modify"_pair_modify.html
command for a discussion. Exceptions to the mixing rules of the
pair_modify command are discussed with the individual pair styles.
For many potentials, if coefficients for type pairs with I != J are
not set explicity by a pair_coeff command, the values are inferred
from the I,I and J,J settings by mixing rules; see the
"pair_modify"_pair_modify.html command for a discussion. Exceptions
to the mixing rules are discussed with the individual pair styles.
:line
@ -83,9 +83,11 @@ the pair_style command, and coefficients specified by the associated
"pair_style none"_pair_none.html - turn off pairwise interactions
"pair_style hybrid"_pair_hybrid.html - define multiple styles of pairwise interactions :ul
"pair_style airebo"_pair_airebo.html - AI-REBO potential
"pair_style buck"_pair_buck.html - Buckingham potential
"pair_style buck/coul/cut"_pair_buck.html - Buckinhham with cutoff Coulomb
"pair_style buck/coul/long"_pair_buck.html - Buckingham with long-range Coulomb
"pair_style colloid"_pair_colloid.html - integrated colloidal potential
"pair_style dpd"_pair_dpd.html - dissipative particle dynamics (DPD)
"pair_style eam"_pair_eam.html - embedded atom method (EAM)
"pair_style eam/alloy"_pair_eam.html - alloy EAM

16
doc/pair_eam.html
View File

@ -118,14 +118,14 @@ file is formatted as follows:
<LI>line 3: Nrho, drho, Nr, dr, cutoff
</UL>
<P>On line 2, all values but the mass are ignored by LAMMPS. The mass is
in atomic mass units (g/cm^3) which is converted by LAMMPS to the
appropriate internal mass <A HREF = "units.html">units</A>. The cubic lattice
constant is in Angstroms. On line 3, Nrho and Nr are the number of
tabulated values in the subsequent arrays, drho and dr are the spacing
in density and distance space for the values in those arrays, and the
specified cutoff becomes the pairwise cutoff used by LAMMPS for the
potential. The units of dr are Angstroms; I'm not sure of the units
for drho - some measure of electron density.
in mass <A HREF = "units.html">units</A> (e.g. mass number or grams/mole for metal
units). The cubic lattice constant is in Angstroms. On line 3, Nrho
and Nr are the number of tabulated values in the subsequent arrays,
drho and dr are the spacing in density and distance space for the
values in those arrays, and the specified cutoff becomes the pairwise
cutoff used by LAMMPS for the potential. The units of dr are
Angstroms; I'm not sure of the units for drho - some measure of
electron density.
</P>
<P>Following the 3 header lines are 3 arrays of tabulated values:
</P>

16
doc/pair_eam.txt
View File

@ -110,14 +110,14 @@ line 2: atomic number, mass, lattice constant, lattice type (e.g. FCC)
line 3: Nrho, drho, Nr, dr, cutoff :ul
On line 2, all values but the mass are ignored by LAMMPS. The mass is
in atomic mass units (g/cm^3) which is converted by LAMMPS to the
appropriate internal mass "units"_units.html. The cubic lattice
constant is in Angstroms. On line 3, Nrho and Nr are the number of
tabulated values in the subsequent arrays, drho and dr are the spacing
in density and distance space for the values in those arrays, and the
specified cutoff becomes the pairwise cutoff used by LAMMPS for the
potential. The units of dr are Angstroms; I'm not sure of the units
for drho - some measure of electron density.
in mass "units"_units.html (e.g. mass number or grams/mole for metal
units). The cubic lattice constant is in Angstroms. On line 3, Nrho
and Nr are the number of tabulated values in the subsequent arrays,
drho and dr are the spacing in density and distance space for the
values in those arrays, and the specified cutoff becomes the pairwise
cutoff used by LAMMPS for the potential. The units of dr are
Angstroms; I'm not sure of the units for drho - some measure of
electron density.
Following the 3 header lines are 3 arrays of tabulated values:

15
doc/pair_gayberne.html
View File

@ -47,14 +47,16 @@ curvatures <A HREF = "#Everaers">(Everaers)</A>:
</CENTER>
<P>The variable names utilized as potential parameters are for the most
part taken from <A HREF = "#Everaers">(Everaers)</A> in order to be consistent with
its RE-squared potential fix. Details on the upsilon and mu
parameters are given <A HREF = "Eqs/pair_gayberne_extra.pdf">here</A>.
Use of this pair style requires the
<A HREF = "fix_nve_asphere.html">fix nve/asphere</A> in order to integrate particle
its RE-squared potential fix. Details on the upsilon and mu
parameters are given <A HREF = "Eqs/pair_gayberne_extra.pdf">here</A>. Use of this pair style requires
the NVE, NVT, or NPT fixes with the <I>asphere</I> extension (e.g. <A HREF = "fix_nve_asphere.html">fix
nve/asphere</A>) in order to integrate particle
rotation. Additionally, <A HREF = "atom_style.html">atom_style ellipsoid</A> should
be used since it defines the rotation state of the ellipsoidal
be used since it defines the rotational state of the ellipsoidal
particles.
</P>
<P>More details of the Gay-Berne formulation are given in the references
listed below and in <A HREF = "Eqs/pair_gayberne_extra.pdf">this document</A>.
</P>
@ -85,8 +87,7 @@ pair of atoms. Thus they are applied to atom type I only.
</P>
<P><B>Restrictions:</B>
</P>
<P>Can only be used if LAMMPS was built with the "asphere" package. Can
only be used with <A HREF = "atom_style.html">atom_style ellipsoid</A>.
<P>Can only be used if LAMMPS was built with the "asphere" package.
</P>
<P>The use of this potential requires additional fixes as described
above. The "shift yes" option currently cannot be used with this

33
doc/pair_gayberne.txt
View File

@ -44,14 +44,16 @@ curvatures "(Everaers)"_#Everaers:
The variable names utilized as potential parameters are for the most
part taken from "(Everaers)"_#Everaers in order to be consistent with
its RE-squared potential fix. Details on the upsilon and mu
parameters are given "here"_Eqs/pair_gayberne_extra.pdf.
Use of this pair style requires the
"fix nve/asphere"_fix_nve_asphere.html in order to integrate particle
its RE-squared potential fix. Details on the upsilon and mu
parameters are given "here"_gbdoc. Use of this pair style requires
the NVE, NVT, or NPT fixes with the {asphere} extension (e.g. "fix
nve/asphere"_fix_nve_asphere.html) in order to integrate particle
rotation. Additionally, "atom_style ellipsoid"_atom_style.html should
be used since it defines the rotation state of the ellipsoidal
be used since it defines the rotational state of the ellipsoidal
particles.
:link(gbdoc,Eqs/pair_gayberne_extra.pdf)
More details of the Gay-Berne formulation are given in the references
listed below and in "this document"_Eqs/pair_gayberne_extra.pdf.
@ -63,12 +65,12 @@ commands:
epsilon = well depth (energy units)
sigma = minimum effective particle radii (distance units)
a = ellipsoid radius in x dimension (distance units)
b = ellipsoid radius in y dimension (distance units)
c = ellipsoid radius in z dimension (distance units)
epsilon_a = relative well depth for side-to-side interactions
epsilon_b = relative well depth for face-to-face interactions
epsilon_c = relative well depth for end-to-end interactions
epsilon_i_a = relative well depth of I for side-to-side interactions
epsilon_i_b = relative well depth of I for face-to-face interactions
epsilon_i_c = relative well depth of I for end-to-end interactions
epsilon_j_a = relative well depth of J for side-to-side interactions
epsilon_j_b = relative well depth of J for face-to-face interactions
epsilon_j_c = relative well depth of J for end-to-end interactions
cutoff (distance units) :ul
The last coefficient is optional. If not specified, the global
@ -82,17 +84,16 @@ pair of atoms. Thus they are applied to atom type I only.
[Restrictions:]
Can only be used if LAMMPS was built with the "asphere" package. Can
only be used with "atom_style ellipsoid"_atom_style.html.
Can only be used if LAMMPS was built with the "asphere" package.
The use of this potential requires additional fixes as described
above. The "shift yes" option currently cannot be used with this
potential to shift energies to 0 at the cutoff due to the anisotropic
dependence of the interaction. Angular velocities are all set to zero
initially. The Gay-Berne potential does not become isotropic as r
increases "(Everaers)"_#Everaers. The distance of closest approach
approximation becomes less accurate as the shape of ellipsoids becomes
more dissimilar (high aspect ratio particles).
increases "(Everaers)"_#Everaers. The distance-of-closest-approach
approximation used by the code becomes less accurate as the shape of
ellipsoids becomes more dissimilar (high-aspect-ratio particles).
[Related commands:]

6
doc/pair_meam.html
View File

@ -142,7 +142,7 @@ rho0(I) = relative density for element I (overwrites value
read from meamf file)
Ec(I,J) = cohesive energy of reference structure for I-J mixture
delta(I,J) = heat of formation for I-J alloy; if Ec_IJ is input as
zero, then WARP sets Ec_IJ = (Ec_II + Ec_JJ)/2 - delta_IJ
zero, then LAMMPS sets Ec_IJ = (Ec_II + Ec_JJ)/2 - delta_IJ
alpha(I,J) = alpha parameter for pair potential between I and J (can
be computed from bulk modulus of reference structure
re(I,J) = equilibrium distance between I and J in the reference
@ -168,6 +168,10 @@ augt1 = integer flag for whether to augment t1 parameter by
1 = augment t1
default = 1
</PRE>
<P>Rc, delr, re are in distance units (Angstroms in the case of metal
units). Ec and delta are in energy units (eV in the case of metal
units).
</P>
<P>Each keyword represents a quantity which is either a scalar, vector,
2d array, or 3d array and must be specified with the correct
corresponding array syntax. The indices I,J,K each run from 1 to N

6
doc/pair_meam.txt
View File

@ -139,7 +139,7 @@ rho0(I) = relative density for element I (overwrites value
read from meamf file)
Ec(I,J) = cohesive energy of reference structure for I-J mixture
delta(I,J) = heat of formation for I-J alloy; if Ec_IJ is input as
zero, then WARP sets Ec_IJ = (Ec_II + Ec_JJ)/2 - delta_IJ
zero, then LAMMPS sets Ec_IJ = (Ec_II + Ec_JJ)/2 - delta_IJ
alpha(I,J) = alpha parameter for pair potential between I and J (can
be computed from bulk modulus of reference structure
re(I,J) = equilibrium distance between I and J in the reference
@ -165,6 +165,10 @@ augt1 = integer flag for whether to augment t1 parameter by
1 = augment t1
default = 1 :pre
Rc, delr, re are in distance units (Angstroms in the case of metal
units). Ec and delta are in energy units (eV in the case of metal
units).
Each keyword represents a quantity which is either a scalar, vector,
2d array, or 3d array and must be specified with the correct
corresponding array syntax. The indices I,J,K each run from 1 to N

13
doc/pair_modify.html
View File

@ -47,12 +47,13 @@ output, but does not affect atom dynamics (forces). Pair styles that
are already 0.0 at their cutoff such as <I>lj/charmm/coul/charmm</I> are
not affected by this setting.
</P>
<P>The <I>mix</I> keyword affects how Lennard-Jones coefficients for epsilon
and sigma are generated for interactions between atoms of type I and
J, when I != J. Coefficients for I = J are set explicitly in the data
file or input script. The <A HREF = "pair_coeff.html">pair_coeff</A> command can be
used in the input script to specify epilon/sigma for a specific I != J
pairing, which overrides the setting of the <I>mix</I> keyword.
<P>The <I>mix</I> keyword affects how Lennard-Jones coefficients for epsilon,
sigma, and the cutoff are generated for interactions between atoms of
type I and J, when I != J. Coefficients for I = J are set explicitly
in the data file or input script. The <A HREF = "pair_coeff.html">pair_coeff</A>
command can be used in the input script to specify epilon/sigma for a
specific I != J pairing, which overrides the setting of the <I>mix</I>
keyword.
</P>
<P>These are the formulas used by the 3 <I>mix</I> options. In each case, the
LJ cutoff is mixed the same way as sigma. Note that some of these

13
doc/pair_modify.txt
View File

@ -41,12 +41,13 @@ output, but does not affect atom dynamics (forces). Pair styles that
are already 0.0 at their cutoff such as {lj/charmm/coul/charmm} are
not affected by this setting.
The {mix} keyword affects how Lennard-Jones coefficients for epsilon
and sigma are generated for interactions between atoms of type I and
J, when I != J. Coefficients for I = J are set explicitly in the data
file or input script. The "pair_coeff"_pair_coeff.html command can be
used in the input script to specify epilon/sigma for a specific I != J
pairing, which overrides the setting of the {mix} keyword.
The {mix} keyword affects how Lennard-Jones coefficients for epsilon,
sigma, and the cutoff are generated for interactions between atoms of
type I and J, when I != J. Coefficients for I = J are set explicitly
in the data file or input script. The "pair_coeff"_pair_coeff.html
command can be used in the input script to specify epilon/sigma for a
specific I != J pairing, which overrides the setting of the {mix}
keyword.
These are the formulas used by the 3 {mix} options. In each case, the
LJ cutoff is mixed the same way as sigma. Note that some of these

14
doc/pair_style.html
View File

@ -17,9 +17,9 @@
</PRE>
<UL><LI>style = one of the following
<UL><LI><I>none</I>, <I>hybrid</I>, <I>buck</I>, <I>buck/coul/cut</I>, <I>buck/coul/long</I>, <I>dpd</I>,
<LI><I>eam</I>, <I>eam/alloy</I> or <I>eam/fs</I>, <I>gran/hertzian</I>, <I>gran/history</I>,
<LI><I>gran/no_history</I>, <I>lj/charmm/coul/charmm</I>,
<UL><LI><I>none</I>, <I>hybrid</I>, <I>airebo</I>, <I>buck</I>, <I>buck/coul/cut</I>, <I>buck/coul/long</I>,
<LI><I>dpd</I>, <I>eam</I>, <I>eam/alloy</I> or <I>eam/fs</I>, <I>gran/hertzian</I>,
<LI><I>gran/history</I>, <I>gran/no_history</I>, <I>lj/charmm/coul/charmm</I>,
<LI><I>lj/charmm/coul/charmm/implicit</I> or <I>lj/charmm/coul/long</I>,
<LI><I>lj/class2</I>, <I>lj/class2/coul/cut</I> or <I>lj/class2/coul/long</I>, <I>lj/cut</I>,
<LI><I>lj/cut/coul/cut</I> or <I>lj/cut/coul/debye</I>, <I>lj/cut/coul/long</I>,
@ -47,8 +47,8 @@ remain in place for the duration of a simulation.
</P>
<P>In LAMMPS, pairwise force fields encompass a variety of interactions,
some of which include many-body effects, e.g. EAM, Stillinger-Weber,
Tersoff, REBO potentials. They are still classed as "pairwise"
potential because the set of interacting atoms changes with time
Tersoff, REBO potentials. They are still classified as "pairwise"
potentials because the set of interacting atoms changes with time
(unlike a bonded system) and thus a neighbor list is used to find
nearby interacting atoms.
</P>
@ -92,9 +92,11 @@ the pair_style command, and coefficients specified by the associated
<UL><LI><A HREF = "pair_none.html">pair_style none</A> - turn off pairwise interactions
<LI><A HREF = "pair_hybrid.html">pair_style hybrid</A> - define multiple styles of pairwise interactions
</UL>
<UL><LI><A HREF = "pair_buck.html">pair_style buck</A> - Buckingham potential
<UL><LI><A HREF = "pair_airebo.html">pair_style airebo</A> - AI-REBO potential
<LI><A HREF = "pair_buck.html">pair_style buck</A> - Buckingham potential
<LI><A HREF = "pair_buck.html">pair_style buck/coul/cut</A> - Buckinhham with cutoff Coulomb
<LI><A HREF = "pair_buck.html">pair_style buck/coul/long</A> - Buckingham with long-range Coulomb
<LI><A HREF = "pair_colloid.html">pair_style colloid</A> - integrated colloidal potential
<LI><A HREF = "pair_dpd.html">pair_style dpd</A> - dissipative particle dynamics (DPD)
<LI><A HREF = "pair_eam.html">pair_style eam</A> - embedded atom method (EAM)
<LI><A HREF = "pair_eam.html">pair_style eam/alloy</A> - alloy EAM

12
doc/pair_style.txt
View File

@ -14,9 +14,9 @@ pair_style style args :pre
style = one of the following :ulb,l
{none}, {hybrid}, {buck}, {buck/coul/cut}, {buck/coul/long}, {dpd},
{eam}, {eam/alloy} or {eam/fs}, {gran/hertzian}, {gran/history},
{gran/no_history}, {lj/charmm/coul/charmm},
{none}, {hybrid}, {airebo}, {buck}, {buck/coul/cut}, {buck/coul/long},
{dpd}, {eam}, {eam/alloy} or {eam/fs}, {gran/hertzian},
{gran/history}, {gran/no_history}, {lj/charmm/coul/charmm},
{lj/charmm/coul/charmm/implicit} or {lj/charmm/coul/long},
{lj/class2}, {lj/class2/coul/cut} or {lj/class2/coul/long}, {lj/cut},
{lj/cut/coul/cut} or {lj/cut/coul/debye}, {lj/cut/coul/long},
@ -44,8 +44,8 @@ remain in place for the duration of a simulation.
In LAMMPS, pairwise force fields encompass a variety of interactions,
some of which include many-body effects, e.g. EAM, Stillinger-Weber,
Tersoff, REBO potentials. They are still classed as "pairwise"
potential because the set of interacting atoms changes with time
Tersoff, REBO potentials. They are still classified as "pairwise"
potentials because the set of interacting atoms changes with time
(unlike a bonded system) and thus a neighbor list is used to find
nearby interacting atoms.
@ -89,9 +89,11 @@ the pair_style command, and coefficients specified by the associated
"pair_style none"_pair_none.html - turn off pairwise interactions
"pair_style hybrid"_pair_hybrid.html - define multiple styles of pairwise interactions :ul
"pair_style airebo"_pair_airebo.html - AI-REBO potential
"pair_style buck"_pair_buck.html - Buckingham potential
"pair_style buck/coul/cut"_pair_buck.html - Buckinhham with cutoff Coulomb
"pair_style buck/coul/long"_pair_buck.html - Buckingham with long-range Coulomb
"pair_style colloid"_pair_colloid.html - integrated colloidal potential
"pair_style dpd"_pair_dpd.html - dissipative particle dynamics (DPD)
"pair_style eam"_pair_eam.html - embedded atom method (EAM)
"pair_style eam/alloy"_pair_eam.html - alloy EAM

94
doc/read_data.html
View File

@ -94,16 +94,19 @@ parallelepiped with triclinic symmetry. See the <A HREF = "region.html">region
prism</A> command for a description of how the extent of the
parallelepiped is defined. The parallelepiped has its "origin" at
(xlo,ylo,zlo) and 3 edge vectors starting from the origin given by a =
(xhi-xlo,0,0); b = (xy,yhi-ylo,0); c = (xz,yz,zhi-zlo).
(xhi-xlo,0,0); b = (xy,yhi-ylo,0); c = (xz,yz,zhi-zlo). Note that if
your simulation will tilt the box, e.g. via the <A HREF = "fix_deform.html">fix
deform</A> command, the simulation box must be triclinic,
even if the tilt factors are initially 0.0.
</P>
<P>The tilt factors (xy,xz,yz) must not skew the box more than half the
distance of the perpendicular box length. For example, if ylo = 2 and
yhi = 12, then the y box length is 10 and the xy tilt factor must be
<P>The tilt factors (xy,xz,yz) can not skew the box more than half the
distance of the parallel box length. For example, if xlo = 2 and xhi
= 12, then the x box length is 10 and the xy tilt factor must be
between -5 and 5. Similarly, both xz and yz must be between
-(zhi-zlo)/2 and +(zhi-zlo)/2. From a mechanics persepctive this is
equivalent to saying the shear strain of the system (sideways
displacement divided by perpendicular box length) must be between -0.5
and 0.5.
-(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation,
since if the maximum tilt factor is 5 (as in this example), then
configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
equivalent.
</P>
<P>When a triclinic system is used, the simulation domain must be
periodic in any dimensions with a non-zero tilt factor, as defined by
@ -135,12 +138,12 @@ back inside the box.
<P>These are the section keywords for the body of the file.
</P>
<UL><LI><I>Atoms, Velocities, Masses, Dipoles</I> = atom-property sections
<UL><LI><I>Atoms, Velocities, Masses, Shapes, Dipoles</I> = atom-property sections
<LI><I>Bonds, Angles, Dihedrals, Impropers</I> = molecular topolgy sections
<LI><I>Pair Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, Improper Coeffs</I> = force field sections
<LI><I>BondBond Coeffs, BondAngle Coeffs, MiddleBondTorsion Coeffs, EndBondTorsion Coeffs, AngleTorsion Coeffs, AngleAngleTorsion Coeffs, BondBond13 Coeffs, AngleAngle Coeffs</I> = class 2 force field sections
</UL>
<P>Each section is now listed in alphabetic order. The format of each
<P>Each section is listed below in alphabetic order. The format of each
section is described including the number of lines it must contain and
rules (if any) for where it can appear in the data file.
</P>
@ -252,11 +255,13 @@ line formats for each <A HREF = "atom_style.html">atom style</A> in LAMMPS:
<TR><TD >atomic</TD><TD > atom-ID atom-type x y z</TD></TR>
<TR><TD >bond</TD><TD > atom-ID molecule-ID atom-type x y z</TD></TR>
<TR><TD >charge</TD><TD > atom-ID atom-type q x y z</TD></TR>
<TR><TD >dipole</TD><TD > atom-ID atom-type q x y z mux muy muz</TD></TR>
<TR><TD >dpd</TD><TD > atom-ID atom-type x y z</TD></TR>
<TR><TD >ellipsoid</TD><TD > atom-ID atom-type x y z quatw quati quatj quatk</TD></TR>
<TR><TD >full</TD><TD > atom-ID molecule-ID atom-type q x y z</TD></TR>
<TR><TD >granular</TD><TD > atom-ID atom-type diameter density x y z</TD></TR>
<TR><TD >molecular</TD><TD > atom-ID molecule-ID atom-type x y z
<TR><TD >molecular</TD><TD > atom-ID molecule-ID atom-type x y z</TD></TR>
<TR><TD >hybrid</TD><TD > atom-ID atom-type x y z sub-style1 sub-style2 ...
</TD></TR></TABLE></DIV>
<P>where the keywords have these meanings:
@ -268,13 +273,14 @@ line formats for each <A HREF = "atom_style.html">atom style</A> in LAMMPS:
<LI>diameter = diameter of atom
<LI>density = density of atom
<LI>x,y,z = coordinates of atom
<LI>mux,muy,muz = direction of dipole moment of atom
<LI>quatw,quati,quatj,quatk = quaternion components for orientation of atom
</UL>
<P>The units for these quantities depend on the unit style; see the
<A HREF = "units.html">units</A> command for details.
</P>
<P>For 2d simulations specify z as 0.0, or a value is within the <I>zlo
zhi</I> setting in the data file header.
<P>For 2d simulations specify z as 0.0, or a value within the <I>zlo zhi</I>
setting in the data file header.
</P>
<P>The atom-ID is used to identify the atom throughout the simulation and
in dump files. Normally, it is a unique value from 1 to Natoms for
@ -291,6 +297,36 @@ is a number from 1 to N, identifying which molecule the atom belongs
to. It can be 0 if it is an unbonded atom or if you don't care to
keep track of molecule assignments.
</P>
<P>The values <I>quatw</I>, <I>quati</I>, <I>quatj</I>, and <I>quatk</I> set the orientation
of the atom as a quaternion (4-vector). Note that the
<A HREF = "shape.html">shape</A> command or "Shapes" section of the data file
specifies the aspect ratios of an ellipsoidal particle, which is
oriented by default with its x-axis along the simulation box's x-axis,
and similarly for y and z. If this body is rotated (via the
right-hand rule) by an angle theta around a unit vector (a,b,c), then
the quaternion that represents its new orientation is given by
(cos(theta/2), a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). These
4 components are quatw, quati, quatj, and quatk as specfied above.
LAMMPS normalizes each atom's quaternion in case (a,b,c) was not a
unit vector.
</P>
<P>For atom_style hybrid, following the 5 initial values (ID,type,x,y,z),
specific values for each sub-style must be listed. The order of the
sub-styles is the same as they were listed in the
<A HREF = "atom_style.html">atom_style</A> command. The sub-style specific values
are those that are not the 5 standard ones (ID,type,x,y,z). For
example, for the "charge" sub-style, a "q" value would appear. For
the "full" sub-style, a "molecule-ID" and "q" would appear. These are
listed in the same order they appear as listed above.
</P>
<P>Thus if
</P>
<PRE>atom_style hybrid charge granular
</PRE>
<P>were used in the input script, each atom line would have these fields:
</P>
<PRE>atom-ID atom-type x y z q diameter density
</PRE>
<P>Atom lines (all lines or none of them) can optionally list 3 final
integer values: nx,ny,nz. For periodic dimensions, they specify which
image of the box the atom is considered to be in. An image of 0 means
@ -301,9 +337,10 @@ during the simulation. The flags can be output with atom snapshots
via the <A HREF = "dump.html">dump</A> command. If nx,ny,nz values are not set in
the data file, LAMMPS initializes them to 0.
</P>
<P>Atom velocities are set to 0.0 when the <I>Atoms</I> section is read. They
may later be set by a <I>Velocities</I> section in the data file or by a
<A HREF = "velocity.html">velocity</A> command in the input script.
<P>Atom velocities and other atom quantities not defined above are set to
0.0 when the <I>Atoms</I> section is read. They may later be set by a
<I>Velocities</I> section in the data file or by a <A HREF = "velocity.html">velocity</A>
or <A HREF = "set.html">set</A> command in the input script.
</P>
<HR>
@ -571,6 +608,30 @@ script.
</P>
<HR>
<P><I>Shapes</I> section:
</P>
<UL><LI>one line per atom type
<LI>line syntax: ID x y z
<PRE> ID = atom type (1-N)
x = x diameter
y = y diameter
z = z diameter
</PRE>
<LI>example:
<PRE> 3 2.0 1.0 1.0
</PRE>
</UL>
<P>This defines the shape of each atom type. This can also be set via
the <A HREF = "mass.html">shape</A> command in the input script. This section
should only be used for atom styles that define a shape, e.g. atom
style dipole or ellipsoid.
</P>
<HR>
<P><I>Velocities</I> section:
</P>
<UL><LI>one line per atom
@ -578,6 +639,7 @@ script.
</UL>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR><TD >all styles except those listed</TD><TD > atom-ID vx vy vz</TD></TR>
<TR><TD >dipole</TD><TD > atom-ID vx vy vz wx wy wz</TD></TR>
<TR><TD >ellipsoid</TD><TD > atom-ID vx vy vz lx ly lz</TD></TR>
<TR><TD >granular</TD><TD > atom-ID vx vy vz wx wy wz
</TD></TR></TABLE></DIV>

89
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View File

@ -89,16 +89,19 @@ parallelepiped with triclinic symmetry. See the "region
prism"_region.html command for a description of how the extent of the
parallelepiped is defined. The parallelepiped has its "origin" at
(xlo,ylo,zlo) and 3 edge vectors starting from the origin given by a =
(xhi-xlo,0,0); b = (xy,yhi-ylo,0); c = (xz,yz,zhi-zlo).
(xhi-xlo,0,0); b = (xy,yhi-ylo,0); c = (xz,yz,zhi-zlo). Note that if
your simulation will tilt the box, e.g. via the "fix
deform"_fix_deform.html command, the simulation box must be triclinic,
even if the tilt factors are initially 0.0.
The tilt factors (xy,xz,yz) must not skew the box more than half the
distance of the perpendicular box length. For example, if ylo = 2 and
yhi = 12, then the y box length is 10 and the xy tilt factor must be
The tilt factors (xy,xz,yz) can not skew the box more than half the
distance of the parallel box length. For example, if xlo = 2 and xhi
= 12, then the x box length is 10 and the xy tilt factor must be
between -5 and 5. Similarly, both xz and yz must be between
-(zhi-zlo)/2 and +(zhi-zlo)/2. From a mechanics persepctive this is
equivalent to saying the shear strain of the system (sideways
displacement divided by perpendicular box length) must be between -0.5
and 0.5.
-(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation,
since if the maximum tilt factor is 5 (as in this example), then
configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
equivalent.
When a triclinic system is used, the simulation domain must be
periodic in any dimensions with a non-zero tilt factor, as defined by
@ -130,7 +133,7 @@ back inside the box.
These are the section keywords for the body of the file.
{Atoms, Velocities, Masses, Dipoles} = atom-property sections
{Atoms, Velocities, Masses, Shapes, Dipoles} = atom-property sections
{Bonds, Angles, Dihedrals, Impropers} = molecular topolgy sections
{Pair Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, \
Improper Coeffs} = force field sections
@ -138,7 +141,7 @@ These are the section keywords for the body of the file.
EndBondTorsion Coeffs, AngleTorsion Coeffs, AngleAngleTorsion Coeffs, \
BondBond13 Coeffs, AngleAngle Coeffs} = class 2 force field sections :ul
Each section is now listed in alphabetic order. The format of each
Each section is listed below in alphabetic order. The format of each
section is described including the number of lines it must contain and
rules (if any) for where it can appear in the data file.
@ -230,11 +233,13 @@ angle: atom-ID molecule-ID atom-type x y z
atomic: atom-ID atom-type x y z
bond: atom-ID molecule-ID atom-type x y z
charge: atom-ID atom-type q x y z
dipole: atom-ID atom-type q x y z mux muy muz
dpd: atom-ID atom-type x y z
ellipsoid: atom-ID atom-type x y z quatw quati quatj quatk
full: atom-ID molecule-ID atom-type q x y z
granular: atom-ID atom-type diameter density x y z
molecular: atom-ID molecule-ID atom-type x y z :tb(s=:)
molecular: atom-ID molecule-ID atom-type x y z
hybrid: atom-ID atom-type x y z sub-style1 sub-style2 ... :tb(s=:)
where the keywords have these meanings:
@ -245,13 +250,14 @@ q = charge on atom
diameter = diameter of atom
density = density of atom
x,y,z = coordinates of atom
mux,muy,muz = direction of dipole moment of atom
quatw,quati,quatj,quatk = quaternion components for orientation of atom :ul
The units for these quantities depend on the unit style; see the
"units"_units.html command for details.
For 2d simulations specify z as 0.0, or a value is within the {zlo
zhi} setting in the data file header.
For 2d simulations specify z as 0.0, or a value within the {zlo zhi}
setting in the data file header.
The atom-ID is used to identify the atom throughout the simulation and
in dump files. Normally, it is a unique value from 1 to Natoms for
@ -268,6 +274,36 @@ is a number from 1 to N, identifying which molecule the atom belongs
to. It can be 0 if it is an unbonded atom or if you don't care to
keep track of molecule assignments.
The values {quatw}, {quati}, {quatj}, and {quatk} set the orientation
of the atom as a quaternion (4-vector). Note that the
"shape"_shape.html command or "Shapes" section of the data file
specifies the aspect ratios of an ellipsoidal particle, which is
oriented by default with its x-axis along the simulation box's x-axis,
and similarly for y and z. If this body is rotated (via the
right-hand rule) by an angle theta around a unit vector (a,b,c), then
the quaternion that represents its new orientation is given by
(cos(theta/2), a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). These
4 components are quatw, quati, quatj, and quatk as specfied above.
LAMMPS normalizes each atom's quaternion in case (a,b,c) was not a
unit vector.
For atom_style hybrid, following the 5 initial values (ID,type,x,y,z),
specific values for each sub-style must be listed. The order of the
sub-styles is the same as they were listed in the
"atom_style"_atom_style.html command. The sub-style specific values
are those that are not the 5 standard ones (ID,type,x,y,z). For
example, for the "charge" sub-style, a "q" value would appear. For
the "full" sub-style, a "molecule-ID" and "q" would appear. These are
listed in the same order they appear as listed above.
Thus if
atom_style hybrid charge granular :pre
were used in the input script, each atom line would have these fields:
atom-ID atom-type x y z q diameter density :pre
Atom lines (all lines or none of them) can optionally list 3 final
integer values: nx,ny,nz. For periodic dimensions, they specify which
image of the box the atom is considered to be in. An image of 0 means
@ -278,9 +314,10 @@ during the simulation. The flags can be output with atom snapshots
via the "dump"_dump.html command. If nx,ny,nz values are not set in
the data file, LAMMPS initializes them to 0.
Atom velocities are set to 0.0 when the {Atoms} section is read. They
may later be set by a {Velocities} section in the data file or by a
"velocity"_velocity.html command in the input script.
Atom velocities and other atom quantities not defined above are set to
0.0 when the {Atoms} section is read. They may later be set by a
{Velocities} section in the data file or by a "velocity"_velocity.html
or "set"_set.html command in the input script.
:line
@ -488,12 +525,32 @@ script.
:line
{Shapes} section:
one line per atom type :ulb,l
line syntax: ID x y z :l
ID = atom type (1-N)
x = x diameter
y = y diameter
z = z diameter :pre
example: :l
3 2.0 1.0 1.0 :pre
:ule
This defines the shape of each atom type. This can also be set via
the "shape"_mass.html command in the input script. This section
should only be used for atom styles that define a shape, e.g. atom
style dipole or ellipsoid.
:line
{Velocities} section:
one line per atom
line syntax: depends on atom style :ul
all styles except those listed: atom-ID vx vy vz
dipole: atom-ID vx vy vz wx wy wz
ellipsoid: atom-ID vx vy vz lx ly lz
granular: atom-ID vx vy vz wx wy wz :tb(s=:)

14
doc/region.html
View File

@ -86,9 +86,7 @@ y-direction located at x = 2.0 and z = 3.0, with a radius of 5.0, and
extending in the y-direction from -5.0 to the upper box boundary.
</P>
<P>For style <I>prism</I>, a parallelepiped is defined (it's too hard to spell
parallelepiped in an input script!). A prism region is used by the
<A HREF = "create_box.html">create_box</A> command to define a triclinic
(non-orthogonal) simulation domain. Think of the parallelepided as
parallelepiped in an input script!). Think of the parallelepided as
initially an axis-aligned orthogonal box with the same xyz lo/hi
parameters as region style <I>block</I> would define. Then, while holding
the (xlo,ylo,zlo) corner point fixed, the box is "skewed" or "tilted"
@ -101,6 +99,16 @@ results in a parallelepiped whose "origin" is at (xlo,ylo,zlo) with 3
edge vectors starting from its origin given by a = (xhi-xlo,0,0); b =
(xy,yhi-ylo,0); c = (xz,yz,zhi-zlo).
</P>
<P>A prism region used with the <A HREF = "create_box.html">create_box</A> command must
have tilt factors (xy,xz,yz) that do not skew the box more than half
the distance of the parallel box length. For example, if xlo = 2 and
xhi = 12, then the x box length is 10 and the xy tilt factor must be
between -5 and 5. Similarly, both xz and yz must be between
-(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation,
since if the maximum tilt factor is 5 (as in this example), then
configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
equivalent.
</P>
<P>The <I>union</I> style creates a region consisting of the volume of all the
listed regions combined. The <I>intesect</I> style creates a region
consisting of the volume that is common to all the listed regions.

14
doc/region.txt
View File

@ -77,9 +77,7 @@ y-direction located at x = 2.0 and z = 3.0, with a radius of 5.0, and
extending in the y-direction from -5.0 to the upper box boundary.
For style {prism}, a parallelepiped is defined (it's too hard to spell
parallelepiped in an input script!). A prism region is used by the
"create_box"_create_box.html command to define a triclinic
(non-orthogonal) simulation domain. Think of the parallelepided as
parallelepiped in an input script!). Think of the parallelepided as
initially an axis-aligned orthogonal box with the same xyz lo/hi
parameters as region style {block} would define. Then, while holding
the (xlo,ylo,zlo) corner point fixed, the box is "skewed" or "tilted"
@ -92,6 +90,16 @@ results in a parallelepiped whose "origin" is at (xlo,ylo,zlo) with 3
edge vectors starting from its origin given by a = (xhi-xlo,0,0); b =
(xy,yhi-ylo,0); c = (xz,yz,zhi-zlo).
A prism region used with the "create_box"_create_box.html command must
have tilt factors (xy,xz,yz) that do not skew the box more than half
the distance of the parallel box length. For example, if xlo = 2 and
xhi = 12, then the x box length is 10 and the xy tilt factor must be
between -5 and 5. Similarly, both xz and yz must be between
-(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation,
since if the maximum tilt factor is 5 (as in this example), then
configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
equivalent.
The {union} style creates a region consisting of the volume of all the
listed regions combined. The {intesect} style creates a region
consisting of the volume that is common to all the listed regions.

3
doc/run.txt
View File

@ -63,8 +63,7 @@ performed and you want a "fix"_fix.html command that ramps some value
of runs and not just a single run. Fixes in this category include
"fix nvt"_fix_nvt.html, "fix npt"_fix_npt.html, "fix
langevin"_fix_langevin.html, "fix temp/rescale"_fix_temp_rescale.html,
"fix volume/rescale"_fix_volume_rescale.html, "fix
deform"_fix_deform.html, and "fix indent"_fix_indent.html. The
"fix deform"_fix_deform.html, and "fix indent"_fix_indent.html. The
"pair_style soft"_pair_style.html potential also ramps its
coefficients in a similar way.

187
doc/set.html
View File

@ -13,86 +13,153 @@
</H3>
<P><B>Syntax:</B>
</P>
<PRE>set ID style value
<PRE>set style ID keyword value ...
</PRE>
<UL><LI>ID = ID of group or atom
<LI>style = <I>atom</I> or <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I> or <I>charge</I> or <I>dipole</I> or <I>type</I> or <I>mol</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>vx</I> or <I>vy</I> or <I>vz</I> or <I>q</I>
<LI>value = value to set selected atom(s) to
<UL><LI>style = <I>atom</I> or <I>group</I> or <I>region</I>
<LI>ID = atom ID or group ID or region ID
<LI>one or more keyword/value pairs may be appended to the args
<LI>keyword = <I>type</I> or <I>type/fraction</I> or <I>mol</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>vx</I> or <I>vy</I> or <I>vz</I> or <I>charge</I> or <I>dipole</I> or <I>dipole/random</I> or <I>quat</I> or <I>quat/random</I> or <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I>
<PRE> <I>type</I> value = atom type
<I>type/fraction</I> values = type fraction seed
type = new atom type
fraction = fraction of selected atoms to set to new atom type
seed = random # seed (8 digits or less)
<I>mol</I> value = molecule ID
<I>x</I>,<I>y</I>,<I>z</I> value = atom coordinate (distance units)
<I>vx</I>,<I>vy</I>,<I>vz</I> value = velocity component (velocity units)
<I>charge</I> value = atomic charge (charge units)
<I>dipole</I> values = x y z
x,y,z = orientation of dipole moment vector
<I>dipole/random</I> value = seed
seed = random # seed (8 digits or less) for dipole moment orientations
<I>quat</I> values = w i j k
w,i,j,k = quaternion components (see below)
<I>quat/random</I> value = seed
seed = random # seed (8 digits or less) for quaternion orientations
<I>bond</I> value = bond type for all bonds between selected atoms
<I>angle</I> value = angle type for all angles bewteen selected atoms
<I>dihedral</I> value = dihedral type for all dihedrals between selected atoms
<I>improper</I> value = improper type for all impropers between selected atoms
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>set solvent atom 2
set edge bond 4
set half charge 0.5
set 100 x 0.5
set 1492 type 3
<PRE>set group solvent type 2
set group solvent type/fraction 2 0.5 12393
set group edge bond 4
set region half charge 0.5
set atom 100 x 0.5 vx 1.0
set atom 1492 type 3
</PRE>
<P><B>Description:</B>
</P>
<P>Set an attribute for a single atom or each atom in a group. The
context depends on the specified <I>style</I>.
</P>
<P>Styles <I>atom</I>, <I>bond</I>, <I>angle</I>, <I>dihedral</I>, <I>improper</I>, <I>charge</I>, and
<I>dipole</I> set attributes for all atoms in a group, so the specified ID
is a group-ID string.
</P>
<P>Styles <I>type</I>, <I>mol</I>, <I>x</I>, <I>y</I>, <I>z</I>, <I>vx</I>, <I>vy</I>, <I>vz</I>, and <I>q</I> set the
attribute of a single atom, so the specified ID is an atom-ID number
(1-N).
</P>
<P>Since atom attributes are assigned by the <A HREF = "read_data.html">read_data</A>,
<P>Set one or more properties of one or more atoms. Since atom
properties are initially assigned by the <A HREF = "read_data.html">read_data</A>,
<A HREF = "read_restart.html">read_restart</A> or <A HREF = "create_atoms.html">create_atoms</A>
commands, this command changes those assignments. This can be useful
for altering pairwise and molecular force interactions, since
force-field coefficients are defined in terms of types. It can also
be used to change the labeling of atoms when they are output in
<A HREF = "dump.html">dump</A> files. It can also be useful for debugging purposes;
i.e. positioning an atom at a precise location to compute subsequent
forces or energy.
for overriding the default values assigned by the
<A HREF = "create_atoms.html">create_atoms</A> command (e.g. charge = 0.0). It can
be useful for altering pairwise and molecular force interactions,
since force-field coefficients are defined in terms of types. It can
be used to change the labeling of atoms by atom type when they are
output in <A HREF = "dump.html">dump</A> files. It can be useful for debugging
purposes; i.e. positioning an atom at a precise location to compute
subsequent forces or energy.
</P>
<P>For style <I>atom</I>, the atom type of all atoms in the group is changed
to the specified value from 1 to ntypes. Note that ntypes must be
within the range the simulation was initialized for. The maximum
number of types is set by the <A HREF = "create_box.html">create_box</A> command or
the <I>atom types</I> field in the header of the data file read by the
<A HREF = "read_data.html">read_data</A> command.
<P>The style <I>atom</I> selects a single atom. The style <I>group</I> selects the
entire group of atoms. The style <I>region</I> selects all atoms in the
geometric region. The associated ID for each of these styles is
either the unique atom ID (typically a number from 1 to N = the number
of atoms in the simulation), the group ID, or the region ID. See the
<A HREF = "group.html">group</A> and <A HREF = "region.html">region</A> commands for details of
how to specify a group or region.
</P>
<P>For style <I>bond</I>, <I>angle</I>, <I>dihedral</I>, or <I>improper</I>, the bond type
(angle type, etc) of all bonds (angles, etc) of atoms in the group is
changed to the specified value from 1 to nbondtypes (angletypes, etc).
All atoms in the bond (angle, etc) must be in the group in order for
the change to be made. The maximum number of types is set by the
<I>bond types</I> (<I>angle types</I>, etc) field in the header of the data
file.
<HR>
<P>Keyword <I>type</I> sets the atom type for all selected atoms. The
specified value must be from 1 to ntypes, where ntypes was set by the
<A HREF = "create_box.html">create_box</A> command or the <I>atom types</I> field in the
header of the data file read by the <A HREF = "read_data.html">read_data</A>
command.
</P>
<P>For style <I>charge</I>, the charge of each atom in the group is set to
the specified value.
<P>Keyword <I>type/fraction</I> sets the atom type for a fraction of the
selected atoms. The actual number of atoms changed is not guaranteed
to be exactly the requested fraction, but should be statisticaly
close. Random numbers are used in such a way that a particular atom
is changed or not changed, regardless of how many processors are being
used.
</P>
<P>For style <I>dipole</I>, the specified value is used as a random number
seed. The dipole moment of each atom in the group is set to a random
orientation with a magnitude determined by the <A HREF = "dipole.html">dipole</A>
command setting for that atom type.
<P>Keyword <I>mol</I> sets the molecule ID for all selected atoms. The <A HREF = "atom_style.html">atom
style</A> being used must support the use of molecule
IDs.
</P>
<P>For styles <I>type</I>, <I>mol</I>, <I>x</I>, <I>y</I>, <I>z</I>, <I>vx</I>, <I>vy</I>, <I>vz</I>, or <I>q</I>, the
corresponding attribute of a single atom with the specified atom-ID is
set to the specified value. E.g. the last example above, sets the
atom-type of atom 1492 to 3. If "type" were replaced by "q", the
charge on atom 1492 would be set to 3; if it were replaced by "mol",
then then the molecule-ID would be set to 3. The values for x,y,z are
in distance units, the values for vx,vy,vz are in velocity units, and
the value for charge is in charge units, as explained by the
<A HREF = "units.html">units</A> command.
<P>Keywords <I>x</I>, <I>y</I>, <I>z</I>, <I>vx</I>, <I>vy</I>, <I>vz</I>, and <I>charge</I> set the
coordinates, velocity, or charge of all selected atoms. For <I>charge</I>,
the <A HREF = "atom_style.html">atom style</A> being used must support the use of
atomic charge.
</P>
<P>Keyword <I>dipole</I> uses the specified x,y,z values as components of a
vector to set as the orientation of the dipole moment vectors of the
selected atoms. The magnitude of the dipole moment for each atom is
set by the <A HREF = "dipole.html">dipole</A> command.
</P>
<P>Keyword <I>dipole/random</I> randomizes the orientation of the dipole
moment vectors of the selected atoms. The magnitude of the dipole
moment for each atom is set by the <A HREF = "dipole.html">dipole</A> command.
Random numbers are used in such a way that the orientation of a
particular atom is the same, regardless of how many processors are
being used.
</P>
<P>Keyword <I>quat</I> uses the specified values as components of a quaternion
(4-vector) to set the orientation of the selected atoms. Note that
the <A HREF = "shape.html">shape</A> command is used to specify the aspect ratios of
an ellipsoidal particle, which is oriented by default with its x-axis
along the simulation box's x-axis, and similarly for y and z. If this
body is rotated (via the right-hand rule) by an angle theta around a
unit vector (a,b,c), then the quaternion that represents its new
orientation is given by (cos(theta/2), a*sin(theta/2), b*sin(theta/2),
c*sin(theta/2)). These 4 components are the arguments w,i,j,k to the
<I>quat</I> keyword. LAMMPS normalizes the quaternion in case (a,b,c) was
not a unit vector.
</P>
<P>Keyword <I>quat/random</I> randomizes the orientation of the quaternion of
the selected atoms. Random numbers are used in such a way that the
orientation of a particular atom is the same, regardless of how many
processors are being used.
</P>
<P>For the <I>dipole</I> and <I>quat</I> keywords, the <A HREF = "atom_style.html">atom style</A>
being used must support the use of dipoles or quaternions.
</P>
<P>Keywords <I>bond</I>, <I>angle</I>, <I>dihedral</I>, and <I>improper</I>, set the bond
type (angle type, etc) of all bonds (angles, etc) of selected atoms to
the specified value from 1 to nbondtypes (nangletypes, etc). All
atoms in a particular bond (angle, etc) must be selected atoms in
order for the change to be made. The value of nbondtype (nangletypes,
etc) was set by the <I>bond types</I> (<I>angle types</I>, etc) field in the
header of the data file read by the <A HREF = "read_data.html">read_data</A>
command.
</P>
<P><B>Restrictions:</B>
</P>
<P>You cannot set an atom attribute (e.g. <I>mol</I> or <I>q</I>) if the
<A HREF = "atom_style.html">atom_style</A> does not have that attribute.
</P>
<P>This command requires inter-processor communication to coordinate the
setting of bond types (angle types, etc). This means that your system
must be ready to perform a simulation before using this command (force
fields setup, atom masses set, etc). This is not necessary to simply
reset atom types.
must be ready to perform a simulation before using one of these
keywords (force fields set, atom mass set, etc). This is not
necessary for other keywords.
</P>
<P>You cannot set the <I>mol</I> or <I>q</I> for an atom if the
<A HREF = "atom_style.html">atom_style</A> does not have those attributes.
<P>Using the <I>region</I> style with the bond (angle, etc) keywords can give
unpredictable results if there are bonds (angles, etc) that straddle
periodic boundaries. This is because the region may only extend up to
the boundary and partner atoms in the bond (angle, etc) may have
coordinates outside the simulation box if they are ghost atoms.
</P>
<P><B>Related commands:</B>
</P>

188
doc/set.txt
View File

@ -10,88 +10,152 @@ set command :h3
[Syntax:]
set ID style value :pre
set style ID keyword value ... :pre
ID = ID of group or atom
style = {atom} or {bond} or {angle} or {dihedral} or {improper} or \
{charge} or {dipole} or {type} or {mol} or {x} or {y} or {z} or \
{vx} or {vy} or {vz} or {q}
value = value to set selected atom(s) to :ul
style = {atom} or {group} or {region} :ulb,l
ID = atom ID or group ID or region ID :l
one or more keyword/value pairs may be appended to the args :l
keyword = {type} or {type/fraction} or {mol} or \
{x} or {y} or {z} or {vx} or {vy} or {vz} or \
{charge} or {dipole} or {dipole/random} or \
{quat} or {quat/random} or \
{bond} or {angle} or {dihedral} or {improper} :l
{type} value = atom type
{type/fraction} values = type fraction seed
type = new atom type
fraction = fraction of selected atoms to set to new atom type
seed = random # seed (8 digits or less)
{mol} value = molecule ID
{x},{y},{z} value = atom coordinate (distance units)
{vx},{vy},{vz} value = velocity component (velocity units)
{charge} value = atomic charge (charge units)
{dipole} values = x y z
x,y,z = orientation of dipole moment vector
{dipole/random} value = seed
seed = random # seed (8 digits or less) for dipole moment orientations
{quat} values = w i j k
w,i,j,k = quaternion components (see below)
{quat/random} value = seed
seed = random # seed (8 digits or less) for quaternion orientations
{bond} value = bond type for all bonds between selected atoms
{angle} value = angle type for all angles bewteen selected atoms
{dihedral} value = dihedral type for all dihedrals between selected atoms
{improper} value = improper type for all impropers between selected atoms :pre
:ule
[Examples:]
set solvent atom 2
set edge bond 4
set half charge 0.5
set 100 x 0.5
set 1492 type 3 :pre
set group solvent type 2
set group solvent type/fraction 2 0.5 12393
set group edge bond 4
set region half charge 0.5
set atom 100 x 0.5 vx 1.0
set atom 1492 type 3 :pre
[Description:]
Set an attribute for a single atom or each atom in a group. The
context depends on the specified {style}.
Styles {atom}, {bond}, {angle}, {dihedral}, {improper}, {charge}, and
{dipole} set attributes for all atoms in a group, so the specified ID
is a group-ID string.
Styles {type}, {mol}, {x}, {y}, {z}, {vx}, {vy}, {vz}, and {q} set the
attribute of a single atom, so the specified ID is an atom-ID number
(1-N).
Since atom attributes are assigned by the "read_data"_read_data.html,
Set one or more properties of one or more atoms. Since atom
properties are initially assigned by the "read_data"_read_data.html,
"read_restart"_read_restart.html or "create_atoms"_create_atoms.html
commands, this command changes those assignments. This can be useful
for altering pairwise and molecular force interactions, since
force-field coefficients are defined in terms of types. It can also
be used to change the labeling of atoms when they are output in
"dump"_dump.html files. It can also be useful for debugging purposes;
i.e. positioning an atom at a precise location to compute subsequent
forces or energy.
for overriding the default values assigned by the
"create_atoms"_create_atoms.html command (e.g. charge = 0.0). It can
be useful for altering pairwise and molecular force interactions,
since force-field coefficients are defined in terms of types. It can
be used to change the labeling of atoms by atom type when they are
output in "dump"_dump.html files. It can be useful for debugging
purposes; i.e. positioning an atom at a precise location to compute
subsequent forces or energy.
For style {atom}, the atom type of all atoms in the group is changed
to the specified value from 1 to ntypes. Note that ntypes must be
within the range the simulation was initialized for. The maximum
number of types is set by the "create_box"_create_box.html command or
the {atom types} field in the header of the data file read by the
"read_data"_read_data.html command.
The style {atom} selects a single atom. The style {group} selects the
entire group of atoms. The style {region} selects all atoms in the
geometric region. The associated ID for each of these styles is
either the unique atom ID (typically a number from 1 to N = the number
of atoms in the simulation), the group ID, or the region ID. See the
"group"_group.html and "region"_region.html commands for details of
how to specify a group or region.
For style {bond}, {angle}, {dihedral}, or {improper}, the bond type
(angle type, etc) of all bonds (angles, etc) of atoms in the group is
changed to the specified value from 1 to nbondtypes (angletypes, etc).
All atoms in the bond (angle, etc) must be in the group in order for
the change to be made. The maximum number of types is set by the
{bond types} ({angle types}, etc) field in the header of the data
file.
:line
For style {charge}, the charge of each atom in the group is set to
the specified value.
Keyword {type} sets the atom type for all selected atoms. The
specified value must be from 1 to ntypes, where ntypes was set by the
"create_box"_create_box.html command or the {atom types} field in the
header of the data file read by the "read_data"_read_data.html
command.
For style {dipole}, the specified value is used as a random number
seed. The dipole moment of each atom in the group is set to a random
orientation with a magnitude determined by the "dipole"_dipole.html
command setting for that atom type.
Keyword {type/fraction} sets the atom type for a fraction of the
selected atoms. The actual number of atoms changed is not guaranteed
to be exactly the requested fraction, but should be statisticaly
close. Random numbers are used in such a way that a particular atom
is changed or not changed, regardless of how many processors are being
used.
For styles {type}, {mol}, {x}, {y}, {z}, {vx}, {vy}, {vz}, or {q}, the
corresponding attribute of a single atom with the specified atom-ID is
set to the specified value. E.g. the last example above, sets the
atom-type of atom 1492 to 3. If "type" were replaced by "q", the
charge on atom 1492 would be set to 3; if it were replaced by "mol",
then then the molecule-ID would be set to 3. The values for x,y,z are
in distance units, the values for vx,vy,vz are in velocity units, and
the value for charge is in charge units, as explained by the
"units"_units.html command.
Keyword {mol} sets the molecule ID for all selected atoms. The "atom
style"_atom_style.html being used must support the use of molecule
IDs.
Keywords {x}, {y}, {z}, {vx}, {vy}, {vz}, and {charge} set the
coordinates, velocity, or charge of all selected atoms. For {charge},
the "atom style"_atom_style.html being used must support the use of
atomic charge.
Keyword {dipole} uses the specified x,y,z values as components of a
vector to set as the orientation of the dipole moment vectors of the
selected atoms. The magnitude of the dipole moment for each atom is
set by the "dipole"_dipole.html command.
Keyword {dipole/random} randomizes the orientation of the dipole
moment vectors of the selected atoms. The magnitude of the dipole
moment for each atom is set by the "dipole"_dipole.html command.
Random numbers are used in such a way that the orientation of a
particular atom is the same, regardless of how many processors are
being used.
Keyword {quat} uses the specified values as components of a quaternion
(4-vector) to set the orientation of the selected atoms. Note that
the "shape"_shape.html command is used to specify the aspect ratios of
an ellipsoidal particle, which is oriented by default with its x-axis
along the simulation box's x-axis, and similarly for y and z. If this
body is rotated (via the right-hand rule) by an angle theta around a
unit vector (a,b,c), then the quaternion that represents its new
orientation is given by (cos(theta/2), a*sin(theta/2), b*sin(theta/2),
c*sin(theta/2)). These 4 components are the arguments w,i,j,k to the
{quat} keyword. LAMMPS normalizes the quaternion in case (a,b,c) was
not a unit vector.
Keyword {quat/random} randomizes the orientation of the quaternion of
the selected atoms. Random numbers are used in such a way that the
orientation of a particular atom is the same, regardless of how many
processors are being used.
For the {dipole} and {quat} keywords, the "atom style"_atom_style.html
being used must support the use of dipoles or quaternions.
Keywords {bond}, {angle}, {dihedral}, and {improper}, set the bond
type (angle type, etc) of all bonds (angles, etc) of selected atoms to
the specified value from 1 to nbondtypes (nangletypes, etc). All
atoms in a particular bond (angle, etc) must be selected atoms in
order for the change to be made. The value of nbondtype (nangletypes,
etc) was set by the {bond types} ({angle types}, etc) field in the
header of the data file read by the "read_data"_read_data.html
command.
[Restrictions:]
You cannot set an atom attribute (e.g. {mol} or {q}) if the
"atom_style"_atom_style.html does not have that attribute.
This command requires inter-processor communication to coordinate the
setting of bond types (angle types, etc). This means that your system
must be ready to perform a simulation before using this command (force
fields setup, atom masses set, etc). This is not necessary to simply
reset atom types.
must be ready to perform a simulation before using one of these
keywords (force fields set, atom mass set, etc). This is not
necessary for other keywords.
You cannot set the {mol} or {q} for an atom if the
"atom_style"_atom_style.html does not have those attributes.
Using the {region} style with the bond (angle, etc) keywords can give
unpredictable results if there are bonds (angles, etc) that straddle
periodic boundaries. This is because the region may only extend up to
the boundary and partner atoms in the bond (angle, etc) may have
coordinates outside the simulation box if they are ghost atoms.
[Related commands:]

2
doc/shape.html
View File

@ -32,7 +32,7 @@ shape 2* 3.0 1.0 1.0
can also be set in the <A HREF = "read_data.html">read_data</A> data file. See the
<A HREF = "units.html">units</A> command for what distance units to use.
</P>
<P>Currently, only <A HREF = "atom_style.html<A HREF = "atom_style.html">>atom_style dipole</A> and atom_style
<P>Currently, only <A HREF = "atom_style.html">atom_style dipole</A> and <A HREF = "atom_style.html">atom_style
ellipsoid</A> require that shapes be set.
</P>
<P>Dipoles use the atom shape to compute a moment of inertia for

21
doc/shape.txt
View File

@ -29,7 +29,7 @@ Set the shape for all atoms of one or more atom types. Shape values
can also be set in the "read_data"_read_data.html data file. See the
"units"_units.html command for what distance units to use.
Currently, only "atom_style dipole"_atom_style.html and atom_style
Currently, only "atom_style dipole"_atom_style.html and "atom_style
ellipsoid"_atom_style.html require that shapes be set.
Dipoles use the atom shape to compute a moment of inertia for
@ -45,14 +45,15 @@ longer in x than in y or z and with a circular cross-section in yz.
Ellipsoids that are spherical can be defined by setting all 3 shape
components the same.
I can be specified in one of two ways. An explicit numeric value can
be used, as in the 1st example above. Or a wild-card asterik can be
used to set the mass for multiple atom types. This takes the form "*"
or "*n" or "n*" or "m*n". If N = the number of atom types, then an
asterik with no numeric values means all types from 1 to N. A leading
asterik means all types from 1 to n (inclusive). A trailing asterik
means all types from n to N (inclusive). A middle asterik means all
types from m to n (inclusive).
The I index can be specified in one of two ways. An explicit numeric
value can be used, as in the 1st example above. Or a wild-card
asterik can be used to set the mass for multiple atom types. This
takes the form "*" or "*n" or "n*" or "m*n". If N = the number of
atom types, then an asterik with no numeric values means all types
from 1 to N. A leading asterik means all types from 1 to n
(inclusive). A trailing asterik means all types from n to N
(inclusive). A middle asterik means all types from m to n
(inclusive).
A line in a data file that specifies shape uses the same format as the
arguments of the shape command in an input script, except that no
@ -60,7 +61,7 @@ wild-card asterik can be used. For example, under the "Shapes"
section of a data file, the line that corresponds to the 1st example
above would be listed as
1 1.0 :pre
1 1.0 1.0 1.0 :pre
[Restrictions:]

17
doc/thermo_modify.html
View File

@ -37,7 +37,7 @@
</UL>
<P><B>Examples:</B>
</P>
<PRE>thermo_modify lost no flush yes
<PRE>thermo_modify lost ignore flush yes
thermo_modify temp myTemp format 3 %15.8g
thermo_modify line multi format float %g
</PRE>
@ -46,6 +46,13 @@ thermo_modify line multi format float %g
<P>Set options for how thermodynamic information is computed and printed
by LAMMPS.
</P>
<P>IMPORTANT NOTE: These options apply to the currently defined thermo
style (thermo_style <I>one</I> by default). When you specify a
<A HREF = "thermo_style.html">thermo_style</A> command, all thermodynamic settings
are restored to their default values. Thus a thermo_style command
will wipe out any options previously specified by the
<A HREF = "thermo_modify.html">thermo_modify</A> command.
</P>
<P>The <I>lost</I> keyword determines whether LAMMPS checks for lost atoms
each time it computes thermodynamics and what it does if atoms are
lost. If the value is <I>ignore</I>, LAMMPS does not check for lost atoms.
@ -87,7 +94,7 @@ temperature ("temp", "press", "ke", "etotal", "enthalpy", "pxx etc",
"tave", "pave"). The specified compute ID must have been previously
defined by the user via the <A HREF = "compute.html">compute</A> command and it must
be a style of compute that calculates a temperature. As described in
the <A HREF = "thermo_style.html">thermo_style</A> command, thermo output has a
the <A HREF = "thermo_style.html">thermo_style</A> command, thermo output uses a
default compute for temperature with ID = <I>thermo_temp</I>. This option
allows the user to override the default.
</P>
@ -97,9 +104,9 @@ pressure ("press", "enthalpy", "pxx etc", "pave"). The specified
compute ID must have been previously defined by the user via the
<A HREF = "compute.html">compute</A> command and it must be a style of compute that
calculates a pressure. As described in the
<A HREF = "thermo_style.html">thermo_style</A> command, thermo output has a default
compute for pressure with ID = <I>thermo_press</I>. This option allows the
user to override the default.
<A HREF = "thermo_style.html">thermo_style</A> command, thermo output uses a default
compute for pressure with ID = <I>thermo_pressure</I>. This option allows
the user to override the default.
</P>
<P>The <I>drot</I> keyword is used to determine how rotational energy is
calculated for dipolar atoms, which is used by the thermo_style

17
doc/thermo_modify.txt
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@ -31,7 +31,7 @@ keyword = {lost} or {norm} or {flush} or {line} or {format} or {temp} or {press}
[Examples:]
thermo_modify lost no flush yes
thermo_modify lost ignore flush yes
thermo_modify temp myTemp format 3 %15.8g
thermo_modify line multi format float %g :pre
@ -40,6 +40,13 @@ thermo_modify line multi format float %g :pre
Set options for how thermodynamic information is computed and printed
by LAMMPS.
IMPORTANT NOTE: These options apply to the currently defined thermo
style (thermo_style {one} by default). When you specify a
"thermo_style"_thermo_style.html command, all thermodynamic settings
are restored to their default values. Thus a thermo_style command
will wipe out any options previously specified by the
"thermo_modify"_thermo_modify.html command.
The {lost} keyword determines whether LAMMPS checks for lost atoms
each time it computes thermodynamics and what it does if atoms are
lost. If the value is {ignore}, LAMMPS does not check for lost atoms.
@ -81,7 +88,7 @@ temperature ("temp", "press", "ke", "etotal", "enthalpy", "pxx etc",
"tave", "pave"). The specified compute ID must have been previously
defined by the user via the "compute"_compute.html command and it must
be a style of compute that calculates a temperature. As described in
the "thermo_style"_thermo_style.html command, thermo output has a
the "thermo_style"_thermo_style.html command, thermo output uses a
default compute for temperature with ID = {thermo_temp}. This option
allows the user to override the default.
@ -91,9 +98,9 @@ pressure ("press", "enthalpy", "pxx etc", "pave"). The specified
compute ID must have been previously defined by the user via the
"compute"_compute.html command and it must be a style of compute that
calculates a pressure. As described in the
"thermo_style"_thermo_style.html command, thermo output has a default
compute for pressure with ID = {thermo_press}. This option allows the
user to override the default.
"thermo_style"_thermo_style.html command, thermo output uses a default
compute for pressure with ID = {thermo_pressure}. This option allows
the user to override the default.
The {drot} keyword is used to determine how rotational energy is
calculated for dipolar atoms, which is used by the thermo_style

44
doc/thermo_style.html
View File

@ -108,43 +108,49 @@ be used to set the one- or multi-line format of the print-out, the
normalization of energy quantities (total or per-atom), and the
numeric precision of each printed value.
</P>
<P>IMPORTANT NOTE: When you specify a <A HREF = "thermo_style.html">thermo_style</A>
command, all thermodynamic settings are restored to their default
values. Thus a thermo_style command will wipe out any options
previously specified by the <A HREF = "thermo_modify.html">thermo_modify</A>
command.
</P>
<HR>
<P>Several of the thermodynamic quantities require a temperature to be
computed: "temp", "press", "ke", "etotal", "enthalpy", "pxx etc",
"tave", "pave". To do this, a compute of style "temp" is created, as
if this command had been issued:
"tave", "pave". By default this is done by using the "thermo_temp"
compute which is created by LAMMPS as if this command had been issued:
</P>
<PRE>compute thermo_temp all temp
</PRE>
<P>See the <A HREF = "compute_temp.html">compute temp</A> command for details. Note
that the ID of the new compute is <I>thermo_temp</I> and the group is
<I>all</I>. You can change the attributes of this temperature (e.g. its
that the ID of this compute is <I>thermo_temp</I> and the group is <I>all</I>.
You can change the attributes of this temperature (e.g. its
degrees-of-freedom) via the <A HREF = "compute_modify.html">compute_modify</A>
command. Alternatively, you can directly assign a new compute (that
calculates temperature) which you have defined, to be used for any
thermodynamic quantity that requires a temperature. This is done via
the <A HREF = "thermo_modify.html">thermo_modify</A> command.
calculates temperature) which you have defined, to be used for
calculating any thermodynamic quantity that requires a temperature.
This is done via the <A HREF = "thermo_modify.html">thermo_modify</A> command.
</P>
<P>Several of the thermodynamic quantities require a pressure to be
computed: "press", "enthalpy", "pxx etc", "pave". To do this, a
compute of style "pressure" is created, as if this command had been
issued:
computed: "press", "enthalpy", "pxx etc", "pave". By default this is
done by using the "thermo_pressure" compute which is created by LAMMPS
as if this command had been issued:
</P>
<PRE>compute thermo_press all pressure thermo_temp
<PRE>compute thermo_pressure all pressure thermo_temp
</PRE>
<P>See the <A HREF = "compute_pressure.html">compute pressure</A> command for details.
Note that the ID of the new compute is <I>thermo_press</I> and the group is
Note that the ID of this compute is <I>thermo_pressure</I> and the group is
<I>all</I>. You can change the attributes of this pressure via the
<A HREF = "compute_modify.html">compute_modify</A> command. Alternatively, you can
directly assign a new compute (that calculates pressure) which you
have defined, to be used for any thermodynamic quantity that requires
a pressure. This is done via the <A HREF = "thermo_modify.html">thermo_modify</A>
command.
have defined, to be used for calculating any thermodynamic quantity
that requires a pressure. This is done via the
<A HREF = "thermo_modify.html">thermo_modify</A> command.
</P>
<P>The <I>drot</I> keyword requires a rotational energy to be compute for
dipolar particles. To do this, a compute of style "rotate/dipole" is
created, as if this command had been issued:
<P>The <I>drot</I> keyword requires a rotational energy to be computed for
point dipole particles. To do this, a compute of style
"rotate/dipole" is created, as if this command had been issued:
</P>
<PRE>compute thermo_rotate_dipole all rotate/dipole
</PRE>
@ -158,7 +164,7 @@ directly assign a new compute which you have defined, to be used for
command. For example, this could be useful if you wish to exclude
certain particles from the compuation.
</P>
<P>The <I>grot</I> keyword requires a rotational energy to be compute for
<P>The <I>grot</I> keyword requires a rotational energy to be computed for
granular particles. To do this, a compute of style "rotate/gran" is
created, as if this command had been issued:
</P>

44
doc/thermo_style.txt
View File

@ -102,43 +102,49 @@ be used to set the one- or multi-line format of the print-out, the
normalization of energy quantities (total or per-atom), and the
numeric precision of each printed value.
IMPORTANT NOTE: When you specify a "thermo_style"_thermo_style.html
command, all thermodynamic settings are restored to their default
values. Thus a thermo_style command will wipe out any options
previously specified by the "thermo_modify"_thermo_modify.html
command.
:line
Several of the thermodynamic quantities require a temperature to be
computed: "temp", "press", "ke", "etotal", "enthalpy", "pxx etc",
"tave", "pave". To do this, a compute of style "temp" is created, as
if this command had been issued:
"tave", "pave". By default this is done by using the "thermo_temp"
compute which is created by LAMMPS as if this command had been issued:
compute thermo_temp all temp :pre
See the "compute temp"_compute_temp.html command for details. Note
that the ID of the new compute is {thermo_temp} and the group is
{all}. You can change the attributes of this temperature (e.g. its
that the ID of this compute is {thermo_temp} and the group is {all}.
You can change the attributes of this temperature (e.g. its
degrees-of-freedom) via the "compute_modify"_compute_modify.html
command. Alternatively, you can directly assign a new compute (that
calculates temperature) which you have defined, to be used for any
thermodynamic quantity that requires a temperature. This is done via
the "thermo_modify"_thermo_modify.html command.
calculates temperature) which you have defined, to be used for
calculating any thermodynamic quantity that requires a temperature.
This is done via the "thermo_modify"_thermo_modify.html command.
Several of the thermodynamic quantities require a pressure to be
computed: "press", "enthalpy", "pxx etc", "pave". To do this, a
compute of style "pressure" is created, as if this command had been
issued:
computed: "press", "enthalpy", "pxx etc", "pave". By default this is
done by using the "thermo_pressure" compute which is created by LAMMPS
as if this command had been issued:
compute thermo_press all pressure thermo_temp :pre
compute thermo_pressure all pressure thermo_temp :pre
See the "compute pressure"_compute_pressure.html command for details.
Note that the ID of the new compute is {thermo_press} and the group is
Note that the ID of this compute is {thermo_pressure} and the group is
{all}. You can change the attributes of this pressure via the
"compute_modify"_compute_modify.html command. Alternatively, you can
directly assign a new compute (that calculates pressure) which you
have defined, to be used for any thermodynamic quantity that requires
a pressure. This is done via the "thermo_modify"_thermo_modify.html
command.
have defined, to be used for calculating any thermodynamic quantity
that requires a pressure. This is done via the
"thermo_modify"_thermo_modify.html command.
The {drot} keyword requires a rotational energy to be compute for
dipolar particles. To do this, a compute of style "rotate/dipole" is
created, as if this command had been issued:
The {drot} keyword requires a rotational energy to be computed for
point dipole particles. To do this, a compute of style
"rotate/dipole" is created, as if this command had been issued:
compute thermo_rotate_dipole all rotate/dipole :pre
@ -152,7 +158,7 @@ directly assign a new compute which you have defined, to be used for
command. For example, this could be useful if you wish to exclude
certain particles from the compuation.
The {grot} keyword requires a rotational energy to be compute for
The {grot} keyword requires a rotational energy to be computed for
granular particles. To do this, a compute of style "rotate/gran" is
created, as if this command had been issued:

3
doc/units.html
View File

@ -45,6 +45,7 @@ uses the thermochemical calorie = 4.184 J.
<LI>temperature = reduced LJ temperature
<LI>pressure = reduced LJ pressure
<LI>charge = reduced LJ charge
<LI>dipole = reduced LJ dipole moment
<LI>electric field = force/charge
</UL>
<P>For style <I>real</I>, these are the units:
@ -58,6 +59,7 @@ uses the thermochemical calorie = 4.184 J.
<LI>temperature = degrees K
<LI>pressure = atmospheres
<LI>charge = multiple of electron charge (+1.0 is a proton)
<LI>dipole = charge*Angstroms
<LI>electric field = volts/Angstrom
</UL>
<P>For style <I>metal</I>, these are the units:
@ -71,6 +73,7 @@ uses the thermochemical calorie = 4.184 J.
<LI>temperature = degrees K
<LI>pressure = bars
<LI>charge = multiple of electron charge (+1.0 is a proton)
<LI>dipole = charge*Angstroms
<LI>electric field = volts/Angstrom
</UL>
<P>This command also sets the timestep size and neighbor skin distance to

3
doc/units.txt
View File

@ -42,6 +42,7 @@ force = epsilon/sigma
temperature = reduced LJ temperature
pressure = reduced LJ pressure
charge = reduced LJ charge
dipole = reduced LJ dipole moment
electric field = force/charge :ul
For style {real}, these are the units:
@ -55,6 +56,7 @@ force = Kcal/mole-Angstrom
temperature = degrees K
pressure = atmospheres
charge = multiple of electron charge (+1.0 is a proton)
dipole = charge*Angstroms
electric field = volts/Angstrom :ul
For style {metal}, these are the units:
@ -68,6 +70,7 @@ force = eV/Angstrom
temperature = degrees K
pressure = bars
charge = multiple of electron charge (+1.0 is a proton)
dipole = charge*Angstroms
electric field = volts/Angstrom :ul
This command also sets the timestep size and neighbor skin distance to

3
doc/variable.html
View File

@ -290,6 +290,9 @@ style to use a global mapping in order to look up the vector indices.
Only atom styles with molecular information create global maps unless
the <A HREF = "atom_modify.html">atom_modify map</A> command is used.
</P>
<P>All <I>universe</I>- and <I>uloop</I>-style variables must have the same number
of values.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "next.html">next</A>, <A HREF = "jump.html">jump</A>, <A HREF = "include.html">include</A>,

3
doc/variable.txt
View File

@ -288,6 +288,9 @@ style to use a global mapping in order to look up the vector indices.
Only atom styles with molecular information create global maps unless
the "atom_modify map"_atom_modify.html command is used.
All {universe}- and {uloop}-style variables must have the same number
of values.
[Related commands:]
"next"_next.html, "jump"_jump.html, "include"_include.html,