mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3550 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
61bb734172
commit
664fa43717
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@ -321,14 +321,14 @@ of each style or click on the style itself for a full description:
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</P>
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<DIV ALIGN=center><TABLE BORDER=1 >
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<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_atom.html">ave/atom</A></TD><TD ><A HREF = "fix_ave_histo.html">ave/histo</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_bond_break.html">bond/break</A></TD><TD ><A HREF = "fix_bond_create.html">bond/create</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_bond_swap.html">bond/swap</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_coord_original.html">coord/original</A></TD><TD ><A HREF = "fix_deform.html">deform</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_dt_reset.html">dt/reset</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_evaporate.html">evaporate</A></TD><TD ><A HREF = "fix_freeze.html">freeze</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><TD ><A HREF = "fix_indent.html">indent</A></TD></TR>
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<TR ALIGN="center"><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_move.html">move</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>
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<TR ALIGN="center"><TD ><A HREF = "fix_npt_sphere.html">npt/sphere</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_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nve_sphere.html">nve/sphere</A></TD><TD ><A HREF = "fix_nvt.html">nvt</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_nvt_sphere.html">nvt/sphere</A></TD><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_press_berendsen.html">press/berendsen</A></TD><TD ><A HREF = "fix_print.html">print</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_rdf.html">rdf</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/bonds</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><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></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A>
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<TR ALIGN="center"><TD ><A HREF = "fix_bond_swap.html">bond/swap</A></TD><TD ><A HREF = "fix_box_relax.html">box/relax</A></TD><TD ><A HREF = "fix_coord_original.html">coord/original</A></TD><TD ><A HREF = "fix_deform.html">deform</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_dt_reset.html">dt/reset</A></TD><TD ><A HREF = "fix_efield.html">efield</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_evaporate.html">evaporate</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><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></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_move.html">move</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><TD ><A HREF = "fix_npt_sphere.html">npt/sphere</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nve_sphere.html">nve/sphere</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_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_nvt_sphere.html">nvt/sphere</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD></TR>
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<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_press_berendsen.html">press/berendsen</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/bonds</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD></TR>
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<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_berendsen.html">temp/berendsen</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A>
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</TD></TR></TABLE></DIV>
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<P>These are fix styles contributed by users, which can be used if
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@ -349,9 +349,9 @@ each style or click on the style itself for a full description:
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<TR ALIGN="center"><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_cna_atom.html">cna/atom</A></TD><TD ><A HREF = "compute_com.html">com</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_damage_atom.html">damage/atom</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD><TD ><A HREF = "compute_event_displace.html">event/displace</A></TD><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_gyration.html">gyration</A></TD><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_msd.html">msd</A></TD><TD ><A HREF = "compute_pe.html">pe</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_property_atom.html">property/atom</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</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></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A>
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<TR ALIGN="center"><TD ><A HREF = "compute_property_atom.html">property/atom</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A>
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</TD></TR></TABLE></DIV>
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<P>These are compute styles contributed by users, which can be used if
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@ -389,7 +389,6 @@ of each style or click on the style itself for a full description:
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"bond/create"_fix_bond_create.html,
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"bond/swap"_fix_bond_swap.html,
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"box/relax"_fix_box_relax.html,
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"com"_fix_com.html,
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"coord/original"_fix_coord_original.html,
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"deform"_fix_deform.html,
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"deposit"_fix_deposit.html,
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@ -400,12 +399,10 @@ of each style or click on the style itself for a full description:
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"evaporate"_fix_evaporate.html,
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"freeze"_fix_freeze.html,
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"gravity"_fix_gravity.html,
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"gyration"_fix_gyration.html,
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"heat"_fix_heat.html,
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"indent"_fix_indent.html,
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"langevin"_fix_langevin.html,
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"lineforce"_fix_lineforce.html,
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"msd"_fix_msd.html,
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"momentum"_fix_momentum.html,
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"move"_fix_move.html,
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"nph"_fix_nph.html,
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@ -427,7 +424,6 @@ of each style or click on the style itself for a full description:
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"pour"_fix_pour.html,
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"press/berendsen"_fix_press_berendsen.html,
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"print"_fix_print.html,
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"rdf"_fix_rdf.html,
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"reax/bonds"_fix_reax_bonds.html,
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"recenter"_fix_recenter.html,
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"rigid"_fix_rigid.html,
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@ -482,6 +478,7 @@ each style or click on the style itself for a full description:
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"pe/atom"_compute_pe_atom.html,
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"pressure"_compute_pressure.html,
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"property/atom"_compute_property_atom.html,
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"rdf"_compute_rdf.html,
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"reduce"_compute_reduce.html,
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"reduce/region"_compute_reduce.html,
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"stress/atom"_compute_stress_atom.html,
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@ -184,6 +184,7 @@ available in LAMMPS:
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<LI><A HREF = "compute_pe_atom.html">pe/atom</A> - potential energy for each atom
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<LI><A HREF = "compute_pressure.html">pressure</A> - total pressure and pressure tensor
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<LI><A HREF = "compute_property_atom.html">property/atom</A> - convert atom attributes to per-atom vectors/arrays
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<LI><A HREF = "compute_rdf.html">rdf</A> - radial distribution function g(r) histogram of group of atoms
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<LI><A HREF = "compute_reduce.html">reduce</A> - combine per-atom quantities into a single global value
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<LI><A HREF = "compute_reduce.html">reduce/region</A> - same as compute reduce, within a region
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<LI><A HREF = "compute_stress_atom.html">stress/atom</A> - stress tensor for each atom
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@ -179,6 +179,7 @@ available in LAMMPS:
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"pe/atom"_compute_pe_atom.html - potential energy for each atom
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"pressure"_compute_pressure.html - total pressure and pressure tensor
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"property/atom"_compute_property_atom.html - convert atom attributes to per-atom vectors/arrays
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"rdf"_compute_rdf.html - radial distribution function g(r) histogram of group of atoms
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"reduce"_compute_reduce.html - combine per-atom quantities into a single global value
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"reduce/region"_compute_reduce.html - same as compute reduce, within a region
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"stress/atom"_compute_stress_atom.html - stress tensor for each atom
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@ -168,7 +168,6 @@ list of fix styles available in LAMMPS:
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<LI><A HREF = "fix_bond_create.html">bond/create</A> - create bonds on the fly
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<LI><A HREF = "fix_bond_swap.html">bond/swap</A> - Monte Carlo bond swapping
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<LI><A HREF = "fix_box_relax.html">box/relax</A> - relax box size during energy minimization
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<LI><A HREF = "fix_com.html">com</A> - compute a center-of-mass
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<LI><A HREF = "fix_coord_original.html">coord/original</A> - store original coords of each atom
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<LI><A HREF = "fix_deform.html">deform</A> - change the simulation box size/shape
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<LI><A HREF = "fix_deposit.html">deposit</A> - add new atoms above a surface
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@ -179,13 +178,11 @@ list of fix styles available in LAMMPS:
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<LI><A HREF = "fix_evaporate.html">evaporate</A> - remove atoms from simulation periodically
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<LI><A HREF = "fix_freeze.html">freeze</A> - freeze atoms in a granular simulation
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<LI><A HREF = "fix_gravity.html">gravity</A> - add gravity to atoms in a granular simulation
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<LI><A HREF = "fix_gyration.html">gyration</A> - compute radius of gyration
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<LI><A HREF = "fix_heat.html">heat</A> - add/subtract momentum-conserving heat
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<LI><A HREF = "fix_indent.html">indent</A> - impose force due to an indenter
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<LI><A HREF = "fix_langevin.html">langevin</A> - Langevin temperature control
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<LI><A HREF = "fix_lineforce.html">lineforce</A> - constrain atoms to move in a line
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<LI><A HREF = "fix_msd.html">msd</A> - compute mean-squared displacement (i.e. diffusion coefficient)
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<LI><A HREF = "fix_momentum.html">momentum</A> - zero the linear and/or angular momentum of a group of atoms
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<LI><A HREF = "fix_momentum.html">momentum</A> - zero the linear and/or angular momentum of a group of atoms
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<LI><A HREF = "fix_move.html">move</A> - move atoms in a prescribed fashion
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<LI><A HREF = "fix_nph.html">nph</A> - constant NPH time integration via Nose/Hoover
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<LI><A HREF = "fix_npt.html">npt</A> - constant NPT time integration via Nose/Hoover
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@ -206,7 +203,6 @@ list of fix styles available in LAMMPS:
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<LI><A HREF = "fix_pour.html">pour</A> - pour new atoms into a granular simulation domain
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<LI><A HREF = "fix_press_berendsen.html">press/berendsen</A> - pressure control by Berendsen barostat
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<LI><A HREF = "fix_print.html">print</A> - print text and variables during a simulation
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<LI><A HREF = "fix_rdf.html">rdf</A> - compute radial distribution functions
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<LI><A HREF = "fix_reax_bonds.html">reax/bonds</A> - write out ReaxFF bond information <A HREF = "fix_recenter.html">recenter</A> - constrain the center-of-mass position of a group of atoms
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<LI><A HREF = "fix_rigid.html">rigid</A> - constrain one or more clusters of atoms to move as a rigid body
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<LI><A HREF = "fix_setforce.html">setforce</A> - set the force on each atom
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@ -163,7 +163,6 @@ list of fix styles available in LAMMPS:
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"bond/create"_fix_bond_create.html - create bonds on the fly
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"bond/swap"_fix_bond_swap.html - Monte Carlo bond swapping
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"box/relax"_fix_box_relax.html - relax box size during energy minimization
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"com"_fix_com.html - compute a center-of-mass
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"coord/original"_fix_coord_original.html - store original coords of each atom
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"deform"_fix_deform.html - change the simulation box size/shape
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"deposit"_fix_deposit.html - add new atoms above a surface
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@ -174,15 +173,11 @@ list of fix styles available in LAMMPS:
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"evaporate"_fix_evaporate.html - remove atoms from simulation periodically
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"freeze"_fix_freeze.html - freeze atoms in a granular simulation
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"gravity"_fix_gravity.html - add gravity to atoms in a granular simulation
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"gyration"_fix_gyration.html - compute radius of gyration
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"heat"_fix_heat.html - add/subtract momentum-conserving heat
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"indent"_fix_indent.html - impose force due to an indenter
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"langevin"_fix_langevin.html - Langevin temperature control
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"lineforce"_fix_lineforce.html - constrain atoms to move in a line
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"msd"_fix_msd.html - compute mean-squared displacement \
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(i.e. diffusion coefficient)
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"momentum"_fix_momentum.html - zero the linear and/or angular momentum \
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of a group of atoms
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"momentum"_fix_momentum.html - zero the linear and/or angular momentum of a group of atoms
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"move"_fix_move.html - move atoms in a prescribed fashion
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"nph"_fix_nph.html - constant NPH time integration via Nose/Hoover
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"npt"_fix_npt.html - constant NPT time integration via Nose/Hoover
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@ -205,7 +200,6 @@ list of fix styles available in LAMMPS:
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"press/berendsen"_fix_press_berendsen.html - pressure control by \
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Berendsen barostat
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"print"_fix_print.html - print text and variables during a simulation
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"rdf"_fix_rdf.html - compute radial distribution functions
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"reax/bonds"_fix_reax_bonds.html - write out ReaxFF bond information \
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"recenter"_fix_recenter.html - constrain the center-of-mass position \
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of a group of atoms
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@ -1,49 +0,0 @@
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<HTML>
|
||||
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
|
||||
</CENTER>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
<HR>
|
||||
|
||||
<H3>fix com command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>fix ID group-ID com N file
|
||||
</PRE>
|
||||
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
|
||||
<LI>com = style name of this fix command
|
||||
<LI>N = compute center-of-mass every this many timesteps
|
||||
<LI>file = filename to write center-of-mass info to
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>fix 1 all com 100 com.out
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Compute the center-of-mass of the group of atoms every N steps,
|
||||
including all effects due to atoms passing thru periodic boundaries.
|
||||
Write the results to the specified file.
|
||||
</P>
|
||||
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
||||
</P>
|
||||
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
|
||||
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
|
||||
are relevant to this fix. No global scalar or vector or per-atom
|
||||
quantities are stored by this fix for access by various <A HREF = "Section_howto.html#4_15">output
|
||||
commands</A>. No parameter of this fix can be
|
||||
used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
|
||||
This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
<P><B>Related commands:</B> none
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -1,48 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
fix com command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID com N file :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command
|
||||
com = style name of this fix command
|
||||
N = compute center-of-mass every this many timesteps
|
||||
file = filename to write center-of-mass info to :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 all com 100 com.out :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Compute the center-of-mass of the group of atoms every N steps,
|
||||
including all effects due to atoms passing thru periodic boundaries.
|
||||
Write the results to the specified file.
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html. None of the "fix_modify"_fix_modify.html options
|
||||
are relevant to this fix. No global scalar or vector or per-atom
|
||||
quantities are stored by this fix for access by various "output
|
||||
commands"_Section_howto.html#4_15. No parameter of this fix can be
|
||||
used with the {start/stop} keywords of the "run"_run.html command.
|
||||
This fix is not invoked during "energy minimization"_minimize.html.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:] none
|
||||
|
||||
[Default:] none
|
||||
|
||||
|
||||
|
||||
|
||||
|
|
@ -1,57 +0,0 @@
|
|||
<HTML>
|
||||
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
|
||||
</CENTER>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
<HR>
|
||||
|
||||
<H3>fix gyration command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>fix ID group-ID gyration N file
|
||||
</PRE>
|
||||
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
|
||||
<LI>gyration = style name of this fix command
|
||||
<LI>N = compute radius-of-gyration every this many timesteps
|
||||
<LI>file = filename to write gyration info to
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>fix 1 all gyration 100 molecule.out
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Compute the radius-of-gyration of the group of atoms every N steps,
|
||||
including all effects due to atoms passing thru periodic boundaries.
|
||||
Write the results to the specified file.
|
||||
</P>
|
||||
<P>Rg is a measure of the size of the group of atoms, and is computed by
|
||||
this formula
|
||||
</P>
|
||||
<CENTER><IMG SRC = "Eqs/fix_gyration.jpg">
|
||||
</CENTER>
|
||||
<P>where M is the total mass of the group and Rcm is the center-of-mass
|
||||
position of the group.
|
||||
</P>
|
||||
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
||||
</P>
|
||||
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
|
||||
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
|
||||
are relevant to this fix. No global scalar or vector or per-atom
|
||||
quantities are stored by this fix for access by various <A HREF = "Section_howto.html#4_15">output
|
||||
commands</A>. No parameter of this fix can be
|
||||
used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
|
||||
This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
<P><B>Related commands:</B> none
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -1,52 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
fix gyration command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID gyration N file :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command
|
||||
gyration = style name of this fix command
|
||||
N = compute radius-of-gyration every this many timesteps
|
||||
file = filename to write gyration info to :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 all gyration 100 molecule.out :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Compute the radius-of-gyration of the group of atoms every N steps,
|
||||
including all effects due to atoms passing thru periodic boundaries.
|
||||
Write the results to the specified file.
|
||||
|
||||
Rg is a measure of the size of the group of atoms, and is computed by
|
||||
this formula
|
||||
|
||||
:c,image(Eqs/fix_gyration.jpg)
|
||||
|
||||
where M is the total mass of the group and Rcm is the center-of-mass
|
||||
position of the group.
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html. None of the "fix_modify"_fix_modify.html options
|
||||
are relevant to this fix. No global scalar or vector or per-atom
|
||||
quantities are stored by this fix for access by various "output
|
||||
commands"_Section_howto.html#4_15. No parameter of this fix can be
|
||||
used with the {start/stop} keywords of the "run"_run.html command.
|
||||
This fix is not invoked during "energy minimization"_minimize.html.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:] none
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -1,89 +0,0 @@
|
|||
<HTML>
|
||||
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
|
||||
</CENTER>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
<HR>
|
||||
|
||||
<H3>fix msd command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>fix ID group-ID msd N file keyword value ...
|
||||
</PRE>
|
||||
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
|
||||
|
||||
<LI>msd = style name of this fix command
|
||||
|
||||
<LI>N = compute mean-squared displacement every this many timesteps
|
||||
|
||||
<LI>file = filename to write mean-squared displacement info to
|
||||
|
||||
<LI>zero or more keyword/value pairs may be appended
|
||||
|
||||
<LI>keyword = <I>com</I>
|
||||
|
||||
<PRE> <I>com</I> value = <I>yes</I> or <I>no</I>
|
||||
</PRE>
|
||||
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>fix 1 all msd 100 diff.out
|
||||
fix 1 all msd 1000 diff.out com yes
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Compute the mean-squared displacement (MSD) of the group of atoms
|
||||
every N steps, including all effects due to atoms passing thru
|
||||
periodic boundaries. The MSD is the square of the displacement of
|
||||
each atom, averaged over all the atoms in the group. The displacement
|
||||
of an atom is from its original position at the time the fix command
|
||||
was issued. The slope of the mean-squared displacement versus time is
|
||||
proportional to the diffusion coefficient of the diffusing atoms.
|
||||
</P>
|
||||
<P>The MSD values versus time are written to the specified file.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: If an atom is part of a rigid body (see the <A HREF = "fix_rigid.html">fix
|
||||
rigid</A> command), it's periodic image flags are altered,
|
||||
and the computed MSD will not reflect its true displacement. See the
|
||||
<A HREF = "fix_rigid.html">fix rigid</A> command for details. Thus, to compute the
|
||||
MSD of rigid bodies as they cross periodic boundaries, you will need
|
||||
to post-process a <A HREF = "dump.html">dump file</A> containing coordinates of the
|
||||
atoms in the bodies.
|
||||
</P>
|
||||
<P>If the <I>com</I> option is set to <I>yes</I> then the effect of any drift
|
||||
in the center-of-mass of the group of atoms is subtracted out before
|
||||
the displacment of each atom is calcluated.
|
||||
</P>
|
||||
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
||||
</P>
|
||||
<P>This fix writes the original coordinates of diffusing atoms to <A HREF = "restart.html">binary
|
||||
restart files</A>, so that the mean-squared displacement
|
||||
will be accurate in a restarted simulation. See the
|
||||
<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify
|
||||
a fix in an input script that reads a restart file, so that the
|
||||
operation of the fix continues in an uninterrupted fashion.
|
||||
</P>
|
||||
<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
|
||||
fix. No global scalar or vector or per-atom quantities are stored by
|
||||
this fix for access by various <A HREF = "Section_howto.html#4_15">output
|
||||
commands</A>. No parameter of this fix can be
|
||||
used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
|
||||
This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "fix_coord_original.html">fix coord/original</A>
|
||||
</P>
|
||||
<P><B>Default:</B>
|
||||
</P>
|
||||
<P>The option default is com = no.
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -1,77 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
fix msd command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID msd N file keyword value ... :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
msd = style name of this fix command :l
|
||||
N = compute mean-squared displacement every this many timesteps :l
|
||||
file = filename to write mean-squared displacement info to :l
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {com} :l
|
||||
{com} value = {yes} or {no} :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 all msd 100 diff.out
|
||||
fix 1 all msd 1000 diff.out com yes :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Compute the mean-squared displacement (MSD) of the group of atoms
|
||||
every N steps, including all effects due to atoms passing thru
|
||||
periodic boundaries. The MSD is the square of the displacement of
|
||||
each atom, averaged over all the atoms in the group. The displacement
|
||||
of an atom is from its original position at the time the fix command
|
||||
was issued. The slope of the mean-squared displacement versus time is
|
||||
proportional to the diffusion coefficient of the diffusing atoms.
|
||||
|
||||
The MSD values versus time are written to the specified file.
|
||||
|
||||
IMPORTANT NOTE: If an atom is part of a rigid body (see the "fix
|
||||
rigid"_fix_rigid.html command), it's periodic image flags are altered,
|
||||
and the computed MSD will not reflect its true displacement. See the
|
||||
"fix rigid"_fix_rigid.html command for details. Thus, to compute the
|
||||
MSD of rigid bodies as they cross periodic boundaries, you will need
|
||||
to post-process a "dump file"_dump.html containing coordinates of the
|
||||
atoms in the bodies.
|
||||
|
||||
If the {com} option is set to {yes} then the effect of any drift
|
||||
in the center-of-mass of the group of atoms is subtracted out before
|
||||
the displacment of each atom is calcluated.
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
This fix writes the original coordinates of diffusing atoms to "binary
|
||||
restart files"_restart.html, so that the mean-squared displacement
|
||||
will be accurate in a restarted simulation. See the
|
||||
"read_restart"_read_restart.html command for info on how to re-specify
|
||||
a fix in an input script that reads a restart file, so that the
|
||||
operation of the fix continues in an uninterrupted fashion.
|
||||
|
||||
None of the "fix_modify"_fix_modify.html options are relevant to this
|
||||
fix. No global scalar or vector or per-atom quantities are stored by
|
||||
this fix for access by various "output
|
||||
commands"_Section_howto.html#4_15. No parameter of this fix can be
|
||||
used with the {start/stop} keywords of the "run"_run.html command.
|
||||
This fix is not invoked during "energy minimization"_minimize.html.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix coord/original"_fix_coord_original.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The option default is com = no.
|
||||
|
|
@ -1,74 +0,0 @@
|
|||
<HTML>
|
||||
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
|
||||
</CENTER>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
<HR>
|
||||
|
||||
<H3>fix rdf command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>fix ID group-ID rdf N file Nbin itype1 jtype1 itype2 jtype2 ...
|
||||
</PRE>
|
||||
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
|
||||
<LI>rdf = style name of this fix command
|
||||
<LI>N = compute radial distribution function (RDF) every this many timesteps
|
||||
<LI>file = filename to write radial distribution function info to
|
||||
<LI>Nbin = number of RDF bins
|
||||
<LI>itypeN = central atom type for RDF pair N
|
||||
<LI>jtypeN = distribution atom type for RDF pair N
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>fix 1 all rdf 500 rdf.out 100 1 1
|
||||
fix 1 fluid rdf 10000 rdf.out 100 1 1 1 2 2 1 2 2
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Compute the radial distribution function (RDF), also known as g(r),
|
||||
and coordination number every N steps. The RDF for each specified
|
||||
atom type pair is histogrammed in Nbin bins from distance 0 to Rc,
|
||||
where Rc = the maximum force cutoff for any pair of atom types. An
|
||||
atom pair only contributes to the RDF if
|
||||
</P>
|
||||
<UL><LI>both atoms are in the fix group
|
||||
<LI>the distance between them is within the maximum force cutoff
|
||||
<LI>their interaction is stored in the neighbor list
|
||||
</UL>
|
||||
<P>Bonded atoms (1-2, 1-3, 1-4 interactions within a molecular topology)
|
||||
with a pairwise weighting factor of 0.0 are not included in the RDF;
|
||||
pairs with a non-zero weighting factor are included. The weighting
|
||||
factor is set by the <A HREF = "special_bonds.html">special_bonds</A> command.
|
||||
</P>
|
||||
<P>The RDF statistics for each timestep are written to the specified
|
||||
file, as are the RDF values averaged over all timesteps.
|
||||
</P>
|
||||
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
||||
</P>
|
||||
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
|
||||
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
|
||||
are relevant to this fix. No global scalar or vector or per-atom
|
||||
quantities are stored by this fix for access by various <A HREF = "Section_howto.html#4_15">output
|
||||
commands</A>. No parameter of this fix can be
|
||||
used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
|
||||
This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
|
||||
</P>
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>The RDF is not computed for distances longer than the force cutoff,
|
||||
since processors (in parallel) don't know atom coordinates for atoms
|
||||
further away than that distance. If you want an RDF for larger <I>r</I>,
|
||||
you'll need to post-process a dump file.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "pair_style.html">pair_style</A>
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -1,69 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
fix rdf command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID rdf N file Nbin itype1 jtype1 itype2 jtype2 ... :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command
|
||||
rdf = style name of this fix command
|
||||
N = compute radial distribution function (RDF) every this many timesteps
|
||||
file = filename to write radial distribution function info to
|
||||
Nbin = number of RDF bins
|
||||
itypeN = central atom type for RDF pair N
|
||||
jtypeN = distribution atom type for RDF pair N :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 all rdf 500 rdf.out 100 1 1
|
||||
fix 1 fluid rdf 10000 rdf.out 100 1 1 1 2 2 1 2 2 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Compute the radial distribution function (RDF), also known as g(r),
|
||||
and coordination number every N steps. The RDF for each specified
|
||||
atom type pair is histogrammed in Nbin bins from distance 0 to Rc,
|
||||
where Rc = the maximum force cutoff for any pair of atom types. An
|
||||
atom pair only contributes to the RDF if
|
||||
|
||||
both atoms are in the fix group
|
||||
the distance between them is within the maximum force cutoff
|
||||
their interaction is stored in the neighbor list :ul
|
||||
|
||||
Bonded atoms (1-2, 1-3, 1-4 interactions within a molecular topology)
|
||||
with a pairwise weighting factor of 0.0 are not included in the RDF;
|
||||
pairs with a non-zero weighting factor are included. The weighting
|
||||
factor is set by the "special_bonds"_special_bonds.html command.
|
||||
|
||||
The RDF statistics for each timestep are written to the specified
|
||||
file, as are the RDF values averaged over all timesteps.
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html. None of the "fix_modify"_fix_modify.html options
|
||||
are relevant to this fix. No global scalar or vector or per-atom
|
||||
quantities are stored by this fix for access by various "output
|
||||
commands"_Section_howto.html#4_15. No parameter of this fix can be
|
||||
used with the {start/stop} keywords of the "run"_run.html command.
|
||||
This fix is not invoked during "energy minimization"_minimize.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
The RDF is not computed for distances longer than the force cutoff,
|
||||
since processors (in parallel) don't know atom coordinates for atoms
|
||||
further away than that distance. If you want an RDF for larger {r},
|
||||
you'll need to post-process a dump file.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_style"_pair_style.html
|
||||
|
||||
[Default:] none
|
||||
Loading…
Reference in New Issue