Loading doc/Section_commands.html +8 −8 Original line number Diff line number Diff line Loading @@ -321,14 +321,14 @@ of each style or click on the style itself for a full description: </P> <DIV ALIGN=center><TABLE 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_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> <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> <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> <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> <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> <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> <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> <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> <TR ALIGN="center"><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A> <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_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><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD></TR> <TR ALIGN="center"><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><TD ><A HREF = "fix_momentum.html">momentum</A></TD></TR> <TR ALIGN="center"><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><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD></TR> <TR ALIGN="center"><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><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD></TR> <TR ALIGN="center"><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><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_store_coord.html">store/coord</A></TD><TD ><A HREF = "fix_store_force.html">store/force</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD></TR> <TR ALIGN="center"><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><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></TR> <TR ALIGN="center"><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A> </TD></TR></TABLE></DIV> <P>These are fix styles contributed by users, which can be used if Loading doc/Section_commands.txt +2 −1 Original line number Diff line number Diff line Loading @@ -389,7 +389,6 @@ of each style or click on the style itself for a full description: "bond/create"_fix_bond_create.html, "bond/swap"_fix_bond_swap.html, "box/relax"_fix_box_relax.html, "coord/original"_fix_coord_original.html, "deform"_fix_deform.html, "deposit"_fix_deposit.html, "drag"_fix_drag.html, Loading Loading @@ -432,6 +431,8 @@ of each style or click on the style itself for a full description: "spring"_fix_spring.html, "spring/rg"_fix_spring_rg.html, "spring/self"_fix_spring_self.html, "store/coord"_fix_store_coord.html, "store/force"_fix_store_force.html, "temp/berendsen"_fix_temp_berendsen.html, "temp/rescale"_fix_temp_rescale.html, "thermal/conductivity"_fix_thermal_conductivity.html, Loading doc/compute_displace_atom.html +9 −9 Original line number Diff line number Diff line Loading @@ -35,20 +35,20 @@ dz*dz). </P> <P>The displacement of an atom is from its original position at the time the compute command was issued. To store the original coordinates, the compute creates its own fix of style "coord/original", as if this the compute creates its own fix of style "store/coord", as if this command had been issued: </P> <PRE>fix compute-ID_coord_original group-ID coord/original <PRE>fix compute-ID_store_coord group-ID store/coord </PRE> <P>See the <A HREF = "fix_coord_original.html">fix coord/original</A> command for details. Note that the ID of the new fix is the compute-ID + underscore + "coord_original", and the group for the new fix is the same as the compute group. <P>See the <A HREF = "fix_coord_original.html">fix store/coord</A> command for details. Note that the ID of the new fix is the compute-ID + underscore + "store_coord", and the group for the new fix is the same as the compute group. </P> <P>The value of the displacement will be 0.0 for atoms not in the specified compute group. </P> <P>IMPORTANT NOTE: Fix coord/original stores the initial coordinates in <P>IMPORTANT NOTE: Fix store/coord stores the initial coordinates in "unwrapped" form, by using the image flags associated with each atom. See the <A HREF = "dump.html">dump custom</A> command for a discussion of "unwrapped" coordinates. See the Atoms section of the Loading Loading @@ -83,8 +83,8 @@ overview of LAMMPS output options. </P> <P><B>Related commands:</B> </P> <P><A HREF = "compute_msd.html">compute msd</A>, <A HREF = "dump.html">dump custom</A>, <A HREF = "fix_coord_original.html">fix coord/original</A> <P><A HREF = "compute_msd.html">compute msd</A>, <A HREF = "dump.html">dump custom</A>, <A HREF = "fix_store_coord.html">fix store/coord</A> </P> <P><B>Default:</B> none </P> Loading doc/compute_displace_atom.txt +8 −8 Original line number Diff line number Diff line Loading @@ -32,20 +32,20 @@ dz*dz). The displacement of an atom is from its original position at the time the compute command was issued. To store the original coordinates, the compute creates its own fix of style "coord/original", as if this the compute creates its own fix of style "store/coord", as if this command had been issued: fix compute-ID_coord_original group-ID coord/original :pre fix compute-ID_store_coord group-ID store/coord :pre See the "fix coord/original"_fix_coord_original.html command for details. Note that the ID of the new fix is the compute-ID + underscore + "coord_original", and the group for the new fix is the same as the compute group. See the "fix store/coord"_fix_coord_original.html command for details. Note that the ID of the new fix is the compute-ID + underscore + "store_coord", and the group for the new fix is the same as the compute group. The value of the displacement will be 0.0 for atoms not in the specified compute group. IMPORTANT NOTE: Fix coord/original stores the initial coordinates in IMPORTANT NOTE: Fix store/coord stores the initial coordinates in "unwrapped" form, by using the image flags associated with each atom. See the "dump custom"_dump.html command for a discussion of "unwrapped" coordinates. See the Atoms section of the Loading Loading @@ -81,6 +81,6 @@ overview of LAMMPS output options. [Related commands:] "compute msd"_compute_msd.html, "dump custom"_dump.html, "fix coord/original"_fix_coord_original.html store/coord"_fix_store_coord.html [Default:] none doc/compute_msd.html +8 −8 Original line number Diff line number Diff line Loading @@ -49,22 +49,22 @@ proportional to the diffusion coefficient of the diffusing atoms. </P> <P>The displacement of an atom is from its original position at the time the compute command was issued. To store the original coordinates, the compute creates its own fix of style "coord/original", as if this the compute creates its own fix of style "store/coord", as if this command had been issued: </P> <PRE>fix compute-ID_coord_original group-ID coord/original <PRE>fix compute-ID_store_coord group-ID store/coord </PRE> <P>See the <A HREF = "fix_coord_original.html">fix coord/original</A> command for <P>See the <A HREF = "fix_store_coord.html">fix store/coord</A> command for details. Note that the ID of the new fix is the compute-ID + underscore + "coord_original", and the group for the new fix is underscore + "store_coord", and the group for the new fix is the same as the compute group. </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. The <I>com</I> option is also passed to the created fix coord/original. is also passed to the created fix store/coord. </P> <P>IMPORTANT NOTE: Fix coord/original stores the initial coordinates in <P>IMPORTANT NOTE: Fix store/coord stores the initial coordinates in "unwrapped" form, by using the image flags associated with each atom. See the <A HREF = "dump.html">dump custom</A> command for a discussion of "unwrapped" coordinates. See the Atoms section of the Loading Loading @@ -102,8 +102,8 @@ number of atoms in the simulation. </P> <P><B>Related commands:</B> </P> <P><A HREF = "compute_displace_atom.html">compute displace_atom</A>, <A HREF = "fix_coord_original.html">fix coord/original</A>, <A HREF = "compute_msd_molecule.html">compute <P><A HREF = "compute_displace_atom.html">compute displace_atom</A>, <A HREF = "fix_store_coord.html">fix store/coord</A>, <A HREF = "compute_msd_molecule.html">compute msd/molecule</A> </P> <P><B>Default:</B> Loading Loading
doc/Section_commands.html +8 −8 Original line number Diff line number Diff line Loading @@ -321,14 +321,14 @@ of each style or click on the style itself for a full description: </P> <DIV ALIGN=center><TABLE 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_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> <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> <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> <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> <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> <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> <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> <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> <TR ALIGN="center"><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A> <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_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><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD></TR> <TR ALIGN="center"><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><TD ><A HREF = "fix_momentum.html">momentum</A></TD></TR> <TR ALIGN="center"><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><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD></TR> <TR ALIGN="center"><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><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD></TR> <TR ALIGN="center"><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><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_store_coord.html">store/coord</A></TD><TD ><A HREF = "fix_store_force.html">store/force</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD></TR> <TR ALIGN="center"><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><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></TR> <TR ALIGN="center"><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A> </TD></TR></TABLE></DIV> <P>These are fix styles contributed by users, which can be used if Loading
doc/Section_commands.txt +2 −1 Original line number Diff line number Diff line Loading @@ -389,7 +389,6 @@ of each style or click on the style itself for a full description: "bond/create"_fix_bond_create.html, "bond/swap"_fix_bond_swap.html, "box/relax"_fix_box_relax.html, "coord/original"_fix_coord_original.html, "deform"_fix_deform.html, "deposit"_fix_deposit.html, "drag"_fix_drag.html, Loading Loading @@ -432,6 +431,8 @@ of each style or click on the style itself for a full description: "spring"_fix_spring.html, "spring/rg"_fix_spring_rg.html, "spring/self"_fix_spring_self.html, "store/coord"_fix_store_coord.html, "store/force"_fix_store_force.html, "temp/berendsen"_fix_temp_berendsen.html, "temp/rescale"_fix_temp_rescale.html, "thermal/conductivity"_fix_thermal_conductivity.html, Loading
doc/compute_displace_atom.html +9 −9 Original line number Diff line number Diff line Loading @@ -35,20 +35,20 @@ dz*dz). </P> <P>The displacement of an atom is from its original position at the time the compute command was issued. To store the original coordinates, the compute creates its own fix of style "coord/original", as if this the compute creates its own fix of style "store/coord", as if this command had been issued: </P> <PRE>fix compute-ID_coord_original group-ID coord/original <PRE>fix compute-ID_store_coord group-ID store/coord </PRE> <P>See the <A HREF = "fix_coord_original.html">fix coord/original</A> command for details. Note that the ID of the new fix is the compute-ID + underscore + "coord_original", and the group for the new fix is the same as the compute group. <P>See the <A HREF = "fix_coord_original.html">fix store/coord</A> command for details. Note that the ID of the new fix is the compute-ID + underscore + "store_coord", and the group for the new fix is the same as the compute group. </P> <P>The value of the displacement will be 0.0 for atoms not in the specified compute group. </P> <P>IMPORTANT NOTE: Fix coord/original stores the initial coordinates in <P>IMPORTANT NOTE: Fix store/coord stores the initial coordinates in "unwrapped" form, by using the image flags associated with each atom. See the <A HREF = "dump.html">dump custom</A> command for a discussion of "unwrapped" coordinates. See the Atoms section of the Loading Loading @@ -83,8 +83,8 @@ overview of LAMMPS output options. </P> <P><B>Related commands:</B> </P> <P><A HREF = "compute_msd.html">compute msd</A>, <A HREF = "dump.html">dump custom</A>, <A HREF = "fix_coord_original.html">fix coord/original</A> <P><A HREF = "compute_msd.html">compute msd</A>, <A HREF = "dump.html">dump custom</A>, <A HREF = "fix_store_coord.html">fix store/coord</A> </P> <P><B>Default:</B> none </P> Loading
doc/compute_displace_atom.txt +8 −8 Original line number Diff line number Diff line Loading @@ -32,20 +32,20 @@ dz*dz). The displacement of an atom is from its original position at the time the compute command was issued. To store the original coordinates, the compute creates its own fix of style "coord/original", as if this the compute creates its own fix of style "store/coord", as if this command had been issued: fix compute-ID_coord_original group-ID coord/original :pre fix compute-ID_store_coord group-ID store/coord :pre See the "fix coord/original"_fix_coord_original.html command for details. Note that the ID of the new fix is the compute-ID + underscore + "coord_original", and the group for the new fix is the same as the compute group. See the "fix store/coord"_fix_coord_original.html command for details. Note that the ID of the new fix is the compute-ID + underscore + "store_coord", and the group for the new fix is the same as the compute group. The value of the displacement will be 0.0 for atoms not in the specified compute group. IMPORTANT NOTE: Fix coord/original stores the initial coordinates in IMPORTANT NOTE: Fix store/coord stores the initial coordinates in "unwrapped" form, by using the image flags associated with each atom. See the "dump custom"_dump.html command for a discussion of "unwrapped" coordinates. See the Atoms section of the Loading Loading @@ -81,6 +81,6 @@ overview of LAMMPS output options. [Related commands:] "compute msd"_compute_msd.html, "dump custom"_dump.html, "fix coord/original"_fix_coord_original.html store/coord"_fix_store_coord.html [Default:] none
doc/compute_msd.html +8 −8 Original line number Diff line number Diff line Loading @@ -49,22 +49,22 @@ proportional to the diffusion coefficient of the diffusing atoms. </P> <P>The displacement of an atom is from its original position at the time the compute command was issued. To store the original coordinates, the compute creates its own fix of style "coord/original", as if this the compute creates its own fix of style "store/coord", as if this command had been issued: </P> <PRE>fix compute-ID_coord_original group-ID coord/original <PRE>fix compute-ID_store_coord group-ID store/coord </PRE> <P>See the <A HREF = "fix_coord_original.html">fix coord/original</A> command for <P>See the <A HREF = "fix_store_coord.html">fix store/coord</A> command for details. Note that the ID of the new fix is the compute-ID + underscore + "coord_original", and the group for the new fix is underscore + "store_coord", and the group for the new fix is the same as the compute group. </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. The <I>com</I> option is also passed to the created fix coord/original. is also passed to the created fix store/coord. </P> <P>IMPORTANT NOTE: Fix coord/original stores the initial coordinates in <P>IMPORTANT NOTE: Fix store/coord stores the initial coordinates in "unwrapped" form, by using the image flags associated with each atom. See the <A HREF = "dump.html">dump custom</A> command for a discussion of "unwrapped" coordinates. See the Atoms section of the Loading Loading @@ -102,8 +102,8 @@ number of atoms in the simulation. </P> <P><B>Related commands:</B> </P> <P><A HREF = "compute_displace_atom.html">compute displace_atom</A>, <A HREF = "fix_coord_original.html">fix coord/original</A>, <A HREF = "compute_msd_molecule.html">compute <P><A HREF = "compute_displace_atom.html">compute displace_atom</A>, <A HREF = "fix_store_coord.html">fix store/coord</A>, <A HREF = "compute_msd_molecule.html">compute msd/molecule</A> </P> <P><B>Default:</B> Loading
