Note that the velocity command can be used to create velocities with zero aggregate linear and/or angular momentum.
+IMPORTANT NOTE: This fix performs its operations at the same point in +the timestep as other time integration fixes, such as fix +nve, fix nvt, or fix npt. +Thus fix recenter should normally be the last such fix specified in +the input script, since the adjustments it makes to atom coordinates +should come after the changes made by time integration. LAMMPS will +warn you if your fixes are not ordered this way. +
Restrictions:
This fix should not be used with an x,y,z setting that causes a large @@ -83,12 +91,6 @@ be lost,especially in parallel. Instead, use the displace_atoms command, which can be used several times in succession to move atoms a large distance.
-This fix should be specified after integration fixes (fix -nve, fix_nvt, fix npt, -etc), because the adjustments it makes to atom coordinates should come -after atom coordinates are changed due to time integration. LAMMPS -will warn you if your fixes are not ordered this way. -
Related commands:
fix momentum, velocity diff --git a/doc/fix_recenter.txt b/doc/fix_recenter.txt index 8aa0e52654..7e3b914ac9 100644 --- a/doc/fix_recenter.txt +++ b/doc/fix_recenter.txt @@ -66,6 +66,14 @@ means a fractional distance between the lo/hi box boundaries, e.g. 0.5 Note that the "velocity"_velocity.html command can be used to create velocities with zero aggregate linear and/or angular momentum. +IMPORTANT NOTE: This fix performs its operations at the same point in +the timestep as other time integration fixes, such as "fix +nve"_fix_nve.html, "fix nvt"_fix_nvt.html, or "fix npt"_fix_npt.html. +Thus fix recenter should normally be the last such fix specified in +the input script, since the adjustments it makes to atom coordinates +should come after the changes made by time integration. LAMMPS will +warn you if your fixes are not ordered this way. + [Restrictions:] This fix should not be used with an x,y,z setting that causes a large @@ -75,12 +83,6 @@ be lost,especially in parallel. Instead, use the "displace_atoms"_displace_atoms.html command, which can be used several times in succession to move atoms a large distance. -This fix should be specified after integration fixes ("fix -nve"_fix_nve.html, "fix_nvt"_fix_nvt.html, "fix npt"_fix_npt.html, -etc), because the adjustments it makes to atom coordinates should come -after atom coordinates are changed due to time integration. LAMMPS -will warn you if your fixes are not ordered this way. - [Related commands:] "fix momentum"_fix_momentum.html, "velocity"_velocity.html diff --git a/doc/fix_wall_reflect.html b/doc/fix_wall_reflect.html index 6e53f52337..e4a4fa5ad2 100644 --- a/doc/fix_wall_reflect.html +++ b/doc/fix_wall_reflect.html @@ -38,12 +38,13 @@ by a distance delta (e.g. due to fix nve), then it put back inside the box by the same delta and the sign of the corresponding component of its velocity is flipped.
-This fix performs its operations at the same point in the timestep as -other time integration fixes, such as fix nve, fix -nvt, or fix npt. It is important that it -be the last such fix specified in the input script, since it changes -the atom positions set by those fixes to insure atoms stay within the -simulation box. +
IMPORTANT NOTE: This fix performs its operations at the same point in +the timestep as other time integration fixes, such as fix +nve, fix nvt, or fix npt. +Thus fix wall/reflect should normally be the last such fix specified +in the input script, since the adjustments it makes to atom +coordinates should come after the changes made by time integration. +LAMMPS will warn you if your fixes are not ordered this way.
Restrictions: none
diff --git a/doc/fix_wall_reflect.txt b/doc/fix_wall_reflect.txt index e9b6c1aacd..66b784eed2 100644 --- a/doc/fix_wall_reflect.txt +++ b/doc/fix_wall_reflect.txt @@ -35,12 +35,13 @@ by a distance delta (e.g. due to "fix nve"_fix_nve.html), then it is put back inside the box by the same delta and the sign of the corresponding component of its velocity is flipped. -This fix performs its operations at the same point in the timestep as -other time integration fixes, such as "fix nve"_fix_nve.html, "fix -nvt"_fix_nvt.html, or "fix npt"_fix_npt.html. It is important that it -be the last such fix specified in the input script, since it changes -the atom positions set by those fixes to insure atoms stay within the -simulation box. +IMPORTANT NOTE: This fix performs its operations at the same point in +the timestep as other time integration fixes, such as "fix +nve"_fix_nve.html, "fix nvt"_fix_nvt.html, or "fix npt"_fix_npt.html. +Thus fix wall/reflect should normally be the last such fix specified +in the input script, since the adjustments it makes to atom +coordinates should come after the changes made by time integration. +LAMMPS will warn you if your fixes are not ordered this way. [Restrictions:] none diff --git a/doc/pair_lj_smooth.html b/doc/pair_lj_smooth.html index 96534eaf62..085ae8fd20 100644 --- a/doc/pair_lj_smooth.html +++ b/doc/pair_lj_smooth.html @@ -34,10 +34,12 @@ applied between the inner and outer cutoff.The polynomial coefficients C1, C2, C3, C4 are computed by LAMMPS to cause the force to vary smoothly from Rin to Rc. At Rin the force and its 1st derivative will match the unsmoothed LJ formula. At Rc the -force and its 1st derivative will be 0.0. IMPORTANT NOTE: this force -smoothing causes the energy to be discontinuous both in its values and -1st derivative. This can lead to poor energy conservation. Plot the -energy and force resulting from this formula via the +force and its 1st derivative will be 0.0. +
+IMPORTANT NOTE: this force smoothing causes the energy to be +discontinuous both in its values and 1st derivative. This can lead to +poor energy conservation and may require the use of a thermostat. +Plot the energy and force resulting from this formula via the pair_write command to see the effect.
The following coefficients must be defined for each pair of atoms diff --git a/doc/pair_lj_smooth.txt b/doc/pair_lj_smooth.txt index 8b603a9e7e..3e678f4567 100644 --- a/doc/pair_lj_smooth.txt +++ b/doc/pair_lj_smooth.txt @@ -31,10 +31,12 @@ applied between the inner and outer cutoff. The polynomial coefficients C1, C2, C3, C4 are computed by LAMMPS to cause the force to vary smoothly from Rin to Rc. At Rin the force and its 1st derivative will match the unsmoothed LJ formula. At Rc the -force and its 1st derivative will be 0.0. IMPORTANT NOTE: this force -smoothing causes the energy to be discontinuous both in its values and -1st derivative. This can lead to poor energy conservation. Plot the -energy and force resulting from this formula via the +force and its 1st derivative will be 0.0. + +IMPORTANT NOTE: this force smoothing causes the energy to be +discontinuous both in its values and 1st derivative. This can lead to +poor energy conservation and may require the use of a thermostat. +Plot the energy and force resulting from this formula via the "pair_write"_pair_write.html command to see the effect. The following coefficients must be defined for each pair of atoms