diff --git a/doc/fix_viscosity.html b/doc/fix_viscosity.html index 2f7fada686..3ae2b1ce58 100644 --- a/doc/fix_viscosity.html +++ b/doc/fix_viscosity.html @@ -98,12 +98,13 @@ momentum and kinetic energy. Thus you should not need to thermostat the system. If you do use a thermostat, you may want to apply it only to the non-swapped dimensions (other than vdim).

-

You should not swap velocities of atoms that are in constrained -molecules, e.g. via fix shake or fix -rigid, since application of the constraints will alter -the amount of transferred momentum. You should, however, be able to -use flexible molecules with this approach. LAMMPS does not check that -this advice is followed. +

LAMMPS does not check, but you should not use this fix to swap +velocities of atoms that are in constrained molecules, e.g. via fix +shake or fix rigid. This is because +application of the constraints will alter the amount of transferred +momentum. You should, however, be able to use flexible molecules. +See the Maginn paper for an example of using this algorithm +in a computation of alcohol molecule properties.

When running a simulation with large, massive particles or molecules in a background solvent, you may want to only exchange momenta bewteen @@ -122,4 +123,9 @@ nvt/sllod

(Muller-Plathe) Muller-Plathe, Phys Rev E, 59, 4894-4898 (1999).

+ + +

(Maginn) Kelkar, Rafferty, Maginn, Siepmann, Fluid Phase Equilibria, +260, 218-231 (2007). +

diff --git a/doc/fix_viscosity.txt b/doc/fix_viscosity.txt index 2a50fbc945..d4dbc512b2 100644 --- a/doc/fix_viscosity.txt +++ b/doc/fix_viscosity.txt @@ -95,12 +95,13 @@ momentum and kinetic energy. Thus you should not need to thermostat the system. If you do use a thermostat, you may want to apply it only to the non-swapped dimensions (other than {vdim}). -You should not swap velocities of atoms that are in constrained -molecules, e.g. via "fix shake"_fix_shake.html or "fix -rigid"_fix_rigid.html, since application of the constraints will alter -the amount of transferred momentum. You should, however, be able to -use flexible molecules with this approach. LAMMPS does not check that -this advice is followed. +LAMMPS does not check, but you should not use this fix to swap +velocities of atoms that are in constrained molecules, e.g. via "fix +shake"_fix_shake.html or "fix rigid"_fix_rigid.html. This is because +application of the constraints will alter the amount of transferred +momentum. You should, however, be able to use flexible molecules. +See the "Maginn paper"_#Maginn for an example of using this algorithm +in a computation of alcohol molecule properties. When running a simulation with large, massive particles or molecules in a background solvent, you may want to only exchange momenta bewteen @@ -117,3 +118,7 @@ nvt/sllod"_fix_nvt_sllod.html :link(Muller-Plathe) [(Muller-Plathe)] Muller-Plathe, Phys Rev E, 59, 4894-4898 (1999). + +:link(Maginn) +[(Maginn)] Kelkar, Rafferty, Maginn, Siepmann, Fluid Phase Equilibria, +260, 218-231 (2007).