Each time the box size or shape is changed, the remap keyword determines whether atom positions are re-mapped to the new box. If remap is set to x (the default), atoms in the fix group are -re-mapped; otherwise they are not. If remap is set to v, then any -atom in the fix group that crosses a periodic boundary will have a -delta added to its velocity equal to the difference in velocities -between the lo and hi boundaries. Note that this velocity difference -can include tilt components, e.g. a delta in the x velocity when an -atom crosses the y periodic boundary. If remap is set to none, -then neither of these remappings take place. +re-mapped; otherwise they are not. Note that their velocities are not +changed, just their positions are altered. If remap is set to v, +then any atom in the fix group that crosses a periodic boundary will +have a delta added to its velocity equal to the difference in +velocities between the lo and hi boundaries. Note that this velocity +difference can include tilt components, e.g. a delta in the x velocity +when an atom crosses the y periodic boundary. If remap is set to +none, then neither of these remappings take place. +
+Conceptually, setting remap to x is forcing the atoms to deform +via an affine transformation that exactly matches the box deformation. +Though the atoms are moving, it is not due to them having a velocity +that matches the box change. This setting is typically appropriate +for solids. Setting remap to v is typically appropriate for +fluids, where you want the atoms to respond to the change in box +size/shape on their own and acquire a velocity that matches the box +change, so that they will naturally move with the box without explicit +remapping of their coordinates.
IMPORTANT NOTE: When non-equilibrium MD (NEMD) simulations are performed using this fix, the option "remap v" should normally be used. This is because fix nvt/sllod adjusts the -atom positions and velocities to provide a velocity profile that +atom positions and velocities to induce a velocity profile that matches the changing box size/shape. Thus atom coordinates should NOT be remapped by fix deform, but velocities SHOULD be when atoms cross periodic boundaries, since that is consistent with maintaining the diff --git a/doc/fix_deform.txt b/doc/fix_deform.txt index c1cce1acb1..0bab5b15af 100644 --- a/doc/fix_deform.txt +++ b/doc/fix_deform.txt @@ -344,18 +344,29 @@ remapped into the new box in the appropriate manner. Each time the box size or shape is changed, the {remap} keyword determines whether atom positions are re-mapped to the new box. If {remap} is set to {x} (the default), atoms in the fix group are -re-mapped; otherwise they are not. If {remap} is set to {v}, then any -atom in the fix group that crosses a periodic boundary will have a -delta added to its velocity equal to the difference in velocities -between the lo and hi boundaries. Note that this velocity difference -can include tilt components, e.g. a delta in the x velocity when an -atom crosses the y periodic boundary. If {remap} is set to {none}, -then neither of these remappings take place. +re-mapped; otherwise they are not. Note that their velocities are not +changed, just their positions are altered. If {remap} is set to {v}, +then any atom in the fix group that crosses a periodic boundary will +have a delta added to its velocity equal to the difference in +velocities between the lo and hi boundaries. Note that this velocity +difference can include tilt components, e.g. a delta in the x velocity +when an atom crosses the y periodic boundary. If {remap} is set to +{none}, then neither of these remappings take place. + +Conceptually, setting {remap} to {x} is forcing the atoms to deform +via an affine transformation that exactly matches the box deformation. +Though the atoms are moving, it is not due to them having a velocity +that matches the box change. This setting is typically appropriate +for solids. Setting {remap} to {v} is typically appropriate for +fluids, where you want the atoms to respond to the change in box +size/shape on their own and acquire a velocity that matches the box +change, so that they will naturally move with the box without explicit +remapping of their coordinates. IMPORTANT NOTE: When non-equilibrium MD (NEMD) simulations are performed using this fix, the option "remap v" should normally be used. This is because "fix nvt/sllod"_fix_nvt_sllod.html adjusts the -atom positions and velocities to provide a velocity profile that +atom positions and velocities to induce a velocity profile that matches the changing box size/shape. Thus atom coordinates should NOT be remapped by fix deform, but velocities SHOULD be when atoms cross periodic boundaries, since that is consistent with maintaining the