IMPORTANT NOTE: If a fix rigid is defined for rigid +bodies, and remap is set to x, then the center-of-mass coordinates +of rigid bodies will be remapped to the changing simulation box. This +will be done regardless of whether atoms in the rigid bodies are in +the fix deform group or not. The velocity of the centers of mass are +not remapped even if remap is set to v, since fix +nvt/sllod does not currently do anything special +for rigid particles. If you wish to perform a NEMD simulation of +rigid particles, you can either thermostat them independently or +include a background fluid and thermostat the fluid via fix +nvt/sllod. +
The units keyword determines the meaning of the distance units used to define various arguments. A box value selects standard distance units as defined by the units command, e.g. Angstroms for diff --git a/doc/fix_deform.txt b/doc/fix_deform.txt index ee92ebb63c..385c5950f0 100644 --- a/doc/fix_deform.txt +++ b/doc/fix_deform.txt @@ -331,6 +331,18 @@ periodic boundaries, since that is consistent with maintaining the velocity profile already created by fix nvt/sllod. LAMMPS will warn you if the {remap} setting is not consistent with fix nvt/sllod. +IMPORTANT NOTE: If a "fix rigid"_fix_rigid.html is defined for rigid +bodies, and {remap} is set to {x}, then the center-of-mass coordinates +of rigid bodies will be remapped to the changing simulation box. This +will be done regardless of whether atoms in the rigid bodies are in +the fix deform group or not. The velocity of the centers of mass are +not remapped even if {remap} is set to {v}, since "fix +nvt/sllod"_fix_nvt_sllod.html does not currently do anything special +for rigid particles. If you wish to perform a NEMD simulation of +rigid particles, you can either thermostat them independently or +include a background fluid and thermostat the fluid via "fix +nvt/sllod"_fix_nvt_sllod. + The {units} keyword determines the meaning of the distance units used to define various arguments. A {box} value selects standard distance units as defined by the "units"_units.html command, e.g. Angstroms for diff --git a/doc/fix_indent.html b/doc/fix_indent.html index 4ed98e394d..27605132ac 100644 --- a/doc/fix_indent.html +++ b/doc/fix_indent.html @@ -122,7 +122,7 @@ indenter always has a radius of its final value R in that case.
IMPORTANT NOTE: If you want the atom/indenter interaction energy to be included in the total potential energy of the system (the quantity -being minimized), you MUST enable the fix_modify +being minimized), you must enable the fix_modify energy option for this fix.
Restrictions: none diff --git a/doc/fix_indent.txt b/doc/fix_indent.txt index c22eeb9c0f..2186996d84 100644 --- a/doc/fix_indent.txt +++ b/doc/fix_indent.txt @@ -113,7 +113,7 @@ indenter always has a radius of its final value R in that case. IMPORTANT NOTE: If you want the atom/indenter interaction energy to be included in the total potential energy of the system (the quantity -being minimized), you MUST enable the "fix_modify"_fix_modify.html +being minimized), you must enable the "fix_modify"_fix_modify.html {energy} option for this fix. [Restrictions:] none diff --git a/doc/fix_msd.html b/doc/fix_msd.html index 94ff529e7c..7140c2caaf 100644 --- a/doc/fix_msd.html +++ b/doc/fix_msd.html @@ -26,12 +26,21 @@
Description:
-Compute the mean-squared displacement of the group of atoms every N -steps, including all effects due to atoms passing thru periodic -boundaries. The slope of the mean-squared displacement versus time is -proportional to the diffusion coefficient of the diffusing atoms. The -"origin" of the displacement for each atom is its position at the time -the fix command was issued. Write the results to the specified file. +
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 slope of the mean-squared displacement +versus time is proportional to the diffusion coefficient of the +diffusing atoms. The "origin" of the displacement for each atom is +its position at the time the fix command was issued. Write the +results to the specified file. +
+IMPORTANT NOTE: If an atom is part of a rigid body (see the fix +rigid command), it's periodic image flags are altered, +and the computed MSD will not reflect its true displacement. See the +fix rigid 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 containing coordinates of the +atomss in the bodies.
Restart, fix_modify, thermo output, run start/stop, minimize info:
diff --git a/doc/fix_msd.txt b/doc/fix_msd.txt index 29657cfecf..3a4b07ca3e 100644 --- a/doc/fix_msd.txt +++ b/doc/fix_msd.txt @@ -23,12 +23,21 @@ fix 1 all msd 100 diff.out :pre [Description:] -Compute the mean-squared displacement of the group of atoms every N -steps, including all effects due to atoms passing thru periodic -boundaries. The slope of the mean-squared displacement versus time is -proportional to the diffusion coefficient of the diffusing atoms. The -"origin" of the displacement for each atom is its position at the time -the fix command was issued. Write the results to the specified file. +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 slope of the mean-squared displacement +versus time is proportional to the diffusion coefficient of the +diffusing atoms. The "origin" of the displacement for each atom is +its position at the time the fix command was issued. Write the +results 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 +atomss in the bodies. [Restart, fix_modify, thermo output, run start/stop, minimize info:] diff --git a/doc/fix_rigid.html b/doc/fix_rigid.html index e6a4d232a4..1ff3d7dbaa 100644 --- a/doc/fix_rigid.html +++ b/doc/fix_rigid.html @@ -87,6 +87,17 @@ effectively immersed in an implicit solvent, i.e. a Brownian dynamics model. Or you can thermostat additional atoms of an explicit solvent directly. +IMPORTANT NOTE: The periodic image flags of atoms in rigid bodies are +modified when the center-of-mass of the rigid body moves across a +periodic boundary. They are not incremented/decremented as they would +be for non-rigid atoms. This change does not affect dynamics, but +means that any diagnostic computation based on the atomic image flag +values must be adjusted accordingly. For example, the fix +msd will not compute the expected mean-squared +displacement for such atoms, and the image flag values written to a +dump file will be different than they would be if the +atoms were not in a rigid body. +
Restart, fix_modify, thermo output, run start/stop, minimize info: