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 compute -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. It also means that if you have bonds +altered so that the rigid body can be reconstructed correctly when it +straddles periodic boundaries. The atom image flags are not +incremented/decremented as they would be for non-rigid atoms. This +means you cannot interpret them as you normally would. For example, +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. +Likewise the compute msd will not compute the +expected mean-squared displacement for such atoms if the body moves +across periodic boundaries. It also means that if you have bonds between a pair of rigid bodies and the bond straddles a periodic boundary, you cannot use the replicate command to -increase the system size. +increase the system size. Note that this fix does define image flags +for each rigid body, which are incremented when the rigid body crosses +a periodic boundary in the usual way. These image flags have the same +meaning as atom images (see the "dump" command) and can be accessed +and output as described below.
These fixes compute a global array of values which can be accessed by various output commands. The number of rows in the array is equal to the number of rigid bodies. The number of -columns is 12. Thus for each rigid body, 12 values are stored: the +columns is 15. Thus for each rigid body, 12 values are stored: the xyz coords of the center of mass (COM), the xyz components of the COM -velocity, the xyz components of the force acting on the COM, and the -xyz components of the torque acting on the COM. The force and torque -values in the array are not affected by the force and torque -keywords in the fix rigid command; they reflect values before any -changes are made by those keywords. +velocity, the xyz components of the force acting on the COM, the xyz +components of the torque acting on the COM, and the xyz image flags of +the COM, which have the same meaning as image flags for atom positions +(see the "dump" command). The force and torque values in the array +are not affected by the force and torque keywords in the fix rigid +command; they reflect values before any changes are made by those +keywords.
The ordering of the rigid bodies (by row in the array) is as follows. For the single keyword there is just one rigid body. For the diff --git a/doc/fix_rigid.txt b/doc/fix_rigid.txt index b02d864ee8..6f4d4df5ce 100644 --- a/doc/fix_rigid.txt +++ b/doc/fix_rigid.txt @@ -231,18 +231,22 @@ The rigid body contribution to the pressure of the system (virial) is also accounted for by this fix. 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 "compute -msd"_compute_msd.html will not compute the expected mean-squared -displacement for such atoms, and the image flag values written to a -"dump file"_dump.html will be different than they would be if the -atoms were not in a rigid body. It also means that if you have bonds +altered so that the rigid body can be reconstructed correctly when it +straddles periodic boundaries. The atom image flags are not +incremented/decremented as they would be for non-rigid atoms. This +means you cannot interpret them as you normally would. For example, +the image flag values written to a "dump file"_dump.html will be +different than they would be if the atoms were not in a rigid body. +Likewise the "compute msd"_compute_msd.html will not compute the +expected mean-squared displacement for such atoms if the body moves +across periodic boundaries. It also means that if you have bonds between a pair of rigid bodies and the bond straddles a periodic boundary, you cannot use the "replicate"_replicate.html command to -increase the system size. +increase the system size. Note that this fix does define image flags +for each rigid body, which are incremented when the rigid body crosses +a periodic boundary in the usual way. These image flags have the same +meaning as atom images (see the "dump" command) and can be accessed +and output as described below. :line @@ -262,13 +266,15 @@ fixes. These fixes compute a global array of values which can be accessed by various "output commands"_Section_howto.html#4_15. The number of rows in the array is equal to the number of rigid bodies. The number of -columns is 12. Thus for each rigid body, 12 values are stored: the +columns is 15. Thus for each rigid body, 12 values are stored: the xyz coords of the center of mass (COM), the xyz components of the COM -velocity, the xyz components of the force acting on the COM, and the -xyz components of the torque acting on the COM. The force and torque -values in the array are not affected by the {force} and {torque} -keywords in the fix rigid command; they reflect values before any -changes are made by those keywords. +velocity, the xyz components of the force acting on the COM, the xyz +components of the torque acting on the COM, and the xyz image flags of +the COM, which have the same meaning as image flags for atom positions +(see the "dump" command). The force and torque values in the array +are not affected by the {force} and {torque} keywords in the fix rigid +command; they reflect values before any changes are made by those +keywords. The ordering of the rigid bodies (by row in the array) is as follows. For the {single} keyword there is just one rigid body. For the