comm_modify keyword value ...
-+comm_modify keyword value ... +
comm_modify mode multi
-comm_modify mode multi group solvent
-comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0
-comm_modify vel yes
-comm_modify mode single cutoff 5.0 vel yes
-comm_modify cutoff/multi * 0.0
-+comm_modify mode multi +comm_modify mode multi group solvent +comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0 +comm_modify vel yes +comm_modify mode single cutoff 5.0 vel yes +comm_modify cutoff/multi * 0.0 +
dist = bond distance -eng = bond energy +engpot = bond potential energy force = bond force+
+engvib = bond kinetic energy of vibration +engrot = bond kinetic energy of rotation +engtrans = bond kinetic energy of translation +omega = magnitude of bond angular velocity +velvib = vibrational velocity along the bond length +
compute 1 all bond/local eng
-compute 1 all bond/local dist eng force
+compute 1 all bond/local engpot
+compute 1 all bond/local dist engpot force
Define a computation that calculates properties of individual bond interactions. The number of datums generated, aggregated across all -processors, equals the number of bonds in the system, modified -by the group parameter as explained below.
-The value dist is the length of the bond.
-The value eng is the interaction energy for the bond.
-The value force is the force acting between the pair of atoms in the +processors, equals the number of bonds in the system, modified by the +group parameter as explained below.
+The value dist is the current length of the bond.
+The value engpot is the potential energy for the bond, +based on the current separation of the pair of atoms in the bond.
+The value force is the magnitude of the force acting between the +pair of atoms in the bond.
+The remaining properties are all computed for motion of the two atoms +relative to the center of mass (COM) velocity of the 2 atoms in the bond.
+The value engvib is the vibrational kinetic energy of the two atoms +in the bond, which is simply 1/2 m1 v1^2 + 1/2 m1 v2^2, where v1 and +v2 are the magnitude of the velocity of the 2 atoms along the bond +direction, after the COM velocity has been subtracted from each.
+The value engrot is the rotationsl kinetic energy of the two atoms +in the bond, which is simply 1/2 m1 v1^2 + 1/2 m1 v2^2, where v1 and +v2 are the magnitude of the velocity of the 2 atoms perpendicular to +the bond direction, after the COM velocity has been subtracted from +each.
+The value engtrans is the translational kinetic energy associated +with the motion of the COM of the system itself, namely 1/2 (m1+m2) +Vcm^2 where Vcm = magnitude of the velocity of the COM.
+Note that these 3 kinetic energy terms are simply a partitioning of +the summed kinetic energy of the 2 atoms themselves. I.e. total KE = +1/2 m1 v1^2 + 1/2 m2 v3^2 = engvib + engrot + engtrans, where v1,v2 +are the magnitude of the velocities of the 2 atoms, without any +adjustment for the COM velocity.
+The value omega is the magnitude of the angular velocity of the +two atoms around their COM position.
+The value velvib is the magnitude of the relative velocity of the +two atoms in the bond towards each other. A negative value means the +2 atoms are moving toward each other; a positive value means they are +moving apart.
+Note that all these properties are computed for the pair of atoms in a +bond, whether the 2 atoms represent a simple diatomic molecule, or are +part of some larger molecule.
The local data stored by this command is generated by looping over all the atoms owned on a processor and their bonds. A bond will only be included if both atoms in the bond are in the specified compute group. @@ -179,8 +216,8 @@ command in a consistent way.
Here is an example of how to do this:
compute 1 all property/local btype batom1 batom2
-compute 2 all bond/local dist eng
-dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2]
+compute 2 all bond/local dist engpot
+dump 1 all local 1000 tmp.dump index c_1[*] c_2[*]
Output info:
This compute calculates a local vector or local array depending on the @@ -191,9 +228,12 @@ local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that uses local values from a compute as input. See this section for an overview of LAMMPS output options.
-The output for dist will be in distance units. The -output for eng will be in energy units. The output for -force will be in force units.
+The output for dist will be in distance units. The +output for velvib will be in velocity units. The output +for omega will be in velocity/distance units. The +output for engtrans, engvib, engrot, and engpot will be in +energy units. The output for force will be in force +units.