+Syntax: +
+compute ID group-ID msd/nongauss keyword values ... ++
com value = yes or no ++ +
Examples: +
+compute 1 all msd/nongauss +compute 1 upper msd/nongauss com yes ++
Description: +
+Define a computation that calculates the mean-squared displacement +(MSD) and non-Gaussian parameter (NGP) of the group of atoms, +including all effects due to atoms passing thru periodic boundaries. +
+A vector of three quantites is calculated by this compute. The first +element of the vector is the total squared dx,dy,dz displacements +drsquared = (dx*dx + dy*dy + dz*dz) of atoms, and the second is the +fourth power of these displacements drfourth = (dx*dx + dy*dy + +dz*dz)*(dx*dx + dy*dy + dz*dz), summed and averaged over atoms in the +group. The 3rd component is the nonGaussian diffusion paramter NGP = +3*drfourth/(5*drsquared*drsquared), i.e. +
+
+The NGP is a commonly used quantity in studies of dynamical +heterogeneity. Its minimum theoretical value (-0.4) occurs when all +atoms have the same displacement magnitude. NGP=0 for Brownian +diffusion, while NGP > 0 when some mobile atoms move faster than +others. +
+If the com option is set to yes then the effect of any drift in +the center-of-mass of the group of atoms is subtracted out before the +displacment of each atom is calcluated. +
+See the compute msd doc page for further IMPORTANT +NOTES, which also apply to this compute. +
+Output info: +
+This compute calculates a global vector of length 3, which can be +accessed by indices 1-3 by any command that uses global vector values +from a compute as input. See this +section for an overview of LAMMPS output +options. +
+The vector values are "intensive". The first vector value will be in +distance^2 units, the second is in distance^4 units, and +the 3rd is dimensionless. +
+Restrictions: +
+This compute is part of the MISC package. It is only enabled if LAMMPS +was built with that package. See the Making +LAMMPS section for more info. +
+Related commands: +
+ +Default: +
+The option default is com = no. +
+ diff --git a/doc/compute_msd_nongauss.txt b/doc/compute_msd_nongauss.txt new file mode 100644 index 0000000000..53d30a9145 --- /dev/null +++ b/doc/compute_msd_nongauss.txt @@ -0,0 +1,80 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +compute msd/nongauss command :h3 + +[Syntax:] + +compute ID group-ID msd/nongauss keyword values ... :pre + +ID, group-ID are documented in "compute"_compute.html command :ulb,l +msd/nongauss = style name of this compute command :l +zero or more keyword/value pairs may be appended :l +keyword = {com} :l + {com} value = {yes} or {no} :pre +:ule + +[Examples:] + +compute 1 all msd/nongauss +compute 1 upper msd/nongauss com yes :pre + +[Description:] + +Define a computation that calculates the mean-squared displacement +(MSD) and non-Gaussian parameter (NGP) of the group of atoms, +including all effects due to atoms passing thru periodic boundaries. + +A vector of three quantites is calculated by this compute. The first +element of the vector is the total squared dx,dy,dz displacements +drsquared = (dx*dx + dy*dy + dz*dz) of atoms, and the second is the +fourth power of these displacements drfourth = (dx*dx + dy*dy + +dz*dz)*(dx*dx + dy*dy + dz*dz), summed and averaged over atoms in the +group. The 3rd component is the nonGaussian diffusion paramter NGP = +3*drfourth/(5*drsquared*drsquared), i.e. + +:c,image(Eqs/compute_msd_nongauss.jpg) + +The NGP is a commonly used quantity in studies of dynamical +heterogeneity. Its minimum theoretical value (-0.4) occurs when all +atoms have the same displacement magnitude. NGP=0 for Brownian +diffusion, while NGP > 0 when some mobile atoms move faster than +others. + +If the {com} option is set to {yes} then the effect of any drift in +the center-of-mass of the group of atoms is subtracted out before the +displacment of each atom is calcluated. + +See the "compute msd"_compute_msd.html doc page for further IMPORTANT +NOTES, which also apply to this compute. + +[Output info:] + +This compute calculates a global vector of length 3, which can be +accessed by indices 1-3 by any command that uses global vector values +from a compute as input. See "this +section"_Section_howto.html#howto_15 for an overview of LAMMPS output +options. + +The vector values are "intensive". The first vector value will be in +distance^2 "units"_units.html, the second is in distance^4 units, and +the 3rd is dimensionless. + +[Restrictions:] + +This compute is part of the MISC package. It is only enabled if LAMMPS +was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +[Related commands:] + +"compute msd"_compute_msd.html + +[Default:] + +The option default is com = no.