forked from lijiext/lammps
94 lines
3.5 KiB
Plaintext
94 lines
3.5 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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compute msd/molecule command :h3
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[Syntax:]
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compute ID group-ID msd/molecule :pre
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ID, group-ID are documented in "compute"_compute.html command
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msd/molecule = style name of this compute command :ul
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[Examples:]
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compute 1 all msd/molecule :pre
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[Description:]
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Define a computation that calculates the mean-squared displacement
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(MSD) of individual molecules. The calculation includes all effects
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due to atoms passing thru periodic boundaries.
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Four quantites are calculated by this compute for each molecule. The
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first 3 quantities are the squared dx,dy,dz displacements of the
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center-of-mass. The 4th component is the total squared displacement,
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i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass.
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The slope of the mean-squared displacement (MSD) versus time is
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proportional to the diffusion coefficient of the diffusing molecules.
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The displacement of the center-of-mass of the molecule is from its
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original center-of-mass position at the time the compute command was
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issued.
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The MSD for a particular molecule is only computed if one or more of
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its atoms are in the specified group. Normally all atoms in the
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molecule should be in the group, however this is not required. LAMMPS
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will warn you if this is not the case. Only atoms in the group
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contribute to the center-of-mass calculation for the molecule, which
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is used to caculate its initial and current position.
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Let Nmolecules be the number of molecules for which the MSD is
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calculated. If not all molecules have atoms in the group, then the
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molecule with the lowest ID is the first of the Nmolecules. The next
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lowest ID is the second, etc, up to Nmolecules.
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IMPORTANT NOTE: The initial coordinates of each molecule are stored in
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"unwrapped" form, by using the image flags associated with each atom.
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See the "dump custom"_dump.html command for a discussion of
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"unwrapped" coordinates. See the Atoms section of the
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"read_data"_read_data.html command for a discussion of image flags and
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how they are set for each atom. You can reset the image flags
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(e.g. to 0) before invoking this compute by using the "set
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image"_set.html command.
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IMPORTANT NOTE: If an atom is part of a rigid body (see the "fix
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rigid"_fix_rigid.html command), it's periodic image flags are altered,
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and its contribution to the MSD may not reflect its true contribution.
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See the "fix rigid"_fix_rigid.html command for details. Thus, to
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compute the MSD of rigid bodies as they cross periodic boundaries, you
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will need to post-process a "dump file"_dump.html containing
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coordinates of the atoms in the bodies.
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IMPORTANT NOTE: Unlike the "compute msd"_compute_msd.html command,
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this compute does not store the initial center-of-mass coorindates of
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its molecules in a restart file. Thus you cannot continue the MSD per
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molecule calculation when running from a "restart
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file"_read_restart.html.
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[Output info:]
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This compute calculates a global array with the number of rows =
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Nmolecules and the number of columns = 4 for dx,dy,dz and the total
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displacement. These values can be accessed by any command that uses
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global array values from a compute as input. See "this
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section"_Section_howto.html#4_15 for an overview of LAMMPS output
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options.
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The array values are "intensive", meaning they are independent of the
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number of atoms in the simulation.
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[Restrictions:] none
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[Related commands:]
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"compute msd"_compute_msd.html
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[Default:] none
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