2009-12-22 01:27:08 +08:00
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
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<H3>compute msd/molecule command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>compute ID group-ID msd/molecule
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
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<LI>msd/molecule = style name of this compute command
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>compute 1 all msd/molecule
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>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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</P>
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<P>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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</P>
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<P>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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</P>
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<P>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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</P>
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<P>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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</P>
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<P>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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</P>
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<P>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 <A HREF = "dump.html">dump custom</A> command for a discussion of
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"unwrapped" coordinates. See the Atoms section of the
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<A HREF = "read_data.html">read_data</A> 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 <A HREF = "set.html">set
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image</A> command.
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</P>
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<P>IMPORTANT NOTE: If an atom is part of a rigid body (see the <A HREF = "fix_rigid.html">fix
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rigid</A> 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 <A HREF = "fix_rigid.html">fix rigid</A> 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 <A HREF = "dump.html">dump file</A> containing
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coordinates of the atoms in the bodies.
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</P>
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<P>IMPORTANT NOTE: Unlike the <A HREF = "compute_msd.html">compute msd</A> 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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2009-12-22 01:34:52 +08:00
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molecule calculation of this compute when running from a <A HREF = "read_restart.html">restart
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2009-12-22 01:27:08 +08:00
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file</A>.
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</P>
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<P><B>Output info:</B>
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</P>
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2009-12-22 01:34:52 +08:00
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<P>This compute calculates a global array where 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 <A HREF = "Section_howto.html#4_15">this
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section</A> for an overview of LAMMPS output
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options.
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</P>
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<P>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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</P>
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<P><B>Restrictions:</B> none
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "compute_msd.html">compute msd</A>
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</P>
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<P><B>Default:</B> none
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</P>
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</HTML>
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