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<p class="caption"><span class="caption-text">User Documentation</span></p>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<p class="caption"><span class="caption-text">Index</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>
<li class="toctree-l1"><a class="reference internal" href="commands.html">Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="computes.html">Computes</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="compute_ackland_atom.html">compute ackland/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_angle.html">compute angle command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_angle_local.html">compute angle/local command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_angmom_chunk.html">compute angmom/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_basal_atom.html">compute basal/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_body_local.html">compute body/local command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_bond.html">compute bond command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_bond_local.html">compute bond/local command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_centro_atom.html">compute centro/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_chunk_atom.html">compute chunk/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_cluster_atom.html">compute cluster/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_cna_atom.html">compute cna/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_com.html">compute com command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_com_chunk.html">compute com/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_contact_atom.html">compute contact/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_coord_atom.html">compute coord/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_damage_atom.html">compute damage/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_dihedral.html">compute dihedral command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_dihedral_local.html">compute dihedral/local command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_dilatation_atom.html">compute dilatation/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_dipole_chunk.html">compute dipole/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_displace_atom.html">compute displace/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_dpd.html">compute dpd command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_dpd_atom.html">compute dpd/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_erotate_asphere.html">compute erotate/asphere command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_erotate_rigid.html">compute erotate/rigid command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_erotate_sphere.html">compute erotate/sphere command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_erotate_sphere_atom.html">compute erotate/sphere/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_event_displace.html">compute event/displace command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_fep.html">compute fep command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_group_group.html">compute group/group command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_gyration.html">compute gyration command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_gyration_chunk.html">compute gyration/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_heat_flux.html">compute heat/flux command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_hexorder_atom.html">compute hexorder/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_improper.html">compute improper command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_improper_local.html">compute improper/local command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_inertia_chunk.html">compute inertia/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_ke.html">compute ke command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_ke_atom.html">compute ke/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_ke_atom_eff.html">compute ke/atom/eff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_ke_eff.html">compute ke/eff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_ke_rigid.html">compute ke/rigid command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_meso_e_atom.html">compute meso/e/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_meso_rho_atom.html">compute meso/rho/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_meso_t_atom.html">compute meso/t/atom command</a></li>
<li class="toctree-l2 current"><a class="current reference internal" href="#">compute msd command</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#syntax">Syntax</a></li>
<li class="toctree-l3"><a class="reference internal" href="#examples">Examples</a></li>
<li class="toctree-l3"><a class="reference internal" href="#description">Description</a></li>
<li class="toctree-l3"><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li class="toctree-l3"><a class="reference internal" href="#related-commands">Related commands</a></li>
<li class="toctree-l3"><a class="reference internal" href="#default">Default</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="compute_msd_chunk.html">compute msd/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_msd_nongauss.html">compute msd/nongauss command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_omega_chunk.html">compute omega/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_orientorder_atom.html">compute orientorder/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_pair.html">compute pair command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_pair_local.html">compute pair/local command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_pe.html">compute pe command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_pe_atom.html">compute pe/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_plasticity_atom.html">compute plasticity/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_pressure.html">compute pressure command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_property_atom.html">compute property/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_property_chunk.html">compute property/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_property_local.html">compute property/local command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_rdf.html">compute rdf command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_reduce.html">compute reduce command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_reduce.html#compute-reduce-region-command">compute reduce/region command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_rigid_local.html">compute rigid/local command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_saed.html">compute saed command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_slice.html">compute slice command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_contact_radius.html">compute smd/contact/radius command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_damage.html">compute smd/damage command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_hourglass_error.html">compute smd/hourglass/error command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_internal_energy.html">compute smd/internal/energy command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_plastic_strain.html">compute smd/plastic/strain command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_plastic_strain_rate.html">compute smd/plastic/strain/rate command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_rho.html">compute smd/rho command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_defgrad.html">compute smd/tlsph/defgrad command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_dt.html">compute smd/tlsph/dt command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_num_neighs.html">compute smd/tlsph/num/neighs command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_shape.html">compute smd/tlsph/shape command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_strain.html">compute smd/tlsph/strain command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_strain_rate.html">compute smd/tlsph/strain/rate command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_tlsph_stress.html">compute smd/tlsph/stress command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_triangle_mesh_vertices.html">compute smd/triangle/mesh/vertices</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_ulsph_num_neighs.html">compute smd/ulsph/num/neighs command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_ulsph_strain.html">compute smd/ulsph/strain command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_ulsph_strain_rate.html">compute smd/ulsph/strain/rate command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_ulsph_stress.html">compute smd/ulsph/stress command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_smd_vol.html">compute smd/vol command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_sna_atom.html">compute sna/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_sna_atom.html#compute-snad-atom-command">compute snad/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_sna_atom.html#compute-snav-atom-command">compute snav/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_stress_atom.html">compute stress/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_tally.html">compute force/tally command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-heat-flux-tally-command">compute heat/flux/tally command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-pe-tally-command">compute pe/tally command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-pe-mol-tally-command">compute pe/mol/tally command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_tally.html#compute-stress-tally-command">compute stress/tally command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp.html">compute temp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp.html#compute-temp-kk-command">compute temp/kk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_asphere.html">compute temp/asphere command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_body.html">compute temp/body command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_chunk.html">compute temp/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_com.html">compute temp/com command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_cs.html">compute temp/cs command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_deform.html">compute temp/deform command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_deform_eff.html">compute temp/deform/eff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_drude.html">compute temp/drude command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_eff.html">compute temp/eff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_partial.html">compute temp/partial command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_profile.html">compute temp/profile command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_ramp.html">compute temp/ramp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_region.html">compute temp/region command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_region_eff.html">compute temp/region/eff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_rotate.html">compute temp/rotate command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_temp_sphere.html">compute temp/sphere command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_ti.html">compute ti command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_torque_chunk.html">compute torque/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_vacf.html">compute vacf command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_vcm_chunk.html">compute vcm/chunk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_voronoi_atom.html">compute voronoi/atom command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_xrd.html">compute xrd command</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
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<div class="section" id="compute-msd-command">
<span id="index-0"></span><h1>compute msd command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">msd</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
</pre></div>
</div>
<ul>
<li><p class="first">ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</p>
</li>
<li><p class="first">msd = style name of this compute command</p>
</li>
<li><p class="first">zero or more keyword/value pairs may be appended</p>
</li>
<li><p class="first">keyword = <em>com</em> or <em>average</em></p>
<pre class="literal-block">
<em>com</em> value = <em>yes</em> or <em>no</em>
<em>average</em> value = <em>yes</em> or <em>no</em>
</pre>
</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">msd</span>
<span class="n">compute</span> <span class="mi">1</span> <span class="n">upper</span> <span class="n">msd</span> <span class="n">com</span> <span class="n">yes</span> <span class="n">average</span> <span class="n">yes</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Define a computation that calculates the mean-squared displacement
(MSD) of the group of atoms, including all effects due to atoms
passing thru periodic boundaries. For computation of the non-Gaussian
parameter of mean-squared displacement, see the <a class="reference internal" href="compute_msd_nongauss.html"><span class="doc">compute msd/nongauss</span></a> command.</p>
<p>A vector of four quantites is calculated by this compute. The first 3
elements of the vector are the squared dx,dy,dz displacements, summed
and averaged over atoms in the group. The 4th element is the total
squared displacement, i.e. (dx*dx + dy*dy + dz*dz), summed and
averaged over atoms in the group.</p>
<p>The slope of the mean-squared displacement (MSD) versus time is
proportional to the diffusion coefficient of the diffusing atoms.</p>
<p>The displacement of an atom is from its reference position. This is
normally the original position at the time
the compute command was issued, unless the <em>average</em> keyword is set to <em>yes</em>.
The value of the displacement will be
0.0 for atoms not in the specified compute group.</p>
<p>If the <em>com</em> option is set to <em>yes</em> 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 calculated.</p>
<p>If the <em>average</em> option is set to <em>yes</em> then the reference position of
an atom is based on the average position of that atom, corrected for
center-of-mass motion if requested. The average position is a running
average over all previous calls to the compute, including the current
call. So on the first call it is current position, on the second call
it is the arithmetic average of the current position and the position
on the first call, and so on. Note that when using this option, the
precise value of the mean square displacement will depend on the
number of times the compute is called. So, for example, changing the
frequency of thermo output may change the computed displacement. Also,
the precise values will be changed if a single simulation is broken up
into two parts, using either multiple run commands or a restart
file. It only makes sense to use this option if the atoms are not
diffusing, so that their average positions relative to the center of
mass of the system are stationary. The most common case is crystalline
solids undergoing thermal motion.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Initial coordinates are stored in &#8220;unwrapped&#8221; form, by using the
image flags associated with each atom. See the <a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a> command for a discussion of &#8220;unwrapped&#8221; coordinates.
See the Atoms section of the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command for a
discussion of image flags and how they are set for each atom. You can
reset the image flags (e.g. to 0) before invoking this compute by
using the <a class="reference internal" href="set.html"><span class="doc">set image</span></a> command.</p>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If you want the quantities calculated by this compute to be
continuous when running from a <a class="reference internal" href="read_restart.html"><span class="doc">restart file</span></a>, then
you should use the same ID for this compute, as in the original run.
This is so that the fix this compute creates to store per-atom
quantities will also have the same ID, and thus be initialized
correctly with atom reference positions from the restart file. When
<em>average</em> is set to yes, then the atom reference positions are
restored correctly, but not the number of samples used obtain them. As
a result, the reference positions from the restart file are combined
with subsequent positions as if they were from a single sample,
instead of many, which will change the values of msd somewhat.</p>
</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global vector of length 4, which can be
accessed by indices 1-4 by any command that uses global vector values
from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview of LAMMPS output
options.</p>
<p>The vector values are &#8220;intensive&#8221;. The vector values will be in
distance^2 <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="compute_msd_nongauss.html"><span class="doc">compute msd/nongauss</span></a>, <a class="reference internal" href="compute_displace_atom.html"><span class="doc">compute displace_atom</span></a>, <a class="reference internal" href="fix_store_state.html"><span class="doc">fix store/state</span></a>, <a class="reference internal" href="compute_msd_chunk.html"><span class="doc">compute msd/chunk</span></a></p>
</div>
<div class="section" id="default">
<h2>Default</h2>
<p>The option default are com = no, average = no.</p>
</div>
</div>
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