git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10149 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/compute_temp_deform.html

@@ -85,6 +85,21 @@ temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
 temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
 langevin</A>.
 </P>
+<P>IMPORTANT NOTE: The temperature calculated by this compute is only
+accurate if the atoms are indeed moving with a stream velocity profile
+that matches the box deformation.  If not, then the compute will
+subtract off an incorrect stream velocity, yielding a bogus thermal
+temperature.  You should NOT assume that your atoms are streaming at
+the same rate the box is deforming.  Rather, you should monitor their
+velocity profile, e.g. via the <A HREF = "fix_ave_spatial.html">fix ave/spatial</A>
+command.  And you can compare the results of this compute to <A HREF = "compute_temp_profile.html">compute
+temp/profile</A>, which actually calculates the
+stream profile before subtracting it.  If the two computes do not give
+roughly the same temperature, then your atoms are not streaming
+consistent with the box deformation.  See the <A HREF = "fix_deform.html">fix
+deform</A> command for more details on ways to get atoms
+to stream consistently with the box deformation.
+</P>
 <P>This compute subtracts out degrees-of-freedom due to fixes that
 constrain molecular motion, such as <A HREF = "fix_shake.html">fix shake</A> and
 <A HREF = "fix_rigid.html">fix rigid</A>.  This means the temperature of groups of

doc/compute_temp_deform.txt

@@ -82,6 +82,21 @@ temp/rescale"_fix_temp_rescale.html, "fix
 temp/berendsen"_fix_temp_berendsen.html, and "fix
 langevin"_fix_langevin.html.
 
+IMPORTANT NOTE: The temperature calculated by this compute is only
+accurate if the atoms are indeed moving with a stream velocity profile
+that matches the box deformation.  If not, then the compute will
+subtract off an incorrect stream velocity, yielding a bogus thermal
+temperature.  You should NOT assume that your atoms are streaming at
+the same rate the box is deforming.  Rather, you should monitor their
+velocity profile, e.g. via the "fix ave/spatial"_fix_ave_spatial.html
+command.  And you can compare the results of this compute to "compute
+temp/profile"_compute_temp_profile.html, which actually calculates the
+stream profile before subtracting it.  If the two computes do not give
+roughly the same temperature, then your atoms are not streaming
+consistent with the box deformation.  See the "fix
+deform"_fix_deform.html command for more details on ways to get atoms
+to stream consistently with the box deformation.
+
 This compute subtracts out degrees-of-freedom due to fixes that
 constrain molecular motion, such as "fix shake"_fix_shake.html and
 "fix rigid"_fix_rigid.html.  This means the temperature of groups of

doc/fix_deform.html

@@ -492,6 +492,28 @@ periodic boundaries, since that is consistent with maintaining the
 velocity profile already created by fix nvt/sllod.  LAMMPS will warn
 you if the <I>remap</I> setting is not consistent with fix nvt/sllod.
 </P>
+<P>IMPORTANT NOTE: For non-equilibrium MD (NEMD) simulations using "remap
+v" it is usually desirable that the fluid (or flowing material,
+e.g. granular particles) stream with a velocity profile consistent
+with the deforming box.  As mentioned above, using a thermostat such
+as <A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A> or <A HREF = "doc/fix_langevin.html">fix
+lavgevin</A> (with a bias provided by <A HREF = "compute_temp_deform.html">compute
+temp/deform</A>), will typically accomplish
+that.  If you do not use a thermostat, then there is no driving force
+pushing the atoms to flow in a manner consistent with the deforming
+box.  E.g. for a shearing system the box deformation velocity may vary
+from 0 at the bottom to 10 at the top of the box.  But the stream
+velocity profile of the atoms may vary from -5 at the bottom to +5 at
+the top.  You can monitor these effects using the <A HREF = "fix_ave_spatial.html">fix
+ave/spatial</A>, <A HREF = "compute_temp_deform.html">compute
+temp/deform</A>, and <A HREF = "compute_temp_profile.html">compute
+temp/profile</A> commands.  One way to induce
+atoms to stream consistent with the box deformation is to give them an
+initial velocity profile, via the <A HREF = "velocity.html">velocity ramp</A>
+command, that matches the box deformation rate.  This also typically
+helps the system come to equilibrium more quickly, even if a
+thermostat is used.
+</P>
 <P>IMPORTANT NOTE: If a <A HREF = "fix_rigid.html">fix rigid</A> is defined for rigid
 bodies, and <I>remap</I> is set to <I>x</I>, then the center-of-mass coordinates
 of rigid bodies will be remapped to the changing simulation box.  This

doc/fix_deform.txt

@@ -482,6 +482,28 @@ periodic boundaries, since that is consistent with maintaining the
 velocity profile already created by fix nvt/sllod.  LAMMPS will warn
 you if the {remap} setting is not consistent with fix nvt/sllod.
 
+IMPORTANT NOTE: For non-equilibrium MD (NEMD) simulations using "remap
+v" it is usually desirable that the fluid (or flowing material,
+e.g. granular particles) stream with a velocity profile consistent
+with the deforming box.  As mentioned above, using a thermostat such
+as "fix nvt/sllod"_fix_nvt_sllod.html or "fix
+lavgevin"_doc/fix_langevin.html (with a bias provided by "compute
+temp/deform"_compute_temp_deform.html), will typically accomplish
+that.  If you do not use a thermostat, then there is no driving force
+pushing the atoms to flow in a manner consistent with the deforming
+box.  E.g. for a shearing system the box deformation velocity may vary
+from 0 at the bottom to 10 at the top of the box.  But the stream
+velocity profile of the atoms may vary from -5 at the bottom to +5 at
+the top.  You can monitor these effects using the "fix
+ave/spatial"_fix_ave_spatial.html, "compute
+temp/deform"_compute_temp_deform.html, and "compute
+temp/profile"_compute_temp_profile.html commands.  One way to induce
+atoms to stream consistent with the box deformation is to give them an
+initial velocity profile, via the "velocity ramp"_velocity.html
+command, that matches the box deformation rate.  This also typically
+helps the system come to equilibrium more quickly, even if a
+thermostat is used.
+
 IMPORTANT NOTE: If a "fix rigid"_fix_rigid.html is defined for rigid
 bodies, and {remap} is set to {x}, then the center-of-mass coordinates
 of rigid bodies will be remapped to the changing simulation box.  This