From 388c4d9cd600d1d4c9bdbf6ace3f90e4ecc50c01 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 28 Jun 2013 16:38:40 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10149 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/compute_temp_deform.html | 15 +++++++++++++++ doc/compute_temp_deform.txt | 15 +++++++++++++++ doc/fix_deform.html | 22 ++++++++++++++++++++++ doc/fix_deform.txt | 22 ++++++++++++++++++++++ 4 files changed, 74 insertions(+) diff --git a/doc/compute_temp_deform.html b/doc/compute_temp_deform.html index def9a12187..1a2af61281 100644 --- a/doc/compute_temp_deform.html +++ b/doc/compute_temp_deform.html @@ -85,6 +85,21 @@ temp/rescale, fix temp/berendsen, and fix langevin.

+

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 +command. And you can compare the results of this compute to compute +temp/profile, 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 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 and fix rigid. This means the temperature of groups of diff --git a/doc/compute_temp_deform.txt b/doc/compute_temp_deform.txt index 02b7ca3c22..e846107c8d 100644 --- a/doc/compute_temp_deform.txt +++ b/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 diff --git a/doc/fix_deform.html b/doc/fix_deform.html index 05e8c0c9a2..f9a7526b51 100644 --- a/doc/fix_deform.html +++ b/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 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 or fix +lavgevin (with a bias provided by compute +temp/deform), 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, compute +temp/deform, and compute +temp/profile 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 +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 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 diff --git a/doc/fix_deform.txt b/doc/fix_deform.txt index e403b2b8f2..018b9b9247 100644 --- a/doc/fix_deform.txt +++ b/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