From f709a723cd9747ff3d70d20d0931685bf974530d Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Wed, 18 Oct 2017 15:26:15 -0600 Subject: [PATCH] cross ref fix deform and new fix nvt/uef --- doc/src/fix_deform.txt | 13 +++++++++---- doc/src/fix_nh_uef.txt | 19 ++++++++++++------- 2 files changed, 21 insertions(+), 11 deletions(-) diff --git a/doc/src/fix_deform.txt b/doc/src/fix_deform.txt index 63d872eded..12d84e8fcb 100644 --- a/doc/src/fix_deform.txt +++ b/doc/src/fix_deform.txt @@ -86,11 +86,16 @@ Change the volume and/or shape of the simulation box during a dynamics run. Orthogonal simulation boxes have 3 adjustable parameters (x,y,z). Triclinic (non-orthogonal) simulation boxes have 6 adjustable parameters (x,y,z,xy,xz,yz). Any or all of them can be -adjusted independently and simultaneously by this command. This fix -can be used to perform non-equilibrium MD (NEMD) simulations of a -continuously strained system. See the "fix +adjusted independently and simultaneously by this command. + +This fix can be used to perform non-equilibrium MD (NEMD) simulations +of a continuously strained system. See the "fix nvt/sllod"_fix_nvt_sllod.html and "compute -temp/deform"_compute_temp_deform.html commands for more details. +temp/deform"_compute_temp_deform.html commands for more details. Note +that simulation of a continuously extended (extensional flow) system +can be modeled using the "USER-UEF +package"_Section_packages.html#USER-UEF and its "fix +commands"_fix_nh_uef.html. For the {x}, {y}, {z} parameters, the associated dimension cannot be shrink-wrapped. For the {xy}, {yz}, {xz} parameters, the associated diff --git a/doc/src/fix_nh_uef.txt b/doc/src/fix_nh_uef.txt index 375904cced..bde1818371 100644 --- a/doc/src/fix_nh_uef.txt +++ b/doc/src/fix_nh_uef.txt @@ -36,18 +36,23 @@ fix biax_npt all npt/uef temp 400 400 100 erate -0.00001 0.000005 x 1 1 3000 :pr [Description:] -This fix is used to simulate non-equilibrium molecular dynamics (NEMD) -under diagonal flow fields, including uniaxial and biaxial flow. -Simulations under extensional flow may be carried out for an -indefinite amount of time. It is an implementation of the boundary -conditions from "(Dobson)"_#Dobson, and also uses numerical lattice -reduction as was proposed by "(Hunt)"_#Hunt. The lattice reduction -algorithm is from "(Semaev)"_Semaev. The fix is intended for +This fix can be used to simulate non-equilibrium molecular dynamics +(NEMD) under diagonal flow fields, including uniaxial and biaxial +flow. Simulations under continuous extensional flow may be carried +out for an indefinite amount of time. It is an implementation of the +boundary conditions from "(Dobson)"_#Dobson, and also uses numerical +lattice reduction as was proposed by "(Hunt)"_#Hunt. The lattice +reduction algorithm is from "(Semaev)"_Semaev. The fix is intended for simulations of homogeneous flows, and integrates the SLLOD equations of motion, originally proposed by Hoover and Ladd (see "(Evans and Morriss)"_#Sllod). Additional detail about this implementation can be found in "(Nicholson and Rutledge)"_#Nicholson. +Note that NEMD simulations of a continuously strained system can be +performed using the "fix deform"_fix_deform.html, "fix +nvt/sllod"_fix_nvt_sllod.html, and "compute +temp/deform"_compute_temp_deform.html commands. + The applied flow field is set by the {eps} keyword. The values {edot_x} and {edot_y} correspond to the strain rates in the xx and yy directions. It is implicitly assumed that the flow field is