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cross ref fix deform and new fix nvt/uef

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This commit is contained in:
Steve Plimpton
2017-10-18 15:26:15 -06:00
parent 6dd55e49cb
commit f709a723cd
2 changed files with 21 additions and 11 deletions
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13
doc/src/fix_deform.txt
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@ -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

19
doc/src/fix_nh_uef.txt
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@ -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