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tweak the docs for the new fix numdiff command

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Steve Plimpton
2020-03-20 07:23:01 -06:00
parent 54c2381632
commit 8b0e5c66ea
2 changed files with 8 additions and 7 deletions
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14
doc/src/fix_numdiff.rst
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@ -29,14 +29,14 @@ Description
Calculate forces through finite difference calculations of energy Calculate forces through finite difference calculations of energy
versus position. These forces can be compared to analytic forces versus position. These forces can be compared to analytic forces
computed by pair styles, bond styles, etc. E.g. for debugging computed by pair styles, bond styles, etc. This can be usefule for
purposes. debugging or other purposes.
The group specified with the command means only atoms within the group The group specified with the command means only atoms within the group
have their averages computed. Results are set to 0.0 for atoms not in have their averages computed. Results are set to 0.0 for atoms not in
the group. the group.
This fix performs a loop over all atoms (in the group). For each atom This fix performs a loop over all atoms in the group. For each atom
and each component of force it adds *delta* to the position, and and each component of force it adds *delta* to the position, and
computes the new energy of the entire system. It then subtracts computes the new energy of the entire system. It then subtracts
*delta* from the original position and again computes the new energy *delta* from the original position and again computes the new energy
@ -66,10 +66,10 @@ by two times *delta*.
.. note:: .. note::
The cost of each energy evaluation is essentially the cost of an MD The cost of each energy evaluation is essentially the cost of an MD
timestep. This invoking this fix once has a cost of 2N timesteps, timestep. Thus invoking this fix for a 3d system once has a cost
where N is the total number of atoms in the system (assuming all atoms of 6N timesteps, where N is the total number of atoms in the system
are included in the group). So this fix can be very expensive to use (assuming all atoms are included in the group). So this fix can be
for large systems. very expensive to use for large systems.
---------- ----------

1
examples/README
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@ -93,6 +93,7 @@ msst: MSST shock dynamics
nb3b: use of nonbonded 3-body harmonic pair style nb3b: use of nonbonded 3-body harmonic pair style
neb: nudged elastic band (NEB) calculation for barrier finding neb: nudged elastic band (NEB) calculation for barrier finding
nemd: non-equilibrium MD of 2d sheared system nemd: non-equilibrium MD of 2d sheared system
numdiff: numerical difference computation of forces
obstacle: flow around two voids in a 2d channel obstacle: flow around two voids in a 2d channel
peptide: dynamics of a small solvated peptide chain (5-mer) peptide: dynamics of a small solvated peptide chain (5-mer)
peri: Peridynamic model of cylinder impacted by indenter peri: Peridynamic model of cylinder impacted by indenter