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Eliminated another initialization error and tweaked rdf-adf example

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Aidan Thompson
2018-10-20 16:46:45 -06:00
parent 8aecefe233
commit 8223f5e0a3
4 changed files with 61 additions and 53 deletions
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16
doc/src/compute_adf.txt
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@ -133,7 +133,7 @@ arguments are specified.
The first ADF value for a bin is calculated from the histogram count by
dividing by the total number of triples satisfying the criteria,
so that the integral of the ADF w.r.t. angle is one i.e. the ADF
so that the integral of the ADF w.r.t. angle is 1, i.e. the ADF
is a probability density function.
The second ADF value is reported as a cumulative sum of
@ -147,9 +147,15 @@ number radial distribution function.
The {ordinate} optional keyword determines
whether the bins are of uniform angular size from zero
to 180 ({degree}), zero to Pi ({radian}), or the
cosine of the angle uniform in the range \[-1,1\] ({cosine}).
Regardless of which is chosen, the first ADF will be normalized
so that the integral w.r.t. the ordinate is one.
cosine of the angle uniform in the range \[-1,1\] ({cosine}).
{cosine} has the advantage of eliminating the {acos()} function
call, which speeds up the compute by 2-3x, and it is also preferred
on physical grounds, because the for uniformly distributed particles
in 3D, the angular probability density w.r.t dtheta is
sin(theta)/2, while for d(cos(theta)), it is 1/2,
Regardless of which ordinate is chosen, the first column of ADF
values is normalized w.r.t. the range of that ordinate, so that
the integral is 1.
The simplest way to output the results of the compute adf calculation
to a file is to use the "fix ave/time"_fix_ave_time.html command, for
@ -177,7 +183,7 @@ the angle in degrees or radians, or the cosine of the angle. Each
subsequent pair of columns gives the first and second kinds of ADF
for a specific set of ({itypeN},{jtypeN},{ktypeN}). The values
in the first ADF column are normalized numbers >= 0.0,
whose integral w.r.t. the ordinate is one,
whose integral w.r.t. the ordinate is 1,
i.e. the first ADF is a normalized probability distribution.
The values in the second ADF column are also numbers >= 0.0.
They are the cumulative density distribution of angles per atom.