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Completed back-porting of Zombie SNAP improvements, particularly noteworthy is reduction in memory footprint, elimination of most multidimensional arrays, elimination of diagonal_style, elimination of Z array in force calculation.

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This commit is contained in:
Aidan Thompson
2019-06-12 16:42:28 -06:00
parent 0559e155f2
commit a973700295
14 changed files with 130 additions and 154 deletions
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39
doc/src/compute_sna_atom.txt
View File

@ -24,12 +24,8 @@ twojmax = band limit for bispectrum components (non-negative integer) :l
R_1, R_2,... = list of cutoff radii, one for each type (distance units) :l
w_1, w_2,... = list of neighbor weights, one for each type :l
zero or more keyword/value pairs may be appended :l
keyword = {diagonal} or {rmin0} or {switchflag} or {bzeroflag} or {quadraticflag} :l
{diagonal} value = {0} or {1} or {2} or {3}
{0} = all j1, j2, j <= twojmax, j2 <= j1
{1} = subset satisfying j1 == j2
{2} = subset satisfying j1 == j2 == j3
{3} = subset satisfying j2 <= j1 <= j
keyword = {rmin0} or {switchflag} or {bzeroflag} or {quadraticflag} :l
// {3} = subset satisfying j2 <= j1 <= j
{rmin0} value = parameter in distance to angle conversion (distance units)
{switchflag} value = {0} or {1}
{0} = do not use switching function
@ -44,7 +40,7 @@ keyword = {diagonal} or {rmin0} or {switchflag} or {bzeroflag} or {quadraticflag
[Examples:]
compute b all sna/atom 1.4 0.99363 6 2.0 2.4 0.75 1.0 diagonal 3 rmin0 0.0
compute b all sna/atom 1.4 0.99363 6 2.0 2.4 0.75 1.0 rmin0 0.0
compute db all sna/atom 1.4 0.95 6 2.0 1.0
compute vb all sna/atom 1.4 0.95 6 2.0 1.0 :pre
@ -151,7 +147,7 @@ The argument {rfac0} and the optional keyword {rmin0} define the
linear mapping from radial distance to polar angle {theta0} on the
3-sphere.
The argument {twojmax} and the keyword {diagonal} define which
The argument {twojmax} defines which
bispectrum components are generated. See section below on output for a
detailed explanation of the number of bispectrum components and the
ordered in which they are listed.
@ -192,25 +188,20 @@ command that includes all pairs in the neighbor list.
Compute {sna/atom} calculates a per-atom array, each column
corresponding to a particular bispectrum component. The total number
of columns and the identity of the bispectrum component contained in
each column depend on the values of {twojmax} and {diagonal}, as
each column depend of the value of {twojmax}, as
described by the following piece of python code:
for j1 in range(0,twojmax+1):
if(diagonal==2):
print j1/2.,j1/2.,j1/2.
elif(diagonal==1):
for j in range(0,min(twojmax,2*j1)+1,2):
print j1/2.,j1/2.,j/2.
elif(diagonal==0):
for j2 in range(0,j1+1):
for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
print j1/2.,j2/2.,j/2.
elif(diagonal==3):
for j2 in range(0,j1+1):
for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
if (j>=j1): print j1/2.,j2/2.,j/2. :pre
for j2 in range(0,j1+1):
for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
if (j>=j1): print j1/2.,j2/2.,j/2. :pre
Compute {snad/atom} evaluates a per-atom array. The columns are
NOTE: the {diagonal} keyword allowing other possible choices
for the number of bispectrum components was removed in 2019,
since all potentials use the value of 3, corresponding to the
above set of bispectrum components.
ompute {snad/atom} evaluates a per-atom array. The columns are
arranged into {ntypes} blocks, listed in order of atom type {I}. Each
block contains three sub-blocks corresponding to the {x}, {y}, and {z}
components of the atom position. Each of these sub-blocks contains
@ -259,7 +250,7 @@ package"_Build_package.html doc page for more info.
[Default:]
The optional keyword defaults are {diagonal} = 0, {rmin0} = 0,
The optional keyword defaults are {rmin0} = 0,
{switchflag} = 1, {bzeroflag} = 1, {quadraticflag} = 0,
:line

8
doc/src/pair_snap.txt
View File

@ -38,7 +38,7 @@ where {B_k^i} is the {k}-th bispectrum component of atom {i},
and {beta_k^alpha_i} is the corresponding linear coefficient
that depends on {alpha_i}, the SNAP element of atom {i}. The
number of bispectrum components used and their definitions
depend on the values of {twojmax} and {diagonalstyle}
depend on the value of {twojmax}
defined in the SNAP parameter file described below.
The bispectrum calculation is described in more detail
in "compute sna/atom"_compute_sna_atom.html.
@ -125,14 +125,13 @@ This line is followed by {ncoeff} coefficients, one per line.
The SNAP parameter file can contain blank and comment lines (start
with #) anywhere. Each non-blank non-comment line must contain one
keyword/value pair. The required keywords are {rcutfac} and
{twojmax}. Optional keywords are {rfac0}, {rmin0}, {diagonalstyle},
{twojmax}. Optional keywords are {rfac0}, {rmin0},
{switchflag}, and {bzeroflag}.
The default values for these keywords are
{rfac0} = 0.99363
{rmin0} = 0.0
{diagonalstyle} = 3
{switchflag} = 0
{bzeroflag} = 1
{quadraticflag} = 1 :ul
@ -144,6 +143,9 @@ If {quadraticflag} is set to 1, then the SNAP energy expression includes the qua
The SNAP element file should contain {K}({K}+1)/2 additional coefficients
for each element, the upper-triangular elements of alpha.
NOTE: The previously used {diagonalstyle} keyword was removed in 2019,
since all known SNAP potentials use the default value of 3.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]: