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Finished documentation and example

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This commit is contained in:
Aidan Thompson
2019-11-19 00:12:57 -07:00
parent b092a9fffa
commit 921d0794bb
2 changed files with 59 additions and 14 deletions
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52
doc/txt/compute_sna_atom.txt
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@ -9,12 +9,14 @@
compute sna/atom command :h3
compute snad/atom command :h3
compute snav/atom command :h3
compute snap command :h3
[Syntax:]
compute ID group-ID sna/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... :pre
compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
compute ID group-ID snap rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
sna/atom = style name of this compute command :l
@ -41,12 +43,17 @@ keyword = {rmin0} or {switchflag} or {bzeroflag} or {quadraticflag} :l
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
compute vb all sna/atom 1.4 0.95 6 2.0 1.0
compute snap all snap 1.4 0.95 6 2.0 1.0 :pre
[Description:]
Define a computation that calculates a set of bispectrum components
for each atom in a group.
Define a computation that calculates a set of quantities related to the
bispectrum components of the atoms in a group. These computes are
used primarily for calculating the dependence of energy, force, and
stress components on the linear coefficients in the
"snap pair_style"_pair_snap.html, which is useful when training a
SNAP potential to match target data.
Bispectrum components of an atom are order parameters characterizing
the radial and angular distribution of neighbor atoms. The detailed
@ -130,6 +137,26 @@ Again, the sum is over all atoms {i'} of atom type {I}. For each atom
virial components, each atom type, and each bispectrum component. See
section below on output for a detailed explanation.
Compute {snap} calculates a global array contains information related
to all three of the preceding per-atom computes {sna/atom}, {snad/atom},
and {snav/atom}. The first row of the array contains the summation of
{sna/atom} over all atoms, but broken out by type. The last six rows
of the array contain the summation of {snav/atom} over all atoms, broken
out by type. In between these are 3*N rows containing the same values
computed by {snad/atom} (these are already summed over all atoms and
broken out by type). The element in the last column of each row contains
the corresponding contribution to potential energy, force, or stress.
These quantities correspond to the user-specified refence potential
that must be subtracted from the target data when fitting SNAP.
The potential energy calculation uses the built in compute {thermo_pe}.
The stess calculation requires that a compute called {snap_press}
be defined using the following command:
compute snap_press all pressure NULL virial :pre
See section below on output for a detailed explanation of the data
layout in the global array.
The value of all bispectrum components will be zero for atoms not in
the group. Neighbor atoms not in the group do not contribute to the
bispectrum of atoms in the group.
@ -214,10 +241,27 @@ block contains six sub-blocks corresponding to the {xx}, {yy}, {zz},
notation. Each of these sub-blocks contains one column for each
bispectrum component, the same as for compute {sna/atom}
Compute {snap} evaluates a global array.
The columns are arranged into
{ntypes} blocks, listed in order of atom type {I}. Each block
contains one column for each bispectrum component, the same as for compute
{sna/atom}. A final column contains the corresponding energy, force component
on an atom, and virial stress component. The rows of the array appear
in the following order:
1 row: {sna/atom} quantities summed for all atoms of type {I}
3*N rows: {snad/atom} quantities, with derivatives w.r.t x, y, and z
coordinate of atom {i} appearing in consecutive rows. The atoms
are sorted based on atom ID.
6 rows: {snav/atom} quantities summed for all atoms of type {I} :ul
For example, if {K} =30 and ntypes=1, the number of columns in the per-atom
arrays generated by {sna/atom}, {snad/atom}, and {snav/atom}
are 30, 90, and 180, respectively. With {quadratic} value=1,
the numbers of columns are 930, 2790, and 5580, respectively.
The number of columns in the global array generated by {snap}
are 31, and 931, respectively, while the number of rows is
1+3*{N} +6, where {N} is the total number of atoms.
If the {quadratic} keyword value is set to 1, then additional
columns are generated, corresponding to

21
examples/snap/in.snap.compute
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@ -1,6 +1,6 @@
# Demonstrate bispectrum computes
# Initialize simulation
# initialize simulation
variable nsteps index 0
variable nrep equal 1
@ -35,14 +35,15 @@ variable radelem1 equal 2.3
variable radelem2 equal 2.0
variable wj1 equal 1.0
variable wj2 equal 0.96
variable snap_options string &
"${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag 0 bzeroflag 0 switchflag 0"
# Setup dummy potential to satisfy cutoff
# set up dummy potential to satisfy cutoff
pair_style zero ${rcutfac}
pair_coeff * *
# Setup reference potential
# set up reference potential
variable zblcutinner equal 4
variable zblcutouter equal 4.8
@ -50,11 +51,11 @@ variable zblz equal 73
pair_style zbl ${zblcutinner} ${zblcutouter}
pair_coeff * * ${zblz} ${zblz}
# set up old-style per-atom computes
# set up per-atom computes
compute b all sna/atom ${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag 0 bzeroflag 0 switchflag 0
compute vb all snav/atom ${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag 0 bzeroflag 0 switchflag 0
compute db all snad/atom ${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag 0 bzeroflag 0 switchflag 0
compute b all sna/atom ${snap_options}
compute vb all snav/atom ${snap_options}
compute db all snad/atom ${snap_options}
# perform sums over atoms
@ -67,9 +68,9 @@ compute bsum2 snapgroup2 reduce sum c_b[*]
compute vbsum all reduce sum c_vb[*]
# fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
# set up new-style global compute
# set up compute snap generating global array
compute snap all snap ${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag 0 bzeroflag 0 switchflag 0
compute snap all snap ${snap_options}
fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector
thermo 100