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added examples/threebody, fix reaxc/speceies/kk

This commit is contained in:
Steve Plimpton 2016-11-04 10:56:04 -06:00
parent d9891abdf4
commit f48b71f46b
28 changed files with 1180 additions and 337 deletions
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4
doc/src/compute_temp_profile.txt
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@ -69,8 +69,8 @@ velocity for each atom. Note that if there is only one atom in the
bin, its thermal velocity will thus be 0.0.
After the spatially-averaged velocity field has been subtracted from
each atom, the temperature is calculated by the formula KE = (dim/2 N
- dim*Nx*Ny*Nz) k T, where KE = total kinetic energy of the group of
each atom, the temperature is calculated by the formula KE = (dim*N
- dim*Nx*Ny*Nz) k T/2, where KE = total kinetic energy of the group of
atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the
simulation, N = number of atoms in the group, k = Boltzmann constant,
and T = temperature. The dim*Nx*Ny*Nz term are degrees of freedom

26
doc/src/fix_reax_bonds.txt
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@ -8,6 +8,7 @@
fix reax/bonds command :h3
fix reax/c/bonds command :h3
fix reax/c/bonds/kk command :h3
[Syntax:]
@ -47,6 +48,31 @@ commands"_Section_howto.html#howto_15. No parameter of this fix can
be used with the {start/stop} keywords of the "run"_run.html command.
This fix is not invoked during "energy minimization"_minimize.html.
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in "Section_accelerate"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section_accelerate"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line
[Restrictions:]
The fix reax/bonds command requires that the "pair_style

26
doc/src/fix_reaxc_species.txt
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@ -7,6 +7,7 @@
:line
fix reax/c/species command :h3
fix reax/c/species/kk command :h3
[Syntax:]
@ -129,6 +130,31 @@ No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in "Section_accelerate"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section_accelerate"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line
[Restrictions:]
The fix species currently only works with

7
doc/src/suffix.txt
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@ -94,6 +94,13 @@ Of course this is also possible by not using any suffix commands, and
explictly appending or not appending the suffix to the relevant
commands in your input script.
NOTE: The default "run_style"_run_style.html verlet is invoked prior to
reading the input script and is therefore not affected by a suffix command
in the input script. The KOKKOS package requires "run_style verlet/kk",
so when using the KOKKOS package it is necessary to either use the command
line "-sf kk" command or add an explicit "run_style verlet" command to the
input script.
[Restrictions:] none
[Related commands:]

74
examples/threebody/BNC.tersoff Normal file
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@ -0,0 +1,74 @@
# DATE: 2013-03-21 CONTRIBUTOR: Cem Sevik CITATION: Kinaci, Haskins, Sevik and Cagin, Phys Rev B, 86, 115410 (2012)
# Tersoff parameters for B, C, and BN-C hybrid based graphene like nano structures
# multiple entries can be added to this file, LAMMPS reads the ones it needs
# these entries are in LAMMPS "metal" units:
# A,B = eV; lambda1,lambda2,lambda3 = 1/Angstroms; R,D = Angstroms
# other quantities are unitless
# Cem Sevik (csevik at anadolu.edu.tr) takes full blame for this
# file. It specifies B-N, B-C, and N-C interaction parameters
# generated and published by the reseacrh group of Prof. Tahir Cagin.
# 1. Physical Review B 84, 085409 2011
# Characterization of thermal transport in low-dimensional boron nitride nanostructures,
#
# 2. Physical Review B 86, 075403 2012
# Influence of disorder on thermal transport properties of boron nitride nanostructures
#
# 3. Physical Review B 86, 075403 2012, Please see for further information about B-C and N-C parameters
# Thermal conductivity of BN-C nanostructures
#
# The file also specifies C-C, interaction parameters
# generated and published by the reseacrh group of Dr. D. A. Broido
# Physical Review B 81, 205441 2010
# Optimized Tersoff and Brenner empirical potential parameters for
# lattice dynamics and phonon thermal transport in carbon nanotubes and graphene
# Users in referring the full parameters can cite the full parameter paper (3) as:
# A. Kinaci, J. B. Haskins, C. Sevik, T. Cagin, Physical Review B 86, 115410 (2012)
# Thermal conductivity of BN-C nanostructures
#
# format of a single entry (one or more lines):
# element 1, element 2, element 3,
# m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A
N B B 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0
N B N 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0
N B C 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0
B N B 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0
B N N 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0
B N C 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0
N N B 3.0 1.0 0.0 17.7959 5.9484 0.00000 0.6184432 0.019251 2.6272721 138.77866 2.0 0.1 2.8293093 128.86866
N N N 3.0 1.0 0.0 17.7959 5.9484 0.00000 0.6184432 0.019251 2.6272721 138.77866 2.0 0.1 2.8293093 128.86866
N N C 3.0 1.0 0.0 17.7959 5.9484 0.00000 0.6184432 0.019251 2.6272721 138.77866 2.0 0.1 2.8293093 128.86866
B B B 3.0 1.0 0.0 0.52629 0.001587 0.5 3.9929061 1.6e-6 2.0774982 43.132016 2.0 0.1 2.2372578 40.0520156
B B N 3.0 1.0 0.0 0.52629 0.001587 0.5 3.9929061 1.6e-6 2.0774982 43.132016 2.0 0.1 2.2372578 40.0520156
B B C 3.0 1.0 0.0 0.52629 0.001587 0.5 3.9929061 1.6e-6 2.0774982 43.132016 2.0 0.1 2.2372578 40.0520156
C C C 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2119 430.00 1.95 0.15 3.4879 1393.6
C C B 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2119 430.00 1.95 0.15 3.4879 1393.6
C C N 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2119 430.00 1.95 0.15 3.4879 1393.6
C B B 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78
C B N 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78
C B C 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78
C N B 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78
C N N 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78
C N C 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78
B C C 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78
B C B 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78
B C N 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78
N C C 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78
N C B 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78
N C N 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78

233
examples/threebody/CdTeZnSeHgS0.sw Normal file
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@ -0,0 +1,233 @@
### DATE: 2013-08-09 CONTRIBUTOR: X. W. Zhou, xzhou@sandia.gov, CITATION: Zhou, Ward, Martin, van Swol, Cruz-Campa, and D. Zubia, Phys. Rev. B, 88, 085309 (2013).
#
# Note that the way the parameters can be entered is not unique.
# As one way, we assume that eps_ijk is equal to eps_ik and
# lambda_ijk is equal to sqrt(lambda_ij*eps_ij*lambda_ik*eps_ik)/eps_ik,
# and all other parameters in the ijk line are for ik.
#
# The twobody ik pair parameters are entered on the i*k lines, where *
# can be any species. This is consistent with the LAMMPS requirement
# that twobody ik parameters be defined on the ikk line. Entries on all
# the other i*k lines are ignored by LAMMPS
#
# These entries are in LAMMPS "metal" units: epsilon = eV;
# sigma = Angstroms; other quantities are unitless
#
# cutoff distance = 4.632
# eps sigma a lambda gamma cos(theta) A B p q tol
Cd Cd Cd 1.182358e+00 2.663951e+00 1.527956e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.674460e-01 4.000000e+00 0.000000e+00 0.000000e+00
Cd Cd Te 1.385284e+00 2.352141e+00 1.810919e+00 3.002537e+01 1.200000e+00 -3.333333e-01 7.049600e+00 8.861252e-01 4.000000e+00 0.000000e+00 0.000000e+00
Cd Cd Zn 6.908179e-01 2.238699e+00 1.812616e+00 4.251831e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.010632e+00 4.000000e+00 0.000000e+00 0.000000e+00
Cd Cd Se 1.352371e+00 2.045165e+00 1.953387e+00 3.038855e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.116149e+00 4.000000e+00 0.000000e+00 0.000000e+00
Cd Cd Hg 4.881231e-01 2.432694e+00 1.677987e+00 5.058167e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.250999e-01 4.000000e+00 0.000000e+00 0.000000e+00
Cd Cd S 1.300376e+00 1.804151e+00 2.124568e+00 3.099013e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.540087e+00 4.000000e+00 0.000000e+00 0.000000e+00
Cd Te Cd 1.182358e+00 2.663951e+00 1.527956e+00 3.517858e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.674460e-01 4.000000e+00 0.000000e+00 0.000000e+00
Cd Te Te 1.385284e+00 2.352141e+00 1.810919e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 8.861252e-01 4.000000e+00 0.000000e+00 0.000000e+00
Cd Te Zn 6.908179e-01 2.238699e+00 1.812616e+00 4.602259e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.010632e+00 4.000000e+00 0.000000e+00 0.000000e+00
Cd Te Se 1.352371e+00 2.045165e+00 1.953387e+00 3.289311e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.116149e+00 4.000000e+00 0.000000e+00 0.000000e+00
Cd Te Hg 4.881231e-01 2.432694e+00 1.677987e+00 5.475051e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.250999e-01 4.000000e+00 0.000000e+00 0.000000e+00
Cd Te S 1.300376e+00 1.804151e+00 2.124568e+00 3.354428e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.540087e+00 4.000000e+00 0.000000e+00 0.000000e+00
Cd Zn Cd 1.182358e+00 2.663951e+00 1.527956e+00 2.484224e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.674460e-01 4.000000e+00 0.000000e+00 0.000000e+00
Cd Zn Te 1.385284e+00 2.352141e+00 1.810919e+00 2.295069e+01 1.200000e+00 -3.333333e-01 7.049600e+00 8.861252e-01 4.000000e+00 0.000000e+00 0.000000e+00
Cd Zn Zn 6.908179e-01 2.238699e+00 1.812616e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.010632e+00 4.000000e+00 0.000000e+00 0.000000e+00
Cd Zn Se 1.352371e+00 2.045165e+00 1.953387e+00 2.322829e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.116149e+00 4.000000e+00 0.000000e+00 0.000000e+00
Cd Zn Hg 4.881231e-01 2.432694e+00 1.677987e+00 3.866344e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.250999e-01 4.000000e+00 0.000000e+00 0.000000e+00
Cd Zn S 1.300376e+00 1.804151e+00 2.124568e+00 2.368813e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.540087e+00 4.000000e+00 0.000000e+00 0.000000e+00
Cd Se Cd 1.182358e+00 2.663951e+00 1.527956e+00 3.475816e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.674460e-01 4.000000e+00 0.000000e+00 0.000000e+00
Cd Se Te 1.385284e+00 2.352141e+00 1.810919e+00 3.211159e+01 1.200000e+00 -3.333333e-01 7.049600e+00 8.861252e-01 4.000000e+00 0.000000e+00 0.000000e+00
Cd Se Zn 6.908179e-01 2.238699e+00 1.812616e+00 4.547256e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.010632e+00 4.000000e+00 0.000000e+00 0.000000e+00
Cd Se Se 1.352371e+00 2.045165e+00 1.953387e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.116149e+00 4.000000e+00 0.000000e+00 0.000000e+00
Cd Se Hg 4.881231e-01 2.432694e+00 1.677987e+00 5.409618e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.250999e-01 4.000000e+00 0.000000e+00 0.000000e+00
Cd Se S 1.300376e+00 1.804151e+00 2.124568e+00 3.314338e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.540087e+00 4.000000e+00 0.000000e+00 0.000000e+00
Cd Hg Cd 1.182358e+00 2.663951e+00 1.527956e+00 2.088207e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.674460e-01 4.000000e+00 0.000000e+00 0.000000e+00
Cd Hg Te 1.385284e+00 2.352141e+00 1.810919e+00 1.929206e+01 1.200000e+00 -3.333333e-01 7.049600e+00 8.861252e-01 4.000000e+00 0.000000e+00 0.000000e+00
Cd Hg Zn 6.908179e-01 2.238699e+00 1.812616e+00 2.731909e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.010632e+00 4.000000e+00 0.000000e+00 0.000000e+00
Cd Hg Se 1.352371e+00 2.045165e+00 1.953387e+00 1.952541e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.116149e+00 4.000000e+00 0.000000e+00 0.000000e+00
Cd Hg Hg 4.881231e-01 2.432694e+00 1.677987e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.250999e-01 4.000000e+00 0.000000e+00 0.000000e+00
Cd Hg S 1.300376e+00 1.804151e+00 2.124568e+00 1.991194e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.540087e+00 4.000000e+00 0.000000e+00 0.000000e+00
Cd S Cd 1.182358e+00 2.663951e+00 1.527956e+00 3.408343e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.674460e-01 4.000000e+00 0.000000e+00 0.000000e+00
Cd S Te 1.385284e+00 2.352141e+00 1.810919e+00 3.148823e+01 1.200000e+00 -3.333333e-01 7.049600e+00 8.861252e-01 4.000000e+00 0.000000e+00 0.000000e+00
Cd S Zn 6.908179e-01 2.238699e+00 1.812616e+00 4.458985e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.010632e+00 4.000000e+00 0.000000e+00 0.000000e+00
Cd S Se 1.352371e+00 2.045165e+00 1.953387e+00 3.186911e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.116149e+00 4.000000e+00 0.000000e+00 0.000000e+00
Cd S Hg 4.881231e-01 2.432694e+00 1.677987e+00 5.304605e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.250999e-01 4.000000e+00 0.000000e+00 0.000000e+00
Cd S S 1.300376e+00 1.804151e+00 2.124568e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.540087e+00 4.000000e+00 0.000000e+00 0.000000e+00
Te Cd Cd 1.385284e+00 2.352141e+00 1.810919e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 8.861252e-01 4.000000e+00 0.000000e+00 0.000000e+00
Te Cd Te 1.849775e+00 2.905254e+00 1.594353e+00 2.812506e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.307283e-01 4.000000e+00 0.000000e+00 0.000000e+00
Te Cd Zn 1.546239e+00 2.056363e+00 1.907922e+00 3.076200e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.255846e+00 4.000000e+00 0.000000e+00 0.000000e+00
Te Cd Se 1.295053e+00 2.231716e+00 1.809645e+00 3.361313e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.005396e+00 4.000000e+00 0.000000e+00 0.000000e+00
Te Cd Hg 1.204715e+00 2.135591e+00 1.892491e+00 3.485063e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.445180e+00 4.000000e+00 0.000000e+00 0.000000e+00
Te Cd S 1.450015e+00 2.297301e+00 1.726905e+00 3.176630e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.794685e-01 4.000000e+00 0.000000e+00 0.000000e+00
Te Te Cd 1.385284e+00 2.352141e+00 1.810919e+00 3.755548e+01 1.200000e+00 -3.333333e-01 7.049600e+00 8.861252e-01 4.000000e+00 0.000000e+00 0.000000e+00
Te Te Te 1.849775e+00 2.905254e+00 1.594353e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.307283e-01 4.000000e+00 0.000000e+00 0.000000e+00
Te Te Zn 1.546239e+00 2.056363e+00 1.907922e+00 3.554713e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.255846e+00 4.000000e+00 0.000000e+00 0.000000e+00
Te Te Se 1.295053e+00 2.231716e+00 1.809645e+00 3.884177e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.005396e+00 4.000000e+00 0.000000e+00 0.000000e+00
Te Te Hg 1.204715e+00 2.135591e+00 1.892491e+00 4.027176e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.445180e+00 4.000000e+00 0.000000e+00 0.000000e+00
Te Te S 1.450015e+00 2.297301e+00 1.726905e+00 3.670765e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.794685e-01 4.000000e+00 0.000000e+00 0.000000e+00
Te Zn Cd 1.385284e+00 2.352141e+00 1.810919e+00 3.433620e+01 1.200000e+00 -3.333333e-01 7.049600e+00 8.861252e-01 4.000000e+00 0.000000e+00 0.000000e+00
Te Zn Te 1.849775e+00 2.905254e+00 1.594353e+00 2.971408e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.307283e-01 4.000000e+00 0.000000e+00 0.000000e+00
Te Zn Zn 1.546239e+00 2.056363e+00 1.907922e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.255846e+00 4.000000e+00 0.000000e+00 0.000000e+00
Te Zn Se 1.295053e+00 2.231716e+00 1.809645e+00 3.551222e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.005396e+00 4.000000e+00 0.000000e+00 0.000000e+00
Te Zn Hg 1.204715e+00 2.135591e+00 1.892491e+00 3.681964e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.445180e+00 4.000000e+00 0.000000e+00 0.000000e+00
Te Zn S 1.450015e+00 2.297301e+00 1.726905e+00 3.356105e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.794685e-01 4.000000e+00 0.000000e+00 0.000000e+00
Te Se Cd 1.385284e+00 2.352141e+00 1.810919e+00 3.142373e+01 1.200000e+00 -3.333333e-01 7.049600e+00 8.861252e-01 4.000000e+00 0.000000e+00 0.000000e+00
Te Se Te 1.849775e+00 2.905254e+00 1.594353e+00 2.719366e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.307283e-01 4.000000e+00 0.000000e+00 0.000000e+00
Te Se Zn 1.546239e+00 2.056363e+00 1.907922e+00 2.974328e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.255846e+00 4.000000e+00 0.000000e+00 0.000000e+00
Te Se Se 1.295053e+00 2.231716e+00 1.809645e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.005396e+00 4.000000e+00 0.000000e+00 0.000000e+00
Te Se Hg 1.204715e+00 2.135591e+00 1.892491e+00 3.369652e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.445180e+00 4.000000e+00 0.000000e+00 0.000000e+00
Te Se S 1.450015e+00 2.297301e+00 1.726905e+00 3.071433e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.794685e-01 4.000000e+00 0.000000e+00 0.000000e+00
Te Hg Cd 1.385284e+00 2.352141e+00 1.810919e+00 3.030791e+01 1.200000e+00 -3.333333e-01 7.049600e+00 8.861252e-01 4.000000e+00 0.000000e+00 0.000000e+00
Te Hg Te 1.849775e+00 2.905254e+00 1.594353e+00 2.622805e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.307283e-01 4.000000e+00 0.000000e+00 0.000000e+00
Te Hg Zn 1.546239e+00 2.056363e+00 1.907922e+00 2.868714e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.255846e+00 4.000000e+00 0.000000e+00 0.000000e+00
Te Hg Se 1.295053e+00 2.231716e+00 1.809645e+00 3.134597e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.005396e+00 4.000000e+00 0.000000e+00 0.000000e+00
Te Hg Hg 1.204715e+00 2.135591e+00 1.892491e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.445180e+00 4.000000e+00 0.000000e+00 0.000000e+00
Te Hg S 1.450015e+00 2.297301e+00 1.726905e+00 2.962370e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.794685e-01 4.000000e+00 0.000000e+00 0.000000e+00
Te S Cd 1.385284e+00 2.352141e+00 1.810919e+00 3.325065e+01 1.200000e+00 -3.333333e-01 7.049600e+00 8.861252e-01 4.000000e+00 0.000000e+00 0.000000e+00
Te S Te 1.849775e+00 2.905254e+00 1.594353e+00 2.877465e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.307283e-01 4.000000e+00 0.000000e+00 0.000000e+00
Te S Zn 1.546239e+00 2.056363e+00 1.907922e+00 3.147250e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.255846e+00 4.000000e+00 0.000000e+00 0.000000e+00
Te S Se 1.295053e+00 2.231716e+00 1.809645e+00 3.438949e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.005396e+00 4.000000e+00 0.000000e+00 0.000000e+00
Te S Hg 1.204715e+00 2.135591e+00 1.892491e+00 3.565557e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.445180e+00 4.000000e+00 0.000000e+00 0.000000e+00
Te S S 1.450015e+00 2.297301e+00 1.726905e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.794685e-01 4.000000e+00 0.000000e+00 0.000000e+00
Zn Cd Cd 6.908179e-01 2.238699e+00 1.812616e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.010632e+00 4.000000e+00 0.000000e+00 0.000000e+00
Zn Cd Te 1.546239e+00 2.056363e+00 1.907922e+00 2.172335e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.255846e+00 4.000000e+00 0.000000e+00 0.000000e+00
Zn Cd Zn 1.392961e+00 2.367650e+00 1.525521e+00 2.288736e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.676279e-01 4.000000e+00 0.000000e+00 0.000000e+00
Zn Cd Se 1.691181e+00 2.028827e+00 1.836907e+00 2.077161e+01 1.200000e+00 -3.333333e-01 7.049600e+00 9.510930e-01 4.000000e+00 0.000000e+00 0.000000e+00
Zn Cd Hg 4.951616e-01 2.239186e+00 1.761363e+00 3.838766e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.461167e-01 4.000000e+00 0.000000e+00 0.000000e+00
Zn Cd S 2.208390e+00 2.323783e+00 1.589241e+00 1.817721e+01 1.200000e+00 -3.333333e-01 7.049600e+00 4.643181e-01 4.000000e+00 0.000000e+00 0.000000e+00
Zn Te Cd 6.908179e-01 2.238699e+00 1.812616e+00 4.862279e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.010632e+00 4.000000e+00 0.000000e+00 0.000000e+00
Zn Te Te 1.546239e+00 2.056363e+00 1.907922e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.255846e+00 4.000000e+00 0.000000e+00 0.000000e+00
Zn Te Zn 1.392961e+00 2.367650e+00 1.525521e+00 3.424146e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.676279e-01 4.000000e+00 0.000000e+00 0.000000e+00
Zn Te Se 1.691181e+00 2.028827e+00 1.836907e+00 3.107611e+01 1.200000e+00 -3.333333e-01 7.049600e+00 9.510930e-01 4.000000e+00 0.000000e+00 0.000000e+00
Zn Te Hg 4.951616e-01 2.239186e+00 1.761363e+00 5.743124e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.461167e-01 4.000000e+00 0.000000e+00 0.000000e+00
Zn Te S 2.208390e+00 2.323783e+00 1.589241e+00 2.719467e+01 1.200000e+00 -3.333333e-01 7.049600e+00 4.643181e-01 4.000000e+00 0.000000e+00 0.000000e+00
Zn Zn Cd 6.908179e-01 2.238699e+00 1.812616e+00 4.614993e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.010632e+00 4.000000e+00 0.000000e+00 0.000000e+00
Zn Zn Te 1.546239e+00 2.056363e+00 1.907922e+00 3.084711e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.255846e+00 4.000000e+00 0.000000e+00 0.000000e+00
Zn Zn Zn 1.392961e+00 2.367650e+00 1.525521e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.676279e-01 4.000000e+00 0.000000e+00 0.000000e+00
Zn Zn Se 1.691181e+00 2.028827e+00 1.836907e+00 2.949563e+01 1.200000e+00 -3.333333e-01 7.049600e+00 9.510930e-01 4.000000e+00 0.000000e+00 0.000000e+00
Zn Zn Hg 4.951616e-01 2.239186e+00 1.761363e+00 5.451040e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.461167e-01 4.000000e+00 0.000000e+00 0.000000e+00
Zn Zn S 2.208390e+00 2.323783e+00 1.589241e+00 2.581160e+01 1.200000e+00 -3.333333e-01 7.049600e+00 4.643181e-01 4.000000e+00 0.000000e+00 0.000000e+00
Zn Se Cd 6.908179e-01 2.238699e+00 1.812616e+00 5.085067e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.010632e+00 4.000000e+00 0.000000e+00 0.000000e+00
Zn Se Te 1.546239e+00 2.056363e+00 1.907922e+00 3.398914e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.255846e+00 4.000000e+00 0.000000e+00 0.000000e+00
Zn Se Zn 1.392961e+00 2.367650e+00 1.525521e+00 3.581039e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.676279e-01 4.000000e+00 0.000000e+00 0.000000e+00
Zn Se Se 1.691181e+00 2.028827e+00 1.836907e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 9.510930e-01 4.000000e+00 0.000000e+00 0.000000e+00
Zn Se Hg 4.951616e-01 2.239186e+00 1.761363e+00 6.006272e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.461167e-01 4.000000e+00 0.000000e+00 0.000000e+00
Zn Se S 2.208390e+00 2.323783e+00 1.589241e+00 2.844072e+01 1.200000e+00 -3.333333e-01 7.049600e+00 4.643181e-01 4.000000e+00 0.000000e+00 0.000000e+00
Zn Hg Cd 6.908179e-01 2.238699e+00 1.812616e+00 2.751535e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.010632e+00 4.000000e+00 0.000000e+00 0.000000e+00
Zn Hg Te 1.546239e+00 2.056363e+00 1.907922e+00 1.839156e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.255846e+00 4.000000e+00 0.000000e+00 0.000000e+00
Zn Hg Zn 1.392961e+00 2.367650e+00 1.525521e+00 1.937704e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.676279e-01 4.000000e+00 0.000000e+00 0.000000e+00
Zn Hg Se 1.691181e+00 2.028827e+00 1.836907e+00 1.758578e+01 1.200000e+00 -3.333333e-01 7.049600e+00 9.510930e-01 4.000000e+00 0.000000e+00 0.000000e+00
Zn Hg Hg 4.951616e-01 2.239186e+00 1.761363e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.461167e-01 4.000000e+00 0.000000e+00 0.000000e+00
Zn Hg S 2.208390e+00 2.323783e+00 1.589241e+00 1.538930e+01 1.200000e+00 -3.333333e-01 7.049600e+00 4.643181e-01 4.000000e+00 0.000000e+00 0.000000e+00
Zn S Cd 6.908179e-01 2.238699e+00 1.812616e+00 5.810847e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.010632e+00 4.000000e+00 0.000000e+00 0.000000e+00
Zn S Te 1.546239e+00 2.056363e+00 1.907922e+00 3.884033e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.255846e+00 4.000000e+00 0.000000e+00 0.000000e+00
Zn S Zn 1.392961e+00 2.367650e+00 1.525521e+00 4.092153e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.676279e-01 4.000000e+00 0.000000e+00 0.000000e+00
Zn S Se 1.691181e+00 2.028827e+00 1.836907e+00 3.713865e+01 1.200000e+00 -3.333333e-01 7.049600e+00 9.510930e-01 4.000000e+00 0.000000e+00 0.000000e+00
Zn S Hg 4.951616e-01 2.239186e+00 1.761363e+00 6.863534e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.461167e-01 4.000000e+00 0.000000e+00 0.000000e+00
Zn S S 2.208390e+00 2.323783e+00 1.589241e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 4.643181e-01 4.000000e+00 0.000000e+00 0.000000e+00
Se Cd Cd 1.352371e+00 2.045165e+00 1.953387e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.116149e+00 4.000000e+00 0.000000e+00 0.000000e+00
Se Cd Te 1.295053e+00 2.231716e+00 1.809645e+00 3.321142e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.005396e+00 4.000000e+00 0.000000e+00 0.000000e+00
Se Cd Zn 1.691181e+00 2.028827e+00 1.836907e+00 2.906271e+01 1.200000e+00 -3.333333e-01 7.049600e+00 9.510930e-01 4.000000e+00 0.000000e+00 0.000000e+00
Se Cd Se 2.400781e+00 2.789002e+00 1.544925e+00 2.439242e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.672131e-01 4.000000e+00 0.000000e+00 0.000000e+00
Se Cd Hg 1.299758e+00 2.113406e+00 1.831821e+00 3.315126e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.150200e+00 4.000000e+00 0.000000e+00 0.000000e+00
Se Cd S 1.307592e+00 2.229392e+00 1.747782e+00 3.305180e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.932325e-01 4.000000e+00 0.000000e+00 0.000000e+00
Se Te Cd 1.352371e+00 2.045165e+00 1.953387e+00 3.180382e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.116149e+00 4.000000e+00 0.000000e+00 0.000000e+00
Se Te Te 1.295053e+00 2.231716e+00 1.809645e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.005396e+00 4.000000e+00 0.000000e+00 0.000000e+00
Se Te Zn 1.691181e+00 2.028827e+00 1.836907e+00 2.844016e+01 1.200000e+00 -3.333333e-01 7.049600e+00 9.510930e-01 4.000000e+00 0.000000e+00 0.000000e+00
Se Te Se 2.400781e+00 2.789002e+00 1.544925e+00 2.386992e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.672131e-01 4.000000e+00 0.000000e+00 0.000000e+00
Se Te Hg 1.299758e+00 2.113406e+00 1.831821e+00 3.244113e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.150200e+00 4.000000e+00 0.000000e+00 0.000000e+00
Se Te S 1.307592e+00 2.229392e+00 1.747782e+00 3.234380e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.932325e-01 4.000000e+00 0.000000e+00 0.000000e+00
Se Zn Cd 1.352371e+00 2.045165e+00 1.953387e+00 3.634382e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.116149e+00 4.000000e+00 0.000000e+00 0.000000e+00
Se Zn Te 1.295053e+00 2.231716e+00 1.809645e+00 3.713938e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.005396e+00 4.000000e+00 0.000000e+00 0.000000e+00
Se Zn Zn 1.691181e+00 2.028827e+00 1.836907e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 9.510930e-01 4.000000e+00 0.000000e+00 0.000000e+00
Se Zn Se 2.400781e+00 2.789002e+00 1.544925e+00 2.727735e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.672131e-01 4.000000e+00 0.000000e+00 0.000000e+00
Se Zn Hg 1.299758e+00 2.113406e+00 1.831821e+00 3.707211e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.150200e+00 4.000000e+00 0.000000e+00 0.000000e+00
Se Zn S 1.307592e+00 2.229392e+00 1.747782e+00 3.696088e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.932325e-01 4.000000e+00 0.000000e+00 0.000000e+00
Se Se Cd 1.352371e+00 2.045165e+00 1.953387e+00 4.330238e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.116149e+00 4.000000e+00 0.000000e+00 0.000000e+00
Se Se Te 1.295053e+00 2.231716e+00 1.809645e+00 4.425026e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.005396e+00 4.000000e+00 0.000000e+00 0.000000e+00
Se Se Zn 1.691181e+00 2.028827e+00 1.836907e+00 3.872260e+01 1.200000e+00 -3.333333e-01 7.049600e+00 9.510930e-01 4.000000e+00 0.000000e+00 0.000000e+00
Se Se Se 2.400781e+00 2.789002e+00 1.544925e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.672131e-01 4.000000e+00 0.000000e+00 0.000000e+00
Se Se Hg 1.299758e+00 2.113406e+00 1.831821e+00 4.417011e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.150200e+00 4.000000e+00 0.000000e+00 0.000000e+00
Se Se S 1.307592e+00 2.229392e+00 1.747782e+00 4.403758e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.932325e-01 4.000000e+00 0.000000e+00 0.000000e+00
Se Hg Cd 1.352371e+00 2.045165e+00 1.953387e+00 3.186153e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.116149e+00 4.000000e+00 0.000000e+00 0.000000e+00
Se Hg Te 1.295053e+00 2.231716e+00 1.809645e+00 3.255898e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.005396e+00 4.000000e+00 0.000000e+00 0.000000e+00
Se Hg Zn 1.691181e+00 2.028827e+00 1.836907e+00 2.849177e+01 1.200000e+00 -3.333333e-01 7.049600e+00 9.510930e-01 4.000000e+00 0.000000e+00 0.000000e+00
Se Hg Se 2.400781e+00 2.789002e+00 1.544925e+00 2.391323e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.672131e-01 4.000000e+00 0.000000e+00 0.000000e+00
Se Hg Hg 1.299758e+00 2.113406e+00 1.831821e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.150200e+00 4.000000e+00 0.000000e+00 0.000000e+00
Se Hg S 1.307592e+00 2.229392e+00 1.747782e+00 3.240249e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.932325e-01 4.000000e+00 0.000000e+00 0.000000e+00
Se S Cd 1.352371e+00 2.045165e+00 1.953387e+00 3.195742e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.116149e+00 4.000000e+00 0.000000e+00 0.000000e+00
Se S Te 1.295053e+00 2.231716e+00 1.809645e+00 3.265696e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.005396e+00 4.000000e+00 0.000000e+00 0.000000e+00
Se S Zn 1.691181e+00 2.028827e+00 1.836907e+00 2.857751e+01 1.200000e+00 -3.333333e-01 7.049600e+00 9.510930e-01 4.000000e+00 0.000000e+00 0.000000e+00
Se S Se 2.400781e+00 2.789002e+00 1.544925e+00 2.398520e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.672131e-01 4.000000e+00 0.000000e+00 0.000000e+00
Se S Hg 1.299758e+00 2.113406e+00 1.831821e+00 3.259780e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.150200e+00 4.000000e+00 0.000000e+00 0.000000e+00
Se S S 1.307592e+00 2.229392e+00 1.747782e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.932325e-01 4.000000e+00 0.000000e+00 0.000000e+00
Hg Cd Cd 4.881231e-01 2.432694e+00 1.677987e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.250999e-01 4.000000e+00 0.000000e+00 0.000000e+00
Hg Cd Te 1.204715e+00 2.135591e+00 1.892491e+00 2.068740e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.445180e+00 4.000000e+00 0.000000e+00 0.000000e+00
Hg Cd Zn 4.951616e-01 2.239186e+00 1.761363e+00 3.226819e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.461167e-01 4.000000e+00 0.000000e+00 0.000000e+00
Hg Cd Se 1.299758e+00 2.113406e+00 1.831821e+00 1.991668e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.150200e+00 4.000000e+00 0.000000e+00 0.000000e+00
Hg Cd Hg 1.272807e+00 2.699097e+00 1.498503e+00 2.012643e+01 1.200000e+00 -3.333333e-01 7.917000e+00 1.211532e+00 4.000000e+00 0.000000e+00 0.000000e+00
Hg Cd S 1.531211e+00 2.025045e+00 1.833708e+00 1.834976e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.184541e+00 4.000000e+00 0.000000e+00 0.000000e+00
Hg Te Cd 4.881231e-01 2.432694e+00 1.677987e+00 5.105765e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.250999e-01 4.000000e+00 0.000000e+00 0.000000e+00
Hg Te Te 1.204715e+00 2.135591e+00 1.892491e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.445180e+00 4.000000e+00 0.000000e+00 0.000000e+00
Hg Te Zn 4.951616e-01 2.239186e+00 1.761363e+00 5.069347e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.461167e-01 4.000000e+00 0.000000e+00 0.000000e+00
Hg Te Se 1.299758e+00 2.113406e+00 1.831821e+00 3.128919e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.150200e+00 4.000000e+00 0.000000e+00 0.000000e+00
Hg Te Hg 1.272807e+00 2.699097e+00 1.498503e+00 3.161872e+01 1.200000e+00 -3.333333e-01 7.917000e+00 1.211532e+00 4.000000e+00 0.000000e+00 0.000000e+00
Hg Te S 1.531211e+00 2.025045e+00 1.833708e+00 2.882756e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.184541e+00 4.000000e+00 0.000000e+00 0.000000e+00
Hg Zn Cd 4.881231e-01 2.432694e+00 1.677987e+00 3.273348e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.250999e-01 4.000000e+00 0.000000e+00 0.000000e+00
Hg Zn Te 1.204715e+00 2.135591e+00 1.892491e+00 2.083602e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.445180e+00 4.000000e+00 0.000000e+00 0.000000e+00
Hg Zn Zn 4.951616e-01 2.239186e+00 1.761363e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.461167e-01 4.000000e+00 0.000000e+00 0.000000e+00
Hg Zn Se 1.299758e+00 2.113406e+00 1.831821e+00 2.005976e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.150200e+00 4.000000e+00 0.000000e+00 0.000000e+00
Hg Zn Hg 1.272807e+00 2.699097e+00 1.498503e+00 2.027102e+01 1.200000e+00 -3.333333e-01 7.917000e+00 1.211532e+00 4.000000e+00 0.000000e+00 0.000000e+00
Hg Zn S 1.531211e+00 2.025045e+00 1.833708e+00 1.848159e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.184541e+00 4.000000e+00 0.000000e+00 0.000000e+00
Hg Se Cd 4.881231e-01 2.432694e+00 1.677987e+00 5.303345e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.250999e-01 4.000000e+00 0.000000e+00 0.000000e+00
Hg Se Te 1.204715e+00 2.135591e+00 1.892491e+00 3.375766e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.445180e+00 4.000000e+00 0.000000e+00 0.000000e+00
Hg Se Zn 4.951616e-01 2.239186e+00 1.761363e+00 5.265518e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.461167e-01 4.000000e+00 0.000000e+00 0.000000e+00
Hg Se Se 1.299758e+00 2.113406e+00 1.831821e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.150200e+00 4.000000e+00 0.000000e+00 0.000000e+00
Hg Se Hg 1.272807e+00 2.699097e+00 1.498503e+00 3.284228e+01 1.200000e+00 -3.333333e-01 7.917000e+00 1.211532e+00 4.000000e+00 0.000000e+00 0.000000e+00
Hg Se S 1.531211e+00 2.025045e+00 1.833708e+00 2.994311e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.184541e+00 4.000000e+00 0.000000e+00 0.000000e+00
Hg Hg Cd 4.881231e-01 2.432694e+00 1.677987e+00 5.248074e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.250999e-01 4.000000e+00 0.000000e+00 0.000000e+00
Hg Hg Te 1.204715e+00 2.135591e+00 1.892491e+00 3.340584e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.445180e+00 4.000000e+00 0.000000e+00 0.000000e+00
Hg Hg Zn 4.951616e-01 2.239186e+00 1.761363e+00 5.210641e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.461167e-01 4.000000e+00 0.000000e+00 0.000000e+00
Hg Hg Se 1.299758e+00 2.113406e+00 1.831821e+00 3.216129e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.150200e+00 4.000000e+00 0.000000e+00 0.000000e+00
Hg Hg Hg 1.272807e+00 2.699097e+00 1.498503e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.917000e+00 1.211532e+00 4.000000e+00 0.000000e+00 0.000000e+00
Hg Hg S 1.531211e+00 2.025045e+00 1.833708e+00 2.963105e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.184541e+00 4.000000e+00 0.000000e+00 0.000000e+00
Hg S Cd 4.881231e-01 2.432694e+00 1.677987e+00 5.756205e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.250999e-01 4.000000e+00 0.000000e+00 0.000000e+00
Hg S Te 1.204715e+00 2.135591e+00 1.892491e+00 3.664028e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.445180e+00 4.000000e+00 0.000000e+00 0.000000e+00
Hg S Zn 4.951616e-01 2.239186e+00 1.761363e+00 5.715148e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.461167e-01 4.000000e+00 0.000000e+00 0.000000e+00
Hg S Se 1.299758e+00 2.113406e+00 1.831821e+00 3.527522e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.150200e+00 4.000000e+00 0.000000e+00 0.000000e+00
Hg S Hg 1.272807e+00 2.699097e+00 1.498503e+00 3.564673e+01 1.200000e+00 -3.333333e-01 7.917000e+00 1.211532e+00 4.000000e+00 0.000000e+00 0.000000e+00
Hg S S 1.531211e+00 2.025045e+00 1.833708e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.184541e+00 4.000000e+00 0.000000e+00 0.000000e+00
S Cd Cd 1.300376e+00 1.804151e+00 2.124568e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.540087e+00 4.000000e+00 0.000000e+00 0.000000e+00
S Cd Te 1.450015e+00 2.297301e+00 1.726905e+00 3.077737e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.794685e-01 4.000000e+00 0.000000e+00 0.000000e+00
S Cd Zn 2.208390e+00 2.323783e+00 1.589241e+00 2.493905e+01 1.200000e+00 -3.333333e-01 7.049600e+00 4.643181e-01 4.000000e+00 0.000000e+00 0.000000e+00
S Cd Se 1.307592e+00 2.229392e+00 1.747782e+00 3.241019e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.932325e-01 4.000000e+00 0.000000e+00 0.000000e+00
S Cd Hg 1.531211e+00 2.025045e+00 1.833708e+00 2.995023e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.184541e+00 4.000000e+00 0.000000e+00 0.000000e+00
S Cd S 2.434871e+00 2.423171e+00 1.711097e+00 2.375088e+01 1.200000e+00 -3.333333e-01 7.917000e+00 1.049688e+00 4.000000e+00 0.000000e+00 0.000000e+00
S Te Cd 1.300376e+00 1.804151e+00 2.124568e+00 3.431904e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.540087e+00 4.000000e+00 0.000000e+00 0.000000e+00
S Te Te 1.450015e+00 2.297301e+00 1.726905e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.794685e-01 4.000000e+00 0.000000e+00 0.000000e+00
S Te Zn 2.208390e+00 2.323783e+00 1.589241e+00 2.633490e+01 1.200000e+00 -3.333333e-01 7.049600e+00 4.643181e-01 4.000000e+00 0.000000e+00 0.000000e+00
S Te Se 1.307592e+00 2.229392e+00 1.747782e+00 3.422421e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.932325e-01 4.000000e+00 0.000000e+00 0.000000e+00
S Te Hg 1.531211e+00 2.025045e+00 1.833708e+00 3.162656e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.184541e+00 4.000000e+00 0.000000e+00 0.000000e+00
S Te S 2.434871e+00 2.423171e+00 1.711097e+00 2.508023e+01 1.200000e+00 -3.333333e-01 7.917000e+00 1.049688e+00 4.000000e+00 0.000000e+00 0.000000e+00
S Zn Cd 1.300376e+00 1.804151e+00 2.124568e+00 4.235326e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.540087e+00 4.000000e+00 0.000000e+00 0.000000e+00
S Zn Te 1.450015e+00 2.297301e+00 1.726905e+00 4.010837e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.794685e-01 4.000000e+00 0.000000e+00 0.000000e+00
S Zn Zn 2.208390e+00 2.323783e+00 1.589241e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 4.643181e-01 4.000000e+00 0.000000e+00 0.000000e+00
S Zn Se 1.307592e+00 2.229392e+00 1.747782e+00 4.223622e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.932325e-01 4.000000e+00 0.000000e+00 0.000000e+00
S Zn Hg 1.531211e+00 2.025045e+00 1.833708e+00 3.903046e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.184541e+00 4.000000e+00 0.000000e+00 0.000000e+00
S Zn S 2.434871e+00 2.423171e+00 1.711097e+00 3.095161e+01 1.200000e+00 -3.333333e-01 7.917000e+00 1.049688e+00 4.000000e+00 0.000000e+00 0.000000e+00
S Se Cd 1.300376e+00 1.804151e+00 2.124568e+00 3.259006e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.540087e+00 4.000000e+00 0.000000e+00 0.000000e+00
S Se Te 1.450015e+00 2.297301e+00 1.726905e+00 3.086266e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.794685e-01 4.000000e+00 0.000000e+00 0.000000e+00
S Se Zn 2.208390e+00 2.323783e+00 1.589241e+00 2.500815e+01 1.200000e+00 -3.333333e-01 7.049600e+00 4.643181e-01 4.000000e+00 0.000000e+00 0.000000e+00
S Se Se 1.307592e+00 2.229392e+00 1.747782e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.932325e-01 4.000000e+00 0.000000e+00 0.000000e+00
S Se Hg 1.531211e+00 2.025045e+00 1.833708e+00 3.003322e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.184541e+00 4.000000e+00 0.000000e+00 0.000000e+00
S Se S 2.434871e+00 2.423171e+00 1.711097e+00 2.381670e+01 1.200000e+00 -3.333333e-01 7.917000e+00 1.049688e+00 4.000000e+00 0.000000e+00 0.000000e+00
S Hg Cd 1.300376e+00 1.804151e+00 2.124568e+00 3.526684e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.540087e+00 4.000000e+00 0.000000e+00 0.000000e+00
S Hg Te 1.450015e+00 2.297301e+00 1.726905e+00 3.339756e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.794685e-01 4.000000e+00 0.000000e+00 0.000000e+00
S Hg Zn 2.208390e+00 2.323783e+00 1.589241e+00 2.706220e+01 1.200000e+00 -3.333333e-01 7.049600e+00 4.643181e-01 4.000000e+00 0.000000e+00 0.000000e+00
S Hg Se 1.307592e+00 2.229392e+00 1.747782e+00 3.516939e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.932325e-01 4.000000e+00 0.000000e+00 0.000000e+00
S Hg Hg 1.531211e+00 2.025045e+00 1.833708e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.184541e+00 4.000000e+00 0.000000e+00 0.000000e+00
S Hg S 2.434871e+00 2.423171e+00 1.711097e+00 2.577288e+01 1.200000e+00 -3.333333e-01 7.917000e+00 1.049688e+00 4.000000e+00 0.000000e+00 0.000000e+00
S S Cd 1.300376e+00 1.804151e+00 2.124568e+00 4.447203e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.540087e+00 4.000000e+00 0.000000e+00 0.000000e+00
S S Te 1.450015e+00 2.297301e+00 1.726905e+00 4.211484e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.794685e-01 4.000000e+00 0.000000e+00 0.000000e+00
S S Zn 2.208390e+00 2.323783e+00 1.589241e+00 3.412585e+01 1.200000e+00 -3.333333e-01 7.049600e+00 4.643181e-01 4.000000e+00 0.000000e+00 0.000000e+00
S S Se 1.307592e+00 2.229392e+00 1.747782e+00 4.434914e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.932325e-01 4.000000e+00 0.000000e+00 0.000000e+00
S S Hg 1.531211e+00 2.025045e+00 1.833708e+00 4.098300e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.184541e+00 4.000000e+00 0.000000e+00 0.000000e+00
S S S 2.434871e+00 2.423171e+00 1.711097e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.917000e+00 1.049688e+00 4.000000e+00 0.000000e+00 0.000000e+00

38
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# DATE: 2015-10-14 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Branicio, Rino, Gan and Tsuzuki, J. Phys Condensed Matter 21 (2009) 095002
#
# Vashishta potential file for InP, Branicio, Rino, Gan and Tsuzuki,
# J. Phys Condensed Matter 21 (2009) 095002
#
# These entries are in LAMMPS "metal" units:
# H = eV*Angstroms^eta; Zi, Zj = |e| (e = electronic charge);
# lambda1, lambda4, rc, r0, gamma = Angstroms;
# D = eV*Angstroms^4; W = eV*Angstroms^6; B = eV;
# other quantities are unitless
# element1 element2 element3
# H eta Zi Zj lambda1 D lambda4
# W rc B gamma r0 C cos(theta)
In In In 273.584 7 -1.21 -1.21 4.5 0.0 2.75
0.0 6.0 0.0 0.0 0.0 0.0 0.0
P P P 1813.06 7 1.21 1.21 4.5 52.7067 2.75
0.0 6.0 0.0 0.0 0.0 0.0 -0.333333333333
In P P 4847.09 9 1.21 -1.21 4.5 26.3533 2.75
270.105 6.0 4.34967 1.0 3.55 7.0 -0.333333333333
P In In 4847.09 9 1.21 -1.21 4.5 26.3533 2.75
270.105 6.0 4.34967 1.0 3.55 7.0 -0.333333333333
In In P 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0
In P In 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0
P In P 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0
P P In 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0

18
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# DATE: 2007-06-11 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Stillinger and Weber, Phys Rev B, 31, 5262, (1985)
# Stillinger-Weber parameters for various elements and mixtures
# multiple entries can be added to this file, LAMMPS reads the ones it needs
# these entries are in LAMMPS "metal" units:
# epsilon = eV; sigma = Angstroms
# other quantities are unitless
# format of a single entry (one or more lines):
# element 1, element 2, element 3,
# epsilon, sigma, a, lambda, gamma, costheta0, A, B, p, q, tol
# Here are the original parameters in metal units, for Silicon from:
#
# Stillinger and Weber, Phys. Rev. B, v. 31, p. 5262, (1985)
#
Si Si Si 2.1683 2.0951 1.80 21.0 1.20 -0.333333333333
7.049556277 0.6022245584 4.0 0.0 0.0

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# Simple regression tests for threebody potentials
# NOTE: These are not intended to represent real materials
units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
# temperature
variable t equal 1800.0
# cubic diamond unit cell
variable a equal 5.431
lattice custom $a &
a1 1.0 0.0 0.0 &
a2 0.0 1.0 0.0 &
a3 0.0 0.0 1.0 &
basis 0.0 0.0 0.0 &
basis 0.0 0.5 0.5 &
basis 0.5 0.0 0.5 &
basis 0.5 0.5 0.0 &
basis 0.25 0.25 0.25 &
basis 0.25 0.75 0.75 &
basis 0.75 0.25 0.75 &
basis 0.75 0.75 0.25
region myreg block 0 4 &
0 4 &
0 4
create_box 8 myreg
create_atoms 1 region myreg &
basis 1 1 &
basis 2 2 &
basis 3 3 &
basis 4 4 &
basis 5 5 &
basis 6 6 &
basis 7 7 &
basis 8 8
mass * 28.06
velocity all create $t 5287287 mom yes rot yes dist gaussian
# Equilibrate using Stillinger-Weber model for silicon
pair_style sw
pair_coeff * * Si.sw Si Si Si Si Si Si Si Si
thermo 10
fix 1 all nvt temp $t $t 0.1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
write_restart restart.equil
# Test Stillinger-Weber model for Cd/Te/Zn/Se/Hg/S
clear
read_restart restart.equil
pair_style sw
pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te
thermo 10
fix 1 all nvt temp $t $t 0.1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
# Test Vashishta model for In/P
clear
read_restart restart.equil
pair_style vashishta
pair_coeff * * InP.vashishta In In In In P P P P
thermo 10
fix 1 all nvt temp $t $t 0.1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100
# Test Tersoff model for B/N/C
clear
read_restart restart.equil
variable fac equal 0.6
change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap
pair_style tersoff
pair_coeff * * BNC.tersoff N N N C B B C B
thermo 10
fix 1 all nvt temp $t $t 0.1
fix_modify 1 energy yes
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100

8
potentials/CdTe.sw
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@ -18,9 +18,11 @@
# sqrt(lambda_ij*epsilon_ij*lambda_ik*epsilon_ik)/lambda_ik, and the
# results are directly entered in this table. Obviously, this
# conversion does not change the two-body parameters epsilon_ijj.
# All other ik pair parameters are entered on the i*k line, where *
# can be any species. This is consistent with the requirement of
# the ik parameter being on the ikk line.
# The twobody ik pair parameters are entered on the i*k lines, where *
# can be any species. This is consistent with the LAMMPS requirement
# that twobody ik parameters be defined on the ikk line. Entries on all
# the other i*k lines are ignored by LAMMPS
# These entries are in LAMMPS "metal" units: epsilon = eV;
# sigma = Angstroms; other quantities are unitless

14
potentials/CdTeZnSeHgS0.sw
View File

@ -1,9 +1,17 @@
### DATE: 2013-08-09 CONTRIBUTOR: X. W. Zhou, xzhou@sandia.gov, CITATION: Zhou, Ward, Martin, van Swol, Cruz-Campa, and D. Zubia, Phys. Rev. B, 88, 085309 (2013).
#
# Note that the way the parameters can be entered is not unique. As one way, we assume that eps_ijk is equal to eps_ik and lambda_ijk is equal to
# sqrt(lambda_ij*eps_ij*lambda_ik*eps_ik)/eps_ik, and all other parameters in the ijk line are for ik.
# Note that the way the parameters can be entered is not unique.
# As one way, we assume that eps_ijk is equal to eps_ik and
# lambda_ijk is equal to sqrt(lambda_ij*eps_ij*lambda_ik*eps_ik)/eps_ik,
# and all other parameters in the ijk line are for ik.
#
# The twobody ik pair parameters are entered on the i*k lines, where *
# can be any species. This is consistent with the LAMMPS requirement
# that twobody ik parameters be defined on the ikk line. Entries on all
# the other i*k lines are ignored by LAMMPS
#
# These entries are in LAMMPS "metal" units: epsilon = eV; sigma = Angstroms; other quantities are unitless;
# These entries are in LAMMPS "metal" units: epsilon = eV;
# sigma = Angstroms; other quantities are unitless
#
# cutoff distance = 4.632
# eps sigma a lambda gamma cos(theta) A B p q tol

74
src/KOKKOS/fix_qeq_reax_kokkos.cpp
View File

@ -37,7 +37,7 @@
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "pair_kokkos.h"
#include "pair_reax_c_kokkos.h"
using namespace LAMMPS_NS;
using namespace FixConst;
@ -62,6 +62,11 @@ FixQEqReaxKokkos<DeviceType>::FixQEqReaxKokkos(LAMMPS *lmp, int narg, char **arg
nmax = nmax = m_cap = 0;
allocated_flag = 0;
reaxc = (PairReaxC *) force->pair_match("reax/c/kk",1);
use_pair_list = 0;
if (reaxc->execution_space == this->execution_space)
use_pair_list = 1;
}
/* ---------------------------------------------------------------------- */
@ -80,29 +85,54 @@ void FixQEqReaxKokkos<DeviceType>::init()
atomKK->k_q.modify<LMPHostType>();
atomKK->k_q.sync<LMPDeviceType>();
FixQEqReax::init();
//FixQEqReax::init();
{
if (!atom->q_flag) error->all(FLERR,"Fix qeq/reax requires atom attribute q");
ngroup = group->count(igroup);
if (ngroup == 0) error->all(FLERR,"Fix qeq/reax group has no atoms");
// need a half neighbor list w/ Newton off and ghost neighbors
// built whenever re-neighboring occurs
if (!use_pair_list) {
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->newton = 2;
neighbor->requests[irequest]->ghost = 1;
}
init_shielding();
init_taper();
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
neighflag = lmp->kokkos->neighflag;
int irequest = neighbor->nrequest - 1;
neighbor->requests[irequest]->
kokkos_host = Kokkos::Impl::is_same<DeviceType,LMPHostType>::value &&
!Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
neighbor->requests[irequest]->
kokkos_device = Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
if (neighflag == FULL) {
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full_cluster = 0;
} else { //if (neighflag == HALF || neighflag == HALFTHREAD)
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 1;
neighbor->requests[irequest]->full_cluster = 0;
neighbor->requests[irequest]->ghost = 1;
if (!use_pair_list) {
int irequest = neighbor->nrequest - 1;
neighbor->requests[irequest]->
kokkos_host = Kokkos::Impl::is_same<DeviceType,LMPHostType>::value &&
!Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
neighbor->requests[irequest]->
kokkos_device = Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
if (neighflag == FULL) {
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full_cluster = 0;
} else { //if (neighflag == HALF || neighflag == HALFTHREAD)
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->full = 0;
neighbor->requests[irequest]->half = 1;
neighbor->requests[irequest]->full_cluster = 0;
neighbor->requests[irequest]->ghost = 1;
}
}
int ntypes = atom->ntypes;
@ -213,6 +243,8 @@ void FixQEqReaxKokkos<DeviceType>::pre_force(int vflag)
k_shield.template sync<DeviceType>();
k_tap.template sync<DeviceType>();
if (use_pair_list)
list = reaxc->list;
NeighListKokkos<DeviceType>* k_list = static_cast<NeighListKokkos<DeviceType>*>(list);
d_numneigh = k_list->d_numneigh;
d_neighbors = k_list->d_neighbors;

2
src/KOKKOS/fix_qeq_reax_kokkos.h
View File

@ -146,7 +146,7 @@ class FixQEqReaxKokkos : public FixQEqReax {
double memory_usage();
protected:
int inum;
int inum,use_pair_list;
int allocated_flag;
typedef Kokkos::DualView<int***,DeviceType> tdual_int_1d;

20
src/KOKKOS/fix_reaxc_species_kokkos.cpp
View File

@ -71,12 +71,6 @@ void FixReaxCSpeciesKokkos::init()
"pair_style reax/c/kk");
FixReaxCSpecies::init();
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->newton = 2;
neighbor->requests[irequest]->ghost = 1;
}
/* ---------------------------------------------------------------------- */
@ -86,12 +80,20 @@ void FixReaxCSpeciesKokkos::FindMolecule()
int i,j,ii,jj,inum,itype,jtype,loop,looptot;
int change,done,anychange;
int *mask = atom->mask;
int *ilist;
double bo_tmp,bo_cut;
double **spec_atom = f_SPECBOND->array_atom;
inum = list->inum;
ilist = list->ilist;
inum = reaxc->list->inum;
typename ArrayTypes<LMPHostType>::t_int_1d ilist;
if (reaxc->execution_space == Host) {
NeighListKokkos<LMPHostType>* k_list = static_cast<NeighListKokkos<LMPHostType>*>(reaxc->list);
k_list->k_ilist.sync<LMPHostType>();
ilist = k_list->k_ilist.h_view;
} else {
NeighListKokkos<LMPDeviceType>* k_list = static_cast<NeighListKokkos<LMPDeviceType>*>(reaxc->list);
k_list->k_ilist.sync<LMPHostType>();
ilist = k_list->k_ilist.h_view;
}
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];

2
src/KOKKOS/fix_wall_reflect_kokkos.h
View File

@ -41,8 +41,6 @@ class FixWallReflectKokkos : public FixWallReflect {
void operator()(TagFixWallReflectPostIntegrate, const int&) const;
protected:
class AtomKokkos *atomKK;
typename AT::t_x_array x;
typename AT::t_v_array v;
typename AT::t_int_1d_randomread mask;

1
src/KOKKOS/neigh_full_kokkos.h
View File

@ -164,6 +164,7 @@ if (GHOST) {
list->gnum = 0;
}
list->k_ilist.template modify<DeviceType>();
}
/* ---------------------------------------------------------------------- */

5
src/KOKKOS/neigh_list_kokkos.cpp
View File

@ -49,8 +49,9 @@ void NeighListKokkos<Device>::grow(int nmax)
if (nmax <= maxatoms) return;
maxatoms = nmax;
d_ilist =
typename ArrayTypes<Device>::t_int_1d("neighlist:ilist",maxatoms);
k_ilist =
DAT::tdual_int_1d("neighlist:ilist",maxatoms);
d_ilist = k_ilist.view<Device>();
d_numneigh =
typename ArrayTypes<Device>::t_int_1d("neighlist:numneigh",maxatoms);
d_neighbors =

3
src/KOKKOS/neigh_list_kokkos.h
View File

@ -71,7 +71,8 @@ public:
void clean_copy();
void grow(int nmax);
typename ArrayTypes<Device>::t_neighbors_2d d_neighbors;
typename ArrayTypes<Device>::t_int_1d d_ilist; // local indices of I atoms
typename DAT::tdual_int_1d k_ilist; // local indices of I atoms
typename ArrayTypes<Device>::t_int_1d d_ilist;
typename ArrayTypes<Device>::t_int_1d d_numneigh; // # of J neighs for each I
typename ArrayTypes<Device>::t_int_1d d_stencil; // # of J neighs for each I
typename ArrayTypes<LMPHostType>::t_int_1d h_stencil; // # of J neighs per I

2
src/KOKKOS/pair_reax_c_kokkos.h
View File

@ -426,8 +426,6 @@ class PairReaxCKokkos : public PairReaxC {
typename AT::t_ffloat_2d_dl d_sum_ovun;
typename AT::t_ffloat_2d_dl d_dBOpx, d_dBOpy, d_dBOpz;
class AtomKokkos *atomKK;
int neighflag,newton_pair, maxnumneigh, maxhb, maxbo;
int nlocal,nall,eflag,vflag;
F_FLOAT cut_nbsq, cut_hbsq, cut_bosq, bo_cut, thb_cut, thb_cutsq;

68
src/KOKKOS/pair_sw_kokkos.cpp
View File

@ -121,6 +121,18 @@ void PairSWKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
EV_FLOAT ev;
EV_FLOAT ev_all;
// build short neighbor list
int max_neighs = d_neighbors.dimension_1();
if ((d_neighbors_short.dimension_1() != max_neighs) ||
(d_neighbors_short.dimension_0() != ignum)) {
d_neighbors_short = Kokkos::View<int**,DeviceType>("SW::neighbors_short",ignum,max_neighs);
}
if (d_numneigh_short.dimension_0()!=ignum)
d_numneigh_short = Kokkos::View<int*,DeviceType>("SW::numneighs_short",ignum);
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagPairSWComputeShortNeigh>(0,neighflag==FULL?ignum:inum), *this);
// loop over neighbor list of my atoms
if (neighflag == HALF) {
@ -174,6 +186,38 @@ void PairSWKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
copymode = 0;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairSWKokkos<DeviceType>::operator()(TagPairSWComputeShortNeigh, const int& ii) const {
const int i = d_ilist[ii];
const X_FLOAT xtmp = x(i,0);
const X_FLOAT ytmp = x(i,1);
const X_FLOAT ztmp = x(i,2);
const int jnum = d_numneigh[i];
int inside = 0;
for (int jj = 0; jj < jnum; jj++) {
int j = d_neighbors(i,jj);
j &= NEIGHMASK;
const X_FLOAT delx = xtmp - x(j,0);
const X_FLOAT dely = ytmp - x(j,1);
const X_FLOAT delz = ztmp - x(j,2);
const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutmax*cutmax) {
d_neighbors_short(i,inside) = j;
inside++;
}
}
d_numneigh_short(i) = inside;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
template<int NEIGHFLAG, int EVFLAG>
KOKKOS_INLINE_FUNCTION
@ -196,14 +240,14 @@ void PairSWKokkos<DeviceType>::operator()(TagPairSWComputeHalf<NEIGHFLAG,EVFLAG>
// two-body interactions, skip half of them
const int jnum = d_numneigh[i];
const int jnum = d_numneigh_short[i];
F_FLOAT fxtmpi = 0.0;
F_FLOAT fytmpi = 0.0;
F_FLOAT fztmpi = 0.0;
for (int jj = 0; jj < jnum; jj++) {
int j = d_neighbors(i,jj);
int j = d_neighbors_short(i,jj);
j &= NEIGHMASK;
const tagint jtag = tag[j];
@ -245,7 +289,7 @@ void PairSWKokkos<DeviceType>::operator()(TagPairSWComputeHalf<NEIGHFLAG,EVFLAG>
const int jnumm1 = jnum - 1;
for (int jj = 0; jj < jnumm1; jj++) {
int j = d_neighbors(i,jj);
int j = d_neighbors_short(i,jj);
j &= NEIGHMASK;
const int jtype = d_map[type[j]];
const int ijparam = d_elem2param(itype,jtype,jtype);
@ -260,7 +304,7 @@ void PairSWKokkos<DeviceType>::operator()(TagPairSWComputeHalf<NEIGHFLAG,EVFLAG>
F_FLOAT fztmpj = 0.0;
for (int kk = jj+1; kk < jnum; kk++) {
int k = d_neighbors(i,kk);
int k = d_neighbors_short(i,kk);
k &= NEIGHMASK;
const int ktype = d_map[type[k]];
const int ikparam = d_elem2param(itype,ktype,ktype);
@ -331,14 +375,14 @@ void PairSWKokkos<DeviceType>::operator()(TagPairSWComputeFullA<NEIGHFLAG,EVFLAG
// two-body interactions
const int jnum = d_numneigh[i];
const int jnum = d_numneigh_short[i];
F_FLOAT fxtmpi = 0.0;
F_FLOAT fytmpi = 0.0;
F_FLOAT fztmpi = 0.0;
for (int jj = 0; jj < jnum; jj++) {
int j = d_neighbors(i,jj);
int j = d_neighbors_short(i,jj);
j &= NEIGHMASK;
const tagint jtag = tag[j];
@ -368,7 +412,7 @@ void PairSWKokkos<DeviceType>::operator()(TagPairSWComputeFullA<NEIGHFLAG,EVFLAG
const int jnumm1 = jnum - 1;
for (int jj = 0; jj < jnumm1; jj++) {
int j = d_neighbors(i,jj);
int j = d_neighbors_short(i,jj);
j &= NEIGHMASK;
const int jtype = d_map[type[j]];
const int ijparam = d_elem2param(itype,jtype,jtype);
@ -380,7 +424,7 @@ void PairSWKokkos<DeviceType>::operator()(TagPairSWComputeFullA<NEIGHFLAG,EVFLAG
if (rsq1 >= d_params[ijparam].cutsq) continue;
for (int kk = jj+1; kk < jnum; kk++) {
int k = d_neighbors(i,kk);
int k = d_neighbors_short(i,kk);
k &= NEIGHMASK;
const int ktype = d_map[type[k]];
const int ikparam = d_elem2param(itype,ktype,ktype);
@ -438,14 +482,14 @@ void PairSWKokkos<DeviceType>::operator()(TagPairSWComputeFullB<NEIGHFLAG,EVFLAG
const X_FLOAT ytmpi = x(i,1);
const X_FLOAT ztmpi = x(i,2);
const int jnum = d_numneigh[i];
const int jnum = d_numneigh_short[i];
F_FLOAT fxtmpi = 0.0;
F_FLOAT fytmpi = 0.0;
F_FLOAT fztmpi = 0.0;
for (int jj = 0; jj < jnum; jj++) {
int j = d_neighbors(i,jj);
int j = d_neighbors_short(i,jj);
j &= NEIGHMASK;
if (j >= nlocal) continue;
const int jtype = d_map[type[j]];
@ -461,10 +505,10 @@ void PairSWKokkos<DeviceType>::operator()(TagPairSWComputeFullB<NEIGHFLAG,EVFLAG
if (rsq1 >= d_params[jiparam].cutsq) continue;
const int j_jnum = d_numneigh[j];
const int j_jnum = d_numneigh_short[j];
for (int kk = 0; kk < j_jnum; kk++) {
int k = d_neighbors(j,kk);
int k = d_neighbors_short(j,kk);
k &= NEIGHMASK;
if (k == i) continue;
const int ktype = d_map[type[k]];

8
src/KOKKOS/pair_sw_kokkos.h
View File

@ -34,6 +34,8 @@ struct TagPairSWComputeFullA{};
template<int NEIGHFLAG, int EVFLAG>
struct TagPairSWComputeFullB{};
struct TagPairSWComputeShortNeigh{};
namespace LAMMPS_NS {
template<class DeviceType>
@ -75,6 +77,9 @@ class PairSWKokkos : public PairSW {
KOKKOS_INLINE_FUNCTION
void operator()(TagPairSWComputeFullB<NEIGHFLAG,EVFLAG>, const int&) const;
KOKKOS_INLINE_FUNCTION
void operator()(TagPairSWComputeShortNeigh, const int&) const;
template<int NEIGHFLAG>
KOKKOS_INLINE_FUNCTION
void ev_tally(EV_FLOAT &ev, const int &i, const int &j,
@ -136,6 +141,9 @@ class PairSWKokkos : public PairSW {
int nlocal,nall,eflag,vflag;
int inum;
Kokkos::View<int**,DeviceType> d_neighbors_short;
Kokkos::View<int*,DeviceType> d_numneigh_short;
friend void pair_virial_fdotr_compute<PairSWKokkos>(PairSWKokkos*);
};

268
src/KOKKOS/pair_tersoff_kokkos.cpp
View File

@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Ray Shan (SNL)
Contributing author: Ray Shan (SNL) and Christian Trott (SNL)
------------------------------------------------------------------------- */
#include <math.h>
@ -191,7 +191,7 @@ void PairTersoffKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
nall = atom->nlocal + atom->nghost;
newton_pair = force->newton_pair;
const int inum = list->inum;
inum = list->inum;
const int ignum = inum + list->gnum;
NeighListKokkos<DeviceType>* k_list = static_cast<NeighListKokkos<DeviceType>*>(list);
d_numneigh = k_list->d_numneigh;
@ -204,6 +204,18 @@ void PairTersoffKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
EV_FLOAT ev;
EV_FLOAT ev_all;
// build short neighbor list
int max_neighs = d_neighbors.dimension_1();
if ((d_neighbors_short.dimension_1() != max_neighs) ||
(d_neighbors_short.dimension_0() != ignum)) {
d_neighbors_short = Kokkos::View<int**,DeviceType>("Tersoff::neighbors_short",ignum,max_neighs);
}
if (d_numneigh_short.dimension_0()!=ignum)
d_numneigh_short = Kokkos::View<int*,DeviceType>("Tersoff::numneighs_short",ignum);
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagPairTersoffComputeShortNeigh>(0,neighflag==FULL?ignum:inum), *this);
if (neighflag == HALF) {
if (evflag)
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairTersoffComputeHalf<HALF,1> >(0,inum),*this,ev);
@ -257,6 +269,35 @@ void PairTersoffKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeShortNeigh, const int& ii) const {
const int i = d_ilist[ii];
const X_FLOAT xtmp = x(i,0);
const X_FLOAT ytmp = x(i,1);
const X_FLOAT ztmp = x(i,2);
const int jnum = d_numneigh[i];
int inside = 0;
for (int jj = 0; jj < jnum; jj++) {
int j = d_neighbors(i,jj);
j &= NEIGHMASK;
const X_FLOAT delx = xtmp - x(j,0);
const X_FLOAT dely = ytmp - x(j,1);
const X_FLOAT delz = ztmp - x(j,2);
const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutmax*cutmax) {
d_neighbors_short(i,inside) = j;
inside++;
}
}
d_numneigh_short(i) = inside;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
template<int NEIGHFLAG, int EVFLAG>
KOKKOS_INLINE_FUNCTION
@ -273,21 +314,22 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeHalf<NEIGHFL
const int itype = type(i);
const int itag = tag(i);
int j,k,jj,kk,jtag,jtype,ktype;
F_FLOAT rsq1, cutsq1, rsq2, cutsq2, rij, rik, bo_ij;
F_FLOAT fi[3], fj[3], fk[3];
X_FLOAT delx1, dely1, delz1, delx2, dely2, delz2;
//const AtomNeighborsConst d_neighbors_i = k_list.get_neighbors_const(i);
const int jnum = d_numneigh[i];
const int jnum = d_numneigh_short[i];
// repulsive
for (jj = 0; jj < jnum; jj++) {
j = d_neighbors(i,jj);
F_FLOAT f_x = 0.0;
F_FLOAT f_y = 0.0;
F_FLOAT f_z = 0.0;
for (int jj = 0; jj < jnum; jj++) {
int j = d_neighbors_short(i,jj);
j &= NEIGHMASK;
jtype = type(j);
jtag = tag(j);
const int jtype = type(j);
const int jtag = tag(j);
if (itag > jtag) {
if ((itag+jtag) % 2 == 0) continue;
@ -315,9 +357,9 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeHalf<NEIGHFL
(tmp_fcd - tmp_fce*paramskk(itype,jtype,jtype).lam1) / r;
const F_FLOAT eng = tmp_fce * paramskk(itype,jtype,jtype).biga * tmp_exp;
a_f(i,0) += delx*frep;
a_f(i,1) += dely*frep;
a_f(i,2) += delz*frep;
f_x += delx*frep;
f_y += dely*frep;
f_z += delz*frep;
a_f(j,0) -= delx*frep;
a_f(j,1) -= dely*frep;
a_f(j,2) -= delz*frep;
@ -330,35 +372,35 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeHalf<NEIGHFL
// attractive: bond order
for (jj = 0; jj < jnum; jj++) {
j = d_neighbors(i,jj);
for (int jj = 0; jj < jnum; jj++) {
int j = d_neighbors_short(i,jj);
j &= NEIGHMASK;
jtype = type(j);
const int jtype = type(j);
delx1 = xtmp - x(j,0);
dely1 = ytmp - x(j,1);
delz1 = ztmp - x(j,2);
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
cutsq1 = paramskk(itype,jtype,jtype).cutsq;
const F_FLOAT delx1 = xtmp - x(j,0);
const F_FLOAT dely1 = ytmp - x(j,1);
const F_FLOAT delz1 = ztmp - x(j,2);
const F_FLOAT rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
const F_FLOAT cutsq1 = paramskk(itype,jtype,jtype).cutsq;
bo_ij = 0.0;
F_FLOAT bo_ij = 0.0;
if (rsq1 > cutsq1) continue;
rij = sqrt(rsq1);
const F_FLOAT rij = sqrt(rsq1);
for (kk = 0; kk < jnum; kk++) {
for (int kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = d_neighbors(i,kk);
int k = d_neighbors_short(i,kk);
k &= NEIGHMASK;
ktype = type(k);
const int ktype = type(k);
delx2 = xtmp - x(k,0);
dely2 = ytmp - x(k,1);
delz2 = ztmp - x(k,2);
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
cutsq2 = paramskk(itype,jtype,ktype).cutsq;
const F_FLOAT delx2 = xtmp - x(k,0);
const F_FLOAT dely2 = ytmp - x(k,1);
const F_FLOAT delz2 = ztmp - x(k,2);
const F_FLOAT rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
const F_FLOAT cutsq2 = paramskk(itype,jtype,ktype).cutsq;
if (rsq2 > cutsq2) continue;
rik = sqrt(rsq2);
const F_FLOAT rik = sqrt(rsq2);
bo_ij += bondorder(itype,jtype,ktype,rij,delx1,dely1,delz1,rik,delx2,dely2,delz2);
}
@ -369,58 +411,64 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeHalf<NEIGHFL
const F_FLOAT bij = ters_bij_k(itype,jtype,jtype,bo_ij);
const F_FLOAT fatt = -0.5*bij * dfa / rij;
const F_FLOAT prefactor = 0.5*fa * ters_dbij(itype,jtype,jtype,bo_ij);
const F_FLOAT eng = 0.5*bij * fa;
a_f(i,0) += delx1*fatt;
a_f(i,1) += dely1*fatt;
a_f(i,2) += delz1*fatt;
a_f(j,0) -= delx1*fatt;
a_f(j,1) -= dely1*fatt;
a_f(j,2) -= delz1*fatt;
f_x += delx1*fatt;
f_y += dely1*fatt;
f_z += delz1*fatt;
F_FLOAT fj_x = -delx1*fatt;
F_FLOAT fj_y = -dely1*fatt;
F_FLOAT fj_z = -delz1*fatt;
if (EVFLAG) {
const F_FLOAT eng = 0.5*bij * fa;
if (eflag) ev.evdwl += eng;
if (vflag_either || eflag_atom)
this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,fatt,delx1,dely1,delz1);
this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,fatt,delx1,dely1,delz1);
}
// attractive: three-body force
for (kk = 0; kk < jnum; kk++) {
for (int kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = d_neighbors(i,kk);
int k = d_neighbors_short(i,kk);
k &= NEIGHMASK;
ktype = type(k);
const int ktype = type(k);
delx2 = xtmp - x(k,0);
dely2 = ytmp - x(k,1);
delz2 = ztmp - x(k,2);
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
cutsq2 = paramskk(itype,jtype,ktype).cutsq;
const F_FLOAT delx2 = xtmp - x(k,0);
const F_FLOAT dely2 = ytmp - x(k,1);
const F_FLOAT delz2 = ztmp - x(k,2);
const F_FLOAT rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
const F_FLOAT cutsq2 = paramskk(itype,jtype,ktype).cutsq;
if (rsq2 > cutsq2) continue;
rik = sqrt(rsq2);
const F_FLOAT rik = sqrt(rsq2);
ters_dthb(itype,jtype,ktype,prefactor,rij,delx1,dely1,delz1,
rik,delx2,dely2,delz2,fi,fj,fk);
rik,delx2,dely2,delz2,fi,fj,fk);
a_f(i,0) += fi[0];
a_f(i,1) += fi[1];
a_f(i,2) += fi[2];
a_f(j,0) += fj[0];
a_f(j,1) += fj[1];
a_f(j,2) += fj[2];
f_x += fi[0];
f_y += fi[1];
f_z += fi[2];
fj_x += fj[0];
fj_y += fj[1];
fj_z += fj[2];
a_f(k,0) += fk[0];
a_f(k,1) += fk[1];
a_f(k,2) += fk[2];
if (vflag_atom) {
F_FLOAT delrij[3], delrik[3];
delrij[0] = -delx1; delrij[1] = -dely1; delrij[2] = -delz1;
delrik[0] = -delx2; delrik[1] = -dely2; delrik[2] = -delz2;
if (vflag_either) this->template v_tally3<NEIGHFLAG>(ev,i,j,k,fj,fk,delrij,delrik);
F_FLOAT delrij[3], delrik[3];
delrij[0] = -delx1; delrij[1] = -dely1; delrij[2] = -delz1;
delrik[0] = -delx2; delrik[1] = -dely2; delrik[2] = -delz2;
if (vflag_either) this->template v_tally3<NEIGHFLAG>(ev,i,j,k,fj,fk,delrij,delrik);
}
}
a_f(j,0) += fj_x;
a_f(j,1) += fj_y;
a_f(j,2) += fj_z;
}
a_f(i,0) += f_x;
a_f(i,1) += f_y;
a_f(i,2) += f_z;
}
template<class DeviceType>
@ -450,12 +498,15 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeFullA<NEIGHF
X_FLOAT delx1, dely1, delz1, delx2, dely2, delz2;
//const AtomNeighborsConst d_neighbors_i = k_list.get_neighbors_const(i);
const int jnum = d_numneigh[i];
const int jnum = d_numneigh_short[i];
// repulsive
F_FLOAT f_x = 0.0;
F_FLOAT f_y = 0.0;
F_FLOAT f_z = 0.0;
for (jj = 0; jj < jnum; jj++) {
j = d_neighbors(i,jj);
j = d_neighbors_short(i,jj);
j &= NEIGHMASK;
const int jtype = type(j);
@ -475,9 +526,9 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeFullA<NEIGHF
(tmp_fcd - tmp_fce*paramskk(itype,jtype,jtype).lam1) / r;
const F_FLOAT eng = tmp_fce * paramskk(itype,jtype,jtype).biga * tmp_exp;
f(i,0) += delx*frep;
f(i,1) += dely*frep;
f(i,2) += delz*frep;
f_x += delx*frep;
f_y += dely*frep;
f_z += delz*frep;
if (EVFLAG) {
if (eflag)
@ -490,7 +541,7 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeFullA<NEIGHF
// attractive: bond order
for (jj = 0; jj < jnum; jj++) {
j = d_neighbors(i,jj);
j = d_neighbors_short(i,jj);
j &= NEIGHMASK;
jtype = type(j);
@ -506,7 +557,7 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeFullA<NEIGHF
for (kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = d_neighbors(i,kk);
k = d_neighbors_short(i,kk);
k &= NEIGHMASK;
ktype = type(k);
@ -530,9 +581,9 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeFullA<NEIGHF
const F_FLOAT prefactor = 0.5*fa * ters_dbij(itype,jtype,jtype,bo_ij);
const F_FLOAT eng = 0.5*bij * fa;
f(i,0) += delx1*fatt;
f(i,1) += dely1*fatt;
f(i,2) += delz1*fatt;
f_x += delx1*fatt;
f_y += dely1*fatt;
f_z += delz1*fatt;
if (EVFLAG) {
if (eflag) ev.evdwl += 0.5*eng;
@ -544,7 +595,7 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeFullA<NEIGHF
for (kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = d_neighbors(i,kk);
k = d_neighbors_short(i,kk);
k &= NEIGHMASK;
ktype = type(k);
@ -559,9 +610,9 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeFullA<NEIGHF
ters_dthb(itype,jtype,ktype,prefactor,rij,delx1,dely1,delz1,
rik,delx2,dely2,delz2,fi,fj,fk);
f(i,0) += fi[0];
f(i,1) += fi[1];
f(i,2) += fi[2];
f_x += fi[0];
f_y += fi[1];
f_z += fi[2];
if (vflag_atom) {
F_FLOAT delrij[3], delrik[3];
@ -571,6 +622,9 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeFullA<NEIGHF
}
}
}
f(i,0) += f_x;
f(i,1) += f_y;
f(i,2) += f_z;
}
template<class DeviceType>
@ -599,12 +653,16 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeFullB<NEIGHF
F_FLOAT fj[3], fk[3];
X_FLOAT delx1, dely1, delz1, delx2, dely2, delz2;
const int jnum = d_numneigh[i];
const int jnum = d_numneigh_short[i];
F_FLOAT f_x = 0.0;
F_FLOAT f_y = 0.0;
F_FLOAT f_z = 0.0;
// attractive: bond order
for (jj = 0; jj < jnum; jj++) {
j = d_neighbors(i,jj);
j = d_neighbors_short(i,jj);
j &= NEIGHMASK;
if (j >= nlocal) continue;
jtype = type(j);
@ -619,10 +677,10 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeFullB<NEIGHF
if (rsq1 > cutsq1) continue;
rij = sqrt(rsq1);
j_jnum = d_numneigh[j];
j_jnum = d_numneigh_short[j];
for (kk = 0; kk < j_jnum; kk++) {
k = d_neighbors(j,kk);
k = d_neighbors_short(j,kk);
if (k == i) continue;
k &= NEIGHMASK;
ktype = type(k);
@ -648,9 +706,9 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeFullB<NEIGHF
const F_FLOAT prefactor = 0.5*fa * ters_dbij(jtype,itype,itype,bo_ij);
const F_FLOAT eng = 0.5*bij * fa;
f(i,0) -= delx1*fatt;
f(i,1) -= dely1*fatt;
f(i,2) -= delz1*fatt;
f_x -= delx1*fatt;
f_y -= dely1*fatt;
f_z -= delz1*fatt;
if (EVFLAG) {
if (eflag)
@ -662,7 +720,7 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeFullB<NEIGHF
// attractive: three-body force
for (kk = 0; kk < j_jnum; kk++) {
k = d_neighbors(j,kk);
k = d_neighbors_short(j,kk);
if (k == i) continue;
k &= NEIGHMASK;
ktype = type(k);
@ -677,9 +735,9 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeFullB<NEIGHF
rik = sqrt(rsq2);
ters_dthbj(jtype,itype,ktype,prefactor,rij,delx1,dely1,delz1,
rik,delx2,dely2,delz2,fj,fk);
f(i,0) += fj[0];
f(i,1) += fj[1];
f(i,2) += fj[2];
f_x += fj[0];
f_y += fj[1];
f_z += fj[2];
if (vflag_atom) {
F_FLOAT delrji[3], delrjk[3];
@ -692,11 +750,14 @@ void PairTersoffKokkos<DeviceType>::operator()(TagPairTersoffComputeFullB<NEIGHF
const F_FLOAT prefactor_jk = 0.5*fa_jk * ters_dbij(jtype,ktype,itype,bo_ij);
ters_dthbk(jtype,ktype,itype,prefactor_jk,rik,delx2,dely2,delz2,
rij,delx1,dely1,delz1,fk);
f(i,0) += fk[0];
f(i,1) += fk[1];
f(i,2) += fk[2];
f_x += fk[0];
f_y += fk[1];
f_z += fk[2];
}
}
f(i,0) += f_x;
f(i,1) += f_y;
f(i,2) += f_z;
}
template<class DeviceType>
@ -749,8 +810,9 @@ double PairTersoffKokkos<DeviceType>::bondorder(const int &i, const int &j, cons
const F_FLOAT costheta = (dx1*dx2 + dy1*dy2 + dz1*dz2)/(rij*rik);
if (int(paramskk(i,j,k).powerm) == 3) arg = pow(paramskk(i,j,k).lam3 * (rij-rik),3.0);
else arg = paramskk(i,j,k).lam3 * (rij-rik);
const F_FLOAT param = paramskk(i,j,k).lam3 * (rij-rik);
if (int(paramskk(i,j,k).powerm) == 3) arg = param*param*param;//pow(paramskk(i,j,k).lam3 * (rij-rik),3.0);
else arg = param;
if (arg > 69.0776) ex_delr = 1.e30;
else if (arg < -69.0776) ex_delr = 0.0;
@ -780,7 +842,6 @@ KOKKOS_INLINE_FUNCTION
double PairTersoffKokkos<DeviceType>::
ters_dgijk(const int &i, const int &j, const int &k, const F_FLOAT &cos) const
{
const F_FLOAT ters_c = paramskk(i,j,k).c * paramskk(i,j,k).c;
const F_FLOAT ters_d = paramskk(i,j,k).d * paramskk(i,j,k).d;
const F_FLOAT hcth = paramskk(i,j,k).h - cos;
@ -838,9 +899,9 @@ double PairTersoffKokkos<DeviceType>::ters_dbij(const int &i, const int &j,
const int &k, const F_FLOAT &bo) const
{
const F_FLOAT tmp = paramskk(i,j,k).beta * bo;
if (tmp > paramskk(i,j,k).c1) return paramskk(i,j,k).beta * -0.5*pow(tmp,-1.5);
if (tmp > paramskk(i,j,k).c1) return paramskk(i,j,k).beta * -0.5/sqrt(tmp*tmp);//*pow(tmp,-1.5);
if (tmp > paramskk(i,j,k).c2)
return paramskk(i,j,k).beta * (-0.5*pow(tmp,-1.5) *
return paramskk(i,j,k).beta * (-0.5/sqrt(tmp*tmp) * //*pow(tmp,-1.5) *
(1.0 - 0.5*(1.0 + 1.0/(2.0*paramskk(i,j,k).powern)) *
pow(tmp,-paramskk(i,j,k).powern)));
if (tmp < paramskk(i,j,k).c4) return 0.0;
@ -883,15 +944,16 @@ void PairTersoffKokkos<DeviceType>::ters_dthb(
fc = ters_fc_k(i,j,k,rik);
dfc = ters_dfc(i,j,k,rik);
if (int(paramskk(i,j,k).powerm) == 3) tmp = pow(paramskk(i,j,k).lam3 * (rij-rik),3.0);
else tmp = paramskk(i,j,k).lam3 * (rij-rik);
const F_FLOAT param = paramskk(i,j,k).lam3 * (rij-rik);
if (int(paramskk(i,j,k).powerm) == 3) tmp = param*param*param;//pow(paramskk(i,j,k).lam3 * (rij-rik),3.0);
else tmp = param;
if (tmp > 69.0776) ex_delr = 1.e30;
else if (tmp < -69.0776) ex_delr = 0.0;
else ex_delr = exp(tmp);
if (int(paramskk(i,j,k).powerm) == 3)
dex_delr = 3.0*pow(paramskk(i,j,k).lam3,3.0) * pow(rij-rik,2.0)*ex_delr;
dex_delr = 3.0*param*param*paramskk(i,j,k).lam3*ex_delr;//pow(rij-rik,2.0)*ex_delr;
else dex_delr = paramskk(i,j,k).lam3 * ex_delr;
cos = vec3_dot(rij_hat,rik_hat);
@ -951,15 +1013,16 @@ void PairTersoffKokkos<DeviceType>::ters_dthbj(
fc = ters_fc_k(i,j,k,rik);
dfc = ters_dfc(i,j,k,rik);
if (int(paramskk(i,j,k).powerm) == 3) tmp = pow(paramskk(i,j,k).lam3 * (rij-rik),3.0);
else tmp = paramskk(i,j,k).lam3 * (rij-rik);
const F_FLOAT param = paramskk(i,j,k).lam3 * (rij-rik);
if (int(paramskk(i,j,k).powerm) == 3) tmp = param*param*param;//pow(paramskk(i,j,k).lam3 * (rij-rik),3.0);
else tmp = param;//paramskk(i,j,k).lam3 * (rij-rik);
if (tmp > 69.0776) ex_delr = 1.e30;
else if (tmp < -69.0776) ex_delr = 0.0;
else ex_delr = exp(tmp);
if (int(paramskk(i,j,k).powerm) == 3)
dex_delr = 3.0*pow(paramskk(i,j,k).lam3,3.0) * pow(rij-rik,2.0)*ex_delr;
dex_delr = 3.0*param*param*paramskk(i,j,k).lam3*ex_delr;//pow(paramskk(i,j,k).lam3,3.0) * pow(rij-rik,2.0)*ex_delr;
else dex_delr = paramskk(i,j,k).lam3 * ex_delr;
cos = vec3_dot(rij_hat,rik_hat);
@ -1012,15 +1075,16 @@ void PairTersoffKokkos<DeviceType>::ters_dthbk(
fc = ters_fc_k(i,j,k,rik);
dfc = ters_dfc(i,j,k,rik);
if (int(paramskk(i,j,k).powerm) == 3) tmp = pow(paramskk(i,j,k).lam3 * (rij-rik),3.0);
else tmp = paramskk(i,j,k).lam3 * (rij-rik);
const F_FLOAT param = paramskk(i,j,k).lam3 * (rij-rik);
if (int(paramskk(i,j,k).powerm) == 3) tmp = param*param*param;//pow(paramskk(i,j,k).lam3 * (rij-rik),3.0);
else tmp = param;//paramskk(i,j,k).lam3 * (rij-rik);
if (tmp > 69.0776) ex_delr = 1.e30;
else if (tmp < -69.0776) ex_delr = 0.0;
else ex_delr = exp(tmp);
if (int(paramskk(i,j,k).powerm) == 3)
dex_delr = 3.0*pow(paramskk(i,j,k).lam3,3.0) * pow(rij-rik,2.0)*ex_delr;
dex_delr = 3.0*param*param*paramskk(i,j,k).lam3*ex_delr;//pow(paramskk(i,j,k).lam3,3.0) * pow(rij-rik,2.0)*ex_delr;
else dex_delr = paramskk(i,j,k).lam3 * ex_delr;
cos = vec3_dot(rij_hat,rik_hat);

10
src/KOKKOS/pair_tersoff_kokkos.h
View File

@ -39,6 +39,8 @@ struct TagPairTersoffComputeFullA{};
template<int NEIGHFLAG, int EVFLAG>
struct TagPairTersoffComputeFullB{};
struct TagPairTersoffComputeShortNeigh{};
template<class DeviceType>
class PairTersoffKokkos : public PairTersoff {
public:
@ -77,6 +79,9 @@ class PairTersoffKokkos : public PairTersoff {
KOKKOS_INLINE_FUNCTION
void operator()(TagPairTersoffComputeFullB<NEIGHFLAG,EVFLAG>, const int&) const;
KOKKOS_INLINE_FUNCTION
void operator()(TagPairTersoffComputeShortNeigh, const int&) const;
KOKKOS_INLINE_FUNCTION
double ters_fc_k(const int &i, const int &j, const int &k, const F_FLOAT &r) const;
@ -184,6 +189,7 @@ class PairTersoffKokkos : public PairTersoff {
// hardwired to space for 15 atom types
//params_ters m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
int inum;
typename AT::t_x_array_randomread x;
typename AT::t_f_array f;
typename AT::t_int_1d_randomread type;
@ -203,10 +209,12 @@ class PairTersoffKokkos : public PairTersoff {
typename ArrayTypes<DeviceType>::t_int_1d_randomread d_numneigh;
//NeighListKokkos<DeviceType> k_list;
class AtomKokkos *atomKK;
int neighflag,newton_pair;
int nlocal,nall,eflag,vflag;
Kokkos::View<int**,DeviceType> d_neighbors_short;
Kokkos::View<int*,DeviceType> d_numneigh_short;
friend void pair_virial_fdotr_compute<PairTersoffKokkos>(PairTersoffKokkos*);
};

235
src/KOKKOS/pair_tersoff_mod_kokkos.cpp
View File

@ -191,7 +191,7 @@ void PairTersoffMODKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
nall = atom->nlocal + atom->nghost;
newton_pair = force->newton_pair;
const int inum = list->inum;
inum = list->inum;
const int ignum = inum + list->gnum;
NeighListKokkos<DeviceType>* k_list = static_cast<NeighListKokkos<DeviceType>*>(list);
d_numneigh = k_list->d_numneigh;
@ -204,6 +204,18 @@ void PairTersoffMODKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
EV_FLOAT ev;
EV_FLOAT ev_all;
// build short neighbor list
int max_neighs = d_neighbors.dimension_1();
if ((d_neighbors_short.dimension_1() != max_neighs) ||
(d_neighbors_short.dimension_0() != ignum)) {
d_neighbors_short = Kokkos::View<int**,DeviceType>("Tersoff::neighbors_short",ignum,max_neighs);
}
if (d_numneigh_short.dimension_0()!=ignum)
d_numneigh_short = Kokkos::View<int*,DeviceType>("Tersoff::numneighs_short",ignum);
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagPairTersoffMODComputeShortNeigh>(0,neighflag==FULL?ignum:inum), *this);
if (neighflag == HALF) {
if (evflag)
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairTersoffMODComputeHalf<HALF,1> >(0,inum),*this,ev);
@ -257,6 +269,35 @@ void PairTersoffMODKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeShortNeigh, const int& ii) const {
const int i = d_ilist[ii];
const X_FLOAT xtmp = x(i,0);
const X_FLOAT ytmp = x(i,1);
const X_FLOAT ztmp = x(i,2);
const int jnum = d_numneigh[i];
int inside = 0;
for (int jj = 0; jj < jnum; jj++) {
int j = d_neighbors(i,jj);
j &= NEIGHMASK;
const X_FLOAT delx = xtmp - x(j,0);
const X_FLOAT dely = ytmp - x(j,1);
const X_FLOAT delz = ztmp - x(j,2);
const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutmax*cutmax) {
d_neighbors_short(i,inside) = j;
inside++;
}
}
d_numneigh_short(i) = inside;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
template<int NEIGHFLAG, int EVFLAG>
KOKKOS_INLINE_FUNCTION
@ -273,21 +314,22 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeHalf<N
const int itype = type(i);
const int itag = tag(i);
int j,k,jj,kk,jtag,jtype,ktype;
F_FLOAT rsq1, cutsq1, rsq2, cutsq2, rij, rik, bo_ij;
F_FLOAT fi[3], fj[3], fk[3];
X_FLOAT delx1, dely1, delz1, delx2, dely2, delz2;
//const AtomNeighborsConst d_neighbors_i = k_list.get_neighbors_const(i);
const int jnum = d_numneigh[i];
const int jnum = d_numneigh_short[i];
// repulsive
for (jj = 0; jj < jnum; jj++) {
j = d_neighbors(i,jj);
F_FLOAT f_x = 0.0;
F_FLOAT f_y = 0.0;
F_FLOAT f_z = 0.0;
for (int jj = 0; jj < jnum; jj++) {
int j = d_neighbors_short(i,jj);
j &= NEIGHMASK;
jtype = type(j);
jtag = tag(j);
const int jtype = type(j);
const int jtag = tag(j);
if (itag > jtag) {
if ((itag+jtag) % 2 == 0) continue;
@ -315,9 +357,9 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeHalf<N
(tmp_fcd - tmp_fce*paramskk(itype,jtype,jtype).lam1) / r;
const F_FLOAT eng = tmp_fce * paramskk(itype,jtype,jtype).biga * tmp_exp;
a_f(i,0) += delx*frep;
a_f(i,1) += dely*frep;
a_f(i,2) += delz*frep;
f_x += delx*frep;
f_y += dely*frep;
f_z += delz*frep;
a_f(j,0) -= delx*frep;
a_f(j,1) -= dely*frep;
a_f(j,2) -= delz*frep;
@ -330,35 +372,35 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeHalf<N
// attractive: bond order
for (jj = 0; jj < jnum; jj++) {
j = d_neighbors(i,jj);
for (int jj = 0; jj < jnum; jj++) {
int j = d_neighbors_short(i,jj);
j &= NEIGHMASK;
jtype = type(j);
const int jtype = type(j);
delx1 = xtmp - x(j,0);
dely1 = ytmp - x(j,1);
delz1 = ztmp - x(j,2);
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
cutsq1 = paramskk(itype,jtype,jtype).cutsq;
const F_FLOAT delx1 = xtmp - x(j,0);
const F_FLOAT dely1 = ytmp - x(j,1);
const F_FLOAT delz1 = ztmp - x(j,2);
const F_FLOAT rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
const F_FLOAT cutsq1 = paramskk(itype,jtype,jtype).cutsq;
bo_ij = 0.0;
F_FLOAT bo_ij = 0.0;
if (rsq1 > cutsq1) continue;
rij = sqrt(rsq1);
const F_FLOAT rij = sqrt(rsq1);
for (kk = 0; kk < jnum; kk++) {
for (int kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = d_neighbors(i,kk);
int k = d_neighbors_short(i,kk);
k &= NEIGHMASK;
ktype = type(k);
const int ktype = type(k);
delx2 = xtmp - x(k,0);
dely2 = ytmp - x(k,1);
delz2 = ztmp - x(k,2);
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
cutsq2 = paramskk(itype,jtype,ktype).cutsq;
const F_FLOAT delx2 = xtmp - x(k,0);
const F_FLOAT dely2 = ytmp - x(k,1);
const F_FLOAT delz2 = ztmp - x(k,2);
const F_FLOAT rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
const F_FLOAT cutsq2 = paramskk(itype,jtype,ktype).cutsq;
if (rsq2 > cutsq2) continue;
rik = sqrt(rsq2);
const F_FLOAT rik = sqrt(rsq2);
bo_ij += bondorder(itype,jtype,ktype,rij,delx1,dely1,delz1,rik,delx2,dely2,delz2);
}
@ -369,58 +411,64 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeHalf<N
const F_FLOAT bij = ters_bij_k(itype,jtype,jtype,bo_ij);
const F_FLOAT fatt = -0.5*bij * dfa / rij;
const F_FLOAT prefactor = 0.5*fa * ters_dbij(itype,jtype,jtype,bo_ij);
const F_FLOAT eng = 0.5*bij * fa;
a_f(i,0) += delx1*fatt;
a_f(i,1) += dely1*fatt;
a_f(i,2) += delz1*fatt;
a_f(j,0) -= delx1*fatt;
a_f(j,1) -= dely1*fatt;
a_f(j,2) -= delz1*fatt;
f_x += delx1*fatt;
f_y += dely1*fatt;
f_z += delz1*fatt;
F_FLOAT fj_x = -delx1*fatt;
F_FLOAT fj_y = -dely1*fatt;
F_FLOAT fj_z = -delz1*fatt;
if (EVFLAG) {
const F_FLOAT eng = 0.5*bij * fa;
if (eflag) ev.evdwl += eng;
if (vflag_either || eflag_atom)
this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,fatt,delx1,dely1,delz1);
this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,fatt,delx1,dely1,delz1);
}
// attractive: three-body force
for (kk = 0; kk < jnum; kk++) {
for (int kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = d_neighbors(i,kk);
int k = d_neighbors_short(i,kk);
k &= NEIGHMASK;
ktype = type(k);
const int ktype = type(k);
delx2 = xtmp - x(k,0);
dely2 = ytmp - x(k,1);
delz2 = ztmp - x(k,2);
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
cutsq2 = paramskk(itype,jtype,ktype).cutsq;
const F_FLOAT delx2 = xtmp - x(k,0);
const F_FLOAT dely2 = ytmp - x(k,1);
const F_FLOAT delz2 = ztmp - x(k,2);
const F_FLOAT rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
const F_FLOAT cutsq2 = paramskk(itype,jtype,ktype).cutsq;
if (rsq2 > cutsq2) continue;
rik = sqrt(rsq2);
const F_FLOAT rik = sqrt(rsq2);
ters_dthb(itype,jtype,ktype,prefactor,rij,delx1,dely1,delz1,
rik,delx2,dely2,delz2,fi,fj,fk);
rik,delx2,dely2,delz2,fi,fj,fk);
a_f(i,0) += fi[0];
a_f(i,1) += fi[1];
a_f(i,2) += fi[2];
a_f(j,0) += fj[0];
a_f(j,1) += fj[1];
a_f(j,2) += fj[2];
f_x += fi[0];
f_y += fi[1];
f_z += fi[2];
fj_x += fj[0];
fj_y += fj[1];
fj_z += fj[2];
a_f(k,0) += fk[0];
a_f(k,1) += fk[1];
a_f(k,2) += fk[2];
if (vflag_atom) {
F_FLOAT delrij[3], delrik[3];
delrij[0] = -delx1; delrij[1] = -dely1; delrij[2] = -delz1;
delrik[0] = -delx2; delrik[1] = -dely2; delrik[2] = -delz2;
if (vflag_either) this->template v_tally3<NEIGHFLAG>(ev,i,j,k,fj,fk,delrij,delrik);
F_FLOAT delrij[3], delrik[3];
delrij[0] = -delx1; delrij[1] = -dely1; delrij[2] = -delz1;
delrik[0] = -delx2; delrik[1] = -dely2; delrik[2] = -delz2;
if (vflag_either) this->template v_tally3<NEIGHFLAG>(ev,i,j,k,fj,fk,delrij,delrik);
}
}
a_f(j,0) += fj_x;
a_f(j,1) += fj_y;
a_f(j,2) += fj_z;
}
a_f(i,0) += f_x;
a_f(i,1) += f_y;
a_f(i,2) += f_z;
}
template<class DeviceType>
@ -450,12 +498,15 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeFullA<
X_FLOAT delx1, dely1, delz1, delx2, dely2, delz2;
//const AtomNeighborsConst d_neighbors_i = k_list.get_neighbors_const(i);
const int jnum = d_numneigh[i];
const int jnum = d_numneigh_short[i];
// repulsive
F_FLOAT f_x = 0.0;
F_FLOAT f_y = 0.0;
F_FLOAT f_z = 0.0;
for (jj = 0; jj < jnum; jj++) {
j = d_neighbors(i,jj);
j = d_neighbors_short(i,jj);
j &= NEIGHMASK;
const int jtype = type(j);
@ -475,9 +526,9 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeFullA<
(tmp_fcd - tmp_fce*paramskk(itype,jtype,jtype).lam1) / r;
const F_FLOAT eng = tmp_fce * paramskk(itype,jtype,jtype).biga * tmp_exp;
f(i,0) += delx*frep;
f(i,1) += dely*frep;
f(i,2) += delz*frep;
f_x += delx*frep;
f_y += dely*frep;
f_z += delz*frep;
if (EVFLAG) {
if (eflag)
@ -490,7 +541,7 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeFullA<
// attractive: bond order
for (jj = 0; jj < jnum; jj++) {
j = d_neighbors(i,jj);
j = d_neighbors_short(i,jj);
j &= NEIGHMASK;
jtype = type(j);
@ -506,7 +557,7 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeFullA<
for (kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = d_neighbors(i,kk);
k = d_neighbors_short(i,kk);
k &= NEIGHMASK;
ktype = type(k);
@ -530,9 +581,9 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeFullA<
const F_FLOAT prefactor = 0.5*fa * ters_dbij(itype,jtype,jtype,bo_ij);
const F_FLOAT eng = 0.5*bij * fa;
f(i,0) += delx1*fatt;
f(i,1) += dely1*fatt;
f(i,2) += delz1*fatt;
f_x += delx1*fatt;
f_y += dely1*fatt;
f_z += delz1*fatt;
if (EVFLAG) {
if (eflag) ev.evdwl += 0.5*eng;
@ -544,7 +595,7 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeFullA<
for (kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = d_neighbors(i,kk);
k = d_neighbors_short(i,kk);
k &= NEIGHMASK;
ktype = type(k);
@ -559,9 +610,9 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeFullA<
ters_dthb(itype,jtype,ktype,prefactor,rij,delx1,dely1,delz1,
rik,delx2,dely2,delz2,fi,fj,fk);
f(i,0) += fi[0];
f(i,1) += fi[1];
f(i,2) += fi[2];
f_x += fi[0];
f_y += fi[1];
f_z += fi[2];
if (vflag_atom) {
F_FLOAT delrij[3], delrik[3];
@ -571,6 +622,9 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeFullA<
}
}
}
f(i,0) += f_x;
f(i,1) += f_y;
f(i,2) += f_z;
}
template<class DeviceType>
@ -599,12 +653,16 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeFullB<
F_FLOAT fj[3], fk[3];
X_FLOAT delx1, dely1, delz1, delx2, dely2, delz2;
const int jnum = d_numneigh[i];
const int jnum = d_numneigh_short[i];
F_FLOAT f_x = 0.0;
F_FLOAT f_y = 0.0;
F_FLOAT f_z = 0.0;
// attractive: bond order
for (jj = 0; jj < jnum; jj++) {
j = d_neighbors(i,jj);
j = d_neighbors_short(i,jj);
j &= NEIGHMASK;
if (j >= nlocal) continue;
jtype = type(j);
@ -619,10 +677,10 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeFullB<
if (rsq1 > cutsq1) continue;
rij = sqrt(rsq1);
j_jnum = d_numneigh[j];
j_jnum = d_numneigh_short[j];
for (kk = 0; kk < j_jnum; kk++) {
k = d_neighbors(j,kk);
k = d_neighbors_short(j,kk);
if (k == i) continue;
k &= NEIGHMASK;
ktype = type(k);
@ -648,9 +706,9 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeFullB<
const F_FLOAT prefactor = 0.5*fa * ters_dbij(jtype,itype,itype,bo_ij);
const F_FLOAT eng = 0.5*bij * fa;
f(i,0) -= delx1*fatt;
f(i,1) -= dely1*fatt;
f(i,2) -= delz1*fatt;
f_x -= delx1*fatt;
f_y -= dely1*fatt;
f_z -= delz1*fatt;
if (EVFLAG) {
if (eflag)
@ -662,7 +720,7 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeFullB<
// attractive: three-body force
for (kk = 0; kk < j_jnum; kk++) {
k = d_neighbors(j,kk);
k = d_neighbors_short(j,kk);
if (k == i) continue;
k &= NEIGHMASK;
ktype = type(k);
@ -677,9 +735,9 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeFullB<
rik = sqrt(rsq2);
ters_dthbj(jtype,itype,ktype,prefactor,rij,delx1,dely1,delz1,
rik,delx2,dely2,delz2,fj,fk);
f(i,0) += fj[0];
f(i,1) += fj[1];
f(i,2) += fj[2];
f_x += fj[0];
f_y += fj[1];
f_z += fj[2];
if (vflag_atom) {
F_FLOAT delrji[3], delrjk[3];
@ -692,11 +750,14 @@ void PairTersoffMODKokkos<DeviceType>::operator()(TagPairTersoffMODComputeFullB<
const F_FLOAT prefactor_jk = 0.5*fa_jk * ters_dbij(jtype,ktype,itype,bo_ij);
ters_dthbk(jtype,ktype,itype,prefactor_jk,rik,delx2,dely2,delz2,
rij,delx1,dely1,delz1,fk);
f(i,0) += fk[0];
f(i,1) += fk[1];
f(i,2) += fk[2];
f_x += fk[0];
f_y += fk[1];
f_z += fk[2];
}
}
f(i,0) += f_x;
f(i,1) += f_y;
f(i,2) += f_z;
}
template<class DeviceType>

10
src/KOKKOS/pair_tersoff_mod_kokkos.h
View File

@ -39,6 +39,8 @@ struct TagPairTersoffMODComputeFullA{};
template<int NEIGHFLAG, int EVFLAG>
struct TagPairTersoffMODComputeFullB{};
struct TagPairTersoffMODComputeShortNeigh{};
template<class DeviceType>
class PairTersoffMODKokkos : public PairTersoffMOD {
public:
@ -77,6 +79,9 @@ class PairTersoffMODKokkos : public PairTersoffMOD {
KOKKOS_INLINE_FUNCTION
void operator()(TagPairTersoffMODComputeFullB<NEIGHFLAG,EVFLAG>, const int&) const;
KOKKOS_INLINE_FUNCTION
void operator()(TagPairTersoffMODComputeShortNeigh, const int&) const;
KOKKOS_INLINE_FUNCTION
double ters_fc_k(const int &i, const int &j, const int &k, const F_FLOAT &r) const;
@ -184,6 +189,7 @@ class PairTersoffMODKokkos : public PairTersoffMOD {
// hardwired to space for 15 atom types
//params_ters m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
int inum;
typename AT::t_x_array_randomread x;
typename AT::t_f_array f;
typename AT::t_int_1d_randomread type;
@ -203,10 +209,12 @@ class PairTersoffMODKokkos : public PairTersoffMOD {
typename ArrayTypes<DeviceType>::t_int_1d_randomread d_numneigh;
//NeighListKokkos<DeviceType> k_list;
class AtomKokkos *atomKK;
int neighflag,newton_pair;
int nlocal,nall,eflag,vflag;
Kokkos::View<int**,DeviceType> d_neighbors_short;
Kokkos::View<int*,DeviceType> d_numneigh_short;
friend void pair_virial_fdotr_compute<PairTersoffMODKokkos>(PairTersoffMODKokkos*);
};

233
src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
View File

@ -205,7 +205,7 @@ void PairTersoffZBLKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
nall = atom->nlocal + atom->nghost;
newton_pair = force->newton_pair;
const int inum = list->inum;
inum = list->inum;
const int ignum = inum + list->gnum;
NeighListKokkos<DeviceType>* k_list = static_cast<NeighListKokkos<DeviceType>*>(list);
d_numneigh = k_list->d_numneigh;
@ -218,6 +218,18 @@ void PairTersoffZBLKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
EV_FLOAT ev;
EV_FLOAT ev_all;
// build short neighbor list
int max_neighs = d_neighbors.dimension_1();
if ((d_neighbors_short.dimension_1() != max_neighs) ||
(d_neighbors_short.dimension_0() != ignum)) {
d_neighbors_short = Kokkos::View<int**,DeviceType>("Tersoff::neighbors_short",ignum,max_neighs);
}
if (d_numneigh_short.dimension_0()!=ignum)
d_numneigh_short = Kokkos::View<int*,DeviceType>("Tersoff::numneighs_short",ignum);
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagPairTersoffZBLComputeShortNeigh>(0,neighflag==FULL?ignum:inum), *this);
if (neighflag == HALF) {
if (evflag)
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairTersoffZBLComputeHalf<HALF,1> >(0,inum),*this,ev);
@ -271,6 +283,35 @@ void PairTersoffZBLKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeShortNeigh, const int& ii) const {
const int i = d_ilist[ii];
const X_FLOAT xtmp = x(i,0);
const X_FLOAT ytmp = x(i,1);
const X_FLOAT ztmp = x(i,2);
const int jnum = d_numneigh[i];
int inside = 0;
for (int jj = 0; jj < jnum; jj++) {
int j = d_neighbors(i,jj);
j &= NEIGHMASK;
const X_FLOAT delx = xtmp - x(j,0);
const X_FLOAT dely = ytmp - x(j,1);
const X_FLOAT delz = ztmp - x(j,2);
const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutmax*cutmax) {
d_neighbors_short(i,inside) = j;
inside++;
}
}
d_numneigh_short(i) = inside;
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
template<int NEIGHFLAG, int EVFLAG>
KOKKOS_INLINE_FUNCTION
@ -287,21 +328,22 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeHalf<N
const int itype = type(i);
const int itag = tag(i);
int j,k,jj,kk,jtag,jtype,ktype;
F_FLOAT rsq1, cutsq1, rsq2, cutsq2, rij, rik, bo_ij;
F_FLOAT fi[3], fj[3], fk[3];
X_FLOAT delx1, dely1, delz1, delx2, dely2, delz2;
//const AtomNeighborsConst d_neighbors_i = k_list.get_neighbors_const(i);
const int jnum = d_numneigh[i];
const int jnum = d_numneigh_short[i];
// repulsive
for (jj = 0; jj < jnum; jj++) {
j = d_neighbors(i,jj);
F_FLOAT f_x = 0.0;
F_FLOAT f_y = 0.0;
F_FLOAT f_z = 0.0;
for (int jj = 0; jj < jnum; jj++) {
int j = d_neighbors_short(i,jj);
j &= NEIGHMASK;
jtype = type(j);
jtag = tag(j);
const int jtype = type(j);
const int jtag = tag(j);
if (itag > jtag) {
if ((itag+jtag) % 2 == 0) continue;
@ -359,9 +401,9 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeHalf<N
eng = (1.0 - fermi_k(itype,jtype,jtype,r)) * eng_z +
fermi_k(itype,jtype,jtype,r) * eng_t;
a_f(i,0) += delx*frep;
a_f(i,1) += dely*frep;
a_f(i,2) += delz*frep;
f_x += delx*frep;
f_y += dely*frep;
f_z += delz*frep;
a_f(j,0) -= delx*frep;
a_f(j,1) -= dely*frep;
a_f(j,2) -= delz*frep;
@ -374,35 +416,35 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeHalf<N
// attractive: bond order
for (jj = 0; jj < jnum; jj++) {
j = d_neighbors(i,jj);
for (int jj = 0; jj < jnum; jj++) {
int j = d_neighbors_short(i,jj);
j &= NEIGHMASK;
jtype = type(j);
const int jtype = type(j);
delx1 = xtmp - x(j,0);
dely1 = ytmp - x(j,1);
delz1 = ztmp - x(j,2);
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
cutsq1 = paramskk(itype,jtype,jtype).cutsq;
const F_FLOAT delx1 = xtmp - x(j,0);
const F_FLOAT dely1 = ytmp - x(j,1);
const F_FLOAT delz1 = ztmp - x(j,2);
const F_FLOAT rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
const F_FLOAT cutsq1 = paramskk(itype,jtype,jtype).cutsq;
bo_ij = 0.0;
F_FLOAT bo_ij = 0.0;
if (rsq1 > cutsq1) continue;
rij = sqrt(rsq1);
const F_FLOAT rij = sqrt(rsq1);
for (kk = 0; kk < jnum; kk++) {
for (int kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = d_neighbors(i,kk);
int k = d_neighbors_short(i,kk);
k &= NEIGHMASK;
ktype = type(k);
const int ktype = type(k);
delx2 = xtmp - x(k,0);
dely2 = ytmp - x(k,1);
delz2 = ztmp - x(k,2);
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
cutsq2 = paramskk(itype,jtype,ktype).cutsq;
const F_FLOAT delx2 = xtmp - x(k,0);
const F_FLOAT dely2 = ytmp - x(k,1);
const F_FLOAT delz2 = ztmp - x(k,2);
const F_FLOAT rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
const F_FLOAT cutsq2 = paramskk(itype,jtype,ktype).cutsq;
if (rsq2 > cutsq2) continue;
rik = sqrt(rsq2);
const F_FLOAT rik = sqrt(rsq2);
bo_ij += bondorder(itype,jtype,ktype,rij,delx1,dely1,delz1,rik,delx2,dely2,delz2);
}
@ -413,58 +455,64 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeHalf<N
const F_FLOAT bij = ters_bij_k(itype,jtype,jtype,bo_ij);
const F_FLOAT fatt = -0.5*bij * dfa / rij;
const F_FLOAT prefactor = 0.5*fa * ters_dbij(itype,jtype,jtype,bo_ij);
const F_FLOAT eng = 0.5*bij * fa;
a_f(i,0) += delx1*fatt;
a_f(i,1) += dely1*fatt;
a_f(i,2) += delz1*fatt;
a_f(j,0) -= delx1*fatt;
a_f(j,1) -= dely1*fatt;
a_f(j,2) -= delz1*fatt;
f_x += delx1*fatt;
f_y += dely1*fatt;
f_z += delz1*fatt;
F_FLOAT fj_x = -delx1*fatt;
F_FLOAT fj_y = -dely1*fatt;
F_FLOAT fj_z = -delz1*fatt;
if (EVFLAG) {
const F_FLOAT eng = 0.5*bij * fa;
if (eflag) ev.evdwl += eng;
if (vflag_either || eflag_atom)
this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,fatt,delx1,dely1,delz1);
this->template ev_tally<NEIGHFLAG>(ev,i,j,eng,fatt,delx1,dely1,delz1);
}
// attractive: three-body force
for (kk = 0; kk < jnum; kk++) {
for (int kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = d_neighbors(i,kk);
int k = d_neighbors_short(i,kk);
k &= NEIGHMASK;
ktype = type(k);
const int ktype = type(k);
delx2 = xtmp - x(k,0);
dely2 = ytmp - x(k,1);
delz2 = ztmp - x(k,2);
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
cutsq2 = paramskk(itype,jtype,ktype).cutsq;
const F_FLOAT delx2 = xtmp - x(k,0);
const F_FLOAT dely2 = ytmp - x(k,1);
const F_FLOAT delz2 = ztmp - x(k,2);
const F_FLOAT rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
const F_FLOAT cutsq2 = paramskk(itype,jtype,ktype).cutsq;
if (rsq2 > cutsq2) continue;
rik = sqrt(rsq2);
const F_FLOAT rik = sqrt(rsq2);
ters_dthb(itype,jtype,ktype,prefactor,rij,delx1,dely1,delz1,
rik,delx2,dely2,delz2,fi,fj,fk);
rik,delx2,dely2,delz2,fi,fj,fk);
a_f(i,0) += fi[0];
a_f(i,1) += fi[1];
a_f(i,2) += fi[2];
a_f(j,0) += fj[0];
a_f(j,1) += fj[1];
a_f(j,2) += fj[2];
f_x += fi[0];
f_y += fi[1];
f_z += fi[2];
fj_x += fj[0];
fj_y += fj[1];
fj_z += fj[2];
a_f(k,0) += fk[0];
a_f(k,1) += fk[1];
a_f(k,2) += fk[2];
if (vflag_atom) {
F_FLOAT delrij[3], delrik[3];
delrij[0] = -delx1; delrij[1] = -dely1; delrij[2] = -delz1;
delrik[0] = -delx2; delrik[1] = -dely2; delrik[2] = -delz2;
if (vflag_either) this->template v_tally3<NEIGHFLAG>(ev,i,j,k,fj,fk,delrij,delrik);
F_FLOAT delrij[3], delrik[3];
delrij[0] = -delx1; delrij[1] = -dely1; delrij[2] = -delz1;
delrik[0] = -delx2; delrik[1] = -dely2; delrik[2] = -delz2;
if (vflag_either) this->template v_tally3<NEIGHFLAG>(ev,i,j,k,fj,fk,delrij,delrik);
}
}
a_f(j,0) += fj_x;
a_f(j,1) += fj_y;
a_f(j,2) += fj_z;
}
a_f(i,0) += f_x;
a_f(i,1) += f_y;
a_f(i,2) += f_z;
}
template<class DeviceType>
@ -498,8 +546,11 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullA<
// repulsive
F_FLOAT f_x = 0.0;
F_FLOAT f_y = 0.0;
F_FLOAT f_z = 0.0;
for (jj = 0; jj < jnum; jj++) {
j = d_neighbors(i,jj);
j = d_neighbors_short(i,jj);
j &= NEIGHMASK;
const int jtype = type(j);
@ -549,9 +600,9 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullA<
eng = (1.0 - fermi_k(itype,jtype,jtype,r)) * eng_z +
fermi_k(itype,jtype,jtype,r) * eng_t;
f(i,0) += delx*frep;
f(i,1) += dely*frep;
f(i,2) += delz*frep;
f_x += delx*frep;
f_y += dely*frep;
f_z += delz*frep;
if (EVFLAG) {
if (eflag)
@ -564,7 +615,7 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullA<
// attractive: bond order
for (jj = 0; jj < jnum; jj++) {
j = d_neighbors(i,jj);
j = d_neighbors_short(i,jj);
j &= NEIGHMASK;
jtype = type(j);
@ -580,7 +631,7 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullA<
for (kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = d_neighbors(i,kk);
k = d_neighbors_short(i,kk);
k &= NEIGHMASK;
ktype = type(k);
@ -604,9 +655,9 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullA<
const F_FLOAT prefactor = 0.5*fa * ters_dbij(itype,jtype,jtype,bo_ij);
const F_FLOAT eng = 0.5*bij * fa;
f(i,0) += delx1*fatt;
f(i,1) += dely1*fatt;
f(i,2) += delz1*fatt;
f_x += delx1*fatt;
f_y += dely1*fatt;
f_z += delz1*fatt;
if (EVFLAG) {
if (eflag) ev.evdwl += 0.5*eng;
@ -618,7 +669,7 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullA<
for (kk = 0; kk < jnum; kk++) {
if (jj == kk) continue;
k = d_neighbors(i,kk);
k = d_neighbors_short(i,kk);
k &= NEIGHMASK;
ktype = type(k);
@ -633,9 +684,9 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullA<
ters_dthb(itype,jtype,ktype,prefactor,rij,delx1,dely1,delz1,
rik,delx2,dely2,delz2,fi,fj,fk);
f(i,0) += fi[0];
f(i,1) += fi[1];
f(i,2) += fi[2];
f_x += fi[0];
f_y += fi[1];
f_z += fi[2];
if (vflag_atom) {
F_FLOAT delrij[3], delrik[3];
@ -645,6 +696,9 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullA<
}
}
}
f(i,0) += f_x;
f(i,1) += f_y;
f(i,2) += f_z;
}
template<class DeviceType>
@ -673,12 +727,16 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullB<
F_FLOAT fj[3], fk[3];
X_FLOAT delx1, dely1, delz1, delx2, dely2, delz2;
const int jnum = d_numneigh[i];
const int jnum = d_numneigh_short[i];
F_FLOAT f_x = 0.0;
F_FLOAT f_y = 0.0;
F_FLOAT f_z = 0.0;
// attractive: bond order
for (jj = 0; jj < jnum; jj++) {
j = d_neighbors(i,jj);
j = d_neighbors_short(i,jj);
j &= NEIGHMASK;
if (j >= nlocal) continue;
jtype = type(j);
@ -693,10 +751,10 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullB<
if (rsq1 > cutsq1) continue;
rij = sqrt(rsq1);
j_jnum = d_numneigh[j];
j_jnum = d_numneigh_short[j];
for (kk = 0; kk < j_jnum; kk++) {
k = d_neighbors(j,kk);
k = d_neighbors_short(j,kk);
if (k == i) continue;
k &= NEIGHMASK;
ktype = type(k);
@ -722,9 +780,9 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullB<
const F_FLOAT prefactor = 0.5*fa * ters_dbij(jtype,itype,itype,bo_ij);
const F_FLOAT eng = 0.5*bij * fa;
f(i,0) -= delx1*fatt;
f(i,1) -= dely1*fatt;
f(i,2) -= delz1*fatt;
f_x -= delx1*fatt;
f_y -= dely1*fatt;
f_z -= delz1*fatt;
if (EVFLAG) {
if (eflag)
@ -736,7 +794,7 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullB<
// attractive: three-body force
for (kk = 0; kk < j_jnum; kk++) {
k = d_neighbors(j,kk);
k = d_neighbors_short(j,kk);
if (k == i) continue;
k &= NEIGHMASK;
ktype = type(k);
@ -751,9 +809,9 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullB<
rik = sqrt(rsq2);
ters_dthbj(jtype,itype,ktype,prefactor,rij,delx1,dely1,delz1,
rik,delx2,dely2,delz2,fj,fk);
f(i,0) += fj[0];
f(i,1) += fj[1];
f(i,2) += fj[2];
f_x += fj[0];
f_y += fj[1];
f_z += fj[2];
if (vflag_atom) {
F_FLOAT delrji[3], delrjk[3];
@ -766,11 +824,14 @@ void PairTersoffZBLKokkos<DeviceType>::operator()(TagPairTersoffZBLComputeFullB<
const F_FLOAT prefactor_jk = 0.5*fa_jk * ters_dbij(jtype,ktype,itype,bo_ij);
ters_dthbk(jtype,ktype,itype,prefactor_jk,rik,delx2,dely2,delz2,
rij,delx1,dely1,delz1,fk);
f(i,0) += fk[0];
f(i,1) += fk[1];
f(i,2) += fk[2];
f_x += fk[0];
f_y += fk[1];
f_z += fk[2];
}
}
f(i,0) += f_x;
f(i,1) += f_y;
f(i,2) += f_z;
}
template<class DeviceType>

9
src/KOKKOS/pair_tersoff_zbl_kokkos.h
View File

@ -39,6 +39,8 @@ struct TagPairTersoffZBLComputeFullA{};
template<int NEIGHFLAG, int EVFLAG>
struct TagPairTersoffZBLComputeFullB{};
struct TagPairTersoffZBLComputeShortNeigh{};
template<class DeviceType>
class PairTersoffZBLKokkos : public PairTersoffZBL {
public:
@ -77,6 +79,8 @@ class PairTersoffZBLKokkos : public PairTersoffZBL {
KOKKOS_INLINE_FUNCTION
void operator()(TagPairTersoffZBLComputeFullB<NEIGHFLAG,EVFLAG>, const int&) const;
KOKKOS_INLINE_FUNCTION
void operator()(TagPairTersoffZBLComputeShortNeigh, const int&) const;
KOKKOS_INLINE_FUNCTION
double ters_fc_k(const int &i, const int &j, const int &k, const F_FLOAT &r) const;
@ -190,6 +194,7 @@ class PairTersoffZBLKokkos : public PairTersoffZBL {
// hardwired to space for 15 atom types
//params_ters m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
int inum;
typename AT::t_x_array_randomread x;
typename AT::t_f_array f;
typename AT::t_int_1d_randomread type;
@ -209,10 +214,12 @@ class PairTersoffZBLKokkos : public PairTersoffZBL {
typename ArrayTypes<DeviceType>::t_int_1d_randomread d_numneigh;
//NeighListKokkos<DeviceType> k_list;
class AtomKokkos *atomKK;
int neighflag,newton_pair;
int nlocal,nall,eflag,vflag;
Kokkos::View<int**,DeviceType> d_neighbors_short;
Kokkos::View<int*,DeviceType> d_numneigh_short;
// ZBL
F_FLOAT global_a_0; // Bohr radius for Coulomb repulsion
F_FLOAT global_epsilon_0; // permittivity of vacuum for Coulomb repulsion

3
src/pair_morse.cpp
View File

@ -176,7 +176,8 @@ void PairMorse::settings(int narg, char **arg)
void PairMorse::coeff(int narg, char **arg)
{
if (narg < 5 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients");
if (narg < 5 || narg > 6)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;