forked from lijiext/lammps
Merge branch 'master' into doc-updates
This commit is contained in:
Axel Kohlmeyer
commit
81f68e06fd
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@ -0,0 +1,10 @@
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|||
\documentclass[12pt]{article}
|
||||
\pagestyle{empty}
|
||||
|
||||
\begin{document}
|
||||
|
||||
\begin{eqnarray*}
|
||||
V_{ij} & = & f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) + c_0 \right]
|
||||
\end{eqnarray*}
|
||||
|
||||
\end{document}
|
||||
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@ -3,7 +3,7 @@
|
|||
\begin{document}
|
||||
|
||||
$$
|
||||
P = \frac{N k_B T}{V} + \frac{\sum_{i}^{N} r_i \bullet f_i}{dV}
|
||||
P = \frac{N k_B T}{V} + \frac{\sum_{i}^{N'} r_i \bullet f_i}{dV}
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
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|
|
@ -4,7 +4,7 @@
|
|||
|
||||
$$
|
||||
P_{IJ} = \frac{\sum_{k}^{N} m_k v_{k_I} v_{k_J}}{V} +
|
||||
\frac{\sum_{k}^{N} r_{k_I} f_{k_J}}{V}
|
||||
\frac{\sum_{k}^{N'} r_{k_I} f_{k_J}}{V}
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
<!-- HTML_ONLY -->
|
||||
<HEAD>
|
||||
<TITLE>LAMMPS Users Manual</TITLE>
|
||||
<META NAME="docnumber" CONTENT="9 Nov 2016 version">
|
||||
<META NAME="docnumber" CONTENT="17 Nov 2016 version">
|
||||
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
|
||||
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
|
||||
</HEAD>
|
||||
|
|
@ -21,7 +21,7 @@
|
|||
<H1></H1>
|
||||
|
||||
LAMMPS Documentation :c,h3
|
||||
9 Nov 2016 version :c,h4
|
||||
17 Nov 2016 version :c,h4
|
||||
|
||||
Version info: :h4
|
||||
|
||||
|
|
|
|||
|
|
@ -981,11 +981,12 @@ KOKKOS, o = USER-OMP, t = OPT.
|
|||
"table (gko)"_pair_table.html,
|
||||
"tersoff (gkio)"_pair_tersoff.html,
|
||||
"tersoff/mod (gko)"_pair_tersoff_mod.html,
|
||||
"tersoff/mod/c (o)"_pair_tersoff_mod.html,
|
||||
"tersoff/zbl (gko)"_pair_tersoff_zbl.html,
|
||||
"tip4p/cut (o)"_pair_coul.html,
|
||||
"tip4p/long (o)"_pair_coul.html,
|
||||
"tri/lj"_pair_tri_lj.html,
|
||||
"vashishta (o)"_pair_vashishta.html,
|
||||
"vashishta (ko)"_pair_vashishta.html,
|
||||
"vashishta/table (o)"_pair_vashishta.html,
|
||||
"yukawa (go)"_pair_yukawa.html,
|
||||
"yukawa/colloid (go)"_pair_yukawa_colloid.html,
|
||||
|
|
@ -995,6 +996,7 @@ These are additional pair styles in USER packages, which can be used
|
|||
if "LAMMPS is built with the appropriate
|
||||
package"_Section_start.html#start_3.
|
||||
|
||||
"agni (o)"_pair_agni.html,
|
||||
"awpmd/cut"_pair_awpmd.html,
|
||||
"buck/mdf"_pair_mdf.html,
|
||||
"coul/cut/soft (o)"_pair_lj_soft.html,
|
||||
|
|
|
|||
|
|
@ -37,12 +37,18 @@ The pressure is computed by the formula
|
|||
|
||||
where N is the number of atoms in the system (see discussion of DOF
|
||||
below), Kb is the Boltzmann constant, T is the temperature, d is the
|
||||
dimensionality of the system (2 or 3 for 2d/3d), V is the system
|
||||
volume (or area in 2d), and the second term is the virial, computed
|
||||
within LAMMPS for all pairwise as well as 2-body, 3-body, and 4-body,
|
||||
and long-range interactions. "Fixes"_fix.html that impose constraints
|
||||
(e.g. the "fix shake"_fix_shake.html command) also contribute to the
|
||||
virial term.
|
||||
dimensionality of the system (2 or 3 for 2d/3d), and V is the system
|
||||
volume (or area in 2d). The second term is the virial, equal to
|
||||
-dU/dV, computed for all pairwise as well as 2-body, 3-body, 4-body,
|
||||
manybody, and long-range interactions, where r_i and f_i are the
|
||||
position and force vector of atom i, and the black dot indicates a dot
|
||||
product. When periodic boundary conditions are used, N' necessarily
|
||||
includes periodic image (ghost) atoms outside the central box, and the
|
||||
position and force vectors of ghost atoms are thus included in the
|
||||
summation. When periodic boundary conditions are not used, N' = N =
|
||||
the number of atoms in the system. "Fixes"_fix.html that impose
|
||||
constraints (e.g. the "fix shake"_fix_shake.html command) also
|
||||
contribute to the virial term.
|
||||
|
||||
A symmetric pressure tensor, stored as a 6-element vector, is also
|
||||
calculated by this compute. The 6 components of the vector are
|
||||
|
|
@ -62,8 +68,9 @@ compute temperature or ke and/or the virial. The {virial} keyword
|
|||
means include all terms except the kinetic energy {ke}.
|
||||
|
||||
Details of how LAMMPS computes the virial efficiently for the entire
|
||||
system, including the effects of periodic boundary conditions is
|
||||
discussed in "(Thompson)"_#Thompson.
|
||||
system, including for manybody potentials and accounting for the
|
||||
effects of periodic boundary conditions are discussed in
|
||||
"(Thompson)"_#Thompson.
|
||||
|
||||
The temperature and kinetic energy tensor is not calculated by this
|
||||
compute, but rather by the temperature compute specified with the
|
||||
|
|
|
|||
|
|
@ -59,6 +59,7 @@ dump_h5md.html
|
|||
dump_image.html
|
||||
dump_modify.html
|
||||
dump_molfile.html
|
||||
dump_nc.html
|
||||
echo.html
|
||||
fix.html
|
||||
fix_modify.html
|
||||
|
|
@ -152,6 +153,7 @@ fix_colvars.html
|
|||
fix_controller.html
|
||||
fix_deform.html
|
||||
fix_deposit.html
|
||||
fix_dpd_energy.html
|
||||
fix_drag.html
|
||||
fix_drude.html
|
||||
fix_drude_transform.html
|
||||
|
|
@ -272,6 +274,7 @@ fix_viscosity.html
|
|||
fix_viscous.html
|
||||
fix_wall.html
|
||||
fix_wall_gran.html
|
||||
fix_wall_gran_region.html
|
||||
fix_wall_piston.html
|
||||
fix_wall_reflect.html
|
||||
fix_wall_region.html
|
||||
|
|
@ -390,6 +393,7 @@ compute_voronoi_atom.html
|
|||
compute_xrd.html
|
||||
|
||||
pair_adp.html
|
||||
pair_agni.html
|
||||
pair_airebo.html
|
||||
pair_awpmd.html
|
||||
pair_beck.html
|
||||
|
|
@ -622,3 +626,4 @@ USER/atc/man_unfix_flux.html
|
|||
USER/atc/man_unfix_nodes.html
|
||||
USER/atc/man_write_atom_weights.html
|
||||
USER/atc/man_write_restart.html
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,128 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
pair_style agni command :h3
|
||||
pair_style agni/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style agni :pre
|
||||
|
||||
[Examples:]
|
||||
pair_style agni
|
||||
pair_coeff * * Al.agni Al
|
||||
|
||||
[Description:]
|
||||
|
||||
Style {agni} style computes the manybody vectorial force components for
|
||||
an atom as
|
||||
|
||||
:c,image(Eqs/pair_agni.jpg)
|
||||
|
||||
{u} labels the individual components, i.e. x, y or z, and {V} is the
|
||||
corresponding atomic fingerprint. {d} is the Euclidean distance between
|
||||
any two atomic fingerprints. A total of N_t reference atomic
|
||||
environments are considered to construct the force field file. {alpha_t}
|
||||
and {l} are the weight coefficients and length scale parameter of the
|
||||
non-linear regression model.
|
||||
|
||||
The method implements the recently proposed machine learning access to
|
||||
atomic forces as discussed extensively in the following publications -
|
||||
"(Botu1)"_#Botu2015adaptive and "(Botu2)"_#Botu2015learning. The premise
|
||||
of the method is to map the atomic enviornment numerically into a
|
||||
fingerprint, and use machine learning methods to create a mapping to the
|
||||
vectorial atomic forces.
|
||||
|
||||
Only a single pair_coeff command is used with the {agni} style which
|
||||
specifies an AGNI potential file containing the parameters of the
|
||||
force field for the needed elements. These are mapped to LAMMPS atom
|
||||
types by specifying N additional arguments after the filename in the
|
||||
pair_coeff command, where N is the number of LAMMPS atom types:
|
||||
|
||||
filename
|
||||
N element names = mapping of AGNI elements to atom types :ul
|
||||
|
||||
See the "pair_coeff"_pair_coeff.html doc page for alternate ways
|
||||
to specify the path for the force field file.
|
||||
|
||||
An AGNI force field is fully specified by the filename which contains the
|
||||
parameters of the force field, i.e., the reference training environments
|
||||
used to construct the machine learning force field. Example force field
|
||||
and input files are provided in the examples/USER/misc/agni directory.
|
||||
|
||||
:line
|
||||
|
||||
Styles with {omp} suffix is 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 5"_Section_accelerate.html
|
||||
of the manual. The accelerated style takes the same arguments and
|
||||
should produce the same results, except for round-off and precision
|
||||
issues.
|
||||
|
||||
The accelerated style is part of the USER-OMP. 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 style 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 5"_Section_accelerate.html of the manual for
|
||||
more instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
||||
|
||||
This pair style does not support the "pair_modify"_pair_modify.html
|
||||
shift, table, and tail options.
|
||||
|
||||
This pair style does not write its information to "binary restart
|
||||
files"_restart.html, since it is stored in potential files. Thus, you
|
||||
need to re-specify the pair_style and pair_coeff commands in an input
|
||||
script that reads a restart file.
|
||||
|
||||
This pair style can only be used via the {pair} keyword of the
|
||||
"run_style respa"_run_style.html command. It does not support the
|
||||
{inner}, {middle}, {outer} keywords.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
Currently, only elemental systems are implemented. Also, the method only
|
||||
provides access to the forces and not energies or stresses. However, one
|
||||
can access the energy via thermodynamic integration of the forces as
|
||||
discussed in "(Botu3)"_#Botu2016construct. This pair style is part
|
||||
of the USER-MISC package. It is only enabled if LAMMPS was built with
|
||||
that package. See the "Making LAMMPS"_Section_start.html#start_3 section
|
||||
for more info.
|
||||
|
||||
The AGNI force field files provided with LAMMPS (see the
|
||||
potentials directory) are parameterized for metal "units"_units.html.
|
||||
You can use the AGNI potential with any LAMMPS units, but you would need
|
||||
to create your own AGNI potential file with coefficients listed in the
|
||||
appropriate units if your simulation doesn't use "metal" units.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Botu2015adaptive)
|
||||
[(Botu1)] V. Botu and R. Ramprasad, Int. J. Quant. Chem., 115(16), 1074 (2015).
|
||||
|
||||
:link(Botu2015learning)
|
||||
[(Botu2)] V. Botu and R. Ramprasad, Phys. Rev. B, 92(9), 094306 (2015).
|
||||
|
||||
:link(Botu2016construct)
|
||||
[(Botu3)] V. Botu, R. Batra, J. Chapman and R. Ramprasad, https://arxiv.org/abs/1610.02098 (2016).
|
||||
|
|
@ -7,32 +7,43 @@
|
|||
:line
|
||||
|
||||
pair_style tersoff/mod command :h3
|
||||
pair_style tersoff/mod/c command :h3
|
||||
pair_style tersoff/mod/gpu command :h3
|
||||
pair_style tersoff/mod/kk command :h3
|
||||
pair_style tersoff/mod/omp command :h3
|
||||
pair_style tersoff/mod/c/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style tersoff/mod :pre
|
||||
|
||||
pair_style tersoff/mod/c :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style tersoff/mod
|
||||
pair_coeff * * Si.tersoff.mod Si Si :pre
|
||||
|
||||
pair_style tersoff/mod/c
|
||||
pair_coeff * * Si.tersoff.modc Si Si :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {tersoff/mod} style computes a bond-order type interatomic
|
||||
potential "(Kumagai)"_#Kumagai based on a 3-body Tersoff potential
|
||||
"(Tersoff_1)"_#Tersoff_1, "(Tersoff_2)"_#Tersoff_2 with modified
|
||||
cutoff function and angular-dependent term, giving the energy E of a
|
||||
system of atoms as
|
||||
The {tersoff/mod} and {tersoff/mod/c} styles computes a bond-order type
|
||||
interatomic potential "(Kumagai)"_#Kumagai based on a 3-body Tersoff
|
||||
potential "(Tersoff_1)"_#Tersoff_1, "(Tersoff_2)"_#Tersoff_2 with
|
||||
modified cutoff function and angular-dependent term, giving the energy
|
||||
E of a system of atoms as
|
||||
|
||||
:c,image(Eqs/pair_tersoff_mod.jpg)
|
||||
|
||||
where f_R is a two-body term and f_A includes three-body interactions.
|
||||
The summations in the formula are over all neighbors J and K of atom I
|
||||
within a cutoff distance = R + D.
|
||||
The {tersoff/mod/c} style differs from {tersoff/mod} only in the
|
||||
formulation of the V_ij term, where it contains an additional c0 term.
|
||||
|
||||
:c,image(Eqs/pair_tersoff_mod_c.jpg)
|
||||
|
||||
The modified cutoff function f_C proposed by "(Murty)"_#Murty and
|
||||
having a continuous second-order differential is employed. The
|
||||
|
|
@ -69,10 +80,11 @@ are placeholders for atom types that will be used with other
|
|||
potentials.
|
||||
|
||||
Tersoff/MOD file in the {potentials} directory of the LAMMPS
|
||||
distribution have a ".tersoff.mod" suffix. Lines that are not blank
|
||||
or comments (starting with #) define parameters for a triplet of
|
||||
elements. The parameters in a single entry correspond to coefficients
|
||||
in the formula above:
|
||||
distribution have a ".tersoff.mod" suffix. Potential files for the
|
||||
{tersoff/mod/c} style have the suffix ".tersoff.modc". Lines that are
|
||||
not blank or comments (starting with #) define parameters for a triplet
|
||||
of elements. The parameters in a single entry correspond to
|
||||
coefficients in the formulae above:
|
||||
|
||||
element 1 (the center atom in a 3-body interaction)
|
||||
element 2 (the atom bonded to the center atom)
|
||||
|
|
@ -93,13 +105,15 @@ c1
|
|||
c2
|
||||
c3
|
||||
c4
|
||||
c5 :ul
|
||||
c5
|
||||
c0 (energy units, tersoff/mod/c only):ul
|
||||
|
||||
The n, eta, lambda2, B, lambda1, and A parameters are only used for
|
||||
two-body interactions. The beta, alpha, c1, c2, c3, c4, c5, h
|
||||
parameters are only used for three-body interactions. The R and D
|
||||
parameters are used for both two-body and three-body interactions. The
|
||||
non-annotated parameters are unitless.
|
||||
parameters are used for both two-body and three-body interactions.
|
||||
The c0 term applies to {tersoff/mod/c} only. The non-annotated
|
||||
parameters are unitless.
|
||||
|
||||
The Tersoff/MOD potential file must contain entries for all the elements
|
||||
listed in the pair_coeff command. It can also contain entries for
|
||||
|
|
|
|||
|
|
@ -8,6 +8,7 @@
|
|||
|
||||
pair_style vashishta command :h3
|
||||
pair_style vashishta/omp command :h3
|
||||
pair_style vashishta/kk command :h3
|
||||
pair_style vashishta/table command :h3
|
||||
pair_style vashishta/table/omp command :h3
|
||||
|
||||
|
|
|
|||
|
|
@ -6,6 +6,7 @@ Pair Styles :h1
|
|||
:maxdepth: 1
|
||||
|
||||
pair_adp
|
||||
pair_agni
|
||||
pair_airebo
|
||||
pair_awpmd
|
||||
pair_beck
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,197 @@
|
|||
Data File created from VASP POSCAR
|
||||
|
||||
181 atoms
|
||||
1 atom types
|
||||
|
||||
0 17.121440767 xlo xhi
|
||||
0 14.8276026536 ylo yhi
|
||||
0 39.3197318979 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 26.982
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 0.0 1.64751140595 15.0
|
||||
2 1 2.85357346116 1.64751140595 15.0
|
||||
3 1 5.70714692232 1.64751140595 15.0
|
||||
4 1 8.56072038348 1.64751140595 15.0
|
||||
5 1 11.4142938446 1.64751140595 15.0
|
||||
6 1 14.2678673058 1.64751140595 15.0
|
||||
7 1 1.42678673058 4.11877851488 15.0
|
||||
8 1 4.28036019174 4.11877851488 15.0
|
||||
9 1 7.1339336529 4.11877851488 15.0
|
||||
10 1 9.98750711406 4.11877851488 15.0
|
||||
11 1 12.8410805752 4.11877851488 15.0
|
||||
12 1 15.6946540364 4.11877851488 15.0
|
||||
13 1 0.0 6.59004562381 15.0
|
||||
14 1 2.85357346116 6.59004562381 15.0
|
||||
15 1 5.70714692232 6.59004562381 15.0
|
||||
16 1 8.56072038348 6.59004562381 15.0
|
||||
17 1 11.4142938446 6.59004562381 15.0
|
||||
18 1 14.2678673058 6.59004562381 15.0
|
||||
19 1 1.42678673058 9.06131273274 15.0
|
||||
20 1 4.28036019174 9.06131273274 15.0
|
||||
21 1 7.1339336529 9.06131273274 15.0
|
||||
22 1 9.98750711406 9.06131273274 15.0
|
||||
23 1 12.8410805752 9.06131273274 15.0
|
||||
24 1 15.6946540364 9.06131273274 15.0
|
||||
25 1 0.0 11.5325798417 15.0
|
||||
26 1 2.85357346116 11.5325798417 15.0
|
||||
27 1 5.70714692232 11.5325798417 15.0
|
||||
28 1 8.56072038348 11.5325798417 15.0
|
||||
29 1 11.4142938446 11.5325798417 15.0
|
||||
30 1 14.2678673058 11.5325798417 15.0
|
||||
31 1 1.42678673058 14.0038469506 15.0
|
||||
32 1 4.28036019174 14.0038469506 15.0
|
||||
33 1 7.1339336529 14.0038469506 15.0
|
||||
34 1 9.98750711406 14.0038469506 15.0
|
||||
35 1 12.8410805752 14.0038469506 15.0
|
||||
36 1 15.6946540364 14.0038469506 15.0
|
||||
37 1 0.0 0.0 17.3299329745
|
||||
38 1 2.85357346116 0.0 17.3299329745
|
||||
39 1 5.70714692232 0.0 17.3299329745
|
||||
40 1 8.56072038348 0.0 17.3299329745
|
||||
41 1 11.4142938446 0.0 17.3299329745
|
||||
42 1 14.2678673058 0.0 17.3299329745
|
||||
43 1 1.42678673058 2.47126710893 17.3299329745
|
||||
44 1 4.28036019174 2.47126710893 17.3299329745
|
||||
45 1 7.1339336529 2.47126710893 17.3299329745
|
||||
46 1 9.98750711406 2.47126710893 17.3299329745
|
||||
47 1 12.8410805752 2.47126710893 17.3299329745
|
||||
48 1 15.6946540364 2.47126710893 17.3299329745
|
||||
49 1 0.0 4.94253421786 17.3299329745
|
||||
50 1 2.85357346116 4.94253421786 17.3299329745
|
||||
51 1 5.70714692232 4.94253421786 17.3299329745
|
||||
52 1 8.56072038348 4.94253421786 17.3299329745
|
||||
53 1 11.4142938446 4.94253421786 17.3299329745
|
||||
54 1 14.2678673058 4.94253421786 17.3299329745
|
||||
55 1 1.42678673058 7.41380132679 17.3299329745
|
||||
56 1 4.28036019174 7.41380132679 17.3299329745
|
||||
57 1 7.1339336529 7.41380132679 17.3299329745
|
||||
58 1 9.98750711406 7.41380132679 17.3299329745
|
||||
59 1 12.8410805752 7.41380132679 17.3299329745
|
||||
60 1 15.6946540364 7.41380132679 17.3299329745
|
||||
61 1 0.0 9.88506843572 17.3299329745
|
||||
62 1 2.85357346116 9.88506843572 17.3299329745
|
||||
63 1 5.70714692232 9.88506843572 17.3299329745
|
||||
64 1 8.56072038348 9.88506843572 17.3299329745
|
||||
65 1 11.4142938446 9.88506843572 17.3299329745
|
||||
66 1 14.2678673058 9.88506843572 17.3299329745
|
||||
67 1 1.42678673058 12.3563355446 17.3299329745
|
||||
68 1 4.28036019174 12.3563355446 17.3299329745
|
||||
69 1 7.1339336529 12.3563355446 17.3299329745
|
||||
70 1 9.98750711406 12.3563355446 17.3299329745
|
||||
71 1 12.8410805752 12.3563355446 17.3299329745
|
||||
72 1 15.6946540364 12.3563355446 17.3299329745
|
||||
73 1 1.42678673058 0.823755702976 19.6598659489
|
||||
74 1 4.28036019174 0.823755702976 19.6598659489
|
||||
75 1 7.1339336529 0.823755702976 19.6598659489
|
||||
76 1 9.98750711406 0.823755702976 19.6598659489
|
||||
77 1 12.8410805752 0.823755702976 19.6598659489
|
||||
78 1 15.6946540364 0.823755702976 19.6598659489
|
||||
79 1 0.0 3.29502281191 19.6598659489
|
||||
80 1 2.85357346116 3.29502281191 19.6598659489
|
||||
81 1 5.70714692232 3.29502281191 19.6598659489
|
||||
82 1 8.56072038348 3.29502281191 19.6598659489
|
||||
83 1 11.4142938446 3.29502281191 19.6598659489
|
||||
84 1 14.2678673058 3.29502281191 19.6598659489
|
||||
85 1 1.42678673058 5.76628992084 19.6598659489
|
||||
86 1 4.28036019174 5.76628992084 19.6598659489
|
||||
87 1 7.1339336529 5.76628992084 19.6598659489
|
||||
88 1 9.98750711406 5.76628992084 19.6598659489
|
||||
89 1 12.8410805752 5.76628992084 19.6598659489
|
||||
90 1 15.6946540364 5.76628992084 19.6598659489
|
||||
91 1 0.0 8.23755702976 19.6598659489
|
||||
92 1 2.85357346116 8.23755702976 19.6598659489
|
||||
93 1 5.70714692232 8.23755702976 19.6598659489
|
||||
94 1 8.56072038348 8.23755702976 19.6598659489
|
||||
95 1 11.4142938446 8.23755702976 19.6598659489
|
||||
96 1 14.2678673058 8.23755702976 19.6598659489
|
||||
97 1 1.42678673058 10.7088241387 19.6598659489
|
||||
98 1 4.28036019174 10.7088241387 19.6598659489
|
||||
99 1 7.1339336529 10.7088241387 19.6598659489
|
||||
100 1 9.98750711406 10.7088241387 19.6598659489
|
||||
101 1 12.8410805752 10.7088241387 19.6598659489
|
||||
102 1 15.6946540364 10.7088241387 19.6598659489
|
||||
103 1 0.0 13.1800912476 19.6598659489
|
||||
104 1 2.85357346116 13.1800912476 19.6598659489
|
||||
105 1 5.70714692232 13.1800912476 19.6598659489
|
||||
106 1 8.56072038348 13.1800912476 19.6598659489
|
||||
107 1 11.4142938446 13.1800912476 19.6598659489
|
||||
108 1 14.2678673058 13.1800912476 19.6598659489
|
||||
109 1 0.0 1.64751140595 21.9897989234
|
||||
110 1 2.85357346116 1.64751140595 21.9897989234
|
||||
111 1 5.70714692232 1.64751140595 21.9897989234
|
||||
112 1 8.56072038348 1.64751140595 21.9897989234
|
||||
113 1 11.4142938446 1.64751140595 21.9897989234
|
||||
114 1 14.2678673058 1.64751140595 21.9897989234
|
||||
115 1 1.42678673058 4.11877851488 21.9897989234
|
||||
116 1 4.28036019174 4.11877851488 21.9897989234
|
||||
117 1 7.1339336529 4.11877851488 21.9897989234
|
||||
118 1 9.98750711406 4.11877851488 21.9897989234
|
||||
119 1 12.8410805752 4.11877851488 21.9897989234
|
||||
120 1 15.6946540364 4.11877851488 21.9897989234
|
||||
121 1 0.0 6.59004562381 21.9897989234
|
||||
122 1 2.85357346116 6.59004562381 21.9897989234
|
||||
123 1 5.70714692232 6.59004562381 21.9897989234
|
||||
124 1 8.56072038348 6.59004562381 21.9897989234
|
||||
125 1 11.4142938446 6.59004562381 21.9897989234
|
||||
126 1 14.2678673058 6.59004562381 21.9897989234
|
||||
127 1 1.42678673058 9.06131273274 21.9897989234
|
||||
128 1 4.28036019174 9.06131273274 21.9897989234
|
||||
129 1 7.1339336529 9.06131273274 21.9897989234
|
||||
130 1 9.98750711406 9.06131273274 21.9897989234
|
||||
131 1 12.8410805752 9.06131273274 21.9897989234
|
||||
132 1 15.6946540364 9.06131273274 21.9897989234
|
||||
133 1 0.0 11.5325798417 21.9897989234
|
||||
134 1 2.85357346116 11.5325798417 21.9897989234
|
||||
135 1 5.70714692232 11.5325798417 21.9897989234
|
||||
136 1 8.56072038348 11.5325798417 21.9897989234
|
||||
137 1 11.4142938446 11.5325798417 21.9897989234
|
||||
138 1 14.2678673058 11.5325798417 21.9897989234
|
||||
139 1 1.42678673058 14.0038469506 21.9897989234
|
||||
140 1 4.28036019174 14.0038469506 21.9897989234
|
||||
141 1 7.1339336529 14.0038469506 21.9897989234
|
||||
142 1 9.98750711406 14.0038469506 21.9897989234
|
||||
143 1 12.8410805752 14.0038469506 21.9897989234
|
||||
144 1 15.6946540364 14.0038469506 21.9897989234
|
||||
145 1 0.0 0.0 24.3197318979
|
||||
146 1 2.85357346116 0.0 24.3197318979
|
||||
147 1 5.70714692232 0.0 24.3197318979
|
||||
148 1 8.56072038348 0.0 24.3197318979
|
||||
149 1 11.4142938446 0.0 24.3197318979
|
||||
150 1 14.2678673058 0.0 24.3197318979
|
||||
151 1 1.42678673058 2.47126710893 24.3197318979
|
||||
152 1 4.28036019174 2.47126710893 24.3197318979
|
||||
153 1 7.1339336529 2.47126710893 24.3197318979
|
||||
154 1 9.98750711406 2.47126710893 24.3197318979
|
||||
155 1 12.8410805752 2.47126710893 24.3197318979
|
||||
156 1 15.6946540364 2.47126710893 24.3197318979
|
||||
157 1 0.0 4.94253421786 24.3197318979
|
||||
158 1 2.85357346116 4.94253421786 24.3197318979
|
||||
159 1 5.70714692232 4.94253421786 24.3197318979
|
||||
160 1 8.56072038348 4.94253421786 24.3197318979
|
||||
161 1 11.4142938446 4.94253421786 24.3197318979
|
||||
162 1 14.2678673058 4.94253421786 24.3197318979
|
||||
163 1 1.42678673058 7.41380132679 24.3197318979
|
||||
164 1 4.28036019174 7.41380132679 24.3197318979
|
||||
165 1 7.1339336529 7.41380132679 24.3197318979
|
||||
166 1 9.98750711406 7.41380132679 24.3197318979
|
||||
167 1 12.8410805752 7.41380132679 24.3197318979
|
||||
168 1 15.6946540364 7.41380132679 24.3197318979
|
||||
169 1 0.0 9.88506843572 24.3197318979
|
||||
170 1 2.85357346116 9.88506843572 24.3197318979
|
||||
171 1 5.70714692232 9.88506843572 24.3197318979
|
||||
172 1 8.56072038348 9.88506843572 24.3197318979
|
||||
173 1 11.4142938446 9.88506843572 24.3197318979
|
||||
174 1 14.2678673058 9.88506843572 24.3197318979
|
||||
175 1 1.42678673058 12.3563355446 24.3197318979
|
||||
176 1 4.28036019174 12.3563355446 24.3197318979
|
||||
177 1 7.1339336529 12.3563355446 24.3197318979
|
||||
178 1 9.98750711406 12.3563355446 24.3197318979
|
||||
179 1 12.8410805752 12.3563355446 24.3197318979
|
||||
180 1 15.6946540364 12.3563355446 24.3197318979
|
||||
181 1 7.1339336529 4.11877851488 26.7197318979
|
||||
|
||||
|
|
@ -0,0 +1,23 @@
|
|||
|
||||
processors * * 1
|
||||
units metal
|
||||
boundary p p f
|
||||
read_data adatom.data
|
||||
|
||||
pair_style agni
|
||||
pair_coeff * * Al_prb.agni Al
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 2 check yes
|
||||
|
||||
timestep 0.0005
|
||||
velocity all create 500 12345
|
||||
fix 1 all nvt temp 250 250 0.2
|
||||
fix 5 all momentum 1 linear 1 1 1
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step ke temp
|
||||
|
||||
# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
|
||||
|
||||
run 1000
|
||||
|
|
@ -0,0 +1,23 @@
|
|||
|
||||
units metal
|
||||
boundary p p p
|
||||
read_data vacancy.data
|
||||
|
||||
pair_style agni
|
||||
pair_coeff * * Al_prb.agni Al
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 2 check yes
|
||||
|
||||
|
||||
timestep 0.0005
|
||||
velocity all create 1000 12345
|
||||
fix 1 all nvt temp 900 900 200
|
||||
fix 5 all momentum 1 linear 1 1 1
|
||||
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step ke etotal temp
|
||||
|
||||
# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
|
||||
|
||||
run 1000
|
||||
|
|
@ -0,0 +1,82 @@
|
|||
LAMMPS (9 Nov 2016)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
processors * * 1
|
||||
units metal
|
||||
boundary p p f
|
||||
read_data adatom.data
|
||||
orthogonal box = (0 0 0) to (17.1214 14.8276 39.3197)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
181 atoms
|
||||
|
||||
pair_style agni
|
||||
pair_coeff * * Al_prb.agni Al
|
||||
Reading potential file Al_prb.agni with DATE: 2016-11-11
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 2 check yes
|
||||
|
||||
timestep 0.0005
|
||||
velocity all create 500 12345
|
||||
fix 1 all nvt temp 250 250 0.2
|
||||
fix 5 all momentum 1 linear 1 1 1
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step ke temp
|
||||
|
||||
# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
|
||||
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 2 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.3
|
||||
ghost atom cutoff = 8.3
|
||||
binsize = 4.15 -> bins = 5 4 10
|
||||
Memory usage per processor = 2.37049 Mbytes
|
||||
Step KinEng Temp
|
||||
0 11.633413 500
|
||||
100 4.049974 174.06646
|
||||
200 5.8983472 253.50889
|
||||
300 5.3667309 230.66021
|
||||
400 4.9343935 212.0785
|
||||
500 5.4054496 232.32432
|
||||
600 6.1779127 265.52452
|
||||
700 6.3749266 273.9921
|
||||
800 6.0701481 260.89283
|
||||
900 6.4582394 277.57286
|
||||
1000 6.4047444 275.27366
|
||||
Loop time of 20.8273 on 1 procs for 1000 steps with 181 atoms
|
||||
|
||||
Performance: 2.074 ns/day, 11.571 hours/ns, 48.014 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 20.79 | 20.79 | 20.79 | 0.0 | 99.82
|
||||
Neigh | 0.022742 | 0.022742 | 0.022742 | 0.0 | 0.11
|
||||
Comm | 0.0040836 | 0.0040836 | 0.0040836 | 0.0 | 0.02
|
||||
Output | 0.00011086 | 0.00011086 | 0.00011086 | 0.0 | 0.00
|
||||
Modify | 0.0089345 | 0.0089345 | 0.0089345 | 0.0 | 0.04
|
||||
Other | | 0.001819 | | | 0.01
|
||||
|
||||
Nlocal: 181 ave 181 max 181 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 562 ave 562 max 562 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 18810 ave 18810 max 18810 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 18810
|
||||
Ave neighs/atom = 103.923
|
||||
Neighbor list builds = 33
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:20
|
||||
|
|
@ -0,0 +1,82 @@
|
|||
LAMMPS (9 Nov 2016)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
processors * * 1
|
||||
units metal
|
||||
boundary p p f
|
||||
read_data adatom.data
|
||||
orthogonal box = (0 0 0) to (17.1214 14.8276 39.3197)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
181 atoms
|
||||
|
||||
pair_style agni
|
||||
pair_coeff * * Al_prb.agni Al
|
||||
Reading potential file Al_prb.agni with DATE: 2016-11-11
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 2 check yes
|
||||
|
||||
timestep 0.0005
|
||||
velocity all create 500 12345
|
||||
fix 1 all nvt temp 250 250 0.2
|
||||
fix 5 all momentum 1 linear 1 1 1
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step ke temp
|
||||
|
||||
# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
|
||||
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 2 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.3
|
||||
ghost atom cutoff = 8.3
|
||||
binsize = 4.15 -> bins = 5 4 10
|
||||
Memory usage per processor = 2.48695 Mbytes
|
||||
Step KinEng Temp
|
||||
0 11.633413 500
|
||||
100 4.049974 174.06646
|
||||
200 5.8983472 253.50889
|
||||
300 5.3667309 230.66021
|
||||
400 4.9343935 212.0785
|
||||
500 5.4054496 232.32432
|
||||
600 6.1779127 265.52451
|
||||
700 6.3749266 273.9921
|
||||
800 6.0701481 260.89283
|
||||
900 6.4582394 277.57286
|
||||
1000 6.4047444 275.27366
|
||||
Loop time of 5.96868 on 4 procs for 1000 steps with 181 atoms
|
||||
|
||||
Performance: 7.238 ns/day, 3.316 hours/ns, 167.541 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.4176 | 5.4602 | 5.5505 | 2.3 | 91.48
|
||||
Neigh | 0.0056074 | 0.0060464 | 0.0062635 | 0.3 | 0.10
|
||||
Comm | 0.39544 | 0.48696 | 0.53111 | 7.9 | 8.16
|
||||
Output | 0.0001545 | 0.00015736 | 0.0001595 | 0.0 | 0.00
|
||||
Modify | 0.010492 | 0.011565 | 0.012588 | 0.9 | 0.19
|
||||
Other | | 0.003794 | | | 0.06
|
||||
|
||||
Nlocal: 45.25 ave 47 max 42 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 2 1
|
||||
Nghost: 374.75 ave 380 max 373 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 4702.5 ave 4868 max 4389 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 1 1
|
||||
|
||||
Total # of neighbors = 18810
|
||||
Ave neighs/atom = 103.923
|
||||
Neighbor list builds = 33
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:05
|
||||
|
|
@ -0,0 +1,82 @@
|
|||
LAMMPS (9 Nov 2016)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
read_data vac.data
|
||||
orthogonal box = (0 0 0) to (8.07113 8.07113 8.07113)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
31 atoms
|
||||
|
||||
pair_style agni
|
||||
pair_coeff * * Al_prb.agni Al
|
||||
Reading potential file Al_prb.agni with DATE: 2016-11-11
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 2 check yes
|
||||
|
||||
|
||||
timestep 0.0005
|
||||
velocity all create 1000 12345
|
||||
fix 1 all nvt temp 900 900 200
|
||||
fix 5 all momentum 1 linear 1 1 1
|
||||
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step ke etotal temp
|
||||
|
||||
# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
|
||||
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 2 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.3
|
||||
ghost atom cutoff = 8.3
|
||||
binsize = 4.15 -> bins = 2 2 2
|
||||
Memory usage per processor = 2.40842 Mbytes
|
||||
Step KinEng TotEng Temp
|
||||
0 3.8778043 3.8778043 1000
|
||||
100 2.8126642 2.8126642 725.32391
|
||||
200 3.7110413 3.7110413 956.9955
|
||||
300 3.2361084 3.2361084 834.52081
|
||||
400 3.4625769 3.4625769 892.92201
|
||||
500 3.4563307 3.4563307 891.31126
|
||||
600 2.8486344 2.8486344 734.59982
|
||||
700 3.1183057 3.1183057 804.14208
|
||||
800 2.9164818 2.9164818 752.09618
|
||||
900 3.464416 3.464416 893.39629
|
||||
1000 3.5954546 3.5954546 927.18825
|
||||
Loop time of 3.86777 on 1 procs for 1000 steps with 31 atoms
|
||||
|
||||
Performance: 11.169 ns/day, 2.149 hours/ns, 258.547 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.8463 | 3.8463 | 3.8463 | 0.0 | 99.44
|
||||
Neigh | 0.011294 | 0.011294 | 0.011294 | 0.0 | 0.29
|
||||
Comm | 0.0057271 | 0.0057271 | 0.0057271 | 0.0 | 0.15
|
||||
Output | 0.00014257 | 0.00014257 | 0.00014257 | 0.0 | 0.00
|
||||
Modify | 0.0029459 | 0.0029459 | 0.0029459 | 0.0 | 0.08
|
||||
Other | | 0.001395 | | | 0.04
|
||||
|
||||
Nlocal: 31 ave 31 max 31 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 878 ave 878 max 878 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 4334 ave 4334 max 4334 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 4334
|
||||
Ave neighs/atom = 139.806
|
||||
Neighbor list builds = 51
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:03
|
||||
|
|
@ -0,0 +1,82 @@
|
|||
LAMMPS (9 Nov 2016)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
read_data vac.data
|
||||
orthogonal box = (0 0 0) to (8.07113 8.07113 8.07113)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
31 atoms
|
||||
|
||||
pair_style agni
|
||||
pair_coeff * * Al_prb.agni Al
|
||||
Reading potential file Al_prb.agni with DATE: 2016-11-11
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 2 check yes
|
||||
|
||||
|
||||
timestep 0.0005
|
||||
velocity all create 1000 12345
|
||||
fix 1 all nvt temp 900 900 200
|
||||
fix 5 all momentum 1 linear 1 1 1
|
||||
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step ke etotal temp
|
||||
|
||||
# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
|
||||
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 2 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.3
|
||||
ghost atom cutoff = 8.3
|
||||
binsize = 4.15 -> bins = 2 2 2
|
||||
Memory usage per processor = 2.3974 Mbytes
|
||||
Step KinEng TotEng Temp
|
||||
0 3.8778044 3.8778044 1000
|
||||
100 2.8126642 2.8126642 725.32391
|
||||
200 3.7110413 3.7110413 956.99549
|
||||
300 3.2361084 3.2361084 834.52081
|
||||
400 3.4625769 3.4625769 892.92201
|
||||
500 3.4563307 3.4563307 891.31126
|
||||
600 2.8486343 2.8486343 734.59981
|
||||
700 3.1183057 3.1183057 804.14208
|
||||
800 2.9164819 2.9164819 752.09618
|
||||
900 3.4644161 3.4644161 893.39631
|
||||
1000 3.5954546 3.5954546 927.18824
|
||||
Loop time of 1.11007 on 4 procs for 1000 steps with 31 atoms
|
||||
|
||||
Performance: 38.916 ns/day, 0.617 hours/ns, 900.843 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.906 | 0.99469 | 1.0291 | 5.1 | 89.61
|
||||
Neigh | 0.0026186 | 0.0027665 | 0.0028622 | 0.2 | 0.25
|
||||
Comm | 0.066125 | 0.10079 | 0.1896 | 16.2 | 9.08
|
||||
Output | 0.00012875 | 0.00014615 | 0.00018787 | 0.2 | 0.01
|
||||
Modify | 0.0080338 | 0.0083079 | 0.00861 | 0.2 | 0.75
|
||||
Other | | 0.003372 | | | 0.30
|
||||
|
||||
Nlocal: 7.75 ave 8 max 7 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Nghost: 623.5 ave 630 max 616 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1083.5 ave 1131 max 988 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 1 1
|
||||
|
||||
Total # of neighbors = 4334
|
||||
Ave neighs/atom = 139.806
|
||||
Neighbor list builds = 51
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:01
|
||||
|
|
@ -0,0 +1,46 @@
|
|||
Data File created from VASP POSCAR
|
||||
|
||||
31 atoms
|
||||
1 atom types
|
||||
|
||||
0 8.071125 xlo xhi
|
||||
0 8.071125 ylo yhi
|
||||
0 8.071125 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 26.9815
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 8.05711986217 3.20498589607 7.09652861184
|
||||
2 1 8.05262255028 3.62006786258 3.16719841667
|
||||
3 1 2.08891866821 1.38430927213 3.14852514324
|
||||
4 1 4.25446836692 3.27689661974 3.35678388118
|
||||
5 1 7.92524269451 7.20500664579 3.03232792051
|
||||
6 1 6.04056771113 7.24499020906 1.11223380379
|
||||
7 1 2.32585852889 5.29910389395 7.31500292009
|
||||
8 1 2.09613190567 1.27658214906 7.44277603054
|
||||
9 1 3.96852985867 7.2805082905 3.37568009522
|
||||
10 1 0.0773420461671 1.29964047903 5.27451616984
|
||||
11 1 7.96501442334 1.24471347504 1.17853896176
|
||||
12 1 2.13035246804 5.36148411996 3.3817805118
|
||||
13 1 2.06211525033 7.25482811482 1.52039033766
|
||||
14 1 3.99735704234 7.4099829467 7.05753768668
|
||||
15 1 3.84113228596 5.1855444403 1.41642147402
|
||||
16 1 0.231862769544 5.38528175164 5.51171817022
|
||||
17 1 0.12718452785 5.35814065671 1.11669573581
|
||||
18 1 8.05303937039 7.38861123542 7.41398359808
|
||||
19 1 1.88506066609 3.17578974033 1.20929473631
|
||||
20 1 4.33739926831 1.37976783613 5.28141762358
|
||||
21 1 2.23200994743 3.12419127088 5.36881641316
|
||||
22 1 6.22871004896 1.34968648416 7.24032447626
|
||||
23 1 6.08380394159 1.16222146146 3.30535465675
|
||||
24 1 6.16629028099 5.22806528503 3.7675179617
|
||||
25 1 4.30194966153 1.14526017671 1.45054175732
|
||||
26 1 6.24221620153 5.05377575942 7.17573714759
|
||||
27 1 3.92820642281 2.9627641757 7.71515743722
|
||||
28 1 4.33686872315 4.73096617728 5.57649231331
|
||||
29 1 6.05033104136 3.51389714904 1.34127903322
|
||||
30 1 6.27311587476 7.19257797516 5.46814369382
|
||||
31 1 1.81274009101 7.47392095028 5.35484578074
|
||||
|
|
@ -114,3 +114,35 @@ neighbor 1.0 bin
|
|||
neigh_modify every 1 delay 10 check yes
|
||||
run 100
|
||||
|
||||
# Test Tersoff/Mod model for Si
|
||||
|
||||
clear
|
||||
read_restart restart.equil
|
||||
|
||||
pair_style tersoff/mod
|
||||
pair_coeff * * Si.tersoff.mod 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
|
||||
|
||||
# Test Tersoff/Mod/C model for Si
|
||||
|
||||
clear
|
||||
read_restart restart.equil
|
||||
|
||||
pair_style tersoff/mod/c
|
||||
pair_coeff * * Si.tersoff.modc 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
|
||||
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,10 @@
|
|||
# DATE: 2016-11-09 CONTRIBUTOR: Ganga P Purja Pun (George Mason University, Fairfax) CITATION: Unknown
|
||||
#
|
||||
# Format:
|
||||
# element1 element2 element3
|
||||
# beta alpha h eta
|
||||
# beta_ters lam2 B R D lam1 A
|
||||
# n c1 c2 c3 c4 c5 C
|
||||
Si Si Si 3.00000000 1.80536502 -0.38136087 2.16152496
|
||||
1 1.39343356 117.78072440 2.87478837 0.33090566 3.18011795 3198.51383127
|
||||
1.98633876 0.20123243 614230.04310619 996439.09714140 3.33560562 25.20963770 -0.00592042
|
||||
|
|
@ -539,6 +539,8 @@
|
|||
|
||||
/pair_adp.cpp
|
||||
/pair_adp.h
|
||||
/pair_agni.cpp
|
||||
/pair_agni.h
|
||||
/pair_airebo.cpp
|
||||
/pair_airebo.h
|
||||
/pair_airebo_morse.cpp
|
||||
|
|
|
|||
|
|
@ -53,6 +53,7 @@ fi
|
|||
|
||||
if (test $1 = "CLASS2") then
|
||||
depend GPU
|
||||
depend KOKKOS
|
||||
depend USER-OMP
|
||||
fi
|
||||
|
||||
|
|
|
|||
|
|
@ -169,6 +169,8 @@ action pair_reax_c_kokkos.cpp pair_reax_c.cpp
|
|||
action pair_reax_c_kokkos.h pair_reax_c.h
|
||||
action pair_sw_kokkos.cpp pair_sw.cpp
|
||||
action pair_sw_kokkos.h pair_sw.h
|
||||
action pair_vashishta_kokkos.cpp pair_vashishta.cpp
|
||||
action pair_vashishta_kokkos.h pair_vashishta.h
|
||||
action pair_table_kokkos.cpp
|
||||
action pair_table_kokkos.h
|
||||
action pair_tersoff_kokkos.cpp pair_tersoff.cpp
|
||||
|
|
|
|||
|
|
@ -83,8 +83,13 @@ class AtomVecKokkos : public AtomVec {
|
|||
std::is_same<typename ViewType::execution_space,LMPDeviceType>::value,
|
||||
Kokkos::CudaHostPinnedSpace,typename ViewType::memory_space>::type,
|
||||
Kokkos::MemoryTraits<Kokkos::Unmanaged> > mirror_type;
|
||||
if(buffer_size < src.capacity())
|
||||
if (buffer_size == 0) {
|
||||
buffer = Kokkos::kokkos_malloc<Kokkos::CudaHostPinnedSpace>(src.capacity());
|
||||
buffer_size = src.capacity();
|
||||
} else if (buffer_size < src.capacity()) {
|
||||
buffer = Kokkos::kokkos_realloc<Kokkos::CudaHostPinnedSpace>(buffer,src.capacity());
|
||||
buffer_size = src.capacity();
|
||||
}
|
||||
return mirror_type( buffer ,
|
||||
src.dimension_0() ,
|
||||
src.dimension_1() ,
|
||||
|
|
@ -104,8 +109,13 @@ class AtomVecKokkos : public AtomVec {
|
|||
std::is_same<typename ViewType::execution_space,LMPDeviceType>::value,
|
||||
Kokkos::CudaHostPinnedSpace,typename ViewType::memory_space>::type,
|
||||
Kokkos::MemoryTraits<Kokkos::Unmanaged> > mirror_type;
|
||||
if(buffer_size < src.capacity())
|
||||
if (buffer_size == 0) {
|
||||
buffer = Kokkos::kokkos_malloc<Kokkos::CudaHostPinnedSpace>(src.capacity()*sizeof(typename ViewType::value_type));
|
||||
buffer_size = src.capacity();
|
||||
} else if (buffer_size < src.capacity()) {
|
||||
buffer = Kokkos::kokkos_realloc<Kokkos::CudaHostPinnedSpace>(buffer,src.capacity()*sizeof(typename ViewType::value_type));
|
||||
buffer_size = src.capacity();
|
||||
}
|
||||
mirror_type tmp_view( (typename ViewType::value_type*)buffer ,
|
||||
src.dimension_0() ,
|
||||
src.dimension_1() ,
|
||||
|
|
|
|||
|
|
@ -21,6 +21,11 @@
|
|||
#include "atom_masks.h"
|
||||
#include "error.h"
|
||||
#include "kokkos.h"
|
||||
#include "force.h"
|
||||
#include "bond.h"
|
||||
#include "angle.h"
|
||||
#include "dihedral.h"
|
||||
#include "improper.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -601,7 +606,19 @@ void NeighborKokkos::build_topology_kokkos() {
|
|||
k_anglelist.modify<LMPDeviceType>();
|
||||
k_dihedrallist.modify<LMPDeviceType>();
|
||||
k_improperlist.modify<LMPDeviceType>();
|
||||
} else {
|
||||
|
||||
// Transfer topology neighbor lists to Host for non-Kokkos styles
|
||||
|
||||
if (force->bond && force->bond->execution_space == Host)
|
||||
k_bondlist.sync<LMPHostType>();
|
||||
if (force->angle && force->angle->execution_space == Host)
|
||||
k_anglelist.sync<LMPHostType>();
|
||||
if (force->dihedral && force->dihedral->execution_space == Host)
|
||||
k_dihedrallist.sync<LMPHostType>();
|
||||
if (force->improper && force->improper->execution_space == Host)
|
||||
k_improperlist.sync<LMPHostType>();
|
||||
|
||||
} else {
|
||||
neighbond_host.build_topology_kk();
|
||||
|
||||
k_bondlist = neighbond_host.k_bondlist;
|
||||
|
|
|
|||
|
|
@ -126,26 +126,26 @@ void PairTersoffKokkos<DeviceType>::setup_params()
|
|||
for (i = 1; i <= n; i++)
|
||||
for (j = 1; j <= n; j++)
|
||||
for (k = 1; k <= n; k++) {
|
||||
m = elem2param[i-1][j-1][k-1];
|
||||
k_params.h_view(i,j,k).powerm = params[m].powerm;
|
||||
k_params.h_view(i,j,k).gamma = params[m].gamma;
|
||||
k_params.h_view(i,j,k).lam3 = params[m].lam3;
|
||||
k_params.h_view(i,j,k).c = params[m].c;
|
||||
k_params.h_view(i,j,k).d = params[m].d;
|
||||
k_params.h_view(i,j,k).h = params[m].h;
|
||||
k_params.h_view(i,j,k).powern = params[m].powern;
|
||||
k_params.h_view(i,j,k).beta = params[m].beta;
|
||||
k_params.h_view(i,j,k).lam2 = params[m].lam2;
|
||||
k_params.h_view(i,j,k).bigb = params[m].bigb;
|
||||
k_params.h_view(i,j,k).bigr = params[m].bigr;
|
||||
k_params.h_view(i,j,k).bigd = params[m].bigd;
|
||||
k_params.h_view(i,j,k).lam1 = params[m].lam1;
|
||||
k_params.h_view(i,j,k).biga = params[m].biga;
|
||||
k_params.h_view(i,j,k).cutsq = params[m].cutsq;
|
||||
k_params.h_view(i,j,k).c1 = params[m].c1;
|
||||
k_params.h_view(i,j,k).c2 = params[m].c2;
|
||||
k_params.h_view(i,j,k).c3 = params[m].c3;
|
||||
k_params.h_view(i,j,k).c4 = params[m].c4;
|
||||
m = elem2param[map[i]][map[j]][map[k]];
|
||||
k_params.h_view(i,j,k).powerm = params[m].powerm;
|
||||
k_params.h_view(i,j,k).gamma = params[m].gamma;
|
||||
k_params.h_view(i,j,k).lam3 = params[m].lam3;
|
||||
k_params.h_view(i,j,k).c = params[m].c;
|
||||
k_params.h_view(i,j,k).d = params[m].d;
|
||||
k_params.h_view(i,j,k).h = params[m].h;
|
||||
k_params.h_view(i,j,k).powern = params[m].powern;
|
||||
k_params.h_view(i,j,k).beta = params[m].beta;
|
||||
k_params.h_view(i,j,k).lam2 = params[m].lam2;
|
||||
k_params.h_view(i,j,k).bigb = params[m].bigb;
|
||||
k_params.h_view(i,j,k).bigr = params[m].bigr;
|
||||
k_params.h_view(i,j,k).bigd = params[m].bigd;
|
||||
k_params.h_view(i,j,k).lam1 = params[m].lam1;
|
||||
k_params.h_view(i,j,k).biga = params[m].biga;
|
||||
k_params.h_view(i,j,k).cutsq = params[m].cutsq;
|
||||
k_params.h_view(i,j,k).c1 = params[m].c1;
|
||||
k_params.h_view(i,j,k).c2 = params[m].c2;
|
||||
k_params.h_view(i,j,k).c3 = params[m].c3;
|
||||
k_params.h_view(i,j,k).c4 = params[m].c4;
|
||||
}
|
||||
|
||||
k_params.template modify<LMPHostType>();
|
||||
|
|
|
|||
|
|
@ -125,27 +125,27 @@ void PairTersoffMODKokkos<DeviceType>::setup_params()
|
|||
for (i = 1; i <= n; i++)
|
||||
for (j = 1; j <= n; j++)
|
||||
for (k = 1; k <= n; k++) {
|
||||
m = elem2param[i-1][j-1][k-1];
|
||||
k_params.h_view(i,j,k).powerm = params[m].powerm;
|
||||
k_params.h_view(i,j,k).lam3 = params[m].lam3;
|
||||
k_params.h_view(i,j,k).h = params[m].h;
|
||||
k_params.h_view(i,j,k).powern = params[m].powern;
|
||||
k_params.h_view(i,j,k).beta = params[m].beta;
|
||||
k_params.h_view(i,j,k).lam2 = params[m].lam2;
|
||||
k_params.h_view(i,j,k).bigb = params[m].bigb;
|
||||
k_params.h_view(i,j,k).bigr = params[m].bigr;
|
||||
k_params.h_view(i,j,k).bigd = params[m].bigd;
|
||||
k_params.h_view(i,j,k).lam1 = params[m].lam1;
|
||||
k_params.h_view(i,j,k).biga = params[m].biga;
|
||||
k_params.h_view(i,j,k).cutsq = params[m].cutsq;
|
||||
k_params.h_view(i,j,k).c1 = params[m].c1;
|
||||
k_params.h_view(i,j,k).c2 = params[m].c2;
|
||||
k_params.h_view(i,j,k).c3 = params[m].c3;
|
||||
k_params.h_view(i,j,k).c4 = params[m].c4;
|
||||
k_params.h_view(i,j,k).c5 = params[m].c5;
|
||||
k_params.h_view(i,j,k).ca1 = params[m].ca1;
|
||||
k_params.h_view(i,j,k).ca4 = params[m].ca4;
|
||||
k_params.h_view(i,j,k).powern_del = params[m].powern_del;
|
||||
m = elem2param[map[i]][map[j]][map[k]];
|
||||
k_params.h_view(i,j,k).powerm = params[m].powerm;
|
||||
k_params.h_view(i,j,k).lam3 = params[m].lam3;
|
||||
k_params.h_view(i,j,k).h = params[m].h;
|
||||
k_params.h_view(i,j,k).powern = params[m].powern;
|
||||
k_params.h_view(i,j,k).beta = params[m].beta;
|
||||
k_params.h_view(i,j,k).lam2 = params[m].lam2;
|
||||
k_params.h_view(i,j,k).bigb = params[m].bigb;
|
||||
k_params.h_view(i,j,k).bigr = params[m].bigr;
|
||||
k_params.h_view(i,j,k).bigd = params[m].bigd;
|
||||
k_params.h_view(i,j,k).lam1 = params[m].lam1;
|
||||
k_params.h_view(i,j,k).biga = params[m].biga;
|
||||
k_params.h_view(i,j,k).cutsq = params[m].cutsq;
|
||||
k_params.h_view(i,j,k).c1 = params[m].c1;
|
||||
k_params.h_view(i,j,k).c2 = params[m].c2;
|
||||
k_params.h_view(i,j,k).c3 = params[m].c3;
|
||||
k_params.h_view(i,j,k).c4 = params[m].c4;
|
||||
k_params.h_view(i,j,k).c5 = params[m].c5;
|
||||
k_params.h_view(i,j,k).ca1 = params[m].ca1;
|
||||
k_params.h_view(i,j,k).ca4 = params[m].ca4;
|
||||
k_params.h_view(i,j,k).powern_del = params[m].powern_del;
|
||||
}
|
||||
|
||||
k_params.template modify<LMPHostType>();
|
||||
|
|
|
|||
|
|
@ -136,30 +136,30 @@ void PairTersoffZBLKokkos<DeviceType>::setup_params()
|
|||
for (i = 1; i <= n; i++)
|
||||
for (j = 1; j <= n; j++)
|
||||
for (k = 1; k <= n; k++) {
|
||||
m = elem2param[i-1][j-1][k-1];
|
||||
k_params.h_view(i,j,k).powerm = params[m].powerm;
|
||||
k_params.h_view(i,j,k).gamma = params[m].gamma;
|
||||
k_params.h_view(i,j,k).lam3 = params[m].lam3;
|
||||
k_params.h_view(i,j,k).c = params[m].c;
|
||||
k_params.h_view(i,j,k).d = params[m].d;
|
||||
k_params.h_view(i,j,k).h = params[m].h;
|
||||
k_params.h_view(i,j,k).powern = params[m].powern;
|
||||
k_params.h_view(i,j,k).beta = params[m].beta;
|
||||
k_params.h_view(i,j,k).lam2 = params[m].lam2;
|
||||
k_params.h_view(i,j,k).bigb = params[m].bigb;
|
||||
k_params.h_view(i,j,k).bigr = params[m].bigr;
|
||||
k_params.h_view(i,j,k).bigd = params[m].bigd;
|
||||
k_params.h_view(i,j,k).lam1 = params[m].lam1;
|
||||
k_params.h_view(i,j,k).biga = params[m].biga;
|
||||
k_params.h_view(i,j,k).cutsq = params[m].cutsq;
|
||||
k_params.h_view(i,j,k).c1 = params[m].c1;
|
||||
k_params.h_view(i,j,k).c2 = params[m].c2;
|
||||
k_params.h_view(i,j,k).c3 = params[m].c3;
|
||||
k_params.h_view(i,j,k).c4 = params[m].c4;
|
||||
k_params.h_view(i,j,k).Z_i = params[m].Z_i;
|
||||
k_params.h_view(i,j,k).Z_j = params[m].Z_j;
|
||||
k_params.h_view(i,j,k).ZBLcut = params[m].ZBLcut;
|
||||
k_params.h_view(i,j,k).ZBLexpscale = params[m].ZBLexpscale;
|
||||
m = elem2param[map[i]][map[j]][map[k]];
|
||||
k_params.h_view(i,j,k).powerm = params[m].powerm;
|
||||
k_params.h_view(i,j,k).gamma = params[m].gamma;
|
||||
k_params.h_view(i,j,k).lam3 = params[m].lam3;
|
||||
k_params.h_view(i,j,k).c = params[m].c;
|
||||
k_params.h_view(i,j,k).d = params[m].d;
|
||||
k_params.h_view(i,j,k).h = params[m].h;
|
||||
k_params.h_view(i,j,k).powern = params[m].powern;
|
||||
k_params.h_view(i,j,k).beta = params[m].beta;
|
||||
k_params.h_view(i,j,k).lam2 = params[m].lam2;
|
||||
k_params.h_view(i,j,k).bigb = params[m].bigb;
|
||||
k_params.h_view(i,j,k).bigr = params[m].bigr;
|
||||
k_params.h_view(i,j,k).bigd = params[m].bigd;
|
||||
k_params.h_view(i,j,k).lam1 = params[m].lam1;
|
||||
k_params.h_view(i,j,k).biga = params[m].biga;
|
||||
k_params.h_view(i,j,k).cutsq = params[m].cutsq;
|
||||
k_params.h_view(i,j,k).c1 = params[m].c1;
|
||||
k_params.h_view(i,j,k).c2 = params[m].c2;
|
||||
k_params.h_view(i,j,k).c3 = params[m].c3;
|
||||
k_params.h_view(i,j,k).c4 = params[m].c4;
|
||||
k_params.h_view(i,j,k).Z_i = params[m].Z_i;
|
||||
k_params.h_view(i,j,k).Z_j = params[m].Z_j;
|
||||
k_params.h_view(i,j,k).ZBLcut = params[m].ZBLcut;
|
||||
k_params.h_view(i,j,k).ZBLexpscale = params[m].ZBLexpscale;
|
||||
}
|
||||
|
||||
k_params.template modify<LMPHostType>();
|
||||
|
|
|
|||
|
|
@ -0,0 +1,961 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Stan Moore (SNL)
|
||||
Anders Hafreager (UiO), andershaf@gmail.com
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <math.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include "pair_vashishta_kokkos.h"
|
||||
#include "kokkos.h"
|
||||
#include "pair_kokkos.h"
|
||||
#include "atom_kokkos.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_request.h"
|
||||
#include "force.h"
|
||||
#include "comm.h"
|
||||
#include "memory.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list_kokkos.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "atom_masks.h"
|
||||
#include "math_const.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
|
||||
#define MAXLINE 1024
|
||||
#define DELTA 4
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
template<class DeviceType>
|
||||
PairVashishtaKokkos<DeviceType>::PairVashishtaKokkos(LAMMPS *lmp) : PairVashishta(lmp)
|
||||
{
|
||||
respa_enable = 0;
|
||||
|
||||
atomKK = (AtomKokkos *) atom;
|
||||
execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
|
||||
datamask_read = X_MASK | F_MASK | TAG_MASK | TYPE_MASK | ENERGY_MASK | VIRIAL_MASK;
|
||||
datamask_modify = F_MASK | ENERGY_MASK | VIRIAL_MASK;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
check if allocated, since class can be destructed when incomplete
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
template<class DeviceType>
|
||||
PairVashishtaKokkos<DeviceType>::~PairVashishtaKokkos()
|
||||
{
|
||||
if (!copymode) {
|
||||
memory->destroy_kokkos(k_eatom,eatom);
|
||||
memory->destroy_kokkos(k_vatom,vatom);
|
||||
eatom = NULL;
|
||||
vatom = NULL;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
template<class DeviceType>
|
||||
void PairVashishtaKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
|
||||
{
|
||||
eflag = eflag_in;
|
||||
vflag = vflag_in;
|
||||
|
||||
if (neighflag == FULL) no_virial_fdotr_compute = 1;
|
||||
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
|
||||
// reallocate per-atom arrays if necessary
|
||||
|
||||
if (eflag_atom) {
|
||||
memory->destroy_kokkos(k_eatom,eatom);
|
||||
memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
|
||||
d_eatom = k_eatom.d_view;
|
||||
}
|
||||
if (vflag_atom) {
|
||||
memory->destroy_kokkos(k_vatom,vatom);
|
||||
memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
|
||||
d_vatom = k_vatom.d_view;
|
||||
}
|
||||
|
||||
atomKK->sync(execution_space,datamask_read);
|
||||
if (eflag || vflag) atomKK->modified(execution_space,datamask_modify);
|
||||
else atomKK->modified(execution_space,F_MASK);
|
||||
|
||||
x = atomKK->k_x.view<DeviceType>();
|
||||
f = atomKK->k_f.view<DeviceType>();
|
||||
tag = atomKK->k_tag.view<DeviceType>();
|
||||
type = atomKK->k_type.view<DeviceType>();
|
||||
nlocal = atom->nlocal;
|
||||
newton_pair = force->newton_pair;
|
||||
nall = atom->nlocal + atom->nghost;
|
||||
|
||||
inum = list->inum;
|
||||
const int ignum = inum + list->gnum;
|
||||
NeighListKokkos<DeviceType>* k_list = static_cast<NeighListKokkos<DeviceType>*>(list);
|
||||
d_ilist = k_list->d_ilist;
|
||||
d_numneigh = k_list->d_numneigh;
|
||||
d_neighbors = k_list->d_neighbors;
|
||||
|
||||
k_list->clean_copy();
|
||||
copymode = 1;
|
||||
|
||||
EV_FLOAT ev;
|
||||
EV_FLOAT ev_all;
|
||||
|
||||
int max_neighs = d_neighbors.dimension_1();
|
||||
|
||||
if ((d_neighbors_short_2body.dimension_1() != max_neighs) ||
|
||||
(d_neighbors_short_2body.dimension_0() != ignum)) {
|
||||
d_neighbors_short_2body = Kokkos::View<int**,DeviceType>("Vashishta::neighbors_short_2body",ignum,max_neighs);
|
||||
}
|
||||
if (d_numneigh_short_2body.dimension_0()!=ignum) {
|
||||
d_numneigh_short_2body = Kokkos::View<int*,DeviceType>("Vashishta::numneighs_short_2body",ignum);
|
||||
}
|
||||
|
||||
if ((d_neighbors_short_3body.dimension_1() != max_neighs) ||
|
||||
(d_neighbors_short_3body.dimension_0() != ignum)) {
|
||||
d_neighbors_short_3body = Kokkos::View<int**,DeviceType>("Vashishta::neighbors_short_3body",ignum,max_neighs);
|
||||
}
|
||||
|
||||
if (d_numneigh_short_3body.dimension_0()!=ignum) {
|
||||
d_numneigh_short_3body = Kokkos::View<int*,DeviceType>("Vashishta::numneighs_short_3body",ignum);
|
||||
}
|
||||
|
||||
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType,TagPairVashishtaComputeShortNeigh>(0,neighflag==FULL?ignum:inum), *this);
|
||||
|
||||
|
||||
|
||||
// loop over neighbor list of my atoms
|
||||
|
||||
if (neighflag == HALF) {
|
||||
if (evflag)
|
||||
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairVashishtaComputeHalf<HALF,1> >(0,inum),*this,ev);
|
||||
else
|
||||
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairVashishtaComputeHalf<HALF,0> >(0,inum),*this);
|
||||
ev_all += ev;
|
||||
} else if (neighflag == HALFTHREAD) {
|
||||
if (evflag)
|
||||
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairVashishtaComputeHalf<HALFTHREAD,1> >(0,inum),*this,ev);
|
||||
else
|
||||
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairVashishtaComputeHalf<HALFTHREAD,0> >(0,inum),*this);
|
||||
ev_all += ev;
|
||||
} else if (neighflag == FULL) {
|
||||
if (evflag)
|
||||
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairVashishtaComputeFullA<FULL,1> >(0,inum),*this,ev);
|
||||
else
|
||||
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairVashishtaComputeFullA<FULL,0> >(0,inum),*this);
|
||||
ev_all += ev;
|
||||
|
||||
if (evflag)
|
||||
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagPairVashishtaComputeFullB<FULL,1> >(0,ignum),*this,ev);
|
||||
else
|
||||
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagPairVashishtaComputeFullB<FULL,0> >(0,ignum),*this);
|
||||
ev_all += ev;
|
||||
}
|
||||
|
||||
if (eflag_global) eng_vdwl += ev_all.evdwl;
|
||||
if (vflag_global) {
|
||||
virial[0] += ev_all.v[0];
|
||||
virial[1] += ev_all.v[1];
|
||||
virial[2] += ev_all.v[2];
|
||||
virial[3] += ev_all.v[3];
|
||||
virial[4] += ev_all.v[4];
|
||||
virial[5] += ev_all.v[5];
|
||||
}
|
||||
|
||||
if (vflag_fdotr) pair_virial_fdotr_compute(this);
|
||||
|
||||
if (eflag_atom) {
|
||||
k_eatom.template modify<DeviceType>();
|
||||
k_eatom.template sync<LMPHostType>();
|
||||
}
|
||||
|
||||
if (vflag_atom) {
|
||||
k_vatom.template modify<DeviceType>();
|
||||
k_vatom.template sync<LMPHostType>();
|
||||
}
|
||||
|
||||
copymode = 0;
|
||||
}
|
||||
|
||||
template<class DeviceType>
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void PairVashishtaKokkos<DeviceType>::operator()(TagPairVashishtaComputeShortNeigh, const int& ii) const {
|
||||
const int i = d_ilist[ii];
|
||||
const int itype = d_map[type[i]];
|
||||
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_2body = 0;
|
||||
int inside_3body = 0;
|
||||
for (int jj = 0; jj < jnum; jj++) {
|
||||
int j = d_neighbors(i,jj);
|
||||
j &= NEIGHMASK;
|
||||
const int jtype = d_map[type[j]];
|
||||
const int ijparam = d_elem2param(itype,jtype,jtype);
|
||||
|
||||
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 < d_params[ijparam].cutsq) {
|
||||
d_neighbors_short_2body(i,inside_2body) = j;
|
||||
inside_2body++;
|
||||
}
|
||||
|
||||
if (rsq < d_params[ijparam].cutsq2) {
|
||||
d_neighbors_short_3body(i,inside_3body) = j;
|
||||
inside_3body++;
|
||||
}
|
||||
}
|
||||
d_numneigh_short_2body(i) = inside_2body;
|
||||
d_numneigh_short_3body(i) = inside_3body;
|
||||
}
|
||||
|
||||
template<class DeviceType>
|
||||
template<int NEIGHFLAG, int EVFLAG>
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void PairVashishtaKokkos<DeviceType>::operator()(TagPairVashishtaComputeHalf<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT& ev) const {
|
||||
|
||||
// The f array is atomic
|
||||
|
||||
Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > a_f = f;
|
||||
|
||||
F_FLOAT delr1[3],delr2[3],fj[3],fk[3];
|
||||
F_FLOAT evdwl = 0.0;
|
||||
F_FLOAT fpair = 0.0;
|
||||
|
||||
const int i = d_ilist[ii];
|
||||
const tagint itag = tag[i];
|
||||
const int itype = d_map[type[i]];
|
||||
const X_FLOAT xtmp = x(i,0);
|
||||
const X_FLOAT ytmp = x(i,1);
|
||||
const X_FLOAT ztmp = x(i,2);
|
||||
|
||||
// two-body interactions, skip half of them
|
||||
|
||||
const int jnum = d_numneigh_short_2body[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_short_2body(i,jj);
|
||||
j &= NEIGHMASK;
|
||||
const tagint jtag = tag[j];
|
||||
|
||||
if (itag > jtag) {
|
||||
if ((itag+jtag) % 2 == 0) continue;
|
||||
} else if (itag < jtag) {
|
||||
if ((itag+jtag) % 2 == 1) continue;
|
||||
} else {
|
||||
if (x(j,2) < ztmp) continue;
|
||||
if (x(j,2) == ztmp && x(j,1) < ytmp) continue;
|
||||
if (x(j,2) == ztmp && x(j,1) == ytmp && x(j,0) < xtmp) continue;
|
||||
}
|
||||
|
||||
const int jtype = d_map[type[j]];
|
||||
|
||||
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;
|
||||
|
||||
const int ijparam = d_elem2param(itype,jtype,jtype);
|
||||
|
||||
twobody(d_params[ijparam],rsq,fpair,eflag,evdwl);
|
||||
|
||||
fxtmpi += delx*fpair;
|
||||
fytmpi += dely*fpair;
|
||||
fztmpi += delz*fpair;
|
||||
a_f(j,0) -= delx*fpair;
|
||||
a_f(j,1) -= dely*fpair;
|
||||
a_f(j,2) -= delz*fpair;
|
||||
|
||||
if (EVFLAG) {
|
||||
if (eflag) ev.evdwl += evdwl;
|
||||
if (vflag_either || eflag_atom) this->template ev_tally<NEIGHFLAG>(ev,i,j,evdwl,fpair,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
|
||||
const int jnumm1 = d_numneigh_short_3body[i];
|
||||
|
||||
for (int jj = 0; jj < jnumm1-1; jj++) {
|
||||
int j = d_neighbors_short_3body(i,jj);
|
||||
j &= NEIGHMASK;
|
||||
const int jtype = d_map[type[j]];
|
||||
const int ijparam = d_elem2param(itype,jtype,jtype);
|
||||
delr1[0] = x(j,0) - xtmp;
|
||||
delr1[1] = x(j,1) - ytmp;
|
||||
delr1[2] = x(j,2) - ztmp;
|
||||
const F_FLOAT rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
|
||||
|
||||
F_FLOAT fxtmpj = 0.0;
|
||||
F_FLOAT fytmpj = 0.0;
|
||||
F_FLOAT fztmpj = 0.0;
|
||||
|
||||
for (int kk = jj+1; kk < jnumm1; kk++) {
|
||||
int k = d_neighbors_short_3body(i,kk);
|
||||
k &= NEIGHMASK;
|
||||
const int ktype = d_map[type[k]];
|
||||
const int ikparam = d_elem2param(itype,ktype,ktype);
|
||||
const int ijkparam = d_elem2param(itype,jtype,ktype);
|
||||
|
||||
delr2[0] = x(k,0) - xtmp;
|
||||
delr2[1] = x(k,1) - ytmp;
|
||||
delr2[2] = x(k,2) - ztmp;
|
||||
const F_FLOAT rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
|
||||
|
||||
threebody(d_params[ijparam],d_params[ikparam],d_params[ijkparam],
|
||||
rsq1,rsq2,delr1,delr2,fj,fk,eflag,evdwl);
|
||||
|
||||
fxtmpi -= fj[0] + fk[0];
|
||||
fytmpi -= fj[1] + fk[1];
|
||||
fztmpi -= fj[2] + fk[2];
|
||||
fxtmpj += fj[0];
|
||||
fytmpj += fj[1];
|
||||
fztmpj += fj[2];
|
||||
a_f(k,0) += fk[0];
|
||||
a_f(k,1) += fk[1];
|
||||
a_f(k,2) += fk[2];
|
||||
|
||||
if (EVFLAG) {
|
||||
if (eflag) ev.evdwl += evdwl;
|
||||
if (vflag_either || eflag_atom) this->template ev_tally3<NEIGHFLAG>(ev,i,j,k,evdwl,0.0,fj,fk,delr1,delr2);
|
||||
}
|
||||
}
|
||||
|
||||
a_f(j,0) += fxtmpj;
|
||||
a_f(j,1) += fytmpj;
|
||||
a_f(j,2) += fztmpj;
|
||||
}
|
||||
|
||||
a_f(i,0) += fxtmpi;
|
||||
a_f(i,1) += fytmpi;
|
||||
a_f(i,2) += fztmpi;
|
||||
}
|
||||
|
||||
template<class DeviceType>
|
||||
template<int NEIGHFLAG, int EVFLAG>
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void PairVashishtaKokkos<DeviceType>::operator()(TagPairVashishtaComputeHalf<NEIGHFLAG,EVFLAG>, const int &ii) const {
|
||||
EV_FLOAT ev;
|
||||
this->template operator()<NEIGHFLAG,EVFLAG>(TagPairVashishtaComputeHalf<NEIGHFLAG,EVFLAG>(), ii, ev);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
template<class DeviceType>
|
||||
template<int NEIGHFLAG, int EVFLAG>
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void PairVashishtaKokkos<DeviceType>::operator()(TagPairVashishtaComputeFullA<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT& ev) const {
|
||||
|
||||
F_FLOAT delr1[3],delr2[3],fj[3],fk[3];
|
||||
F_FLOAT evdwl = 0.0;
|
||||
F_FLOAT fpair = 0.0;
|
||||
|
||||
const int i = d_ilist[ii];
|
||||
|
||||
const tagint itag = tag[i];
|
||||
const int itype = d_map[type[i]];
|
||||
const X_FLOAT xtmp = x(i,0);
|
||||
const X_FLOAT ytmp = x(i,1);
|
||||
const X_FLOAT ztmp = x(i,2);
|
||||
|
||||
// two-body interactions
|
||||
|
||||
const int jnum = d_numneigh_short_2body[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_short_2body(i,jj);
|
||||
j &= NEIGHMASK;
|
||||
const tagint jtag = tag[j];
|
||||
|
||||
const int jtype = d_map[type[j]];
|
||||
|
||||
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;
|
||||
|
||||
const int ijparam = d_elem2param(itype,jtype,jtype);
|
||||
|
||||
twobody(d_params[ijparam],rsq,fpair,eflag,evdwl);
|
||||
|
||||
fxtmpi += delx*fpair;
|
||||
fytmpi += dely*fpair;
|
||||
fztmpi += delz*fpair;
|
||||
|
||||
if (EVFLAG) {
|
||||
if (eflag) ev.evdwl += 0.5*evdwl;
|
||||
if (vflag_either || eflag_atom) this->template ev_tally<NEIGHFLAG>(ev,i,j,evdwl,fpair,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
|
||||
const int jnumm1 = d_numneigh_short_3body[i];
|
||||
|
||||
for (int jj = 0; jj < jnumm1-1; jj++) {
|
||||
int j = d_neighbors_short_3body(i,jj);
|
||||
j &= NEIGHMASK;
|
||||
const int jtype = d_map[type[j]];
|
||||
const int ijparam = d_elem2param(itype,jtype,jtype);
|
||||
delr1[0] = x(j,0) - xtmp;
|
||||
delr1[1] = x(j,1) - ytmp;
|
||||
delr1[2] = x(j,2) - ztmp;
|
||||
const F_FLOAT rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
|
||||
|
||||
for (int kk = jj+1; kk < jnumm1; kk++) {
|
||||
int k = d_neighbors_short_3body(i,kk);
|
||||
k &= NEIGHMASK;
|
||||
const int ktype = d_map[type[k]];
|
||||
const int ikparam = d_elem2param(itype,ktype,ktype);
|
||||
const int ijkparam = d_elem2param(itype,jtype,ktype);
|
||||
|
||||
delr2[0] = x(k,0) - xtmp;
|
||||
delr2[1] = x(k,1) - ytmp;
|
||||
delr2[2] = x(k,2) - ztmp;
|
||||
const F_FLOAT rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
|
||||
|
||||
threebody(d_params[ijparam],d_params[ikparam],d_params[ijkparam],
|
||||
rsq1,rsq2,delr1,delr2,fj,fk,eflag,evdwl);
|
||||
|
||||
fxtmpi -= fj[0] + fk[0];
|
||||
fytmpi -= fj[1] + fk[1];
|
||||
fztmpi -= fj[2] + fk[2];
|
||||
|
||||
if (EVFLAG) {
|
||||
if (eflag) ev.evdwl += evdwl;
|
||||
if (vflag_either || eflag_atom) this->template ev_tally3<NEIGHFLAG>(ev,i,j,k,evdwl,0.0,fj,fk,delr1,delr2);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
f(i,0) += fxtmpi;
|
||||
f(i,1) += fytmpi;
|
||||
f(i,2) += fztmpi;
|
||||
}
|
||||
|
||||
template<class DeviceType>
|
||||
template<int NEIGHFLAG, int EVFLAG>
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void PairVashishtaKokkos<DeviceType>::operator()(TagPairVashishtaComputeFullA<NEIGHFLAG,EVFLAG>, const int &ii) const {
|
||||
EV_FLOAT ev;
|
||||
this->template operator()<NEIGHFLAG,EVFLAG>(TagPairVashishtaComputeFullA<NEIGHFLAG,EVFLAG>(), ii, ev);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
template<class DeviceType>
|
||||
template<int NEIGHFLAG, int EVFLAG>
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void PairVashishtaKokkos<DeviceType>::operator()(TagPairVashishtaComputeFullB<NEIGHFLAG,EVFLAG>, const int &ii, EV_FLOAT& ev) const {
|
||||
|
||||
F_FLOAT delr1[3],delr2[3],fj[3],fk[3];
|
||||
F_FLOAT evdwl = 0.0;
|
||||
F_FLOAT fpair = 0.0;
|
||||
|
||||
const int i = d_ilist[ii];
|
||||
|
||||
const int itype = d_map[type[i]];
|
||||
const X_FLOAT xtmpi = x(i,0);
|
||||
const X_FLOAT ytmpi = x(i,1);
|
||||
const X_FLOAT ztmpi = x(i,2);
|
||||
|
||||
const int jnum = d_numneigh_short_3body[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_short_3body(i,jj);
|
||||
j &= NEIGHMASK;
|
||||
if (j >= nlocal) continue;
|
||||
const int jtype = d_map[type[j]];
|
||||
const int jiparam = d_elem2param(jtype,itype,itype);
|
||||
const X_FLOAT xtmpj = x(j,0);
|
||||
const X_FLOAT ytmpj = x(j,1);
|
||||
const X_FLOAT ztmpj = x(j,2);
|
||||
|
||||
delr1[0] = xtmpi - xtmpj;
|
||||
delr1[1] = ytmpi - ytmpj;
|
||||
delr1[2] = ztmpi - ztmpj;
|
||||
const F_FLOAT rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
|
||||
|
||||
const int j_jnum = d_numneigh_short_3body[j];
|
||||
|
||||
for (int kk = 0; kk < j_jnum; kk++) {
|
||||
int k = d_neighbors_short_3body(j,kk);
|
||||
k &= NEIGHMASK;
|
||||
if (k == i) continue;
|
||||
const int ktype = d_map[type[k]];
|
||||
const int jkparam = d_elem2param(jtype,ktype,ktype);
|
||||
const int jikparam = d_elem2param(jtype,itype,ktype);
|
||||
|
||||
delr2[0] = x(k,0) - xtmpj;
|
||||
delr2[1] = x(k,1) - ytmpj;
|
||||
delr2[2] = x(k,2) - ztmpj;
|
||||
const F_FLOAT rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
|
||||
|
||||
if (vflag_atom)
|
||||
threebody(d_params[jiparam],d_params[jkparam],d_params[jikparam],
|
||||
rsq1,rsq2,delr1,delr2,fj,fk,eflag,evdwl);
|
||||
else
|
||||
threebodyj(d_params[jiparam],d_params[jkparam],d_params[jikparam],
|
||||
rsq1,rsq2,delr1,delr2,fj);
|
||||
|
||||
fxtmpi += fj[0];
|
||||
fytmpi += fj[1];
|
||||
fztmpi += fj[2];
|
||||
|
||||
if (EVFLAG)
|
||||
if (vflag_atom || eflag_atom) ev_tally3_atom(ev,i,evdwl,0.0,fj,fk,delr1,delr2);
|
||||
}
|
||||
}
|
||||
|
||||
f(i,0) += fxtmpi;
|
||||
f(i,1) += fytmpi;
|
||||
f(i,2) += fztmpi;
|
||||
}
|
||||
|
||||
template<class DeviceType>
|
||||
template<int NEIGHFLAG, int EVFLAG>
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void PairVashishtaKokkos<DeviceType>::operator()(TagPairVashishtaComputeFullB<NEIGHFLAG,EVFLAG>, const int &ii) const {
|
||||
EV_FLOAT ev;
|
||||
this->template operator()<NEIGHFLAG,EVFLAG>(TagPairVashishtaComputeFullB<NEIGHFLAG,EVFLAG>(), ii, ev);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
template<class DeviceType>
|
||||
void PairVashishtaKokkos<DeviceType>::coeff(int narg, char **arg)
|
||||
{
|
||||
PairVashishta::coeff(narg,arg);
|
||||
|
||||
// sync map
|
||||
|
||||
int n = atom->ntypes;
|
||||
|
||||
DAT::tdual_int_1d k_map = DAT::tdual_int_1d("pair:map",n+1);
|
||||
HAT::t_int_1d h_map = k_map.h_view;
|
||||
|
||||
for (int i = 1; i <= n; i++)
|
||||
h_map[i] = map[i];
|
||||
|
||||
k_map.template modify<LMPHostType>();
|
||||
k_map.template sync<DeviceType>();
|
||||
|
||||
d_map = k_map.d_view;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init specific to this pair style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
template<class DeviceType>
|
||||
void PairVashishtaKokkos<DeviceType>::init_style()
|
||||
{
|
||||
PairVashishta::init_style();
|
||||
|
||||
// irequest = neigh request made by parent class
|
||||
|
||||
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;
|
||||
|
||||
// always request a full neighbor list
|
||||
|
||||
if (neighflag == FULL || neighflag == HALF || neighflag == HALFTHREAD) {
|
||||
neighbor->requests[irequest]->full = 1;
|
||||
neighbor->requests[irequest]->half = 0;
|
||||
neighbor->requests[irequest]->full_cluster = 0;
|
||||
if (neighflag == FULL)
|
||||
neighbor->requests[irequest]->ghost = 1;
|
||||
else
|
||||
neighbor->requests[irequest]->ghost = 0;
|
||||
} else {
|
||||
error->all(FLERR,"Cannot use chosen neighbor list style with pair vashishta/kk");
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
template<class DeviceType>
|
||||
void PairVashishtaKokkos<DeviceType>::setup_params()
|
||||
{
|
||||
PairVashishta::setup_params();
|
||||
|
||||
// sync elem2param and params
|
||||
|
||||
tdual_int_3d k_elem2param = tdual_int_3d("pair:elem2param",nelements,nelements,nelements);
|
||||
t_host_int_3d h_elem2param = k_elem2param.h_view;
|
||||
|
||||
tdual_param_1d k_params = tdual_param_1d("pair:params",nparams);
|
||||
t_host_param_1d h_params = k_params.h_view;
|
||||
|
||||
for (int i = 0; i < nelements; i++)
|
||||
for (int j = 0; j < nelements; j++)
|
||||
for (int k = 0; k < nelements; k++)
|
||||
h_elem2param(i,j,k) = elem2param[i][j][k];
|
||||
|
||||
for (int m = 0; m < nparams; m++)
|
||||
h_params[m] = params[m];
|
||||
|
||||
k_elem2param.template modify<LMPHostType>();
|
||||
k_elem2param.template sync<DeviceType>();
|
||||
k_params.template modify<LMPHostType>();
|
||||
k_params.template sync<DeviceType>();
|
||||
|
||||
d_elem2param = k_elem2param.d_view;
|
||||
d_params = k_params.d_view;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
template<class DeviceType>
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void PairVashishtaKokkos<DeviceType>::twobody(const Param& param, const F_FLOAT& rsq, F_FLOAT& fforce,
|
||||
const int& eflag, F_FLOAT& eng) const
|
||||
{
|
||||
F_FLOAT r,rinvsq,r4inv,r6inv,reta,lam1r,lam4r,vc2,vc3;
|
||||
r = sqrt(rsq);
|
||||
rinvsq = 1.0/rsq;
|
||||
r4inv = rinvsq*rinvsq;
|
||||
r6inv = rinvsq*r4inv;
|
||||
reta = pow(r,-param.eta);
|
||||
lam1r = r*param.lam1inv;
|
||||
lam4r = r*param.lam4inv;
|
||||
vc2 = param.zizj * exp(-lam1r)/r;
|
||||
vc3 = param.mbigd * r4inv*exp(-lam4r);
|
||||
|
||||
fforce = (param.dvrc*r
|
||||
- (4.0*vc3 + lam4r*vc3+param.big6w*r6inv
|
||||
- param.heta*reta - vc2 - lam1r*vc2)
|
||||
) * rinvsq;
|
||||
|
||||
if (eflag) eng = param.bigh*reta + vc2 - vc3 - param.bigw*r6inv - r*param.dvrc + param.c0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
template<class DeviceType>
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void PairVashishtaKokkos<DeviceType>::threebody(const Param& paramij, const Param& paramik, const Param& paramijk,
|
||||
const F_FLOAT& rsq1, const F_FLOAT& rsq2,
|
||||
F_FLOAT *delr1, F_FLOAT *delr2,
|
||||
F_FLOAT *fj, F_FLOAT *fk, const int& eflag, F_FLOAT& eng) const
|
||||
{
|
||||
F_FLOAT r1,rinvsq1,rainv1,gsrainv1,gsrainvsq1,expgsrainv1;
|
||||
F_FLOAT r2,rinvsq2,rainv2,gsrainv2,gsrainvsq2,expgsrainv2;
|
||||
F_FLOAT rinv12,cs,delcs,delcssq,facexp,facrad,frad1,frad2,pcsinv,pcsinvsq,pcs;
|
||||
F_FLOAT facang,facang12,csfacang,csfac1,csfac2;
|
||||
|
||||
r1 = sqrt(rsq1);
|
||||
rinvsq1 = 1.0/rsq1;
|
||||
rainv1 = 1.0/(r1 - paramij.r0);
|
||||
gsrainv1 = paramij.gamma * rainv1;
|
||||
gsrainvsq1 = gsrainv1*rainv1/r1;
|
||||
expgsrainv1 = exp(gsrainv1);
|
||||
|
||||
r2 = sqrt(rsq2);
|
||||
rinvsq2 = 1.0/rsq2;
|
||||
rainv2 = 1.0/(r2 - paramik.r0);
|
||||
gsrainv2 = paramik.gamma * rainv2;
|
||||
gsrainvsq2 = gsrainv2*rainv2/r2;
|
||||
expgsrainv2 = exp(gsrainv2);
|
||||
|
||||
rinv12 = 1.0/(r1*r2);
|
||||
cs = (delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2]) * rinv12;
|
||||
delcs = cs - paramijk.costheta;
|
||||
delcssq = delcs*delcs;
|
||||
pcsinv = paramijk.bigc*delcssq + 1.0;
|
||||
pcsinvsq = pcsinv*pcsinv;
|
||||
pcs = delcssq/pcsinv;
|
||||
|
||||
facexp = expgsrainv1*expgsrainv2;
|
||||
|
||||
facrad = paramijk.bigb * facexp * pcs;
|
||||
frad1 = facrad*gsrainvsq1;
|
||||
frad2 = facrad*gsrainvsq2;
|
||||
facang = paramijk.big2b * facexp * delcs/pcsinvsq;
|
||||
facang12 = rinv12*facang;
|
||||
csfacang = cs*facang;
|
||||
csfac1 = rinvsq1*csfacang;
|
||||
|
||||
fj[0] = delr1[0]*(frad1+csfac1)-delr2[0]*facang12;
|
||||
fj[1] = delr1[1]*(frad1+csfac1)-delr2[1]*facang12;
|
||||
fj[2] = delr1[2]*(frad1+csfac1)-delr2[2]*facang12;
|
||||
|
||||
csfac2 = rinvsq2*csfacang;
|
||||
|
||||
fk[0] = delr2[0]*(frad2+csfac2)-delr1[0]*facang12;
|
||||
fk[1] = delr2[1]*(frad2+csfac2)-delr1[1]*facang12;
|
||||
fk[2] = delr2[2]*(frad2+csfac2)-delr1[2]*facang12;
|
||||
|
||||
if (eflag) eng = facrad;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
template<class DeviceType>
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void PairVashishtaKokkos<DeviceType>::threebodyj(const Param& paramij, const Param& paramik, const Param& paramijk,
|
||||
const F_FLOAT& rsq1, const F_FLOAT& rsq2, F_FLOAT *delr1, F_FLOAT *delr2, F_FLOAT *fj) const
|
||||
{
|
||||
F_FLOAT r1,rinvsq1,rainv1,gsrainv1,gsrainvsq1,expgsrainv1;
|
||||
F_FLOAT r2,rinvsq2,rainv2,gsrainv2,gsrainvsq2,expgsrainv2;
|
||||
F_FLOAT rinv12,cs,delcs,delcssq,facexp,facrad,frad1,frad2,pcsinv,pcsinvsq,pcs;
|
||||
F_FLOAT facang,facang12,csfacang,csfac1,csfac2;
|
||||
|
||||
r1 = sqrt(rsq1);
|
||||
rinvsq1 = 1.0/rsq1;
|
||||
rainv1 = 1.0/(r1 - paramij.r0);
|
||||
gsrainv1 = paramij.gamma * rainv1;
|
||||
gsrainvsq1 = gsrainv1*rainv1/r1;
|
||||
expgsrainv1 = exp(gsrainv1);
|
||||
|
||||
r2 = sqrt(rsq2);
|
||||
rinvsq2 = 1.0/rsq2;
|
||||
rainv2 = 1.0/(r2 - paramik.r0);
|
||||
gsrainv2 = paramik.gamma * rainv2;
|
||||
gsrainvsq2 = gsrainv2*rainv2/r2;
|
||||
expgsrainv2 = exp(gsrainv2);
|
||||
|
||||
rinv12 = 1.0/(r1*r2);
|
||||
cs = (delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2]) * rinv12;
|
||||
delcs = cs - paramijk.costheta;
|
||||
delcssq = delcs*delcs;
|
||||
pcsinv = paramijk.bigc*delcssq + 1.0;
|
||||
pcsinvsq = pcsinv*pcsinv;
|
||||
pcs = delcssq/pcsinv;
|
||||
|
||||
facexp = expgsrainv1*expgsrainv2;
|
||||
|
||||
facrad = paramijk.bigb * facexp * pcs;
|
||||
frad1 = facrad*gsrainvsq1;
|
||||
frad2 = facrad*gsrainvsq2;
|
||||
facang = paramijk.big2b * facexp * delcs/pcsinvsq;
|
||||
facang12 = rinv12*facang;
|
||||
csfacang = cs*facang;
|
||||
csfac1 = rinvsq1*csfacang;
|
||||
|
||||
fj[0] = delr1[0]*(frad1+csfac1)-delr2[0]*facang12;
|
||||
fj[1] = delr1[1]*(frad1+csfac1)-delr2[1]*facang12;
|
||||
fj[2] = delr1[2]*(frad1+csfac1)-delr2[2]*facang12;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
template<class DeviceType>
|
||||
template<int NEIGHFLAG>
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void PairVashishtaKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, const int &j,
|
||||
const F_FLOAT &epair, const F_FLOAT &fpair, const F_FLOAT &delx,
|
||||
const F_FLOAT &dely, const F_FLOAT &delz) const
|
||||
{
|
||||
const int VFLAG = vflag_either;
|
||||
|
||||
// The eatom and vatom arrays are atomic for half/thread neighbor list
|
||||
|
||||
Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_eatom = k_eatom.view<DeviceType>();
|
||||
Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_vatom = k_vatom.view<DeviceType>();
|
||||
|
||||
|
||||
if (eflag_atom) {
|
||||
const E_FLOAT epairhalf = 0.5 * epair;
|
||||
v_eatom[i] += epairhalf;
|
||||
if (NEIGHFLAG != FULL)
|
||||
v_eatom[j] += epairhalf;
|
||||
}
|
||||
|
||||
if (VFLAG) {
|
||||
const E_FLOAT v0 = delx*delx*fpair;
|
||||
const E_FLOAT v1 = dely*dely*fpair;
|
||||
const E_FLOAT v2 = delz*delz*fpair;
|
||||
const E_FLOAT v3 = delx*dely*fpair;
|
||||
const E_FLOAT v4 = delx*delz*fpair;
|
||||
const E_FLOAT v5 = dely*delz*fpair;
|
||||
|
||||
if (vflag_global) {
|
||||
if (NEIGHFLAG != FULL) {
|
||||
ev.v[0] += v0;
|
||||
ev.v[1] += v1;
|
||||
ev.v[2] += v2;
|
||||
ev.v[3] += v3;
|
||||
ev.v[4] += v4;
|
||||
ev.v[5] += v5;
|
||||
} else {
|
||||
ev.v[0] += 0.5*v0;
|
||||
ev.v[1] += 0.5*v1;
|
||||
ev.v[2] += 0.5*v2;
|
||||
ev.v[3] += 0.5*v3;
|
||||
ev.v[4] += 0.5*v4;
|
||||
ev.v[5] += 0.5*v5;
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_atom) {
|
||||
v_vatom(i,0) += 0.5*v0;
|
||||
v_vatom(i,1) += 0.5*v1;
|
||||
v_vatom(i,2) += 0.5*v2;
|
||||
v_vatom(i,3) += 0.5*v3;
|
||||
v_vatom(i,4) += 0.5*v4;
|
||||
v_vatom(i,5) += 0.5*v5;
|
||||
|
||||
if (NEIGHFLAG != FULL) {
|
||||
v_vatom(j,0) += 0.5*v0;
|
||||
v_vatom(j,1) += 0.5*v1;
|
||||
v_vatom(j,2) += 0.5*v2;
|
||||
v_vatom(j,3) += 0.5*v3;
|
||||
v_vatom(j,4) += 0.5*v4;
|
||||
v_vatom(j,5) += 0.5*v5;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
tally eng_vdwl and virial into global and per-atom accumulators
|
||||
called by SW and hbond potentials, newton_pair is always on
|
||||
virial = riFi + rjFj + rkFk = (rj-ri) Fj + (rk-ri) Fk = drji*fj + drki*fk
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
template<class DeviceType>
|
||||
template<int NEIGHFLAG>
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void PairVashishtaKokkos<DeviceType>::ev_tally3(EV_FLOAT &ev, const int &i, const int &j, int &k,
|
||||
const F_FLOAT &evdwl, const F_FLOAT &ecoul,
|
||||
F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drji, F_FLOAT *drki) const
|
||||
{
|
||||
F_FLOAT epairthird,v[6];
|
||||
|
||||
const int VFLAG = vflag_either;
|
||||
|
||||
// The eatom and vatom arrays are atomic for half/thread neighbor list
|
||||
|
||||
Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_eatom = k_eatom.view<DeviceType>();
|
||||
Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<AtomicF<NEIGHFLAG>::value> > v_vatom = k_vatom.view<DeviceType>();
|
||||
|
||||
if (eflag_atom) {
|
||||
epairthird = THIRD * (evdwl + ecoul);
|
||||
v_eatom[i] += epairthird;
|
||||
if (NEIGHFLAG != FULL) {
|
||||
v_eatom[j] += epairthird;
|
||||
v_eatom[k] += epairthird;
|
||||
}
|
||||
}
|
||||
|
||||
if (VFLAG) {
|
||||
v[0] = drji[0]*fj[0] + drki[0]*fk[0];
|
||||
v[1] = drji[1]*fj[1] + drki[1]*fk[1];
|
||||
v[2] = drji[2]*fj[2] + drki[2]*fk[2];
|
||||
v[3] = drji[0]*fj[1] + drki[0]*fk[1];
|
||||
v[4] = drji[0]*fj[2] + drki[0]*fk[2];
|
||||
v[5] = drji[1]*fj[2] + drki[1]*fk[2];
|
||||
|
||||
if (vflag_global) {
|
||||
ev.v[0] += v[0];
|
||||
ev.v[1] += v[1];
|
||||
ev.v[2] += v[2];
|
||||
ev.v[3] += v[3];
|
||||
ev.v[4] += v[4];
|
||||
ev.v[5] += v[5];
|
||||
}
|
||||
|
||||
if (vflag_atom) {
|
||||
v_vatom(i,0) += THIRD*v[0]; v_vatom(i,1) += THIRD*v[1];
|
||||
v_vatom(i,2) += THIRD*v[2]; v_vatom(i,3) += THIRD*v[3];
|
||||
v_vatom(i,4) += THIRD*v[4]; v_vatom(i,5) += THIRD*v[5];
|
||||
|
||||
if (NEIGHFLAG != FULL) {
|
||||
v_vatom(j,0) += THIRD*v[0]; v_vatom(j,1) += THIRD*v[1];
|
||||
v_vatom(j,2) += THIRD*v[2]; v_vatom(j,3) += THIRD*v[3];
|
||||
v_vatom(j,4) += THIRD*v[4]; v_vatom(j,5) += THIRD*v[5];
|
||||
|
||||
v_vatom(k,0) += THIRD*v[0]; v_vatom(k,1) += THIRD*v[1];
|
||||
v_vatom(k,2) += THIRD*v[2]; v_vatom(k,3) += THIRD*v[3];
|
||||
v_vatom(k,4) += THIRD*v[4]; v_vatom(k,5) += THIRD*v[5];
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
tally eng_vdwl and virial into global and per-atom accumulators
|
||||
called by SW and hbond potentials, newton_pair is always on
|
||||
virial = riFi + rjFj + rkFk = (rj-ri) Fj + (rk-ri) Fk = drji*fj + drki*fk
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
template<class DeviceType>
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void PairVashishtaKokkos<DeviceType>::ev_tally3_atom(EV_FLOAT &ev, const int &i,
|
||||
const F_FLOAT &evdwl, const F_FLOAT &ecoul,
|
||||
F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drji, F_FLOAT *drki) const
|
||||
{
|
||||
F_FLOAT epairthird,v[6];
|
||||
|
||||
const int VFLAG = vflag_either;
|
||||
|
||||
if (eflag_atom) {
|
||||
epairthird = THIRD * (evdwl + ecoul);
|
||||
d_eatom[i] += epairthird;
|
||||
}
|
||||
|
||||
if (VFLAG) {
|
||||
v[0] = drji[0]*fj[0] + drki[0]*fk[0];
|
||||
v[1] = drji[1]*fj[1] + drki[1]*fk[1];
|
||||
v[2] = drji[2]*fj[2] + drki[2]*fk[2];
|
||||
v[3] = drji[0]*fj[1] + drki[0]*fk[1];
|
||||
v[4] = drji[0]*fj[2] + drki[0]*fk[2];
|
||||
v[5] = drji[1]*fj[2] + drki[1]*fk[2];
|
||||
|
||||
if (vflag_atom) {
|
||||
d_vatom(i,0) += THIRD*v[0]; d_vatom(i,1) += THIRD*v[1];
|
||||
d_vatom(i,2) += THIRD*v[2]; d_vatom(i,3) += THIRD*v[3];
|
||||
d_vatom(i,4) += THIRD*v[4]; d_vatom(i,5) += THIRD*v[5];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
template class PairVashishtaKokkos<LMPDeviceType>;
|
||||
#ifdef KOKKOS_HAVE_CUDA
|
||||
template class PairVashishtaKokkos<LMPHostType>;
|
||||
#endif
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,162 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(vashishta/kk,PairVashishtaKokkos<LMPDeviceType>)
|
||||
PairStyle(vashishta/kk/device,PairVashishtaKokkos<LMPDeviceType>)
|
||||
PairStyle(vashishta/kk/host,PairVashishtaKokkos<LMPHostType>)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_VASHISHTA_KOKKOS_H
|
||||
#define LMP_PAIR_VASHISHTA_KOKKOS_H
|
||||
|
||||
#include "pair_vashishta.h"
|
||||
#include "pair_kokkos.h"
|
||||
|
||||
template<int NEIGHFLAG, int EVFLAG>
|
||||
struct TagPairVashishtaComputeHalf{};
|
||||
|
||||
template<int NEIGHFLAG, int EVFLAG>
|
||||
struct TagPairVashishtaComputeFullA{};
|
||||
|
||||
template<int NEIGHFLAG, int EVFLAG>
|
||||
struct TagPairVashishtaComputeFullB{};
|
||||
|
||||
struct TagPairVashishtaComputeShortNeigh{};
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
template<class DeviceType>
|
||||
class PairVashishtaKokkos : public PairVashishta {
|
||||
public:
|
||||
enum {EnabledNeighFlags=FULL};
|
||||
enum {COUL_FLAG=0};
|
||||
typedef DeviceType device_type;
|
||||
typedef ArrayTypes<DeviceType> AT;
|
||||
typedef EV_FLOAT value_type;
|
||||
|
||||
PairVashishtaKokkos(class LAMMPS *);
|
||||
virtual ~PairVashishtaKokkos();
|
||||
virtual void compute(int, int);
|
||||
virtual void coeff(int, char **);
|
||||
virtual void init_style();
|
||||
|
||||
template<int NEIGHFLAG, int EVFLAG>
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void operator()(TagPairVashishtaComputeHalf<NEIGHFLAG,EVFLAG>, const int&, EV_FLOAT&) const;
|
||||
|
||||
template<int NEIGHFLAG, int EVFLAG>
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void operator()(TagPairVashishtaComputeHalf<NEIGHFLAG,EVFLAG>, const int&) const;
|
||||
|
||||
template<int NEIGHFLAG, int EVFLAG>
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void operator()(TagPairVashishtaComputeFullA<NEIGHFLAG,EVFLAG>, const int&, EV_FLOAT&) const;
|
||||
|
||||
template<int NEIGHFLAG, int EVFLAG>
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void operator()(TagPairVashishtaComputeFullA<NEIGHFLAG,EVFLAG>, const int&) const;
|
||||
|
||||
template<int NEIGHFLAG, int EVFLAG>
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void operator()(TagPairVashishtaComputeFullB<NEIGHFLAG,EVFLAG>, const int&, EV_FLOAT&) const;
|
||||
|
||||
template<int NEIGHFLAG, int EVFLAG>
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void operator()(TagPairVashishtaComputeFullB<NEIGHFLAG,EVFLAG>, const int&) const;
|
||||
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void operator()(TagPairVashishtaComputeShortNeigh, const int&) const;
|
||||
|
||||
template<int NEIGHFLAG>
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void ev_tally(EV_FLOAT &ev, const int &i, const int &j,
|
||||
const F_FLOAT &epair, const F_FLOAT &fpair, const F_FLOAT &delx,
|
||||
const F_FLOAT &dely, const F_FLOAT &delz) const;
|
||||
|
||||
template<int NEIGHFLAG>
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void ev_tally3(EV_FLOAT &ev, const int &i, const int &j, int &k,
|
||||
const F_FLOAT &evdwl, const F_FLOAT &ecoul,
|
||||
F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drji, F_FLOAT *drki) const;
|
||||
|
||||
KOKKOS_INLINE_FUNCTION
|
||||
void ev_tally3_atom(EV_FLOAT &ev, const int &i,
|
||||
const F_FLOAT &evdwl, const F_FLOAT &ecoul,
|
||||
F_FLOAT *fj, F_FLOAT *fk, F_FLOAT *drji, F_FLOAT *drki) const;
|
||||
|
||||
protected:
|
||||
typedef Kokkos::DualView<int***,DeviceType> tdual_int_3d;
|
||||
typedef typename tdual_int_3d::t_dev_const_randomread t_int_3d_randomread;
|
||||
typedef typename tdual_int_3d::t_host t_host_int_3d;
|
||||
|
||||
t_int_3d_randomread d_elem2param;
|
||||
DAT::t_int_1d_randomread d_map;
|
||||
|
||||
typedef Kokkos::DualView<Param*,DeviceType> tdual_param_1d;
|
||||
typedef typename tdual_param_1d::t_dev t_param_1d;
|
||||
typedef typename tdual_param_1d::t_host t_host_param_1d;
|
||||
|
||||
t_param_1d d_params;
|
||||
|
||||
virtual void setup_params();
|
||||
void twobody(const Param&, const F_FLOAT&, F_FLOAT&, const int&, F_FLOAT&) const;
|
||||
void threebody(const Param&, const Param&, const Param&, const F_FLOAT&, const F_FLOAT&, F_FLOAT *, F_FLOAT *,
|
||||
F_FLOAT *, F_FLOAT *, const int&, F_FLOAT&) const;
|
||||
void threebodyj(const Param&, const Param&, const Param&, const F_FLOAT&, const F_FLOAT&, F_FLOAT *, F_FLOAT *,
|
||||
F_FLOAT *) const;
|
||||
|
||||
typename ArrayTypes<DeviceType>::t_x_array_randomread x;
|
||||
typename ArrayTypes<DeviceType>::t_f_array f;
|
||||
typename ArrayTypes<DeviceType>::t_tagint_1d tag;
|
||||
typename ArrayTypes<DeviceType>::t_int_1d_randomread type;
|
||||
|
||||
DAT::tdual_efloat_1d k_eatom;
|
||||
DAT::tdual_virial_array k_vatom;
|
||||
DAT::t_efloat_1d d_eatom;
|
||||
DAT::t_virial_array d_vatom;
|
||||
|
||||
DAT::t_int_1d_randomread d_type2frho;
|
||||
DAT::t_int_2d_randomread d_type2rhor;
|
||||
DAT::t_int_2d_randomread d_type2z2r;
|
||||
|
||||
typename ArrayTypes<DeviceType>::t_neighbors_2d d_neighbors;
|
||||
typename ArrayTypes<DeviceType>::t_int_1d_randomread d_ilist;
|
||||
typename ArrayTypes<DeviceType>::t_int_1d_randomread d_numneigh;
|
||||
//NeighListKokkos<DeviceType> k_list;
|
||||
|
||||
int neighflag,newton_pair;
|
||||
int nlocal,nall,eflag,vflag;
|
||||
|
||||
int inum;
|
||||
Kokkos::View<int**,DeviceType> d_neighbors_short_2body;
|
||||
Kokkos::View<int*,DeviceType> d_numneigh_short_2body;
|
||||
Kokkos::View<int**,DeviceType> d_neighbors_short_3body;
|
||||
Kokkos::View<int*,DeviceType> d_numneigh_short_3body;
|
||||
friend void pair_virial_fdotr_compute<PairVashishtaKokkos>(PairVashishtaKokkos*);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Cannot use chosen neighbor list style with pair vashishta/kk
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
*/
|
||||
|
|
@ -33,10 +33,10 @@ template<class DeviceType>
|
|||
class RegBlockKokkos : public RegBlock {
|
||||
friend class FixPour;
|
||||
|
||||
public:
|
||||
typedef DeviceType device_type;
|
||||
typedef ArrayTypes<DeviceType> AT;
|
||||
|
||||
public:
|
||||
RegBlockKokkos(class LAMMPS *, int, char **);
|
||||
~RegBlockKokkos();
|
||||
void match_all_kokkos(int, DAT::t_int_1d);
|
||||
|
|
|
|||
|
|
@ -7,7 +7,7 @@ SHELL = /bin/sh
|
|||
# specify flags and libraries needed for your compiler
|
||||
|
||||
CC = mpicxx -cxx=icc
|
||||
CCFLAGS = -g -O3
|
||||
CCFLAGS = -g -O3 -restrict
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
|
|
|
|||
|
|
@ -7,7 +7,7 @@ SHELL = /bin/sh
|
|||
# specify flags and libraries needed for your compiler
|
||||
|
||||
CC = icc
|
||||
CCFLAGS = -g -O3
|
||||
CCFLAGS = -g -O3 -restrict
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
|
|
|
|||
|
|
@ -8,7 +8,7 @@ SHELL = /bin/sh
|
|||
|
||||
export OMPI_CXX = icc
|
||||
CC = mpicxx
|
||||
CCFLAGS = -g -O3
|
||||
CCFLAGS = -g -O3 -restrict
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
|
|
|
|||
|
|
@ -7,7 +7,7 @@ SHELL = /bin/sh
|
|||
# specify flags and libraries needed for your compiler
|
||||
|
||||
CC = icc
|
||||
CCFLAGS = -g -O3
|
||||
CCFLAGS = -g -O3 -restrict
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
|
|
|
|||
|
|
@ -7,7 +7,7 @@ SHELL = /bin/sh
|
|||
# specify flags and libraries needed for your compiler
|
||||
|
||||
CC = icc
|
||||
CCFLAGS = -g -O3
|
||||
CCFLAGS = -g -O3 -restrict
|
||||
SHFLAGS = -fPIC
|
||||
DEPFLAGS = -M
|
||||
|
||||
|
|
|
|||
|
|
@ -49,6 +49,7 @@ class PairTersoff : public Pair {
|
|||
double ZBLcut,ZBLexpscale;
|
||||
double c5,ca1,ca4; // added for TersoffMOD
|
||||
double powern_del;
|
||||
double c0; // added for TersoffMODC
|
||||
};
|
||||
|
||||
Param *params; // parameter set for an I-J-K interaction
|
||||
|
|
|
|||
|
|
@ -30,7 +30,7 @@ class PairTersoffMOD : public PairTersoff {
|
|||
~PairTersoffMOD() {}
|
||||
|
||||
protected:
|
||||
void read_file(char *);
|
||||
virtual void read_file(char *);
|
||||
virtual void setup_params();
|
||||
double zeta(Param *, double, double, double *, double *);
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,196 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Ganga P Purja Pun (George Mason University, Fairfax)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <math.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include "pair_tersoff_mod_c.h"
|
||||
#include "atom.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "neigh_request.h"
|
||||
#include "force.h"
|
||||
#include "comm.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
#include "math_const.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
|
||||
#define MAXLINE 1024
|
||||
#define DELTA 4
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairTersoffMODC::read_file(char *file)
|
||||
{
|
||||
int params_per_line = 21;
|
||||
char **words = new char*[params_per_line+1];
|
||||
|
||||
memory->sfree(params);
|
||||
params = NULL;
|
||||
nparams = maxparam = 0;
|
||||
|
||||
// open file on proc 0
|
||||
|
||||
FILE *fp;
|
||||
if (comm->me == 0) {
|
||||
fp = force->open_potential(file);
|
||||
if (fp == NULL) {
|
||||
char str[128];
|
||||
sprintf(str,"Cannot open Tersoff potential file %s",file);
|
||||
error->one(FLERR,str);
|
||||
}
|
||||
}
|
||||
|
||||
// read each line out of file, skipping blank lines or leading '#'
|
||||
// store line of params if all 3 element tags are in element list
|
||||
|
||||
int n,nwords,ielement,jelement,kelement;
|
||||
char line[MAXLINE],*ptr;
|
||||
int eof = 0;
|
||||
|
||||
while (1) {
|
||||
if (comm->me == 0) {
|
||||
ptr = fgets(line,MAXLINE,fp);
|
||||
if (ptr == NULL) {
|
||||
eof = 1;
|
||||
fclose(fp);
|
||||
} else n = strlen(line) + 1;
|
||||
}
|
||||
MPI_Bcast(&eof,1,MPI_INT,0,world);
|
||||
if (eof) break;
|
||||
MPI_Bcast(&n,1,MPI_INT,0,world);
|
||||
MPI_Bcast(line,n,MPI_CHAR,0,world);
|
||||
|
||||
// strip comment, skip line if blank
|
||||
|
||||
if ((ptr = strchr(line,'#'))) *ptr = '\0';
|
||||
nwords = atom->count_words(line);
|
||||
if (nwords == 0) continue;
|
||||
|
||||
// concatenate additional lines until have params_per_line words
|
||||
|
||||
while (nwords < params_per_line) {
|
||||
n = strlen(line);
|
||||
if (comm->me == 0) {
|
||||
ptr = fgets(&line[n],MAXLINE-n,fp);
|
||||
if (ptr == NULL) {
|
||||
eof = 1;
|
||||
fclose(fp);
|
||||
} else n = strlen(line) + 1;
|
||||
}
|
||||
MPI_Bcast(&eof,1,MPI_INT,0,world);
|
||||
if (eof) break;
|
||||
MPI_Bcast(&n,1,MPI_INT,0,world);
|
||||
MPI_Bcast(line,n,MPI_CHAR,0,world);
|
||||
if ((ptr = strchr(line,'#'))) *ptr = '\0';
|
||||
nwords = atom->count_words(line);
|
||||
}
|
||||
|
||||
if (nwords != params_per_line)
|
||||
error->all(FLERR,"Incorrect format in Tersoff potential file");
|
||||
|
||||
// words = ptrs to all words in line
|
||||
|
||||
nwords = 0;
|
||||
words[nwords++] = strtok(line," \t\n\r\f");
|
||||
while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
|
||||
|
||||
// ielement,jelement,kelement = 1st args
|
||||
// if all 3 args are in element list, then parse this line
|
||||
// else skip to next line
|
||||
|
||||
for (ielement = 0; ielement < nelements; ielement++)
|
||||
if (strcmp(words[0],elements[ielement]) == 0) break;
|
||||
if (ielement == nelements) continue;
|
||||
for (jelement = 0; jelement < nelements; jelement++)
|
||||
if (strcmp(words[1],elements[jelement]) == 0) break;
|
||||
if (jelement == nelements) continue;
|
||||
for (kelement = 0; kelement < nelements; kelement++)
|
||||
if (strcmp(words[2],elements[kelement]) == 0) break;
|
||||
if (kelement == nelements) continue;
|
||||
|
||||
// load up parameter settings and error check their values
|
||||
|
||||
if (nparams == maxparam) {
|
||||
maxparam += DELTA;
|
||||
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
|
||||
"pair:params");
|
||||
}
|
||||
|
||||
params[nparams].ielement = ielement;
|
||||
params[nparams].jelement = jelement;
|
||||
params[nparams].kelement = kelement;
|
||||
params[nparams].powerm = atof(words[3]);
|
||||
params[nparams].lam3 = atof(words[4]);
|
||||
params[nparams].h = atof(words[5]);
|
||||
params[nparams].powern = atof(words[6]);
|
||||
params[nparams].beta = atof(words[7]);
|
||||
params[nparams].lam2 = atof(words[8]);
|
||||
params[nparams].bigb = atof(words[9]);
|
||||
params[nparams].bigr = atof(words[10]);
|
||||
params[nparams].bigd = atof(words[11]);
|
||||
params[nparams].lam1 = atof(words[12]);
|
||||
params[nparams].biga = atof(words[13]);
|
||||
params[nparams].powern_del = atof(words[14]);
|
||||
params[nparams].c1 = atof(words[15]);
|
||||
params[nparams].c2 = atof(words[16]);
|
||||
params[nparams].c3 = atof(words[17]);
|
||||
params[nparams].c4 = atof(words[18]);
|
||||
params[nparams].c5 = atof(words[19]);
|
||||
params[nparams].c0 = atof(words[20]);
|
||||
|
||||
// currently only allow m exponent of 1
|
||||
|
||||
params[nparams].powermint = int(params[nparams].powerm);
|
||||
|
||||
if (
|
||||
params[nparams].lam3 < 0.0 || params[nparams].powern < 0.0 ||
|
||||
params[nparams].beta < 0.0 || params[nparams].lam2 < 0.0 ||
|
||||
params[nparams].bigb < 0.0 || params[nparams].bigr < 0.0 ||
|
||||
params[nparams].bigd < 0.0 ||
|
||||
params[nparams].bigd > params[nparams].bigr ||
|
||||
params[nparams].lam3 < 0.0 || params[nparams].biga < 0.0 ||
|
||||
params[nparams].powerm - params[nparams].powermint != 0.0 ||
|
||||
(params[nparams].powermint != 3 && params[nparams].powermint != 1))
|
||||
error->all(FLERR,"Illegal Tersoff parameter");
|
||||
|
||||
nparams++;
|
||||
}
|
||||
|
||||
delete [] words;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairTersoffMODC::repulsive(Param *param, double rsq, double &fforce,
|
||||
int eflag, double &eng)
|
||||
{
|
||||
double r,tmp_fc,tmp_fc_d,tmp_exp;
|
||||
|
||||
r = sqrt(rsq);
|
||||
tmp_fc = ters_fc(r,param);
|
||||
tmp_fc_d = ters_fc_d(r,param);
|
||||
tmp_exp = exp(-param->lam1 * r);
|
||||
fforce = -param->biga * tmp_exp * (tmp_fc_d - tmp_fc * param->lam1) / r - param->c0 * tmp_fc_d / r;
|
||||
if (eflag) eng = tmp_fc * param->biga * tmp_exp + param->c0 * tmp_fc;
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,66 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(tersoff/mod/c,PairTersoffMODC)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_TERSOFF_MOD_C_H
|
||||
#define LMP_PAIR_TERSOFF_MOD_C_H
|
||||
|
||||
#include "pair_tersoff_mod.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairTersoffMODC : public PairTersoffMOD {
|
||||
public:
|
||||
PairTersoffMODC(class LAMMPS *lmp) : PairTersoffMOD(lmp) {};
|
||||
~PairTersoffMODC() {}
|
||||
|
||||
protected:
|
||||
void read_file(char *);
|
||||
void repulsive(Param *, double, double &, int, double &);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Cannot open Tersoff potential file %s
|
||||
|
||||
The specified potential file cannot be opened. Check that the path
|
||||
and name are correct.
|
||||
|
||||
E: Incorrect format in Tersoff potential file
|
||||
|
||||
Incorrect number of words per line in the potential file.
|
||||
|
||||
E: Illegal Tersoff parameter
|
||||
|
||||
One or more of the coefficients defined in the potential file is
|
||||
invalid.
|
||||
|
||||
E: Potential file has duplicate entry
|
||||
|
||||
The potential file has more than one entry for the same element.
|
||||
|
||||
E: Potential file is missing an entry
|
||||
|
||||
The potential file does not have a needed entry.
|
||||
|
||||
*/
|
||||
|
|
@ -64,6 +64,8 @@ PairVashishta::PairVashishta(LAMMPS *lmp) : Pair(lmp)
|
|||
|
||||
PairVashishta::~PairVashishta()
|
||||
{
|
||||
if (copymode) return;
|
||||
|
||||
if (elements)
|
||||
for (int i = 0; i < nelements; i++) delete [] elements[i];
|
||||
delete [] elements;
|
||||
|
|
|
|||
|
|
@ -34,7 +34,6 @@ class PairVashishta : public Pair {
|
|||
double init_one(int, int);
|
||||
void init_style();
|
||||
|
||||
protected:
|
||||
struct Param {
|
||||
double bigb,gamma,r0,bigc,costheta;
|
||||
double bigh,eta,zi,zj;
|
||||
|
|
@ -45,7 +44,7 @@ class PairVashishta : public Pair {
|
|||
double lam1rc,lam4rc,vrcc2,vrcc3,vrc,dvrc,c0;
|
||||
int ielement,jelement,kelement;
|
||||
};
|
||||
|
||||
protected:
|
||||
double cutmax; // max cutoff for all elements
|
||||
int nelements; // # of unique elements
|
||||
char **elements; // names of unique elements
|
||||
|
|
|
|||
|
|
@ -55,7 +55,8 @@ static const char cite_fix_orient_fcc[] =
|
|||
|
||||
FixOrientFCC::FixOrientFCC(LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix(lmp, narg, arg),
|
||||
xifilename(NULL), chifilename(NULL), order(NULL), nbr(NULL), sort(NULL), list(NULL)
|
||||
xifilename(NULL), chifilename(NULL), order(NULL), nbr(NULL),
|
||||
sort(NULL), list(NULL)
|
||||
{
|
||||
if (lmp->citeme) lmp->citeme->add(cite_fix_orient_fcc);
|
||||
|
||||
|
|
|
|||
|
|
@ -62,7 +62,12 @@ static const char cite_fix_poems[] =
|
|||
------------------------------------------------------------------------- */
|
||||
|
||||
FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix(lmp, narg, arg)
|
||||
Fix(lmp, narg, arg), step_respa(NULL), natom2body(NULL),
|
||||
atom2body(NULL), displace(NULL), nrigid(NULL), masstotal(NULL),
|
||||
xcm(NULL), vcm(NULL), fcm(NULL), inertia(NULL), ex_space(NULL),
|
||||
ey_space(NULL), ez_space(NULL), angmom(NULL), omega(NULL),
|
||||
torque(NULL), sum(NULL), all(NULL), jointbody(NULL),
|
||||
xjoint(NULL), freelist(NULL), poems(NULL)
|
||||
{
|
||||
if (lmp->citeme) lmp->citeme->add(cite_fix_poems);
|
||||
|
||||
|
|
|
|||
|
|
@ -28,12 +28,10 @@
|
|||
#ifndef LMP_INTEL_PREPROCESS_H
|
||||
#define LMP_INTEL_PREPROCESS_H
|
||||
|
||||
#ifndef LAMMPS_MEMALIGN
|
||||
#error Please set -DLAMMPS_MEMALIGN=64 in CCFLAGS for your LAMMPS makefile.
|
||||
#else
|
||||
#if (LAMMPS_MEMALIGN != 64)
|
||||
#error Please set -DLAMMPS_MEMALIGN=64 in CCFLAGS for your LAMMPS makefile.
|
||||
#endif
|
||||
// LAMMPS_MEMALIGN is set to 64 by default for -DLMP_USER_INTEL
|
||||
// so we only need to error out in case of a different alignment
|
||||
#if LAMMPS_MEMALIGN && (LAMMPS_MEMALIGN != 64)
|
||||
#error Please set -DLAMMPS_MEMALIGN=64 in CCFLAGS of your LAMMPS makefile for USER-INTEL package
|
||||
#endif
|
||||
|
||||
#if defined(_OPENMP)
|
||||
|
|
|
|||
|
|
@ -49,6 +49,7 @@ improper_style cossq, Georgios Vogiatzis, gvog at chemeng.ntua.gr, 25 May 12
|
|||
improper_style fourier, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12
|
||||
improper_style ring, Georgios Vogiatzis, gvog at chemeng.ntua.gr, 25 May 12
|
||||
improper_style distance, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
|
||||
pair_style agni, Axel Kohlmeyer, akohlmey at gmail.com, 9 Nov 16
|
||||
pair_style buck/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
|
||||
pair_style coul/diel, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11
|
||||
pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11
|
||||
|
|
|
|||
|
|
@ -0,0 +1,508 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing authors: Axel Kohlmeyer (Temple U), Venkatesh Botu
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <math.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include "pair_agni.h"
|
||||
#include "atom.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_request.h"
|
||||
#include "force.h"
|
||||
#include "comm.h"
|
||||
#include "memory.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "citeme.h"
|
||||
#include "math_special.h"
|
||||
#include "math_const.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathSpecial;
|
||||
|
||||
static const char cite_pair_agni[] =
|
||||
"pair agni command:\n\n"
|
||||
"@article{botu2015adaptive,\n"
|
||||
" author = {Botu, Venkatesh and Ramprasad, Rampi},\n"
|
||||
" title = {Adaptive machine learning framework to"
|
||||
" accelerate ab initio molecular dynamics},\n"
|
||||
" journal = {International Journal of Quantum Chemistry},\n"
|
||||
" volume = {115},\n"
|
||||
" number = {16},\n"
|
||||
" pages = {1074--1083},\n"
|
||||
" year = {2015},\n"
|
||||
" publisher = {Wiley Online Library}\n"
|
||||
"}\n\n"
|
||||
"@article{botu2015learning,\n"
|
||||
" author = {Botu, Venkatesh and Ramprasad, Rampi},\n"
|
||||
" title = {Learning scheme to predict atomic forces"
|
||||
" and accelerate materials simulations},\n"
|
||||
" journal = {Physical Review B},\n"
|
||||
" volume = {92},\n"
|
||||
" number = {9},\n"
|
||||
" pages = {094306},\n"
|
||||
" year = {2015},\n"
|
||||
" publisher = {APS}\n"
|
||||
"}\n\n";
|
||||
|
||||
#define AGNI_VERSION 1
|
||||
#define MAXLINE 10240
|
||||
#define MAXWORD 40
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairAGNI::PairAGNI(LAMMPS *lmp) : Pair(lmp)
|
||||
{
|
||||
if (lmp->citeme) lmp->citeme->add(cite_pair_agni);
|
||||
|
||||
single_enable = 0;
|
||||
restartinfo = 0;
|
||||
one_coeff = 1;
|
||||
manybody_flag = 1;
|
||||
|
||||
no_virial_fdotr_compute = 1;
|
||||
|
||||
nelements = 0;
|
||||
elements = NULL;
|
||||
elem2param = NULL;
|
||||
nparams = 0;
|
||||
params = NULL;
|
||||
map = NULL;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
check if allocated, since class can be destructed when incomplete
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
PairAGNI::~PairAGNI()
|
||||
{
|
||||
if (elements)
|
||||
for (int i = 0; i < nelements; i++) delete [] elements[i];
|
||||
delete [] elements;
|
||||
if (params) {
|
||||
for (int i = 0; i < nparams; ++i) {
|
||||
int n = params[i].numeta;
|
||||
for (int j = 0; j < n; ++j) {
|
||||
delete [] params[i].xU[j];
|
||||
}
|
||||
delete [] params[i].eta;
|
||||
delete [] params[i].alpha;
|
||||
delete [] params[i].xU;
|
||||
delete [] params[i].yU;
|
||||
}
|
||||
memory->destroy(params);
|
||||
params = NULL;
|
||||
}
|
||||
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
delete [] map;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairAGNI::compute(int eflag, int vflag)
|
||||
{
|
||||
int i,j,k,ii,jj,inum,jnum,itype;
|
||||
double xtmp,ytmp,ztmp,delx,dely,delz;
|
||||
double rsq;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
int *type = atom->type;
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
double fxtmp,fytmp,fztmp;
|
||||
double *Vx, *Vy, *Vz;
|
||||
|
||||
// loop over full neighbor list of my atoms
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
itype = map[type[i]];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
fxtmp = fytmp = fztmp = 0.0;
|
||||
|
||||
const Param &iparam = params[elem2param[itype]];
|
||||
Vx = new double[iparam.numeta];
|
||||
Vy = new double[iparam.numeta];
|
||||
Vz = new double[iparam.numeta];
|
||||
memset(Vx,0,iparam.numeta*sizeof(double));
|
||||
memset(Vy,0,iparam.numeta*sizeof(double));
|
||||
memset(Vz,0,iparam.numeta*sizeof(double));
|
||||
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
|
||||
if ((rsq > 0.0) && (rsq < iparam.cutsq)) {
|
||||
const double r = sqrt(rsq);
|
||||
const double cF = 0.5*(cos((MathConst::MY_PI*r)/iparam.cut)+1.0);
|
||||
const double wX = cF*delx/r;
|
||||
const double wY = cF*dely/r;
|
||||
const double wZ = cF*delz/r;
|
||||
|
||||
for (k = 0; k < iparam.numeta; ++k) {
|
||||
const double e = exp(-(iparam.eta[k]*rsq));
|
||||
Vx[k] += wX*e;
|
||||
Vy[k] += wY*e;
|
||||
Vz[k] += wZ*e;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
for (j = 0; j < iparam.numtrain; ++j) {
|
||||
double kx = 0.0;
|
||||
double ky = 0.0;
|
||||
double kz = 0.0;
|
||||
|
||||
for(int k = 0; k < iparam.numeta; ++k) {
|
||||
const double xu = iparam.xU[k][j];
|
||||
kx += square(Vx[k] - xu);
|
||||
ky += square(Vy[k] - xu);
|
||||
kz += square(Vz[k] - xu);
|
||||
}
|
||||
const double e = -0.5/(square(iparam.sigma));
|
||||
fxtmp += iparam.alpha[j]*exp(kx*e);
|
||||
fytmp += iparam.alpha[j]*exp(ky*e);
|
||||
fztmp += iparam.alpha[j]*exp(kz*e);
|
||||
}
|
||||
fxtmp += iparam.b;
|
||||
fytmp += iparam.b;
|
||||
fztmp += iparam.b;
|
||||
f[i][0] += fxtmp;
|
||||
f[i][1] += fytmp;
|
||||
f[i][2] += fztmp;
|
||||
|
||||
if (evflag) ev_tally_xyz_full(i,0.0,0.0,fxtmp,fytmp,fztmp,delx,dely,delz);
|
||||
|
||||
delete [] Vx;
|
||||
delete [] Vy;
|
||||
delete [] Vz;
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairAGNI::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
|
||||
memory->create(setflag,n+1,n+1,"pair:setflag");
|
||||
memory->create(cutsq,n+1,n+1,"pair:cutsq");
|
||||
map = new int[n+1];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairAGNI::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 0) error->all(FLERR,"Illegal pair_style command");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairAGNI::coeff(int narg, char **arg)
|
||||
{
|
||||
int i,j,n;
|
||||
|
||||
if (!allocated) allocate();
|
||||
|
||||
if (narg != 3 + atom->ntypes)
|
||||
error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
|
||||
// insure I,J args are * *
|
||||
|
||||
if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
|
||||
error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
|
||||
// read args that map atom types to elements in potential file
|
||||
// map[i] = which element the Ith atom type is, -1 if NULL
|
||||
// nelements = # of unique elements
|
||||
// elements = list of element names
|
||||
|
||||
if (elements) {
|
||||
for (i = 0; i < nelements; i++) delete [] elements[i];
|
||||
delete [] elements;
|
||||
}
|
||||
elements = new char*[atom->ntypes];
|
||||
for (i = 0; i < atom->ntypes; i++) elements[i] = NULL;
|
||||
|
||||
nelements = 0;
|
||||
for (i = 3; i < narg; i++) {
|
||||
if (strcmp(arg[i],"NULL") == 0) {
|
||||
map[i-2] = -1;
|
||||
continue;
|
||||
}
|
||||
for (j = 0; j < nelements; j++)
|
||||
if (strcmp(arg[i],elements[j]) == 0) break;
|
||||
map[i-2] = j;
|
||||
if (j == nelements) {
|
||||
n = strlen(arg[i]) + 1;
|
||||
elements[j] = new char[n];
|
||||
strcpy(elements[j],arg[i]);
|
||||
nelements++;
|
||||
}
|
||||
}
|
||||
|
||||
// read potential file and initialize potential parameters
|
||||
|
||||
read_file(arg[2]);
|
||||
setup_params();
|
||||
|
||||
// clear setflag since coeff() called once with I,J = * *
|
||||
|
||||
n = atom->ntypes;
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
setflag[i][j] = 0;
|
||||
|
||||
// set setflag i,j for type pairs where both are mapped to elements
|
||||
|
||||
int count = 0;
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
if (map[i] >= 0 && map[j] >= 0) {
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init specific to this pair style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairAGNI::init_style()
|
||||
{
|
||||
// need a full neighbor list
|
||||
|
||||
int irequest = neighbor->request(this,instance_me);
|
||||
neighbor->requests[irequest]->half = 0;
|
||||
neighbor->requests[irequest]->full = 1;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairAGNI::init_one(int i, int j)
|
||||
{
|
||||
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
|
||||
|
||||
return cutmax;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairAGNI::read_file(char *file)
|
||||
{
|
||||
memory->sfree(params);
|
||||
params = NULL;
|
||||
nparams = 0;
|
||||
|
||||
// open file on proc 0 only
|
||||
// then read line by line and broadcast the line to all MPI ranks
|
||||
|
||||
FILE *fp;
|
||||
if (comm->me == 0) {
|
||||
fp = force->open_potential(file);
|
||||
if (fp == NULL) {
|
||||
char str[128];
|
||||
sprintf(str,"Cannot open AGNI potential file %s",file);
|
||||
error->one(FLERR,str);
|
||||
}
|
||||
}
|
||||
|
||||
int i,j,n,nwords,curparam,wantdata;
|
||||
char line[MAXLINE],*ptr;
|
||||
int eof = 0;
|
||||
char **words = new char*[MAXWORD+1];
|
||||
|
||||
while (1) {
|
||||
n = 0;
|
||||
if (comm->me == 0) {
|
||||
ptr = fgets(line,MAXLINE,fp);
|
||||
if (ptr == NULL) {
|
||||
eof = 1;
|
||||
fclose(fp);
|
||||
} else n = strlen(line) + 1;
|
||||
}
|
||||
MPI_Bcast(&eof,1,MPI_INT,0,world);
|
||||
if (eof) break;
|
||||
MPI_Bcast(&n,1,MPI_INT,0,world);
|
||||
MPI_Bcast(line,n,MPI_CHAR,0,world);
|
||||
|
||||
// strip comment, skip line if blank
|
||||
|
||||
if ((ptr = strchr(line,'#'))) *ptr = '\0';
|
||||
nwords = atom->count_words(line);
|
||||
if (nwords == 0) continue;
|
||||
|
||||
if (nwords > MAXWORD)
|
||||
error->all(FLERR,"Increase MAXWORD and recompile");
|
||||
|
||||
// words = ptrs to all words in line
|
||||
|
||||
nwords = 0;
|
||||
words[nwords++] = strtok(line," \t\n\r\f");
|
||||
while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
|
||||
--nwords;
|
||||
|
||||
if ((nwords == 2) && (strcmp(words[0],"generation") == 0)) {
|
||||
int ver = atoi(words[1]);
|
||||
if (ver != AGNI_VERSION)
|
||||
error->all(FLERR,"Incompatible AGNI potential file version");
|
||||
if ((ver == 1) && (nelements != 1))
|
||||
error->all(FLERR,"Cannot handle multi-element systems with this potential");
|
||||
|
||||
} else if ((nwords == 2) && (strcmp(words[0],"n_elements") == 0)) {
|
||||
nparams = atoi(words[1]);
|
||||
if ((nparams < 1) || params) // sanity check
|
||||
error->all(FLERR,"Invalid AGNI potential file");
|
||||
params = memory->create(params,nparams,"pair:params");
|
||||
memset(params,0,nparams*sizeof(Param));
|
||||
curparam = -1;
|
||||
|
||||
} else if (params && (nwords == nparams+1) && (strcmp(words[0],"element") == 0)) {
|
||||
wantdata = -1;
|
||||
for (i = 0; i < nparams; ++i) {
|
||||
for (j = 0; j < nelements; ++j)
|
||||
if (strcmp(words[i+1],elements[j]) == 0) break;
|
||||
if (j == nelements)
|
||||
error->all(FLERR,"No suitable parameters for requested element found");
|
||||
else params[i].ielement = j;
|
||||
}
|
||||
} else if (params && (nwords == 2) && (strcmp(words[0],"interaction") == 0)) {
|
||||
for (i = 0; i < nparams; ++i)
|
||||
if (strcmp(words[1],elements[params[i].ielement]) == 0) curparam = i;
|
||||
} else if ((curparam >=0) && (nwords == 1) && (strcmp(words[0],"endVar") == 0)) {
|
||||
int numtrain = params[curparam].numtrain;
|
||||
int numeta = params[curparam].numeta;
|
||||
params[curparam].alpha = new double[numtrain];
|
||||
params[curparam].yU = new double[numtrain];
|
||||
params[curparam].xU = new double*[numeta];
|
||||
for (i = 0; i < numeta; ++i)
|
||||
params[curparam].xU[i] = new double[numtrain];
|
||||
|
||||
wantdata = curparam;
|
||||
curparam = -1;
|
||||
} else if ((curparam >=0) && (nwords == 2) && (strcmp(words[0],"Rc") == 0)) {
|
||||
params[curparam].cut = atof(words[1]);
|
||||
} else if ((curparam >=0) && (nwords == 2) && (strcmp(words[0],"Rs") == 0)) {
|
||||
; // ignored
|
||||
} else if ((curparam >=0) && (nwords == 2) && (strcmp(words[0],"neighbors") == 0)) {
|
||||
; // ignored
|
||||
} else if ((curparam >=0) && (nwords == 2) && (strcmp(words[0],"sigma") == 0)) {
|
||||
params[curparam].sigma = atof(words[1]);
|
||||
} else if ((curparam >=0) && (nwords == 2) && (strcmp(words[0],"lambda") == 0)) {
|
||||
params[curparam].lambda = atof(words[1]);
|
||||
} else if ((curparam >=0) && (nwords == 2) && (strcmp(words[0],"b") == 0)) {
|
||||
params[curparam].b = atof(words[1]);
|
||||
} else if ((curparam >=0) && (nwords == 2) && (strcmp(words[0],"n_train") == 0)) {
|
||||
params[curparam].numtrain = atoi(words[1]);
|
||||
} else if ((curparam >=0) && (nwords > 1) && (strcmp(words[0],"eta") == 0)) {
|
||||
params[curparam].numeta = nwords-1;
|
||||
params[curparam].eta = new double[nwords-1];
|
||||
for (i = 0, j = 1 ; j < nwords; ++i, ++j)
|
||||
params[curparam].eta[i] = atof(words[j]);
|
||||
} else if (params && (wantdata >=0) && (nwords == params[wantdata].numeta+3)) {
|
||||
n = (int) atof(words[0]);
|
||||
for (i = 0; i < params[wantdata].numeta; ++i) {
|
||||
params[wantdata].xU[i][n] = atof(words[i+1]);
|
||||
}
|
||||
params[wantdata].yU[n] = atof(words[params[wantdata].numeta+1]);
|
||||
params[wantdata].alpha[n] = atof(words[params[wantdata].numeta+2]);
|
||||
|
||||
} else {
|
||||
if (comm->me == 0)
|
||||
error->warning(FLERR,"Ignoring unknown content in AGNI potential file.");
|
||||
}
|
||||
}
|
||||
|
||||
delete [] words;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairAGNI::setup_params()
|
||||
{
|
||||
int i,m,n;
|
||||
double rtmp;
|
||||
|
||||
// set elem2param for all elements
|
||||
|
||||
memory->destroy(elem2param);
|
||||
memory->create(elem2param,nelements,"pair:elem2param");
|
||||
|
||||
for (i = 0; i < nelements; i++) {
|
||||
n = -1;
|
||||
for (m = 0; m < nparams; m++) {
|
||||
if (i == params[m].ielement) {
|
||||
if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
|
||||
n = m;
|
||||
}
|
||||
}
|
||||
if (n < 0) error->all(FLERR,"Potential file is missing an entry");
|
||||
elem2param[i] = n;
|
||||
}
|
||||
|
||||
// compute parameter values derived from inputs
|
||||
|
||||
// set cutsq using shortcut to reduce neighbor list for accelerated
|
||||
// calculations. cut must remain unchanged as it is a potential parameter
|
||||
// (cut = a*sigma)
|
||||
|
||||
cutmax = 0.0;
|
||||
for (m = 0; m < nparams; m++) {
|
||||
rtmp = params[m].cut;
|
||||
params[m].cutsq = rtmp * rtmp;
|
||||
if (rtmp > cutmax) cutmax = rtmp;
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,85 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(agni,PairAGNI)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_AGNI_H
|
||||
#define LMP_PAIR_AGNI_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairAGNI : public Pair {
|
||||
public:
|
||||
PairAGNI(class LAMMPS *);
|
||||
virtual ~PairAGNI();
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
virtual void coeff(int, char **);
|
||||
virtual double init_one(int, int);
|
||||
virtual void init_style();
|
||||
|
||||
struct Param {
|
||||
double cut,cutsq;
|
||||
double *eta,**xU,*yU,*alpha;
|
||||
double sigma,lambda,b;
|
||||
int numeta,numtrain,ielement;
|
||||
};
|
||||
|
||||
protected:
|
||||
double cutmax; // max cutoff for all elements
|
||||
int nelements; // # of unique atom type labels
|
||||
char **elements; // names of unique elements
|
||||
int *elem2param; // mapping from element pairs to parameters
|
||||
int *map; // mapping from atom types to elements
|
||||
int nparams; // # of stored parameter sets
|
||||
Param *params; // parameter set for an I-J interaction
|
||||
|
||||
virtual void allocate();
|
||||
void read_file(char *);
|
||||
virtual void setup_params();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Incorrect args for pair coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
E: Cannot open AGNI potential file %s
|
||||
|
||||
The specified AGNI potential file cannot be opened. Check that the path
|
||||
and name are correct.
|
||||
|
||||
E: Incorrect format in AGNI potential file
|
||||
|
||||
The potential file is not compatible with the AGNI pair style
|
||||
implementation in this LAMMPS version.
|
||||
|
||||
*/
|
||||
|
|
@ -0,0 +1,299 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
This software is distributed under the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Axel Kohlmeyer (Temple U)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <math.h>
|
||||
#include <string.h>
|
||||
#include <stdint.h>
|
||||
#include "pair_agni_omp.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "math_special.h"
|
||||
#include "math_const.h"
|
||||
|
||||
#include "suffix.h"
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathSpecial;
|
||||
|
||||
/*
|
||||
Copyright (c) 2012,2013 Axel Kohlmeyer <akohlmey@gmail.com>
|
||||
All rights reserved.
|
||||
|
||||
Redistribution and use in source and binary forms, with or without
|
||||
modification, are permitted provided that the following conditions
|
||||
are met:
|
||||
|
||||
* Redistributions of source code must retain the above copyright
|
||||
notice, this list of conditions and the following disclaimer.
|
||||
* Redistributions in binary form must reproduce the above copyright
|
||||
notice, this list of conditions and the following disclaimer in the
|
||||
documentation and/or other materials provided with the distribution.
|
||||
* Neither the name of the <organization> nor the
|
||||
names of its contributors may be used to endorse or promote products
|
||||
derived from this software without specific prior written permission.
|
||||
|
||||
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
|
||||
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
|
||||
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
|
||||
ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
|
||||
DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
|
||||
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
|
||||
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
|
||||
ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
|
||||
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
|
||||
THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
||||
*/
|
||||
|
||||
/* faster versions of 2**x, e**x, and 10**x in single and double precision.
|
||||
*
|
||||
* Based on the Cephes math library 2.8
|
||||
*/
|
||||
|
||||
/* internal definitions for the fastermath library */
|
||||
|
||||
/* IEEE 754 double precision floating point data manipulation */
|
||||
typedef union
|
||||
{
|
||||
double f;
|
||||
uint64_t u;
|
||||
struct {int32_t i0,i1;};
|
||||
} udi_t;
|
||||
#define FM_DOUBLE_BIAS 1023
|
||||
#define FM_DOUBLE_EMASK 2146435072
|
||||
#define FM_DOUBLE_MBITS 20
|
||||
#define FM_DOUBLE_MMASK 1048575
|
||||
#define FM_DOUBLE_EZERO 1072693248
|
||||
|
||||
/* generate 2**num in floating point by bitshifting */
|
||||
#define FM_DOUBLE_INIT_EXP(var,num) \
|
||||
var.i0 = 0; \
|
||||
var.i1 = (((int) num) + FM_DOUBLE_BIAS) << 20
|
||||
|
||||
/* double precision constants */
|
||||
#define FM_DOUBLE_LOG2OFE 1.4426950408889634074
|
||||
#define FM_DOUBLE_LOGEOF2 6.9314718055994530942e-1
|
||||
#define FM_DOUBLE_LOG2OF10 3.32192809488736234789
|
||||
#define FM_DOUBLE_LOG10OF2 3.0102999566398119521e-1
|
||||
#define FM_DOUBLE_LOG10OFE 4.3429448190325182765e-1
|
||||
#define FM_DOUBLE_SQRT2 1.41421356237309504880
|
||||
#define FM_DOUBLE_SQRTH 0.70710678118654752440
|
||||
|
||||
/* optimizer friendly implementation of exp2(x).
|
||||
*
|
||||
* strategy:
|
||||
*
|
||||
* split argument into an integer part and a fraction:
|
||||
* ipart = floor(x+0.5);
|
||||
* fpart = x - ipart;
|
||||
*
|
||||
* compute exp2(ipart) from setting the ieee754 exponent
|
||||
* compute exp2(fpart) using a pade' approximation for x in [-0.5;0.5[
|
||||
*
|
||||
* the result becomes: exp2(x) = exp2(ipart) * exp2(fpart)
|
||||
*/
|
||||
|
||||
static const double fm_exp2_q[] = {
|
||||
/* 1.00000000000000000000e0, */
|
||||
2.33184211722314911771e2,
|
||||
4.36821166879210612817e3
|
||||
};
|
||||
static const double fm_exp2_p[] = {
|
||||
2.30933477057345225087e-2,
|
||||
2.02020656693165307700e1,
|
||||
1.51390680115615096133e3
|
||||
};
|
||||
|
||||
static double fm_exp2(double x)
|
||||
{
|
||||
double ipart, fpart, px, qx;
|
||||
udi_t epart;
|
||||
|
||||
ipart = floor(x+0.5);
|
||||
fpart = x - ipart;
|
||||
FM_DOUBLE_INIT_EXP(epart,ipart);
|
||||
|
||||
x = fpart*fpart;
|
||||
|
||||
px = fm_exp2_p[0];
|
||||
px = px*x + fm_exp2_p[1];
|
||||
qx = x + fm_exp2_q[0];
|
||||
px = px*x + fm_exp2_p[2];
|
||||
qx = qx*x + fm_exp2_q[1];
|
||||
|
||||
px = px * fpart;
|
||||
|
||||
x = 1.0 + 2.0*(px/(qx-px));
|
||||
return epart.f*x;
|
||||
}
|
||||
|
||||
static double fm_exp(double x)
|
||||
{
|
||||
#if defined(__BYTE_ORDER__)
|
||||
#if __BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__
|
||||
return fm_exp2(FM_DOUBLE_LOG2OFE * (x));
|
||||
#endif
|
||||
#endif
|
||||
return exp(x);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairAGNIOMP::PairAGNIOMP(LAMMPS *lmp) :
|
||||
PairAGNI(lmp), ThrOMP(lmp, THR_PAIR)
|
||||
{
|
||||
suffix_flag |= Suffix::OMP;
|
||||
respa_enable = 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairAGNIOMP::compute(int eflag, int vflag)
|
||||
{
|
||||
if (eflag || vflag) {
|
||||
ev_setup(eflag,vflag);
|
||||
} else evflag = vflag_fdotr = 0;
|
||||
|
||||
const int nall = atom->nlocal + atom->nghost;
|
||||
const int nthreads = comm->nthreads;
|
||||
const int inum = list->inum;
|
||||
|
||||
#if defined(_OPENMP)
|
||||
#pragma omp parallel default(none) shared(eflag,vflag)
|
||||
#endif
|
||||
{
|
||||
int ifrom, ito, tid;
|
||||
|
||||
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
|
||||
ThrData *thr = fix->get_thr(tid);
|
||||
thr->timer(Timer::START);
|
||||
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
|
||||
|
||||
if (evflag) eval<1>(ifrom, ito, thr);
|
||||
else eval<0>(ifrom, ito, thr);
|
||||
|
||||
thr->timer(Timer::PAIR);
|
||||
reduce_thr(this, eflag, vflag, thr);
|
||||
} // end of omp parallel region
|
||||
}
|
||||
|
||||
template <int EVFLAG>
|
||||
void PairAGNIOMP::eval(int iifrom, int iito, ThrData * const thr)
|
||||
{
|
||||
int i,j,k,ii,jj,itype,jnum;
|
||||
double xtmp,ytmp,ztmp,delx,dely,delz;
|
||||
double rsq;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
|
||||
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
|
||||
const int * _noalias const type = atom->type;
|
||||
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
double fxtmp,fytmp,fztmp;
|
||||
double *Vx, *Vy, *Vz;
|
||||
|
||||
// loop over full neighbor list of my atoms
|
||||
|
||||
for (ii = iifrom; ii < iito; ++ii) {
|
||||
|
||||
i = ilist[ii];
|
||||
itype = map[type[i]];
|
||||
xtmp = x[i].x;
|
||||
ytmp = x[i].y;
|
||||
ztmp = x[i].z;
|
||||
fxtmp = fytmp = fztmp = 0.0;
|
||||
|
||||
const Param &iparam = params[elem2param[itype]];
|
||||
Vx = new double[iparam.numeta];
|
||||
Vy = new double[iparam.numeta];
|
||||
Vz = new double[iparam.numeta];
|
||||
memset(Vx,0,iparam.numeta*sizeof(double));
|
||||
memset(Vy,0,iparam.numeta*sizeof(double));
|
||||
memset(Vz,0,iparam.numeta*sizeof(double));
|
||||
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j].x;
|
||||
dely = ytmp - x[j].y;
|
||||
delz = ztmp - x[j].z;
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
|
||||
if ((rsq > 0.0) && (rsq < iparam.cutsq)) {
|
||||
const double r = sqrt(rsq);
|
||||
const double cF = 0.5*(cos((MathConst::MY_PI*r)/iparam.cut)+1.0);
|
||||
const double wX = cF*delx/r;
|
||||
const double wY = cF*dely/r;
|
||||
const double wZ = cF*delz/r;
|
||||
|
||||
for (k = 0; k < iparam.numeta; ++k) {
|
||||
const double e = fm_exp(-(iparam.eta[k]*rsq));
|
||||
Vx[k] += wX*e;
|
||||
Vy[k] += wY*e;
|
||||
Vz[k] += wZ*e;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
for (j = 0; j < iparam.numtrain; ++j) {
|
||||
double kx = 0.0;
|
||||
double ky = 0.0;
|
||||
double kz = 0.0;
|
||||
|
||||
for(int k = 0; k < iparam.numeta; ++k) {
|
||||
const double xu = iparam.xU[k][j];
|
||||
kx += square(Vx[k] - xu);
|
||||
ky += square(Vy[k] - xu);
|
||||
kz += square(Vz[k] - xu);
|
||||
}
|
||||
const double e = -0.5/(square(iparam.sigma));
|
||||
fxtmp += iparam.alpha[j]*fm_exp(kx*e);
|
||||
fytmp += iparam.alpha[j]*fm_exp(ky*e);
|
||||
fztmp += iparam.alpha[j]*fm_exp(kz*e);
|
||||
}
|
||||
fxtmp += iparam.b;
|
||||
fytmp += iparam.b;
|
||||
fztmp += iparam.b;
|
||||
f[i].x += fxtmp;
|
||||
f[i].y += fytmp;
|
||||
f[i].z += fztmp;
|
||||
|
||||
if (EVFLAG) ev_tally_xyz_full_thr(this,i,0.0,0.0,
|
||||
fxtmp,fytmp,fztmp,
|
||||
delx,dely,delz,thr);
|
||||
delete [] Vx;
|
||||
delete [] Vy;
|
||||
delete [] Vz;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairAGNIOMP::memory_usage()
|
||||
{
|
||||
double bytes = memory_usage_thr();
|
||||
bytes += PairAGNI::memory_usage();
|
||||
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -0,0 +1,48 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Axel Kohlmeyer (Temple U)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(agni/omp,PairAGNIOMP)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_AGNI_OMP_H
|
||||
#define LMP_PAIR_AGNI_OMP_H
|
||||
|
||||
#include "pair_agni.h"
|
||||
#include "thr_omp.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairAGNIOMP : public PairAGNI, public ThrOMP {
|
||||
|
||||
public:
|
||||
PairAGNIOMP(class LAMMPS *);
|
||||
|
||||
virtual void compute(int, int);
|
||||
virtual double memory_usage();
|
||||
|
||||
private:
|
||||
template <int EVFLAG>
|
||||
void eval(int ifrom, int ito, ThrData * const thr);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -0,0 +1,253 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
This software is distributed under the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Axel Kohlmeyer (Temple U)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <math.h>
|
||||
#include "pair_tersoff_mod_c_omp.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
|
||||
#include "suffix.h"
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairTersoffMODCOMP::PairTersoffMODCOMP(LAMMPS *lmp) :
|
||||
PairTersoffMODC(lmp), ThrOMP(lmp, THR_PAIR)
|
||||
{
|
||||
suffix_flag |= Suffix::OMP;
|
||||
respa_enable = 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairTersoffMODCOMP::compute(int eflag, int vflag)
|
||||
{
|
||||
if (eflag || vflag) {
|
||||
ev_setup(eflag,vflag);
|
||||
} else evflag = vflag_fdotr = vflag_atom = 0;
|
||||
|
||||
const int nall = atom->nlocal + atom->nghost;
|
||||
const int nthreads = comm->nthreads;
|
||||
const int inum = list->inum;
|
||||
|
||||
#if defined(_OPENMP)
|
||||
#pragma omp parallel default(none) shared(eflag,vflag)
|
||||
#endif
|
||||
{
|
||||
int ifrom, ito, tid;
|
||||
|
||||
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
|
||||
ThrData *thr = fix->get_thr(tid);
|
||||
thr->timer(Timer::START);
|
||||
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
|
||||
|
||||
if (evflag) {
|
||||
if (eflag) {
|
||||
if (vflag_atom) eval<1,1,1>(ifrom, ito, thr);
|
||||
else eval<1,1,0>(ifrom, ito, thr);
|
||||
} else {
|
||||
if (vflag_atom) eval<1,0,1>(ifrom, ito, thr);
|
||||
else eval<1,0,0>(ifrom, ito, thr);
|
||||
}
|
||||
} else eval<0,0,0>(ifrom, ito, thr);
|
||||
|
||||
thr->timer(Timer::PAIR);
|
||||
reduce_thr(this, eflag, vflag, thr);
|
||||
} // end of omp parallel region
|
||||
}
|
||||
|
||||
template <int EVFLAG, int EFLAG, int VFLAG_ATOM>
|
||||
void PairTersoffMODCOMP::eval(int iifrom, int iito, ThrData * const thr)
|
||||
{
|
||||
int i,j,k,ii,jj,kk,jnum;
|
||||
tagint itag,jtag;
|
||||
int itype,jtype,ktype,iparam_ij,iparam_ijk;
|
||||
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
|
||||
double rsq,rsq1,rsq2;
|
||||
double delr1[3],delr2[3],fi[3],fj[3],fk[3];
|
||||
double zeta_ij,prefactor;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = 0.0;
|
||||
|
||||
const dbl3_t * _noalias const x = (dbl3_t *) atom->x[0];
|
||||
dbl3_t * _noalias const f = (dbl3_t *) thr->get_f()[0];
|
||||
const tagint * _noalias const tag = atom->tag;
|
||||
const int * _noalias const type = atom->type;
|
||||
const int nlocal = atom->nlocal;
|
||||
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
double fxtmp,fytmp,fztmp;
|
||||
|
||||
// loop over full neighbor list of my atoms
|
||||
|
||||
for (ii = iifrom; ii < iito; ++ii) {
|
||||
|
||||
i = ilist[ii];
|
||||
itag = tag[i];
|
||||
itype = map[type[i]];
|
||||
xtmp = x[i].x;
|
||||
ytmp = x[i].y;
|
||||
ztmp = x[i].z;
|
||||
fxtmp = fytmp = fztmp = 0.0;
|
||||
|
||||
// two-body interactions, skip half of them
|
||||
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
j &= NEIGHMASK;
|
||||
jtag = tag[j];
|
||||
|
||||
if (itag > jtag) {
|
||||
if ((itag+jtag) % 2 == 0) continue;
|
||||
} else if (itag < jtag) {
|
||||
if ((itag+jtag) % 2 == 1) continue;
|
||||
} else {
|
||||
if (x[j].z < ztmp) continue;
|
||||
if (x[j].z == ztmp && x[j].y < ytmp) continue;
|
||||
if (x[j].z == ztmp && x[j].y == ytmp && x[j].x < xtmp) continue;
|
||||
}
|
||||
|
||||
jtype = map[type[j]];
|
||||
|
||||
delx = xtmp - x[j].x;
|
||||
dely = ytmp - x[j].y;
|
||||
delz = ztmp - x[j].z;
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
|
||||
iparam_ij = elem2param[itype][jtype][jtype];
|
||||
if (rsq > params[iparam_ij].cutsq) continue;
|
||||
|
||||
repulsive(¶ms[iparam_ij],rsq,fpair,EFLAG,evdwl);
|
||||
|
||||
fxtmp += delx*fpair;
|
||||
fytmp += dely*fpair;
|
||||
fztmp += delz*fpair;
|
||||
f[j].x -= delx*fpair;
|
||||
f[j].y -= dely*fpair;
|
||||
f[j].z -= delz*fpair;
|
||||
|
||||
if (EVFLAG) ev_tally_thr(this,i,j,nlocal,/* newton_pair */ 1,
|
||||
evdwl,0.0,fpair,delx,dely,delz,thr);
|
||||
}
|
||||
|
||||
// three-body interactions
|
||||
// skip immediately if I-J is not within cutoff
|
||||
double fjxtmp,fjytmp,fjztmp;
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
j &= NEIGHMASK;
|
||||
jtype = map[type[j]];
|
||||
iparam_ij = elem2param[itype][jtype][jtype];
|
||||
|
||||
delr1[0] = x[j].x - xtmp;
|
||||
delr1[1] = x[j].y - ytmp;
|
||||
delr1[2] = x[j].z - ztmp;
|
||||
rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
|
||||
if (rsq1 > params[iparam_ij].cutsq) continue;
|
||||
|
||||
// accumulate bondorder zeta for each i-j interaction via loop over k
|
||||
|
||||
fjxtmp = fjytmp = fjztmp = 0.0;
|
||||
zeta_ij = 0.0;
|
||||
|
||||
for (kk = 0; kk < jnum; kk++) {
|
||||
if (jj == kk) continue;
|
||||
k = jlist[kk];
|
||||
k &= NEIGHMASK;
|
||||
ktype = map[type[k]];
|
||||
iparam_ijk = elem2param[itype][jtype][ktype];
|
||||
|
||||
delr2[0] = x[k].x - xtmp;
|
||||
delr2[1] = x[k].y - ytmp;
|
||||
delr2[2] = x[k].z - ztmp;
|
||||
rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
|
||||
if (rsq2 > params[iparam_ijk].cutsq) continue;
|
||||
|
||||
zeta_ij += zeta(¶ms[iparam_ijk],rsq1,rsq2,delr1,delr2);
|
||||
}
|
||||
|
||||
// pairwise force due to zeta
|
||||
|
||||
force_zeta(¶ms[iparam_ij],rsq1,zeta_ij,fpair,prefactor,EFLAG,evdwl);
|
||||
|
||||
fxtmp += delr1[0]*fpair;
|
||||
fytmp += delr1[1]*fpair;
|
||||
fztmp += delr1[2]*fpair;
|
||||
fjxtmp -= delr1[0]*fpair;
|
||||
fjytmp -= delr1[1]*fpair;
|
||||
fjztmp -= delr1[2]*fpair;
|
||||
|
||||
if (EVFLAG) ev_tally_thr(this,i,j,nlocal,/* newton_pair */ 1,evdwl,0.0,
|
||||
-fpair,-delr1[0],-delr1[1],-delr1[2],thr);
|
||||
|
||||
// attractive term via loop over k
|
||||
|
||||
for (kk = 0; kk < jnum; kk++) {
|
||||
if (jj == kk) continue;
|
||||
k = jlist[kk];
|
||||
k &= NEIGHMASK;
|
||||
ktype = map[type[k]];
|
||||
iparam_ijk = elem2param[itype][jtype][ktype];
|
||||
|
||||
delr2[0] = x[k].x - xtmp;
|
||||
delr2[1] = x[k].y - ytmp;
|
||||
delr2[2] = x[k].z - ztmp;
|
||||
rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
|
||||
if (rsq2 > params[iparam_ijk].cutsq) continue;
|
||||
|
||||
attractive(¶ms[iparam_ijk],prefactor,
|
||||
rsq1,rsq2,delr1,delr2,fi,fj,fk);
|
||||
|
||||
fxtmp += fi[0];
|
||||
fytmp += fi[1];
|
||||
fztmp += fi[2];
|
||||
fjxtmp += fj[0];
|
||||
fjytmp += fj[1];
|
||||
fjztmp += fj[2];
|
||||
f[k].x += fk[0];
|
||||
f[k].y += fk[1];
|
||||
f[k].z += fk[2];
|
||||
|
||||
if (VFLAG_ATOM) v_tally3_thr(i,j,k,fj,fk,delr1,delr2,thr);
|
||||
}
|
||||
f[j].x += fjxtmp;
|
||||
f[j].y += fjytmp;
|
||||
f[j].z += fjztmp;
|
||||
}
|
||||
f[i].x += fxtmp;
|
||||
f[i].y += fytmp;
|
||||
f[i].z += fztmp;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairTersoffMODCOMP::memory_usage()
|
||||
{
|
||||
double bytes = memory_usage_thr();
|
||||
bytes += PairTersoffMOD::memory_usage();
|
||||
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -0,0 +1,43 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Axel Kohlmeyer (Temple U)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(tersoff/mod/c/omp,PairTersoffMODCOMP)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_TERSOFF_MOD_C_OMP_H
|
||||
#define LMP_PAIR_TERSOFF_MOD_C_OMP_H
|
||||
|
||||
#include "pair_tersoff_mod_c.h"
|
||||
#include "thr_omp.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairTersoffMODCOMP : public PairTersoffMODC, public ThrOMP {
|
||||
|
||||
public:
|
||||
PairTersoffMODCOMP(class LAMMPS *);
|
||||
|
||||
virtual void compute(int, int);
|
||||
virtual double memory_usage();
|
||||
|
||||
private:
|
||||
template <int EVFLAG, int EFLAG, int VFLAG_ATOM>
|
||||
void eval(int ifrom, int ito, ThrData * const thr);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -557,6 +557,37 @@ void ThrOMP::ev_tally_xyz_thr(Pair * const pair, const int i, const int j,
|
|||
}
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
tally eng_vdwl and virial into global and per-atom accumulators
|
||||
for virial, have delx,dely,delz and fx,fy,fz
|
||||
called when using full neighbor lists
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ThrOMP::ev_tally_xyz_full_thr(Pair * const pair, const int i,
|
||||
const double evdwl, const double ecoul,
|
||||
const double fx, const double fy,
|
||||
const double fz, const double delx,
|
||||
const double dely, const double delz,
|
||||
ThrData * const thr)
|
||||
{
|
||||
|
||||
if (pair->eflag_either)
|
||||
e_tally_thr(pair,i,i,i+1,0,0.5*evdwl,ecoul,thr);
|
||||
|
||||
if (pair->vflag_either) {
|
||||
double v[6];
|
||||
v[0] = 0.5*delx*fx;
|
||||
v[1] = 0.5*dely*fy;
|
||||
v[2] = 0.5*delz*fz;
|
||||
v[3] = 0.5*delx*fy;
|
||||
v[4] = 0.5*delx*fz;
|
||||
v[5] = 0.5*dely*fz;
|
||||
|
||||
v_tally_thr(pair,i,i,i+1,0,v,thr);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
tally eng_vdwl and virial into global and per-atom accumulators
|
||||
called by SW and hbond potentials, newton_pair is always on
|
||||
|
|
|
|||
|
|
@ -118,6 +118,9 @@ class ThrOMP {
|
|||
const int, const double, const double, const double,
|
||||
const double, const double, const double,
|
||||
const double, const double, ThrData * const);
|
||||
void ev_tally_xyz_full_thr(Pair * const, const int, const double, const double,
|
||||
const double, const double, const double,
|
||||
const double, const double, const double, ThrData * const);
|
||||
void ev_tally3_thr(Pair * const, const int, const int, const int, const double,
|
||||
const double, const double * const, const double * const,
|
||||
const double * const, const double * const, ThrData * const);
|
||||
|
|
|
|||
|
|
@ -1423,7 +1423,7 @@ void PairSMTBQ::tabqeq()
|
|||
{
|
||||
gam = dgam = dza = dzb = d2zaa = d2zab =
|
||||
d2zbb = d2zra = d2zrb = d2gamr2 = 0.0 ;
|
||||
aCoeff = bCoeff = dij = 0.0 ;
|
||||
dij = 0.0 ;
|
||||
|
||||
s = static_cast<double>(k)*ds ; r = sqrt(s) ;
|
||||
if (k==0) r=10e-30;
|
||||
|
|
@ -1438,7 +1438,6 @@ void PairSMTBQ::tabqeq()
|
|||
|
||||
// Cutting Fonction
|
||||
|
||||
|
||||
if (dij < 0.01 && ii==0)
|
||||
{
|
||||
ii=2;
|
||||
|
|
@ -1452,7 +1451,6 @@ void PairSMTBQ::tabqeq()
|
|||
ddij = aCoeff*(r- rc-nang) *(2+bCoeff*(r-rc-nang))*exp(bCoeff*r);
|
||||
}
|
||||
|
||||
|
||||
if (r > (rc+nang)) {dij = 0.0 ; ddij = 0.0;}
|
||||
|
||||
fafb[k][m] = potqn[k] - dij ;
|
||||
|
|
@ -1471,7 +1469,6 @@ void PairSMTBQ::tabqeq()
|
|||
rb = ROxSurf;
|
||||
zb = (2.0*params[j].ne + 1.0)/(4.0*rb); }
|
||||
|
||||
|
||||
ii = 0 ; nang =cang= 5.0 ;
|
||||
// --------------------------
|
||||
for (k = 0; k < kmax+5; k++)
|
||||
|
|
|
|||
|
|
@ -42,7 +42,10 @@ using namespace voro;
|
|||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ComputeVoronoi::ComputeVoronoi(LAMMPS *lmp, int narg, char **arg) :
|
||||
Compute(lmp, narg, arg)
|
||||
Compute(lmp, narg, arg), con_mono(NULL), con_poly(NULL),
|
||||
radstr(NULL), voro(NULL), edge(NULL), sendvector(NULL),
|
||||
rfield(NULL), tags(NULL), occvec(NULL), sendocc(NULL),
|
||||
lroot(NULL), lnext(NULL), faces(NULL)
|
||||
{
|
||||
int sgroup;
|
||||
|
||||
|
|
|
|||
|
|
@ -44,8 +44,9 @@ enum{PERATOM,LOCAL};
|
|||
|
||||
ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) :
|
||||
Compute(lmp, narg, arg),
|
||||
nvalues(0), which(NULL), argindex(NULL), flavor(NULL), value2index(NULL), ids(NULL),
|
||||
onevec(NULL), replace(NULL), indices(NULL), owner(NULL), idregion(NULL), varatom(NULL)
|
||||
nvalues(0), which(NULL), argindex(NULL), flavor(NULL),
|
||||
value2index(NULL), ids(NULL), onevec(NULL), replace(NULL), indices(NULL),
|
||||
owner(NULL), idregion(NULL), varatom(NULL)
|
||||
{
|
||||
int iarg = 0;
|
||||
if (strcmp(style,"reduce") == 0) {
|
||||
|
|
|
|||
|
|
@ -22,6 +22,10 @@
|
|||
#include "tbb/scalable_allocator.h"
|
||||
#endif
|
||||
|
||||
#if defined(LMP_USER_INTEL) && !defined(LAMMPS_MEMALIGN)
|
||||
#define LAMMPS_MEMALIGN 64
|
||||
#endif
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
|
|
|||
|
|
@ -48,6 +48,10 @@ methods:
|
|||
#ifndef LAMMPS_MY_PAGE_H
|
||||
#define LAMMPS_MY_PAGE_H
|
||||
|
||||
#if defined(LMP_USER_INTEL) && !defined(LAMMPS_MEMALIGN)
|
||||
#define LAMMPS_MEMALIGN 64
|
||||
#endif
|
||||
|
||||
#include <stdlib.h>
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
|
|
|
|||
|
|
@ -1 +1 @@
|
|||
#define LAMMPS_VERSION "9 Nov 2016"
|
||||
#define LAMMPS_VERSION "17 Nov 2016"
|
||||
|
|
|
|||
Loading…
Reference in New Issue