Merge pull request #278 from akohlmey/pair-agni
Implementation of the AGNI manybody potential
This commit is contained in:
sjplimp
BIN
doc/src/Eqs/pair_agni.jpg
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doc/src/Eqs/pair_agni.jpg
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@ -995,6 +995,7 @@ These are additional pair styles in USER packages, which can be used
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if "LAMMPS is built with the appropriate
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package"_Section_start.html#start_3.
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"agni (o)"_pair_agni.html,
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"awpmd/cut"_pair_awpmd.html,
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"buck/mdf"_pair_mdf.html,
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"coul/cut/soft (o)"_pair_lj_soft.html,
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@ -59,6 +59,7 @@ dump_h5md.html
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dump_image.html
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dump_modify.html
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dump_molfile.html
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dump_nc.html
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echo.html
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fix.html
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fix_modify.html
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@ -152,6 +153,7 @@ fix_colvars.html
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fix_controller.html
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fix_deform.html
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fix_deposit.html
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fix_dpd_energy.html
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fix_drag.html
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fix_drude.html
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fix_drude_transform.html
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@ -272,6 +274,7 @@ fix_viscosity.html
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fix_viscous.html
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fix_wall.html
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fix_wall_gran.html
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fix_wall_gran_region.html
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fix_wall_piston.html
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fix_wall_reflect.html
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fix_wall_region.html
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@ -390,6 +393,7 @@ compute_voronoi_atom.html
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compute_xrd.html
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pair_adp.html
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pair_agni.html
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pair_airebo.html
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pair_awpmd.html
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pair_beck.html
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@ -622,3 +626,4 @@ USER/atc/man_unfix_flux.html
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USER/atc/man_unfix_nodes.html
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USER/atc/man_write_atom_weights.html
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USER/atc/man_write_restart.html
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128
doc/src/pair_agni.txt
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128
doc/src/pair_agni.txt
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@ -0,0 +1,128 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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pair_style agni command :h3
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pair_style agni/omp command :h3
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[Syntax:]
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pair_style agni :pre
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[Examples:]
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pair_style agni
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pair_coeff * * Al.agni Al
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[Description:]
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Style {agni} style computes the manybody vectorial force components for
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an atom as
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:c,image(Eqs/pair_agni.jpg)
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{u} labels the individual components, i.e. x, y or z, and {V} is the
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corresponding atomic fingerprint. {d} is the Euclidean distance between
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any two atomic fingerprints. A total of N_t reference atomic
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environments are considered to construct the force field file. {alpha_t}
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and {l} are the weight coefficients and length scale parameter of the
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non-linear regression model.
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The method implements the recently proposed machine learning access to
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atomic forces as discussed extensively in the following publications -
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"(Botu1)"_#Botu2015adaptive and "(Botu2)"_#Botu2015learning. The premise
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of the method is to map the atomic enviornment numerically into a
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fingerprint, and use machine learning methods to create a mapping to the
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vectorial atomic forces.
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Only a single pair_coeff command is used with the {agni} style which
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specifies an AGNI potential file containing the parameters of the
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force field for the needed elements. These are mapped to LAMMPS atom
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types by specifying N additional arguments after the filename in the
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pair_coeff command, where N is the number of LAMMPS atom types:
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filename
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N element names = mapping of AGNI elements to atom types :ul
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See the "pair_coeff"_pair_coeff.html doc page for alternate ways
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to specify the path for the force field file.
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An AGNI force field is fully specified by the filename which contains the
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parameters of the force field, i.e., the reference training environments
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used to construct the machine learning force field. Example force field
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and input files are provided in the examples/USER/misc/agni directory.
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:line
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Styles with {omp} suffix is functionally the same as the corresponding
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style without the suffix. They have been optimized to run faster, depending
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on your available hardware, as discussed in "Section 5"_Section_accelerate.html
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of the manual. The accelerated style takes the same arguments and
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should produce the same results, except for round-off and precision
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issues.
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The accelerated style is part of the USER-OMP. They are only enabled if
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LAMMPS was built with those packages. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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You can specify the accelerated style explicitly in your input script
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by including their suffix, or you can use the "-suffix command-line
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switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
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use the "suffix"_suffix.html command in your input script.
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See "Section 5"_Section_accelerate.html of the manual for
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more instructions on how to use the accelerated styles effectively.
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:line
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[Mixing, shift, table, tail correction, restart, rRESPA info]:
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This pair style does not support the "pair_modify"_pair_modify.html
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shift, table, and tail options.
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This pair style does not write its information to "binary restart
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files"_restart.html, since it is stored in potential files. Thus, you
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need to re-specify the pair_style and pair_coeff commands in an input
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script that reads a restart file.
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This pair style can only be used via the {pair} keyword of the
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"run_style respa"_run_style.html command. It does not support the
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{inner}, {middle}, {outer} keywords.
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:line
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[Restrictions:]
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Currently, only elemental systems are implemented. Also, the method only
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provides access to the forces and not energies or stresses. However, one
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can access the energy via thermodynamic integration of the forces as
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discussed in "(Botu3)"_#Botu2016construct. This pair style is part
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of the USER-MISC package. It is only enabled if LAMMPS was built with
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that package. See the "Making LAMMPS"_Section_start.html#start_3 section
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for more info.
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The AGNI force field files provided with LAMMPS (see the
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potentials directory) are parameterized for metal "units"_units.html.
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You can use the AGNI potential with any LAMMPS units, but you would need
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to create your own AGNI potential file with coefficients listed in the
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appropriate units if your simulation doesn't use "metal" units.
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[Related commands:]
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"pair_coeff"_pair_coeff.html
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[Default:] none
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:line
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||||
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:link(Botu2015adaptive)
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[(Botu1)] V. Botu and R. Ramprasad, Int. J. Quant. Chem., 115(16), 1074 (2015).
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:link(Botu2015learning)
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[(Botu2)] V. Botu and R. Ramprasad, Phys. Rev. B, 92(9), 094306 (2015).
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:link(Botu2016construct)
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[(Botu3)] V. Botu, R. Batra, J. Chapman and R. Ramprasad, https://arxiv.org/abs/1610.02098 (2016).
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@ -6,6 +6,7 @@ Pair Styles :h1
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:maxdepth: 1
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pair_adp
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pair_agni
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pair_airebo
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pair_awpmd
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pair_beck
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1019
examples/USER/misc/agni/Al_prb.agni
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1019
examples/USER/misc/agni/Al_prb.agni
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File diff suppressed because it is too large
Load Diff
197
examples/USER/misc/agni/adatom.data
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197
examples/USER/misc/agni/adatom.data
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@ -0,0 +1,197 @@
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Data File created from VASP POSCAR
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181 atoms
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1 atom types
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0 17.121440767 xlo xhi
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0 14.8276026536 ylo yhi
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||||
0 39.3197318979 zlo zhi
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Masses
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||||
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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
|
||||
|
||||
23
examples/USER/misc/agni/in.adatom
Normal file
23
examples/USER/misc/agni/in.adatom
Normal file
@ -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
|
||||
23
examples/USER/misc/agni/in.vacancy
Normal file
23
examples/USER/misc/agni/in.vacancy
Normal file
@ -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
|
||||
82
examples/USER/misc/agni/log.9Nov16.adatom.g++.1
Normal file
82
examples/USER/misc/agni/log.9Nov16.adatom.g++.1
Normal file
@ -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
|
||||
82
examples/USER/misc/agni/log.9Nov16.adatom.g++.4
Normal file
82
examples/USER/misc/agni/log.9Nov16.adatom.g++.4
Normal file
@ -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
|
||||
82
examples/USER/misc/agni/log.9Nov16.vacancy.g++.1
Normal file
82
examples/USER/misc/agni/log.9Nov16.vacancy.g++.1
Normal file
@ -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
|
||||
82
examples/USER/misc/agni/log.9Nov16.vacancy.g++.4
Normal file
82
examples/USER/misc/agni/log.9Nov16.vacancy.g++.4
Normal file
@ -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
|
||||
46
examples/USER/misc/agni/vacancy.data
Normal file
46
examples/USER/misc/agni/vacancy.data
Normal file
@ -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
|
||||
1019
potentials/Al_prb.agni
Normal file
1019
potentials/Al_prb.agni
Normal file
File diff suppressed because it is too large
Load Diff
2
src/.gitignore
vendored
2
src/.gitignore
vendored
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
508
src/USER-MISC/pair_agni.cpp
Normal file
508
src/USER-MISC/pair_agni.cpp
Normal file
@ -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 author: Axel Kohlmeyer (Temple U)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#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;
|
||||
}
|
||||
}
|
||||
|
||||
85
src/USER-MISC/pair_agni.h
Normal file
85
src/USER-MISC/pair_agni.h
Normal file
@ -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.
|
||||
|
||||
*/
|
||||
299
src/USER-OMP/pair_agni_omp.cpp
Normal file
299
src/USER-OMP/pair_agni_omp.cpp
Normal file
@ -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;
|
||||
}
|
||||
48
src/USER-OMP/pair_agni_omp.h
Normal file
48
src/USER-OMP/pair_agni_omp.h
Normal file
@ -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
|
||||
@ -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);
|
||||
|
||||
Reference in New Issue
Block a user