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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if "LAMMPS is built with the appropriate
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package"_Section_start.html#start_3.
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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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"awpmd/cut"_pair_awpmd.html,
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"buck/mdf"_pair_mdf.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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"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_image.html
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dump_modify.html
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dump_modify.html
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dump_molfile.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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echo.html
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fix.html
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fix.html
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fix_modify.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_controller.html
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fix_deform.html
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fix_deform.html
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fix_deposit.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_drag.html
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fix_drude.html
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fix_drude.html
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fix_drude_transform.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_viscous.html
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fix_wall.html
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fix_wall.html
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fix_wall_gran.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_piston.html
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fix_wall_reflect.html
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fix_wall_reflect.html
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fix_wall_region.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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compute_xrd.html
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pair_adp.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_airebo.html
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pair_awpmd.html
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pair_awpmd.html
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pair_beck.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_unfix_nodes.html
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USER/atc/man_write_atom_weights.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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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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: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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:maxdepth: 1
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pair_adp
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pair_adp
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pair_agni
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pair_airebo
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pair_airebo
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pair_awpmd
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pair_awpmd
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pair_beck
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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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1 26.982
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Atoms
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1 1 0.0 1.64751140595 15.0
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2 1 2.85357346116 1.64751140595 15.0
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3 1 5.70714692232 1.64751140595 15.0
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4 1 8.56072038348 1.64751140595 15.0
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5 1 11.4142938446 1.64751140595 15.0
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6 1 14.2678673058 1.64751140595 15.0
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7 1 1.42678673058 4.11877851488 15.0
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8 1 4.28036019174 4.11877851488 15.0
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9 1 7.1339336529 4.11877851488 15.0
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10 1 9.98750711406 4.11877851488 15.0
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11 1 12.8410805752 4.11877851488 15.0
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12 1 15.6946540364 4.11877851488 15.0
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13 1 0.0 6.59004562381 15.0
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14 1 2.85357346116 6.59004562381 15.0
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15 1 5.70714692232 6.59004562381 15.0
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16 1 8.56072038348 6.59004562381 15.0
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17 1 11.4142938446 6.59004562381 15.0
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18 1 14.2678673058 6.59004562381 15.0
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19 1 1.42678673058 9.06131273274 15.0
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20 1 4.28036019174 9.06131273274 15.0
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21 1 7.1339336529 9.06131273274 15.0
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22 1 9.98750711406 9.06131273274 15.0
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23 1 12.8410805752 9.06131273274 15.0
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24 1 15.6946540364 9.06131273274 15.0
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25 1 0.0 11.5325798417 15.0
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26 1 2.85357346116 11.5325798417 15.0
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||||||
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27 1 5.70714692232 11.5325798417 15.0
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||||||
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28 1 8.56072038348 11.5325798417 15.0
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29 1 11.4142938446 11.5325798417 15.0
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||||||
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30 1 14.2678673058 11.5325798417 15.0
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||||||
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31 1 1.42678673058 14.0038469506 15.0
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||||||
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32 1 4.28036019174 14.0038469506 15.0
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||||||
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33 1 7.1339336529 14.0038469506 15.0
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||||||
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34 1 9.98750711406 14.0038469506 15.0
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||||||
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35 1 12.8410805752 14.0038469506 15.0
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||||||
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36 1 15.6946540364 14.0038469506 15.0
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||||||
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37 1 0.0 0.0 17.3299329745
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||||||
|
38 1 2.85357346116 0.0 17.3299329745
|
||||||
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39 1 5.70714692232 0.0 17.3299329745
|
||||||
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40 1 8.56072038348 0.0 17.3299329745
|
||||||
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41 1 11.4142938446 0.0 17.3299329745
|
||||||
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42 1 14.2678673058 0.0 17.3299329745
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||||||
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43 1 1.42678673058 2.47126710893 17.3299329745
|
||||||
|
44 1 4.28036019174 2.47126710893 17.3299329745
|
||||||
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45 1 7.1339336529 2.47126710893 17.3299329745
|
||||||
|
46 1 9.98750711406 2.47126710893 17.3299329745
|
||||||
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47 1 12.8410805752 2.47126710893 17.3299329745
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||||||
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48 1 15.6946540364 2.47126710893 17.3299329745
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||||||
|
49 1 0.0 4.94253421786 17.3299329745
|
||||||
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50 1 2.85357346116 4.94253421786 17.3299329745
|
||||||
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51 1 5.70714692232 4.94253421786 17.3299329745
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||||||
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52 1 8.56072038348 4.94253421786 17.3299329745
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53 1 11.4142938446 4.94253421786 17.3299329745
|
||||||
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54 1 14.2678673058 4.94253421786 17.3299329745
|
||||||
|
55 1 1.42678673058 7.41380132679 17.3299329745
|
||||||
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56 1 4.28036019174 7.41380132679 17.3299329745
|
||||||
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57 1 7.1339336529 7.41380132679 17.3299329745
|
||||||
|
58 1 9.98750711406 7.41380132679 17.3299329745
|
||||||
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59 1 12.8410805752 7.41380132679 17.3299329745
|
||||||
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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
|
||||||
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64 1 8.56072038348 9.88506843572 17.3299329745
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||||||
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65 1 11.4142938446 9.88506843572 17.3299329745
|
||||||
|
66 1 14.2678673058 9.88506843572 17.3299329745
|
||||||
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67 1 1.42678673058 12.3563355446 17.3299329745
|
||||||
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68 1 4.28036019174 12.3563355446 17.3299329745
|
||||||
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69 1 7.1339336529 12.3563355446 17.3299329745
|
||||||
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70 1 9.98750711406 12.3563355446 17.3299329745
|
||||||
|
71 1 12.8410805752 12.3563355446 17.3299329745
|
||||||
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72 1 15.6946540364 12.3563355446 17.3299329745
|
||||||
|
73 1 1.42678673058 0.823755702976 19.6598659489
|
||||||
|
74 1 4.28036019174 0.823755702976 19.6598659489
|
||||||
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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.cpp
|
||||||
/pair_adp.h
|
/pair_adp.h
|
||||||
|
/pair_agni.cpp
|
||||||
|
/pair_agni.h
|
||||||
/pair_airebo.cpp
|
/pair_airebo.cpp
|
||||||
/pair_airebo.h
|
/pair_airebo.h
|
||||||
/pair_airebo_morse.cpp
|
/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 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 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
|
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 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 coul/diel, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11
|
||||||
pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 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++ -*- ----------------------------------------------------------
|
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Axel Kohlmeyer (Temple U)
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------------------------------------------------------------------------- */
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#ifdef PAIR_CLASS
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PairStyle(agni/omp,PairAGNIOMP)
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#else
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#ifndef LMP_PAIR_AGNI_OMP_H
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#define LMP_PAIR_AGNI_OMP_H
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#include "pair_agni.h"
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#include "thr_omp.h"
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namespace LAMMPS_NS {
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class PairAGNIOMP : public PairAGNI, public ThrOMP {
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public:
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PairAGNIOMP(class LAMMPS *);
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virtual void compute(int, int);
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virtual double memory_usage();
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private:
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template <int EVFLAG>
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void eval(int ifrom, int ito, ThrData * const thr);
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};
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}
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#endif
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#endif
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@ -557,6 +557,37 @@ void ThrOMP::ev_tally_xyz_thr(Pair * const pair, const int i, const int j,
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}
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}
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}
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}
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/* ----------------------------------------------------------------------
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tally eng_vdwl and virial into global and per-atom accumulators
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for virial, have delx,dely,delz and fx,fy,fz
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called when using full neighbor lists
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------------------------------------------------------------------------- */
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void ThrOMP::ev_tally_xyz_full_thr(Pair * const pair, const int i,
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const double evdwl, const double ecoul,
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const double fx, const double fy,
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const double fz, const double delx,
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const double dely, const double delz,
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ThrData * const thr)
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{
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if (pair->eflag_either)
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e_tally_thr(pair,i,i,i+1,0,0.5*evdwl,ecoul,thr);
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if (pair->vflag_either) {
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double v[6];
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v[0] = 0.5*delx*fx;
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v[1] = 0.5*dely*fy;
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v[2] = 0.5*delz*fz;
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v[3] = 0.5*delx*fy;
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v[4] = 0.5*delx*fz;
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v[5] = 0.5*dely*fz;
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v_tally_thr(pair,i,i,i+1,0,v,thr);
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}
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}
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||||||
/* ----------------------------------------------------------------------
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/* ----------------------------------------------------------------------
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||||||
tally eng_vdwl and virial into global and per-atom accumulators
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tally eng_vdwl and virial into global and per-atom accumulators
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||||||
called by SW and hbond potentials, newton_pair is always on
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called by SW and hbond potentials, newton_pair is always on
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@ -118,6 +118,9 @@ class ThrOMP {
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const int, const double, const double, const double,
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const int, const double, const double, const double,
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const double, const double, const double,
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const double, const double, const double,
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const double, const double, ThrData * const);
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const double, const double, ThrData * const);
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||||||
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void ev_tally_xyz_full_thr(Pair * const, const int, const double, const double,
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const double, const double, const double,
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const double, const double, const double, ThrData * const);
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||||||
void ev_tally3_thr(Pair * const, const int, const int, const int, const double,
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void ev_tally3_thr(Pair * const, const int, const int, const int, const double,
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||||||
const double, const double * const, const double * const,
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const double, const double * const, const double * const,
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||||||
const double * const, const double * const, ThrData * const);
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const double * const, const double * const, ThrData * const);
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||||||
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|||||||
Reference in New Issue
Block a user