diff --git a/doc/src/Eqs/pair_agni.jpg b/doc/src/Eqs/pair_agni.jpg new file mode 100644 index 0000000000..e0842225c6 Binary files /dev/null and b/doc/src/Eqs/pair_agni.jpg differ diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index f3ffd5bff2..28575624ca 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -995,6 +995,7 @@ These are additional pair styles in USER packages, which can be used if "LAMMPS is built with the appropriate package"_Section_start.html#start_3. +"agni (o)"_pair_agni.html, "awpmd/cut"_pair_awpmd.html, "buck/mdf"_pair_mdf.html, "coul/cut/soft (o)"_pair_lj_soft.html, diff --git a/doc/src/pair_agni.txt b/doc/src/pair_agni.txt new file mode 100644 index 0000000000..08490c601a --- /dev/null +++ b/doc/src/pair_agni.txt @@ -0,0 +1,128 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +pair_style agni command :h3 +pair_style agni/omp command :h3 + +[Syntax:] + +pair_style agni :pre + +[Examples:] +pair_style agni +pair_coeff * * Al.agni Al + +[Description:] + +Style {agni} style computes the manybody vectorial force components for +an atom as + +:c,image(Eqs/pair_agni.jpg) + +{u} labels the individual components, i.e. x, y or z, and {V} is the +corresponding atomic fingerprint. {d} is the Euclidean distance between +any two atomic fingerprints. A total of N_t reference atomic +environments are considered to construct the force field file. {alpha_t} +and {l} are the weight coefficients and length scale parameter of the +non-linear regression model. + +The method implements the recently proposed machine learning access to +atomic forces as discussed extensively in the following publications - +"(Botu1)"_#Botu2015adaptive and "(Botu2)"_#Botu2015learning. The premise +of the method is to map the atomic enviornment numerically into a +fingerprint, and use machine learning methods to create a mapping to the +vectorial atomic forces. + +Only a single pair_coeff command is used with the {agni} style which +specifies an AGNI potential file containing the parameters of the +force field for the needed elements. These are mapped to LAMMPS atom +types by specifying N additional arguments after the filename in the +pair_coeff command, where N is the number of LAMMPS atom types: + +filename +N element names = mapping of AGNI elements to atom types :ul + +See the "pair_coeff"_pair_coeff.html doc page for alternate ways +to specify the path for the force field file. + +An AGNI force field is fully specified by the filename which contains the +parameters of the force field, i.e., the reference training environments +used to construct the machine learning force field. Example force field +and input files are provided in the examples/USER/misc/agni directory. + +:line + +Styles with {omp} suffix is functionally the same as the corresponding +style without the suffix. They have been optimized to run faster, depending +on your available hardware, as discussed in "Section 5"_Section_accelerate.html +of the manual. The accelerated style takes the same arguments and +should produce the same results, except for round-off and precision +issues. + +The accelerated style is part of the USER-OMP. They are only enabled if +LAMMPS was built with those packages. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +You can specify the accelerated style explicitly in your input script +by including their suffix, or you can use the "-suffix command-line +switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can +use the "suffix"_suffix.html command in your input script. + +See "Section 5"_Section_accelerate.html of the manual for +more instructions on how to use the accelerated styles effectively. + +:line + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +This pair style does not support the "pair_modify"_pair_modify.html +shift, table, and tail options. + +This pair style does not write its information to "binary restart +files"_restart.html, since it is stored in potential files. Thus, you +need to re-specify the pair_style and pair_coeff commands in an input +script that reads a restart file. + +This pair style can only be used via the {pair} keyword of the +"run_style respa"_run_style.html command. It does not support the +{inner}, {middle}, {outer} keywords. + +:line + +[Restrictions:] + +Currently, only elemental systems are implemented. Also, the method only +provides access to the forces and not energies or stresses. However, one +can access the energy via thermodynamic integration of the forces as +discussed in "(Botu3)"_#Botu2016construct. This pair style is part +of the USER-MISC package. It is only enabled if LAMMPS was built with +that package. See the "Making LAMMPS"_Section_start.html#start_3 section +for more info. + +The AGNI force field files provided with LAMMPS (see the +potentials directory) are parameterized for metal "units"_units.html. +You can use the AGNI potential with any LAMMPS units, but you would need +to create your own AGNI potential file with coefficients listed in the +appropriate units if your simulation doesn't use "metal" units. + +[Related commands:] + +"pair_coeff"_pair_coeff.html + +[Default:] none + +:line + +:link(Botu2015adaptive) +[(Botu1)] V. Botu and R. Ramprasad, Int. J. Quant. Chem., 115(16), 1074 (2015). + +:link(Botu2015learning) +[(Botu2)] V. Botu and R. Ramprasad, Phys. Rev. B, 92(9), 094306 (2015). + +:link(Botu2016construct) +[(Botu3)] V. Botu, R. Batra, J. Chapman and R. Ramprasad, https://arxiv.org/abs/1610.02098 (2016). diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 164b31e64b..3e10c6a76b 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -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