Loading doc/src/fix_msst.txt +27 −19 Original line number Diff line number Diff line Loading @@ -25,7 +25,7 @@ keyword = {q} or {mu} or {p0} or {v0} or {e0} or {tscale} or {beta} or {dftb} :l {e0} value = initial total energy (energy units) {tscale} value = reduction in initial temperature (unitless fraction between 0.0 and 1.0) {dftb} value = {yes} or {no} for whether using MSST in conjunction with DFTB+ {beta} value = scale factor on energy contribution of DFTB+ :pre {beta} value = scale factor for improved energy conservation :pre :ule [Examples:] Loading Loading @@ -72,6 +72,14 @@ be calculated on the first step, after the energy specified by {tscale} is removed. The value of {e0} is not used in the dynamical equations, but is used in calculating the deviation from the Hugoniot. The keyword {beta} is a scaling term that can be added to the MSST ionic equations of motion to account for drift in the conserved quantity during long timescale simulations, similar to a Berendson thermostat. See "(Reed)"_#Reed and "(Goldman)"_#Goldman for more details. The value of {beta} must be between 0.0 and 1.0 inclusive. A value of 0.0 means no contribution, a value of 1.0 means a full contribution. Values of shockvel less than a critical value determined by the material response will not have compressive solutions. This will be reflected in lack of significant change of the volume in the MSST. Loading @@ -95,23 +103,15 @@ or "_MSST_pe". The group for the new computes is "all". :line The {dftb} and {beta} keywords are to allow this fix to be used when LAMMPS is being driven by DFTB+, a density-functional tight-binding code. If the keyword {dftb} is used with a value of {yes}, then the MSST equations are altered to account for an energy contribution compute by DFTB+. In this case, you must define a "fix external"_fix_external.html command in your input script, which is used to callback to DFTB+ during the LAMMPS timestepping. DFTB+ will communicate its info to LAMMPS via that fix. The keyword {beta} is a scale factor on the DFTB+ energy contribution. The value of {beta} must be between 0.0 and 1.0 inclusive. A value of 0.0 means no contribution, a value of 1.0 means a full contribution. (July 2017) More information about these keywords and the use of LAMMPS with DFTB+ will be added to the LAMMMPS documention soon. The {dftb} keyword is to allow this fix to be used when LAMMPS is being driven by DFTB+, a density-functional tight-binding code. If the keyword {dftb} is used with a value of {yes}, then the MSST equations are altered to account for the electron entropy contribution to the Hugonio relations and total energy. See "(Reed2)"_#Reed2 and "(Goldman)"_#Goldman for details on this contribution. In this case, you must define a "fix external"_fix_external.html command in your input script, which is used to callback to DFTB+ during the LAMMPS timestepping. DFTB+ will communicate its info to LAMMPS via that fix. :line Loading Loading @@ -182,4 +182,12 @@ timestep. :line :link(Reed) [(Reed)] Reed, Fried, and Joannopoulos, Phys. Rev. Lett., 90, 235503 (2003). [(Reed)] Reed, Fried, and Joannopoulos, Phys. Rev. Lett., 90, 235503 (2003). :link(Reed2) [(Reed2)] Reed, J. Phys. Chem. C, 116, 2205 (2012). :link(Goldman) [(Goldman)] Goldman, Srinivasan, Hamel, Fried, Gaus, and Elstner, J. Phys. Chem. C, 117, 7885 (2013). doc/src/pair_kim.txt +27 −6 Original line number Diff line number Diff line Loading @@ -27,13 +27,34 @@ pair_coeff * * Ar Ar :pre [Description:] This pair style is a wrapper on the "Knowledge Base for Interatomic Models (KIM)"_https://openkim.org repository of interatomic potentials, so that they can be used by LAMMPS scripts. Models (OpenKIM)"_https://openkim.org repository of interatomic potentials, so that they can be used by LAMMPS scripts. In KIM lingo, a potential is a "model" and a model contains both the analytic formulas that define the potential as well as the parameters needed to run it for one or more materials, including coefficients and cutoffs. Note that in LAMMPS lingo, a KIM model driver is a pair style (e.g. EAM or Tersoff). A KIM model is a pair style for a particular element or alloy and set of parameters, e.g. EAM for Cu with a specific EAM potential file. See the current list of "KIM model drivers"_https://openkim.org/kim-items/model-drivers/alphabetical. See the current list of all "KIM models"_https://openkim.org/kim-items/models/by-model-drivers See the list of "example KIM models"_https://openkim.org/kim-api which are included in the KIM library by default, in the "What is in the KIM API source package?" section. To use this pair style, you must first download and install the KIM API library from the "OpenKIM website"_https://openkim.org. The "KIM section of Section packages"_Section_packages.html#kim-package has instructions on how to do this with a simple make command, when building LAMMPS. See the examples/kim dir for an input script that uses a KIM model (potential) for Lennard-Jones. :line The argument {virialmode} determines how the global virial is calculated. If {KIMvirial} is specified, the KIM model performs the Loading examples/COUPLE/README +2 −2 Original line number Diff line number Diff line Loading @@ -41,8 +41,8 @@ fortran a simple wrapper on the LAMMPS library API that can be called from Fortran fortran2 a more sophisticated wrapper on the LAMMPS library API that can be called from Fortran fortran3 wrapper written by Nir Goldman (LLNL), as an fortran_dftb wrapper written by Nir Goldman (LLNL), as an extension to fortran2, used for calling LAMMPS from Fortran DFTB+ code from Fortran DFTB+ tight-binding code Each sub-directory has its own README with more details. examples/COUPLE/fortran3/LAMMPS-wrapper.cpp→examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp +0 −0 File moved. View file examples/COUPLE/fortran3/LAMMPS-wrapper.h→examples/COUPLE/fortran_dftb/LAMMPS-wrapper.h +0 −0 File moved. View file Loading
doc/src/fix_msst.txt +27 −19 Original line number Diff line number Diff line Loading @@ -25,7 +25,7 @@ keyword = {q} or {mu} or {p0} or {v0} or {e0} or {tscale} or {beta} or {dftb} :l {e0} value = initial total energy (energy units) {tscale} value = reduction in initial temperature (unitless fraction between 0.0 and 1.0) {dftb} value = {yes} or {no} for whether using MSST in conjunction with DFTB+ {beta} value = scale factor on energy contribution of DFTB+ :pre {beta} value = scale factor for improved energy conservation :pre :ule [Examples:] Loading Loading @@ -72,6 +72,14 @@ be calculated on the first step, after the energy specified by {tscale} is removed. The value of {e0} is not used in the dynamical equations, but is used in calculating the deviation from the Hugoniot. The keyword {beta} is a scaling term that can be added to the MSST ionic equations of motion to account for drift in the conserved quantity during long timescale simulations, similar to a Berendson thermostat. See "(Reed)"_#Reed and "(Goldman)"_#Goldman for more details. The value of {beta} must be between 0.0 and 1.0 inclusive. A value of 0.0 means no contribution, a value of 1.0 means a full contribution. Values of shockvel less than a critical value determined by the material response will not have compressive solutions. This will be reflected in lack of significant change of the volume in the MSST. Loading @@ -95,23 +103,15 @@ or "_MSST_pe". The group for the new computes is "all". :line The {dftb} and {beta} keywords are to allow this fix to be used when LAMMPS is being driven by DFTB+, a density-functional tight-binding code. If the keyword {dftb} is used with a value of {yes}, then the MSST equations are altered to account for an energy contribution compute by DFTB+. In this case, you must define a "fix external"_fix_external.html command in your input script, which is used to callback to DFTB+ during the LAMMPS timestepping. DFTB+ will communicate its info to LAMMPS via that fix. The keyword {beta} is a scale factor on the DFTB+ energy contribution. The value of {beta} must be between 0.0 and 1.0 inclusive. A value of 0.0 means no contribution, a value of 1.0 means a full contribution. (July 2017) More information about these keywords and the use of LAMMPS with DFTB+ will be added to the LAMMMPS documention soon. The {dftb} keyword is to allow this fix to be used when LAMMPS is being driven by DFTB+, a density-functional tight-binding code. If the keyword {dftb} is used with a value of {yes}, then the MSST equations are altered to account for the electron entropy contribution to the Hugonio relations and total energy. See "(Reed2)"_#Reed2 and "(Goldman)"_#Goldman for details on this contribution. In this case, you must define a "fix external"_fix_external.html command in your input script, which is used to callback to DFTB+ during the LAMMPS timestepping. DFTB+ will communicate its info to LAMMPS via that fix. :line Loading Loading @@ -182,4 +182,12 @@ timestep. :line :link(Reed) [(Reed)] Reed, Fried, and Joannopoulos, Phys. Rev. Lett., 90, 235503 (2003). [(Reed)] Reed, Fried, and Joannopoulos, Phys. Rev. Lett., 90, 235503 (2003). :link(Reed2) [(Reed2)] Reed, J. Phys. Chem. C, 116, 2205 (2012). :link(Goldman) [(Goldman)] Goldman, Srinivasan, Hamel, Fried, Gaus, and Elstner, J. Phys. Chem. C, 117, 7885 (2013).
doc/src/pair_kim.txt +27 −6 Original line number Diff line number Diff line Loading @@ -27,13 +27,34 @@ pair_coeff * * Ar Ar :pre [Description:] This pair style is a wrapper on the "Knowledge Base for Interatomic Models (KIM)"_https://openkim.org repository of interatomic potentials, so that they can be used by LAMMPS scripts. Models (OpenKIM)"_https://openkim.org repository of interatomic potentials, so that they can be used by LAMMPS scripts. In KIM lingo, a potential is a "model" and a model contains both the analytic formulas that define the potential as well as the parameters needed to run it for one or more materials, including coefficients and cutoffs. Note that in LAMMPS lingo, a KIM model driver is a pair style (e.g. EAM or Tersoff). A KIM model is a pair style for a particular element or alloy and set of parameters, e.g. EAM for Cu with a specific EAM potential file. See the current list of "KIM model drivers"_https://openkim.org/kim-items/model-drivers/alphabetical. See the current list of all "KIM models"_https://openkim.org/kim-items/models/by-model-drivers See the list of "example KIM models"_https://openkim.org/kim-api which are included in the KIM library by default, in the "What is in the KIM API source package?" section. To use this pair style, you must first download and install the KIM API library from the "OpenKIM website"_https://openkim.org. The "KIM section of Section packages"_Section_packages.html#kim-package has instructions on how to do this with a simple make command, when building LAMMPS. See the examples/kim dir for an input script that uses a KIM model (potential) for Lennard-Jones. :line The argument {virialmode} determines how the global virial is calculated. If {KIMvirial} is specified, the KIM model performs the Loading
examples/COUPLE/README +2 −2 Original line number Diff line number Diff line Loading @@ -41,8 +41,8 @@ fortran a simple wrapper on the LAMMPS library API that can be called from Fortran fortran2 a more sophisticated wrapper on the LAMMPS library API that can be called from Fortran fortran3 wrapper written by Nir Goldman (LLNL), as an fortran_dftb wrapper written by Nir Goldman (LLNL), as an extension to fortran2, used for calling LAMMPS from Fortran DFTB+ code from Fortran DFTB+ tight-binding code Each sub-directory has its own README with more details.
examples/COUPLE/fortran3/LAMMPS-wrapper.cpp→examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp +0 −0 File moved. View file
examples/COUPLE/fortran3/LAMMPS-wrapper.h→examples/COUPLE/fortran_dftb/LAMMPS-wrapper.h +0 −0 File moved. View file
