Loading src/USER-HMA/READMEdeleted 100644 → 0 +0 −30 Original line number Diff line number Diff line The HMA package implements the compute hma command for LAMMPS, which implements harmonically-mapped averaging for crystalline solids. The current implementation handles atomic crystals. Computing the heat capacity relies on being able to compute the second derivative of the energy with respect to atom positions. This capability is provided by the single2 method in Pair, but is currently only implemented for the shifted-force LJ potential (lj/smooth/linear). Pair::single2 takes a single pair and (like Pair::single) returns the energy and sets the force as an out parameter, but also sets the elements of 6-element double array out parameter, which are the unique components of the atomic Hessian tensor for the pair. A helper method exists (Pair::pairTensor), which will compute the tensor from linear derivatives and the vector between the positions. HMA Heat capacity can be computed for other models by implementing single2 in those Pair classes. More information about HMA is available in these publications: A. J. Schultz, D. A. Kofke, “Comprehensive high-precision high-accuracy equation of state and coexistence properties for classical Lennard-Jones crystals and low-temperature fluid phases”, J. Chem. Phys. 149, 204508 (2018) https://dx.doi.org/10.1063/1.5053714 S. G. Moustafa, A. J. Schultz, D. A. Kofke, “Harmonically Assisted Methods for Computing the Free Energy of Classical Crystals by Molecular Simulation: A Comparative Study”, J. Chem. Theory Comput. 13, 825-834 (2017) https://dx.doi.org/10.1021/acs.jctc.6b01082 S. G. Moustafa, A. J. Schultz, D. A. Kofke, “Very fast averaging of thermal properties of crystals by molecular simulation”, Phys. Rev. E 92, 043303 (2015) https://dx.doi.org/10.1103/PhysRevE.92.043303 src/USER-HMA/compute_hma.cpp +32 −0 Original line number Diff line number Diff line Loading @@ -11,6 +11,38 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- This compute implements harmonically-mapped averaging for crystalline solids. The current implementation handles atomic crystals. Computing the heat capacity relies on being able to compute the second derivative of the energy with respect to atom positions. This capability is provided by the single2 method in Pair, but is currently only implemented for the shifted-force LJ potential (lj/smooth/linear). Pair::single2 takes a single pair and (like Pair::single) returns the energy and sets the force as an out parameter, but also sets the elements of 6-element double array out parameter, which are the unique components of the atomic Hessian tensor for the pair. A helper method exists (Pair::pairTensor), which will compute the tensor from linear derivatives and the vector between the positions. HMA Heat capacity can be computed for other models by implementing single2 in those Pair classes. More information about HMA is available in these publications: A. J. Schultz, D. A. Kofke, “Comprehensive high-precision high-accuracy equation of state and coexistence properties for classical Lennard-Jones crystals and low-temperature fluid phases”, J. Chem. Phys. 149, 204508 (2018) https://dx.doi.org/10.1063/1.5053714 S. G. Moustafa, A. J. Schultz, D. A. Kofke, “Harmonically Assisted Methods for Computing the Free Energy of Classical Crystals by Molecular Simulation: A Comparative Study”, J. Chem. Theory Comput. 13, 825-834 (2017) https://dx.doi.org/10.1021/acs.jctc.6b01082 S. G. Moustafa, A. J. Schultz, D. A. Kofke, “Very fast averaging of thermal properties of crystals by molecular simulation”, Phys. Rev. E 92, 043303 (2015) https://dx.doi.org/10.1103/PhysRevE.92.043303 ------------------------------------------------------------------------- */ #include <cmath> #include <cstring> #include <mpi.h> Loading Loading
src/USER-HMA/READMEdeleted 100644 → 0 +0 −30 Original line number Diff line number Diff line The HMA package implements the compute hma command for LAMMPS, which implements harmonically-mapped averaging for crystalline solids. The current implementation handles atomic crystals. Computing the heat capacity relies on being able to compute the second derivative of the energy with respect to atom positions. This capability is provided by the single2 method in Pair, but is currently only implemented for the shifted-force LJ potential (lj/smooth/linear). Pair::single2 takes a single pair and (like Pair::single) returns the energy and sets the force as an out parameter, but also sets the elements of 6-element double array out parameter, which are the unique components of the atomic Hessian tensor for the pair. A helper method exists (Pair::pairTensor), which will compute the tensor from linear derivatives and the vector between the positions. HMA Heat capacity can be computed for other models by implementing single2 in those Pair classes. More information about HMA is available in these publications: A. J. Schultz, D. A. Kofke, “Comprehensive high-precision high-accuracy equation of state and coexistence properties for classical Lennard-Jones crystals and low-temperature fluid phases”, J. Chem. Phys. 149, 204508 (2018) https://dx.doi.org/10.1063/1.5053714 S. G. Moustafa, A. J. Schultz, D. A. Kofke, “Harmonically Assisted Methods for Computing the Free Energy of Classical Crystals by Molecular Simulation: A Comparative Study”, J. Chem. Theory Comput. 13, 825-834 (2017) https://dx.doi.org/10.1021/acs.jctc.6b01082 S. G. Moustafa, A. J. Schultz, D. A. Kofke, “Very fast averaging of thermal properties of crystals by molecular simulation”, Phys. Rev. E 92, 043303 (2015) https://dx.doi.org/10.1103/PhysRevE.92.043303
src/USER-HMA/compute_hma.cpp +32 −0 Original line number Diff line number Diff line Loading @@ -11,6 +11,38 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- This compute implements harmonically-mapped averaging for crystalline solids. The current implementation handles atomic crystals. Computing the heat capacity relies on being able to compute the second derivative of the energy with respect to atom positions. This capability is provided by the single2 method in Pair, but is currently only implemented for the shifted-force LJ potential (lj/smooth/linear). Pair::single2 takes a single pair and (like Pair::single) returns the energy and sets the force as an out parameter, but also sets the elements of 6-element double array out parameter, which are the unique components of the atomic Hessian tensor for the pair. A helper method exists (Pair::pairTensor), which will compute the tensor from linear derivatives and the vector between the positions. HMA Heat capacity can be computed for other models by implementing single2 in those Pair classes. More information about HMA is available in these publications: A. J. Schultz, D. A. Kofke, “Comprehensive high-precision high-accuracy equation of state and coexistence properties for classical Lennard-Jones crystals and low-temperature fluid phases”, J. Chem. Phys. 149, 204508 (2018) https://dx.doi.org/10.1063/1.5053714 S. G. Moustafa, A. J. Schultz, D. A. Kofke, “Harmonically Assisted Methods for Computing the Free Energy of Classical Crystals by Molecular Simulation: A Comparative Study”, J. Chem. Theory Comput. 13, 825-834 (2017) https://dx.doi.org/10.1021/acs.jctc.6b01082 S. G. Moustafa, A. J. Schultz, D. A. Kofke, “Very fast averaging of thermal properties of crystals by molecular simulation”, Phys. Rev. E 92, 043303 (2015) https://dx.doi.org/10.1103/PhysRevE.92.043303 ------------------------------------------------------------------------- */ #include <cmath> #include <cstring> #include <mpi.h> Loading
