diff --git a/src/USER-HMA/README b/src/USER-HMA/README deleted file mode 100644 index b27999341b..0000000000 --- a/src/USER-HMA/README +++ /dev/null @@ -1,30 +0,0 @@ -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 diff --git a/src/USER-HMA/compute_hma.cpp b/src/USER-HMA/compute_hma.cpp index bedcda769d..15cadbdd45 100644 --- a/src/USER-HMA/compute_hma.cpp +++ b/src/USER-HMA/compute_hma.cpp @@ -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 #include #include