diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 0ab1b5e4fd..b5050b8c4b 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -76,6 +76,7 @@ as contained in the file name. "USER-EFF"_#PKG-USER-EFF, "USER-FEP"_#PKG-USER-FEP, "USER-H5MD"_#PKG-USER-H5MD, +"USER-HMA"_#PKG-USER-HMA, "USER-INTEL"_#PKG-USER-INTEL, "USER-LB"_#PKG-USER-LB, "USER-MANIFOLD"_#PKG-USER-MANIFOLD, @@ -1373,6 +1374,25 @@ lib/h5md/README :line +USER-HMA package :link(PKG-USER-HMA),h4 + +[Contents:] + +Harmonically mapped averaging for efficient calculation of properties of +crystalline solids. The compute hma can specify use of HMA for calculation of +potential energy, pressure and heat capacity. + +[Author:] Apoorva Purohit, Andrew Schultz and David Kofke (University at +Buffalo, NY, USA) + +[Supporting info:] + +examples/USER/hma/README +src/USER-HMA/README +"compute hma"_compute_hma.html :ul + +:line + USER-INTEL package :link(PKG-USER-INTEL),h4 [Contents:] diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt index 4210f617ef..3ce2a458b6 100644 --- a/doc/src/Packages_user.txt +++ b/doc/src/Packages_user.txt @@ -51,6 +51,7 @@ Package, Description, Doc page, Example, Library "USER-EFF"_Packages_details.html#PKG-USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, no "USER-FEP"_Packages_details.html#PKG-USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, no "USER-H5MD"_Packages_details.html#PKG-USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, n/a, ext +"USER-HMA"_Packages_details.html#PKG-USER-HMA, compute properties via HMA,"compute hma"_compute_hma.html, USER/hma, no "USER-INTEL"_Packages_details.html#PKG-USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no "USER-LB"_Packages_details.html#PKG-USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, no "USER-MANIFOLD"_Packages_details.html#PKG-USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, no diff --git a/doc/src/compute_hma.txt b/doc/src/compute_hma.txt index c4ade07ad7..340881bf68 100644 --- a/doc/src/compute_hma.txt +++ b/doc/src/compute_hma.txt @@ -61,7 +61,7 @@ The pressure is computed by the formula: \end\{equation\} where \(\rho\) is the number density of the system, \(\Delta \hat P\) is the -difference between theh harmonic and lattice pressure, and \(P_\{vir\}\) is +difference between the harmonic and lattice pressure, and \(P_\{vir\}\) is the virial pressure computed as the sum of pair, bond, angle, dihedral, improper, kspace (long-range), and fix contributions to the force on each atom. Although the method will work for any value of \(\Delta \hat P\) @@ -76,13 +76,13 @@ U_\{HMA\}^2 \right> - \left^2 \right)/T + \frac\{1\}\{4 T\} \left< F\bullet\Delta r + \Delta r \bullet \Phi \bullet \Delta r \right> \end\{equation\} -where \(\Phi\) is the Hessian of second derivatives. The compute hma command +where \(\Phi\) is the Hessian matrix. The compute hma command computes the full expression for \(C_V\) except for the \(\left^2\) in the variance term, which can be obtained by passing the {u} keyword; you must add this extra contribution to the \(C_V\) value reported by this compute. The variance term can cause significant roundoff error when computing \(C_V\). To address this, the {anharmonic} -keyword can be passed and/or the output format can be speicified with more +keyword can be passed and/or the output format can be specified with more digits. thermo_modify format float '%22.15e' :pre