Add bits to Packages_details, Packages_user, fix up typos

This commit is contained in:
Andrew Schultz 2019-06-10 16:13:34 -04:00
parent ad8fd4a2a4
commit 5c9c15025a
3 changed files with 24 additions and 3 deletions

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@ -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:]

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@ -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

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@ -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<U_\{HMA\}\right>^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
\(\left<U_\{HMA\}^2\right>^2\) 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