Add bits to Packages_details, Packages_user, fix up typos (5c9c1502) · Commits · 郑智淋 / lammps

doc/src/Packages_details.txt

+20 −0

Original line number	Diff line number	Diff line
		@@ -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:]

+1 −0

Original line number	Diff line number	Diff line
		@@ -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

+3 −3

Original line number	Diff line number	Diff line
		@@ -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