sync with GH (45e50b46) · Commits · 郑智淋 / lammps

doc/src/Section_howto.txt

+1 −1

Original line number	Diff line number	Diff line
		@@ -2123,7 +2123,7 @@ thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33
		run 100000
		variable v equal (v_v11+v_v22+v_v33)/3.0
		variable ndens equal count(all)/vol
		print "average viscosity: $v \[Pa.s/] @ $T K, $\{ndens\} /A^3" :pre
		print "average viscosity: $v \[Pa.s\] @ $T K, $\{ndens\} /A^3" :pre

		The fifth method is related to the above Green-Kubo method,
		but uses the Einstein formulation, analogous to the Einstein

+1 −1

Original line number	Diff line number	Diff line
		@@ -845,7 +845,7 @@ PYTHON package :link(PYTHON),h5
		Contents: A "python"_python.html command which allow you to execute
		Python code from a LAMMPS input script. The code can be in a separate
		file or embedded in the input script itself. See "Section
		11.2"_Section_python.html#py-2 for an overview of using Python from
		11.2"_Section_python.html#py_2 for an overview of using Python from
		LAMMPS and for other ways to use LAMMPS and Python together.

		Building with the PYTHON package assumes you have a Python shared

+6 −6

Original line number	Diff line number	Diff line
		@@ -56,7 +56,7 @@ CMAP :pre

		1 1 8 10 12 18 20
		2 5 18 20 22 25 27
		...
		\[...\]
		N 3 314 315 317 318 330 :pre

		The first column is an index from 1 to N to enumerate the CMAP terms;
		@@ -66,7 +66,7 @@ remaining 5 columns are the atom IDs of the atoms in the two 4-atom
		dihedrals that overlap to create the CMAP 5-body interaction. Note
		that the "crossterm" and "CMAP" keywords for the header and body
		sections match those specified in the read_data command following the
		data file name; see the "read_data"_doc/read_data.html doc page for
		data file name; see the "read_data"_read_data.html doc page for
		more details.

		A data file containing CMAP crossterms can be generated from a PDB
		@@ -124,9 +124,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.

		:line

		(Buck)
		Buck, Bouguet-Bonnet, Pastor, MacKerell Jr., Biophys J, 90, L36
		:link(Buck)
		[(Buck)] Buck, Bouguet-Bonnet, Pastor, MacKerell Jr., Biophys J, 90, L36
		(2006).

		(Brooks)
		Brooks, Brooks, MacKerell Jr., J Comput Chem, 30, 1545 (2009).
		:link(Brooks)
		[(Brooks)] Brooks, Brooks, MacKerell Jr., J Comput Chem, 30, 1545 (2009).

+1 −0

+1 −0