Merge pull request #481 from akohlmey/collected-small-changes (683f3d9d) · Commits · 郑智淋 / lammps

doc/Makefile

+1 −1

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		@@ -158,7 +158,7 @@ $(VENV):
		@( \
		virtualenv -p $(PYTHON) $(VENV); \
		. $(VENV)/bin/activate; \
		pip install Sphinx; \
		pip install Sphinx==1.5.6; \
		pip install sphinxcontrib-images; \
		deactivate;\
		)

doc/src/dihedral_spherical.txt

+9 −8

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		@@ -15,9 +15,9 @@ dihedral_style spherical :pre
		[Examples:]

		dihedral_coeff 1 1 286.1 1 124 1 1 90.0 0 1 90.0 0
		dihedral_coeff 1 3 286.1 1 114 1 1 90 0 1 90.0 0 &
		17.3 0 0.0 0 1 158 1 0 0.0 0 &
		15.1 0 0.0 0 0 0.0 0 1 167.3 1 :pre
		dihedral_coeff 1 3 69.3 1 93.9 1 1 90 0 1 90 0 &
		49.1 0 0.00 0 1 74.4 1 0 0.00 0 &
		25.2 0 0.00 0 0 0.00 0 1 48.1 1

		[Description:]

		@@ -35,13 +35,14 @@ the dihedral interaction even if it requires adding additional terms to
		the expansion (as was done in the second example). A careful choice of
		parameters can prevent singularities that occur with traditional
		force-fields whenever theta1 or theta2 approach 0 or 180 degrees.

		The last example above corresponds to an interaction with a single energy
		minima located at phi=114, theta1=158, theta2=167.3 degrees, and it remains
		minima located near phi=93.9, theta1=74.4, theta2=48.1 degrees, and it remains
		numerically stable at all angles (phi, theta1, theta2). In this example,
		the coefficients 17.3, and 15.1 can be physically interpreted as the
		the coefficients 49.1, and 25.2 can be physically interpreted as the
		harmonic spring constants for theta1 and theta2 around their minima.
		The coefficient 286.1 is the harmonic spring constant for phi after
		division by sin(158)*sin(167.3) (the minima positions for theta1 and theta2).
		The coefficient 69.3 is the harmonic spring constant for phi after
		division by sin(74.4)*sin(48.1) (the minima positions for theta1 and theta2).

		The following coefficients must be defined for each dihedral type via the
		"dihedral_coeff"_dihedral_coeff.html command as in the example above, or in

doc/src/pair_gauss.txt

+1 −1

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		@@ -128,7 +128,7 @@ The B parameter is converted to a distance (sigma), before mixing
		afterwards (using B=sigma^2).
		Negative A values are converted to positive A values (using abs(A))
		before mixing, and converted back after mixing
		(by multiplying by sign(Ai)*sign(Aj)).
		(by multiplying by min(sign(Ai),sign(Aj))).
		This way, if either particle is repulsive (if Ai<0 or Aj<0),
		then the default interaction between both particles will be repulsive.

doc/src/pair_meam_spline.txt

+2 −2

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		@@ -33,7 +33,7 @@ atoms J, I, and K centered on atom I. The five functions Phi, U, rho,
		f, and g are represented by cubic splines.

		The {meam/spline} style also supports a new style multicomponent
		modified embedded-atom method (MEAM) potential "(Zhang)"_#Zhang1, where
		modified embedded-atom method (MEAM) potential "(Zhang)"_#Zhang4, where
		the total energy E is given by

		:c,image(Eqs/pair_meam_spline_multicomponent.jpg)
		@@ -164,5 +164,5 @@ for more info.
		Kress, Modelling Simulation Materials Science Engineering, 8, 825
		(2000).

		:link(Zhang1)
		:link(Zhang4)
		[(Zhang)] Zhang and Trinkle, Computational Materials Science, 124, 204-210 (2016).

doc/src/rerun.txt

+1 −1

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		@@ -15,7 +15,7 @@ rerun file1 file2 ... keyword args ... :pre
		file1,file2,... = dump file(s) to read :ulb,l
		one or more keywords may be appended, keyword {dump} must appear and be last :l
		keyword = {first} or {last} or {every} or {skip} or {start} or {stop} or {dump}
		{first} args = Nfirts
		{first} args = Nfirst
		Nfirst = dump timestep to start on
		{last} args = Nlast
		Nlast = dumptimestep to stop on

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