Merge branch 'master' of https://github.com/lammps/lammps into USER-DPD_es_RNG (29df5a53) · Commits · 郑智淋 / lammps

doc/src/Section_commands.txt

+6 −5

Original line number	Diff line number	Diff line
		@@ -637,10 +637,10 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
		"rigid/nve (o)"_fix_rigid.html,
		"rigid/nvt (o)"_fix_rigid.html,
		"rigid/small (o)"_fix_rigid.html,
		"rigid/small/nph (o)"_fix_rigid.html,
		"rigid/small/npt (o)"_fix_rigid.html,
		"rigid/small/nve (o)"_fix_rigid.html,
		"rigid/small/nvt (o)"_fix_rigid.html,
		"rigid/small/nph"_fix_rigid.html,
		"rigid/small/npt"_fix_rigid.html,
		"rigid/small/nve"_fix_rigid.html,
		"rigid/small/nvt"_fix_rigid.html,
		"setforce (k)"_fix_setforce.html,
		"shake"_fix_shake.html,
		"spring"_fix_spring.html,
		@@ -1023,7 +1023,7 @@ KOKKOS, o = USER-OMP, t = OPT.
		"tri/lj"_pair_tri_lj.html,
		"vashishta (ko)"_pair_vashishta.html,
		"vashishta/table (o)"_pair_vashishta.html,
		"yukawa (go)"_pair_yukawa.html,
		"yukawa (gok)"_pair_yukawa.html,
		"yukawa/colloid (go)"_pair_yukawa_colloid.html,
		"zbl (go)"_pair_zbl.html :tb(c=4,ea=c)

		@@ -1045,6 +1045,7 @@ package"_Section_start.html#start_3.
		"edpd"_pair_meso.html,
		"eff/cut"_pair_eff.html,
		"exp6/rx"_pair_exp6_rx.html,
		"extep"_pair_extep.html,
		"gauss/cut"_pair_gauss.html,
		"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
		"lennard/mdf"_pair_mdf.html,

doc/src/compute_dihedral_local.txt

+2 −2

Original line number	Diff line number	Diff line
		@@ -27,8 +27,8 @@ compute 1 all dihedral/local phi :pre

		Define a computation that calculates properties of individual dihedral
		interactions. The number of datums generated, aggregated across all
		processors, equals the number of angles in the system, modified by the
		group parameter as explained below.
		processors, equals the number of dihedral angles in the system, modified
		by the group parameter as explained below.

		The value {phi} is the dihedral angle, as defined in the diagram on
		the "dihedral_style"_dihedral_style.html doc page.

doc/src/create_atoms.txt

+16 −14

Original line number	Diff line number	Diff line
		@@ -36,9 +36,9 @@ keyword = {mol} or {basis} or {remap} or {var} or {set} or {units} :l
		{set} values = dim name
		dim = {x} or {y} or {z}
		name = name of variable to set with x, y, or z atom position
		{rotate} values = Rx Ry Rz theta
		Rx,Ry,Rz = rotation vector for single molecule
		{rotate} values = theta Rx Ry Rz
		theta = rotation angle for single molecule (degrees)
		Rx,Ry,Rz = rotation vector for single molecule
		{units} value = {lattice} or {box}
		{lattice} = the geometry is defined in lattice units
		{box} = the geometry is defined in simulation box units :pre
		@@ -227,28 +227,30 @@ the sinusoid would appear to be "smoother". Also note the use of the
		converts lattice spacings to distance. Click on the image for a
		larger version.

		dimension 2
		variable x equal 100
		variable y equal 25
		lattice hex 0.8442
		region box block 0 $x 0 $y -0.5 0.5
		create_box 1 box :pre

		variable xx equal 0.0
		variable yy equal 0.0
		variable xx internal 0.0
		variable yy internal 0.0
		variable v equal "(0.2v_yylat * cos(v_xx/xlat * 2.0PI4.0/v_x) + 0.5v_yylat - v_yy) > 0.0"
		create_atoms 1 box var v set x xx set y yy :pre
		create_atoms 1 box var v set x xx set y yy
		write_dump all atom sinusoid.lammpstrj :pre

		:c,image(JPG/sinusoid_small.jpg,JPG/sinusoid.jpg)

		The {rotate} keyword can be used with the {single} style, when adding
		a single molecule to specify the orientation at which the molecule is
		inserted. The axis of rotation is determined by the rotation vector
		(Rx,Ry,Rz) that goes through the insertion point. The specified
		{theta} determines the angle of rotation around that axis. Note that
		the direction of rotation for the atoms around the rotation axis is
		consistent with the right-hand rule: if your right-hand's thumb points
		along {R}, then your fingers wrap around the axis in the direction of
		rotation.
		The {rotate} keyword can only be used with the {single} style and
		when adding a single molecule. It allows to specify the orientation
		at which the molecule is inserted. The axis of rotation is
		determined by the rotation vector (Rx,Ry,Rz) that goes through the
		insertion point. The specified {theta} determines the angle of
		rotation around that axis. Note that the direction of rotation for
		the atoms around the rotation axis is consistent with the right-hand
		rule: if your right-hand's thumb points along {R}, then your fingers
		wrap around the axis in the direction of rotation.

		The {units} keyword determines the meaning of the distance units used
		to specify the coordinates of the one particle created by the {single}

doc/src/create_bonds.txt

+1 −1

Original line number	Diff line number	Diff line
		@@ -18,7 +18,7 @@ style = {many} or {single/bond} or {single/angle} or {single/dihedral} :ule,l
		group2-ID = ID of second group, bonds will be between atoms in the 2 groups
		btype = bond type of created bonds
		rmin = minimum distance between pair of atoms to bond together
		rmax = minimum distance between pair of atoms to bond together
		rmax = maximum distance between pair of atoms to bond together
		{single/bond} args = btype batom1 batom2
		btype = bond type of new bond
		batom1,batom2 = atom IDs for two atoms in bond

doc/src/fix_rigid.txt

+8 −2

Original line number	Diff line number	Diff line
		@@ -7,11 +7,17 @@
		:line

		fix rigid command :h3
		fix rigid/omp command :h3
		fix rigid/nve command :h3
		fix rigid/nve/omp command :h3
		fix rigid/nvt command :h3
		fix rigid/nvt/omp command :h3
		fix rigid/npt command :h3
		fix rigid/npt/omp command :h3
		fix rigid/nph command :h3
		fix rigid/nph/omp command :h3
		fix rigid/small command :h3
		fix rigid/small/omp command :h3
		fix rigid/nve/small command :h3
		fix rigid/nvt/small command :h3
		fix rigid/npt/small command :h3

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