(59c0f01a) · Commits · 郑智淋 / lammps

doc/region.html

+31 −7

Original line number	Diff line number	Diff line
		@@ -17,7 +17,7 @@
		</PRE>
		<UL><LI>ID = user-assigned name for the region

		<LI>style = <I>block</I> or <I>sphere</I> or <I>cylinder</I> or <I>union</I> or <I>intersect</I>
		<LI>style = <I>block</I> or <I>sphere</I> or <I>cylinder</I> or <I>prism</I> or <I>union</I> or <I>intersect</I>

		<PRE> <I>block</I> args = xlo xhi ylo yhi zlo zhi
		xlo,xhi,ylo,yhi,zlo,zhi = bounds of block in all
		@@ -30,6 +30,12 @@
		c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
		radius = cylinder radius (distance units)
		lo,hi = bounds of cylinder in dim (distance units)
		<I>prism</I> args = xlo xhi ylo yhi zlo zhi yxtilt zxtilt zytilt
		xlo,xhi,ylo,yhi,zlo,zhi = bounds of untilted prism in all
		dimensions (distance units)
		yxtilt = distance to shift upper y in x direction (distance units)
		zxtilt = distance to shift upper z in x direction (distance units)
		zytilt = distance to shift upper z in y direction (distance units)
		<I>union</I> args = N reg-ID1 reg-ID2 ...
		N = # of regions to follow, must be 2 or greater
		reg-ID1,reg-ID2, ... = IDs of regions to join together
		@@ -55,6 +61,7 @@
		<PRE>region 1 block -3.0 5.0 INF 10.0 INF INF
		region 2 sphere 0.0 0.0 0.0 5 side out
		region void cylinder y 2 3 5 -5.0 INF units box
		region 1 prism 0 10 0 10 0 10 2 0 0
		region outside union 4 side1 side2 side3 side4
		</PRE>
		<P><B>Description:</B>
		@@ -65,10 +72,10 @@ atoms via the <A HREF = "create_atoms.html">create_atoms</A> command. Or the at
		in the region can be identified as a group via the <A HREF = "group.html">group</A>
		command, or deleted via the <A HREF = "delete_atoms.html">delete_atoms</A> command.
		</P>
		<P>The lo/hi values for <I>block</I> or <I>cylinder</I> styles can be specified
		as INF which means they extend all the way to the global simulation
		box boundary. If a region is defined before the simulation box has
		been created (via <A HREF = "create_box.html">create_box</A> or
		<P>The lo/hi values for <I>block</I> or <I>cylinder</I> or <I>prism</I> styles can be
		specified as INF which means they extend all the way to the global
		simulation box boundary. If a region is defined before the simulation
		box has been created (via <A HREF = "create_box.html">create_box</A> or
		<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
		commands), then an INF parameter cannot be used.
		</P>
		@@ -79,6 +86,19 @@ third example above specifes a cylinder with its axis in the
		y-direction located at x = 2.0 and z = 3.0, with a radius of 5.0, and
		extending in the y-direction from -5.0 to the upper box boundary.
		</P>
		<P>For style <I>prism</I>, a tilted block is defined. The bounds of the
		untilted axis-aligned block are specified in the same way as for the
		<I>block</I> style. A tilt factor for each dimension with respect to
		another dimension is also specified. If the lower xy face of the
		prism is initially a rectangle (untilted), then the yxtilt factor
		specifies how far the upper y edge of that face is shifted in the x
		direction (skewing that face, keeping the xy face a parallelogram). A
		plus or minus value can be chosen; 0.0 would be no tilt. Similarly,
		zxtilt and zytilt describe how far the upper xy face of the prism is
		translated in the x and y directions to further tilt the prism. The
		final prism shape remains a parallelipiped, with opposing pairs of the
		6 faces remaining parallel to each other.
		</P>
		<P>The <I>union</I> style creates a region consisting of the volume of all the
		listed regions combined. The <I>intesect</I> style creates a region
		consisting of the volume that is common to all the listed regions.
		@@ -96,11 +116,15 @@ both of the spheres.
		to define the region. A <I>box</I> value selects standard distance units
		as defined by the <A HREF = "units.html">units</A> command, e.g. Angstroms for units
		= real or metal. A <I>lattice</I> value means the distance units are in
		cubic lattice spacings. The <A HREF = "lattice.html">lattice</A> command must first
		be used to define a lattice.
		lattice spacings. The <A HREF = "lattice.html">lattice</A> command must have been
		previously used to define the lattice spacing.
		</P>
		<P><B>Restrictions:</B> none
		</P>
		<P>A prism cannot be of 0.0 thickness in any dimension; use a small z
		thickness for 2d simulations. For 2d simulations, the zxtilt and
		zytilt parameters must be 0.0.
		</P>
		<P><B>Related commands:</B>
		</P>
		<P><A HREF = "lattice.html">lattice</A>, <A HREF = "create_atoms.html">create_atoms</A>,

doc/region.txt

+31 −7

Original line number	Diff line number	Diff line
		@@ -13,7 +13,7 @@ region command :h3
		region ID style args keyword value ... :pre

		ID = user-assigned name for the region :ulb,l
		style = {block} or {sphere} or {cylinder} or {union} or {intersect} :l
		style = {block} or {sphere} or {cylinder} or {prism} or {union} or {intersect} :l
		{block} args = xlo xhi ylo yhi zlo zhi
		xlo,xhi,ylo,yhi,zlo,zhi = bounds of block in all
		dimensions (distance units)
		@@ -25,6 +25,12 @@ style = {block} or {sphere} or {cylinder} or {union} or {intersect} :l
		c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
		radius = cylinder radius (distance units)
		lo,hi = bounds of cylinder in dim (distance units)
		{prism} args = xlo xhi ylo yhi zlo zhi yxtilt zxtilt zytilt
		xlo,xhi,ylo,yhi,zlo,zhi = bounds of untilted prism in all
		dimensions (distance units)
		yxtilt = distance to shift upper y in x direction (distance units)
		zxtilt = distance to shift upper z in x direction (distance units)
		zytilt = distance to shift upper z in y direction (distance units)
		{union} args = N reg-ID1 reg-ID2 ...
		N = # of regions to follow, must be 2 or greater
		reg-ID1,reg-ID2, ... = IDs of regions to join together
		@@ -46,6 +52,7 @@ keyword = {side} or {units} :l
		region 1 block -3.0 5.0 INF 10.0 INF INF
		region 2 sphere 0.0 0.0 0.0 5 side out
		region void cylinder y 2 3 5 -5.0 INF units box
		region 1 prism 0 10 0 10 0 10 2 0 0
		region outside union 4 side1 side2 side3 side4 :pre

		[Description:]
		@@ -56,10 +63,10 @@ atoms via the "create_atoms"_create_atoms.html command. Or the atoms
		in the region can be identified as a group via the "group"_group.html
		command, or deleted via the "delete_atoms"_delete_atoms.html command.

		The lo/hi values for {block} or {cylinder} styles can be specified
		as INF which means they extend all the way to the global simulation
		box boundary. If a region is defined before the simulation box has
		been created (via "create_box"_create_box.html or
		The lo/hi values for {block} or {cylinder} or {prism} styles can be
		specified as INF which means they extend all the way to the global
		simulation box boundary. If a region is defined before the simulation
		box has been created (via "create_box"_create_box.html or
		"read_data"_read_data.html or "read_restart"_read_restart.html
		commands), then an INF parameter cannot be used.

		@@ -70,6 +77,19 @@ third example above specifes a cylinder with its axis in the
		y-direction located at x = 2.0 and z = 3.0, with a radius of 5.0, and
		extending in the y-direction from -5.0 to the upper box boundary.

		For style {prism}, a tilted block is defined. The bounds of the
		untilted axis-aligned block are specified in the same way as for the
		{block} style. A tilt factor for each dimension with respect to
		another dimension is also specified. If the lower xy face of the
		prism is initially a rectangle (untilted), then the yxtilt factor
		specifies how far the upper y edge of that face is shifted in the x
		direction (skewing that face, keeping the xy face a parallelogram). A
		plus or minus value can be chosen; 0.0 would be no tilt. Similarly,
		zxtilt and zytilt describe how far the upper xy face of the prism is
		translated in the x and y directions to further tilt the prism. The
		final prism shape remains a parallelipiped, with opposing pairs of the
		6 faces remaining parallel to each other.

		The {union} style creates a region consisting of the volume of all the
		listed regions combined. The {intesect} style creates a region
		consisting of the volume that is common to all the listed regions.
		@@ -87,11 +107,15 @@ The {units} keyword determines the meaning of the distance units used
		to define the region. A {box} value selects standard distance units
		as defined by the "units"_units.html command, e.g. Angstroms for units
		= real or metal. A {lattice} value means the distance units are in
		cubic lattice spacings. The "lattice"_lattice.html command must first
		be used to define a lattice.
		lattice spacings. The "lattice"_lattice.html command must have been
		previously used to define the lattice spacing.

		[Restrictions:] none

		A prism cannot be of 0.0 thickness in any dimension; use a small z
		thickness for 2d simulations. For 2d simulations, the zxtilt and
		zytilt parameters must be 0.0.

		[Related commands:]

		"lattice"_lattice.html, "create_atoms"_create_atoms.html,

potentials/si.sw

+5 −3

Original line number	Diff line number	Diff line
		# Stillinger-Weber parameters for various elements and mixtures
		# multiple elements can be added to this file, LAMMPS reads the ones it needs
		# multiple entries can be added to this file, LAMMPS reads the ones it needs

		# format of a line:
		# format of an entry (one or more lines):
		# element 1, element 2, element 3
		# epsilon, sigma, littlea, lambda, gamma, costheta, biga, bigb, powerp, powerq

		Si Si Si 2.1683 2.0951 1.80 21.0 1.20 -0.333333333333 7.049556277 0.6022245584 4.0 0.0
		Si Si Si 2.1683 2.0951 1.80 21.0 1.20 -0.333333333333
		7.049556277 0.6022245584 4.0 0.0

src/MAKE/Makefile.tbird

+1 −1

Original line number	Diff line number	Diff line
		@@ -5,7 +5,7 @@ SHELL = /bin/sh

		# System-specific settings

		FFTW = /apps/libraries/fftw/nwcc
		FFTW = /apps/libraries/fftw

		CC = mpicxx
		CCFLAGS = -O -DFFT_FFTW -I${FFTW}/include

src/fix_wall_reflect.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -12,7 +12,7 @@
		------------------------------------------------------------------------- */

		#ifndef FIX_WALL_REFLECT_H
		#define FIX_WALL_REFELCT_H
		#define FIX_WALL_REFLECT_H

		#include "fix.h"

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