forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14442 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
5bba67f290
commit
3e36b2b16b
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@ -208,8 +208,12 @@ same, regardless of how many processors are being used.</p>
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around a rotation axis <em>R</em> = (Rx,Ry,Rz) that goes thru a point <em>P</em> =
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(Px,Py,Pz). The direction of rotation for the atoms around the
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rotation axis is consistent with the right-hand rule: if your
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right-hand’s thumb points along <em>R</em>, then your fingers wrap around the
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right-hand thumb points along <em>R</em>, then your fingers wrap around the
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axis in the direction of positive theta.</p>
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<p>If the defined <a class="reference internal" href="atom_style.html"><em>atom_style</em></a> assigns an orientation to
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each atom (<a class="reference internal" href="atom_style.html"><em>atom styles</em></a> ellipsoid, line, tri, body),
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then that property is also updated appropriately to correspond to the
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atom’s rotation.</p>
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<p>Distance units for displacements and the origin point of the <em>rotate</em>
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style are determined by the setting of <em>box</em> or <em>lattice</em> for the
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<em>units</em> keyword. <em>Box</em> means distance units as defined by the
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@ -86,9 +86,14 @@ The {rotate} style rotates each atom in the group by the angle {theta}
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around a rotation axis {R} = (Rx,Ry,Rz) that goes thru a point {P} =
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(Px,Py,Pz). The direction of rotation for the atoms around the
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rotation axis is consistent with the right-hand rule: if your
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right-hand's thumb points along {R}, then your fingers wrap around the
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right-hand thumb points along {R}, then your fingers wrap around the
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axis in the direction of positive theta.
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If the defined "atom_style"_atom_style.html assigns an orientation to
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each atom ("atom styles"_atom_style.html ellipsoid, line, tri, body),
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then that property is also updated appropriately to correspond to the
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atom's rotation.
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Distance units for displacements and the origin point of the {rotate}
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style are determined by the setting of {box} or {lattice} for the
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{units} keyword. {Box} means distance units as defined by the
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@ -143,18 +143,23 @@
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<li>color = atom attribute that determines color of each atom</li>
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<li>diameter = atom attribute that determines size of each atom</li>
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<li>zero or more keyword/value pairs may be appended</li>
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<li>keyword = <em>adiam</em> or <em>atom</em> or <em>body</em> or <em>bond</em> or <em>size</em> or <em>view</em> or <em>center</em> or <em>up</em> or <em>zoom</em> or <em>persp</em> or <em>box</em> or <em>axes</em> or <em>subbox</em> or <em>shiny</em> or <em>ssao</em></li>
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<li>keyword = <em>atom</em> or <em>adiam</em> or <em>bond</em> or <em>line</em> or <em>tri</em> or <em>body</em> or <em>size</em> or <em>view</em> or <em>center</em> or <em>up</em> or <em>zoom</em> or <em>persp</em> or <em>box</em> or <em>axes</em> or <em>subbox</em> or <em>shiny</em> or <em>ssao</em></li>
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</ul>
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<pre class="literal-block">
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<em>adiam</em> value = number = numeric value for atom diameter (distance units)
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<em>atom</em> = yes/no = do or do not draw atoms
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<em>body</em> = yes/no bflag1 bflag2
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yes/no = do or do not draw atoms as bodies
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bflag1,bflag2 = 2 numeric flags to affect how bodies are drawn
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<em>adiam</em> size = numeric value for atom diameter (distance units)
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<em>bond</em> values = color width = color and width of bonds
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color = <em>atom</em> or <em>type</em> or <em>none</em>
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width = number or <em>atom</em> or <em>type</em> or <em>none</em>
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number = numeric value for bond width (distance units)
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<em>line</em> = color width
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color = <em>type</em>
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width = numeric value for line width (distance units)
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<em>tri</em> = color
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color = <em>type</em>
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<em>body</em> = color bflag1 bflag2
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color = <em>type</em>
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bflag1,bflag2 = 2 numeric flags to affect how bodies are drawn
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<em>size</em> values = width height = size of images
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width = width of image in # of pixels
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height = height of image in # of pixels
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@ -350,26 +355,15 @@ will likely not need to change. The <a class="reference internal" href="dump_mo
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also has options specific to the dump image style, particularly for
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assigning colors to atoms, bonds, and other image features.</p>
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<hr class="docutils" />
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<p>The <em>adiam</em> keyword allows you to override the <em>diameter</em> setting to a
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per-atom attribute with a specified numeric value. All atoms will be
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drawn with that diameter, e.g. 1.5, which is in whatever distance
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<a class="reference internal" href="units.html"><em>units</em></a> the input script defines, e.g. Angstroms.</p>
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<p>The <em>atom</em> keyword allow you to turn off the drawing of all atoms,
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if the specified value is <em>no</em>.</p>
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<p>The <em>body</em> keyword can be used when <a class="reference internal" href="atom_style.html"><em>atom_style body</em></a>
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is used to define body particles with internal state
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(e.g. sub-particles). The <a class="reference internal" href="body.html"><em>body</em></a> doc page descibes the body
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styles LAMMPS currently supports, and provides more details as to the
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kind of body particles they represent and how they are drawn by this
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dump image command. For all the body styles, individual atoms can be
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either a body particle or a usual point (non-body) particle. If the
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<em>body</em> keyword is set to <em>yes</em>, then atoms which are body particles
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are drawn by the method defined by the body style. Non-body particles
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the same way they would be if the <em>body</em> keyword is <em>no</em>, i.e. as
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spheres. The <em>bflag1</em> and <em>bflag2</em> settings are numerical values
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which are passed to the body style to affect how the drawing of a body
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particle is done. See the <a class="reference internal" href="body.html"><em>body</em></a> doc page for a description
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of what these parameters mean for each body style.</p>
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<p>The <em>atom</em> keyword allow you to turn off the drawing of all atoms, if
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the specified value is <em>no</em>. Note that this will not turn off the
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drawing of particles that are represented as lines, triangles, or
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bodies, as discussed below. These particles can be drawn separately
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if the <em>line</em>, <em>tri</em>, or <em>body</em> keywords are used.</p>
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<p>The <em>adiam</em> keyword allows you to override the <em>diameter</em> setting to
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set a single numeric <em>size</em>. All atoms will be drawn with that
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diameter, e.g. 1.5, which is in whatever distance <a class="reference internal" href="units.html"><em>units</em></a>
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the input script defines, e.g. Angstroms.</p>
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<p>The <em>bond</em> keyword allows to you to alter how bonds are drawn. A bond
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is only drawn if both atoms in the bond are being drawn due to being
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in the specified group and due to other selection criteria
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@ -405,6 +399,59 @@ of the 2 atoms in the bond.</p>
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<p>If <em>type</em> is specified for the <em>width</em> value then the diameter of each
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bond is determined by its bond type. By default all types have
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diameter 0.5. This mapping can be changed by the <a class="reference internal" href="dump_modify.html"><em>dump_modify bdiam</em></a> command.</p>
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<p>The <em>line</em> keyword can be used when <a class="reference internal" href="atom_style.html"><em>atom_style line</em></a>
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is used to define particles as line segments, and will draw them as
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lines. If this keyword is not used, such particles will be drawn as
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spheres, the same as if they were regular atoms. The only setting
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currently allowed for the <em>color</em> value is <em>type</em>, which will color
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the lines according to the atom type of the particle. By default the
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mapping of types to colors is as follows:</p>
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<ul class="simple">
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<li>type 1 = red</li>
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<li>type 2 = green</li>
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<li>type 3 = blue</li>
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<li>type 4 = yellow</li>
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<li>type 5 = aqua</li>
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<li>type 6 = cyan</li>
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</ul>
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<p>and repeats itself for types > 6. There is not yet an option to
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change this via the <a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a> command.</p>
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<p>The line <em>width</em> can only be a numeric value, which specifies that all
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lines will be drawn as cylinders with that diameter, e.g. 1.0, which
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is in whatever distance <a class="reference internal" href="units.html"><em>units</em></a> the input script defines,
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e.g. Angstroms.</p>
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<p>The <em>tri</em> keyword can be used when <a class="reference internal" href="atom_style.html"><em>atom_style tri</em></a> is
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used to define particles as triangles, and will draw them as
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triangles. If this keyword is not used, such particles will be drawn
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as spheres, the same as if they were regular atoms. The only setting
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currently allowed for the <em>color</em> value is <em>type</em>, which will color
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the triangles according to the atom type of the particle. By default
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the mapping of types to colors is as follows:</p>
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<ul class="simple">
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<li>type 1 = red</li>
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<li>type 2 = green</li>
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<li>type 3 = blue</li>
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<li>type 4 = yellow</li>
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<li>type 5 = aqua</li>
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<li>type 6 = cyan</li>
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</ul>
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<p>and repeats itself for types > 6. There is not yet an option to
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change this via the <a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a> command.</p>
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<p>The <em>body</em> keyword can be used when <a class="reference internal" href="atom_style.html"><em>atom_style body</em></a>
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is used to define body particles with internal state
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(e.g. sub-particles), and will drawn them in a manner specific to the
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body style. If this keyword is not used, such particles will be drawn
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as spheres, the same as if they were regular atoms.</p>
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<p>The <a class="reference internal" href="body.html"><em>body</em></a> doc page descibes the body styles LAMMPS
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currently supports, and provides more details as to the kind of body
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particles they represent and how they are drawn by this dump image
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command. For all the body styles, individual atoms can be either a
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body particle or a usual point (non-body) particle. Non-body
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particles will be drawn the same way they would be as a regular atom.
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The <em>bflag1</em> and <em>bflag2</em> settings are numerical values which are
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passed to the body style to affect how the drawing of a body particle
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is done. See the <a class="reference internal" href="body.html"><em>body</em></a> doc page for a description of what
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these parameters mean for each body style.</p>
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<hr class="docutils" />
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<p>The <em>size</em> keyword sets the width and height of the created images,
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i.e. the number of pixels in each direction.</p>
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@ -21,16 +21,21 @@ file = name of file to write image to :l
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color = atom attribute that determines color of each atom :l
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diameter = atom attribute that determines size of each atom :l
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zero or more keyword/value pairs may be appended :l
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keyword = {adiam} or {atom} or {body} or {bond} or {size} or {view} or {center} or {up} or {zoom} or {persp} or {box} or {axes} or {subbox} or {shiny} or {ssao} :l
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{adiam} value = number = numeric value for atom diameter (distance units)
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keyword = {atom} or {adiam} or {bond} or {line} or {tri} or {body} or {size} or {view} or {center} or {up} or {zoom} or {persp} or {box} or {axes} or {subbox} or {shiny} or {ssao} :l
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{atom} = yes/no = do or do not draw atoms
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{body} = yes/no bflag1 bflag2
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yes/no = do or do not draw atoms as bodies
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bflag1,bflag2 = 2 numeric flags to affect how bodies are drawn
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{adiam} size = numeric value for atom diameter (distance units)
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{bond} values = color width = color and width of bonds
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color = {atom} or {type} or {none}
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width = number or {atom} or {type} or {none}
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number = numeric value for bond width (distance units)
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{line} = color width
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color = {type}
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width = numeric value for line width (distance units)
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{tri} = color
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color = {type}
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{body} = color bflag1 bflag2
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color = {type}
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bflag1,bflag2 = 2 numeric flags to affect how bodies are drawn
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{size} values = width height = size of images
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width = width of image in # of pixels
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height = height of image in # of pixels
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@ -234,28 +239,16 @@ assigning colors to atoms, bonds, and other image features.
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:line
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The {adiam} keyword allows you to override the {diameter} setting to a
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per-atom attribute with a specified numeric value. All atoms will be
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drawn with that diameter, e.g. 1.5, which is in whatever distance
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"units"_units.html the input script defines, e.g. Angstroms.
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The {atom} keyword allow you to turn off the drawing of all atoms, if
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the specified value is {no}. Note that this will not turn off the
|
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drawing of particles that are represented as lines, triangles, or
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bodies, as discussed below. These particles can be drawn separately
|
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if the {line}, {tri}, or {body} keywords are used.
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The {atom} keyword allow you to turn off the drawing of all atoms,
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if the specified value is {no}.
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The {body} keyword can be used when "atom_style body"_atom_style.html
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is used to define body particles with internal state
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(e.g. sub-particles). The "body"_body.html doc page descibes the body
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styles LAMMPS currently supports, and provides more details as to the
|
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kind of body particles they represent and how they are drawn by this
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dump image command. For all the body styles, individual atoms can be
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either a body particle or a usual point (non-body) particle. If the
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{body} keyword is set to {yes}, then atoms which are body particles
|
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are drawn by the method defined by the body style. Non-body particles
|
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the same way they would be if the {body} keyword is {no}, i.e. as
|
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spheres. The {bflag1} and {bflag2} settings are numerical values
|
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which are passed to the body style to affect how the drawing of a body
|
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particle is done. See the "body"_body.html doc page for a description
|
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of what these parameters mean for each body style.
|
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The {adiam} keyword allows you to override the {diameter} setting to
|
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set a single numeric {size}. All atoms will be drawn with that
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diameter, e.g. 1.5, which is in whatever distance "units"_units.html
|
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the input script defines, e.g. Angstroms.
|
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|
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The {bond} keyword allows to you to alter how bonds are drawn. A bond
|
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is only drawn if both atoms in the bond are being drawn due to being
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@ -300,6 +293,64 @@ bond is determined by its bond type. By default all types have
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diameter 0.5. This mapping can be changed by the "dump_modify
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bdiam"_dump_modify.html command.
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The {line} keyword can be used when "atom_style line"_atom_style.html
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is used to define particles as line segments, and will draw them as
|
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lines. If this keyword is not used, such particles will be drawn as
|
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spheres, the same as if they were regular atoms. The only setting
|
||||
currently allowed for the {color} value is {type}, which will color
|
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the lines according to the atom type of the particle. By default the
|
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mapping of types to colors is as follows:
|
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|
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type 1 = red
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type 2 = green
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type 3 = blue
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type 4 = yellow
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type 5 = aqua
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type 6 = cyan :ul
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|
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and repeats itself for types > 6. There is not yet an option to
|
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change this via the "dump_modify"_dump_modify.html command.
|
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|
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The line {width} can only be a numeric value, which specifies that all
|
||||
lines will be drawn as cylinders with that diameter, e.g. 1.0, which
|
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is in whatever distance "units"_units.html the input script defines,
|
||||
e.g. Angstroms.
|
||||
|
||||
The {tri} keyword can be used when "atom_style tri"_atom_style.html is
|
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used to define particles as triangles, and will draw them as
|
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triangles. If this keyword is not used, such particles will be drawn
|
||||
as spheres, the same as if they were regular atoms. The only setting
|
||||
currently allowed for the {color} value is {type}, which will color
|
||||
the triangles according to the atom type of the particle. By default
|
||||
the mapping of types to colors is as follows:
|
||||
|
||||
type 1 = red
|
||||
type 2 = green
|
||||
type 3 = blue
|
||||
type 4 = yellow
|
||||
type 5 = aqua
|
||||
type 6 = cyan :ul
|
||||
|
||||
and repeats itself for types > 6. There is not yet an option to
|
||||
change this via the "dump_modify"_dump_modify.html command.
|
||||
|
||||
The {body} keyword can be used when "atom_style body"_atom_style.html
|
||||
is used to define body particles with internal state
|
||||
(e.g. sub-particles), and will drawn them in a manner specific to the
|
||||
body style. If this keyword is not used, such particles will be drawn
|
||||
as spheres, the same as if they were regular atoms.
|
||||
|
||||
The "body"_body.html doc page descibes the body styles LAMMPS
|
||||
currently supports, and provides more details as to the kind of body
|
||||
particles they represent and how they are drawn by this dump image
|
||||
command. For all the body styles, individual atoms can be either a
|
||||
body particle or a usual point (non-body) particle. Non-body
|
||||
particles will be drawn the same way they would be as a regular atom.
|
||||
The {bflag1} and {bflag2} settings are numerical values which are
|
||||
passed to the body style to affect how the drawing of a body particle
|
||||
is done. See the "body"_body.html doc page for a description of what
|
||||
these parameters mean for each body style.
|
||||
|
||||
:line
|
||||
|
||||
The {size} keyword sets the width and height of the created images,
|
||||
|
|
|
|||
|
|
@ -249,16 +249,17 @@ fix 1 boundary move variable v_x NULL NULL v_v NULL NULL
|
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</div>
|
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<p>The <em>rotate</em> style rotates atoms around a rotation axis <em>R</em> =
|
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(Rx,Ry,Rz) that goes thru a point <em>P</em> = (Px,Py,Pz). The <em>period</em> of
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the rotation is also specified. This style also sets the velocity of
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each atom to (omega cross Rperp) where omega is its angular velocity
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around the rotation axis and Rperp is a perpendicular vector from the
|
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rotation axis to the atom. If the defined
|
||||
<a class="reference internal" href="atom_style.html"><em>atom_style</em></a> assigns an angular velocity to each atom,
|
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then each atom’s angular velocity is also set to omega. Note that the
|
||||
direction of rotation for the atoms around the rotation axis is
|
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consistent with the right-hand rule: if your right-hand’s thumb points
|
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along <em>R</em>, then your fingers wrap around the axis in the direction of
|
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rotation.</p>
|
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the rotation is also specified. The direction of rotation for the
|
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atoms around the rotation axis is consistent with the right-hand rule:
|
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if your right-hand thumb points along <em>R</em>, then your fingers wrap
|
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around the axis in the direction of rotation.</p>
|
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<p>This style also sets the velocity of each atom to (omega cross Rperp)
|
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where omega is its angular velocity around the rotation axis and Rperp
|
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is a perpendicular vector from the rotation axis to the atom. If the
|
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defined <a class="reference internal" href="atom_style.html"><em>atom_style</em></a> assigns an angular velocity or
|
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angular moementum or orientation to each atom (<a class="reference internal" href="atom_style.html"><em>atom styles</em></a> sphere, ellipsoid, line, tri, body), then
|
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those properties are also updated appropriately to correspond to the
|
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atom’s motion and rotation over time.</p>
|
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<p>The <em>variable</em> style allows the position and velocity components of
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each atom to be set by formulas specified via the
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<a class="reference internal" href="variable.html"><em>variable</em></a> command. Each of the 6 variables is
|
||||
|
|
|
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|
|
@ -122,16 +122,19 @@ fix 1 boundary move variable v_x NULL NULL v_v NULL NULL :pre
|
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|
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The {rotate} style rotates atoms around a rotation axis {R} =
|
||||
(Rx,Ry,Rz) that goes thru a point {P} = (Px,Py,Pz). The {period} of
|
||||
the rotation is also specified. This style also sets the velocity of
|
||||
each atom to (omega cross Rperp) where omega is its angular velocity
|
||||
around the rotation axis and Rperp is a perpendicular vector from the
|
||||
rotation axis to the atom. If the defined
|
||||
"atom_style"_atom_style.html assigns an angular velocity to each atom,
|
||||
then each atom's angular velocity is also set to omega. 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 rotation is also specified. The direction of rotation for the
|
||||
atoms around the rotation axis is consistent with the right-hand rule:
|
||||
if your right-hand thumb points along {R}, then your fingers wrap
|
||||
around the axis in the direction of rotation.
|
||||
|
||||
This style also sets the velocity of each atom to (omega cross Rperp)
|
||||
where omega is its angular velocity around the rotation axis and Rperp
|
||||
is a perpendicular vector from the rotation axis to the atom. If the
|
||||
defined "atom_style"_atom_style.html assigns an angular velocity or
|
||||
angular moementum or orientation to each atom ("atom
|
||||
styles"_atom_style.html sphere, ellipsoid, line, tri, body), then
|
||||
those properties are also updated appropriately to correspond to the
|
||||
atom's motion and rotation over time.
|
||||
|
||||
The {variable} style allows the position and velocity components of
|
||||
each atom to be set by formulas specified via the
|
||||
|
|
|
|||
|
|
@ -200,15 +200,15 @@ time for future use in a calculation or output. See the discussion of
|
|||
inputs.</p>
|
||||
<p>If <em>N</em> is not zero, then the attributes will be updated every <em>N</em>
|
||||
steps.</p>
|
||||
<div class="admonition warning">
|
||||
<p class="first admonition-title">Warning</p>
|
||||
<p class="last">Actually, only atom attributes specified by keywords
|
||||
like <em>xu</em> or <em>vy</em> or <em>radius</em> are initially stored immediately at the
|
||||
point in your input script when the fix is defined. Attributes
|
||||
specified by a compute, fix, or variable are not initially stored
|
||||
until the first run following the fix definition begins. This is
|
||||
because calculating those attributes may require quantities that are
|
||||
not defined in between runs.</p>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">Actually, only atom attributes specified by keywords like <em>xu</em>
|
||||
or <em>vy</em> or <em>radius</em> are initially stored immediately at the point in
|
||||
your input script when the fix is defined. Attributes specified by a
|
||||
compute, fix, or variable are not initially stored until the first run
|
||||
following the fix definition begins. This is because calculating
|
||||
those attributes may require quantities that are not defined in
|
||||
between runs.</p>
|
||||
</div>
|
||||
<p>The list of possible attributes is the same as that used by the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command, which describes their meaning.</p>
|
||||
<p>If the <em>com</em> keyword is set to <em>yes</em> then the <em>xu</em>, <em>yu</em>, and <em>zu</em>
|
||||
|
|
|
|||
|
|
@ -74,13 +74,13 @@ inputs.
|
|||
If {N} is not zero, then the attributes will be updated every {N}
|
||||
steps.
|
||||
|
||||
IMPORTANT NOTE: Actually, only atom attributes specified by keywords
|
||||
like {xu} or {vy} or {radius} are initially stored immediately at the
|
||||
point in your input script when the fix is defined. Attributes
|
||||
specified by a compute, fix, or variable are not initially stored
|
||||
until the first run following the fix definition begins. This is
|
||||
because calculating those attributes may require quantities that are
|
||||
not defined in between runs.
|
||||
NOTE: Actually, only atom attributes specified by keywords like {xu}
|
||||
or {vy} or {radius} are initially stored immediately at the point in
|
||||
your input script when the fix is defined. Attributes specified by a
|
||||
compute, fix, or variable are not initially stored until the first run
|
||||
following the fix definition begins. This is because calculating
|
||||
those attributes may require quantities that are not defined in
|
||||
between runs.
|
||||
|
||||
The list of possible attributes is the same as that used by the "dump
|
||||
custom"_dump.html command, which describes their meaning.
|
||||
|
|
|
|||
|
|
@ -189,7 +189,7 @@ more instructions on how to use the accelerated styles effectively.</p>
|
|||
<hr class="docutils" />
|
||||
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
|
||||
<p>For atom type pairs I,J and I != J, coeffiecients must be specified.
|
||||
No default miture rules are used.</p>
|
||||
No default mixing rules are used.</p>
|
||||
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift
|
||||
option for the energy of the pair interaction.</p>
|
||||
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option is not relevant
|
||||
|
|
|
|||
|
|
@ -74,7 +74,7 @@ more instructions on how to use the accelerated styles effectively.
|
|||
[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
||||
|
||||
For atom type pairs I,J and I != J, coeffiecients must be specified.
|
||||
No default miture rules are used.
|
||||
No default mixing rules are used.
|
||||
|
||||
This pair style does not support the "pair_modify"_pair_modify.html shift
|
||||
option for the energy of the pair interaction.
|
||||
|
|
|
|||
|
|
@ -139,8 +139,9 @@
|
|||
<div class="section" id="examples">
|
||||
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
|
||||
<div class="highlight-python"><div class="highlight"><pre>pair_style line/lj 3.0
|
||||
pair_coeff * * 1.0 1.0
|
||||
pair_coeff 1 1 1.0 1.5 2.5
|
||||
pair_coeff * * 1.0 1.0 1.0 0.8 1.12
|
||||
pair_coeff 1 2 1.0 2.0 1.0 1.5 1.12 5.0
|
||||
pair_coeff 1 2 1.0 0.0 1.0 1.0 2.5
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
|
|
@ -154,44 +155,77 @@ N1*N2 Lennard-Jones interactions. Interactions between a line segment
|
|||
with N spherical particles and a point particle are treated as the
|
||||
pairwise sum of N Lennard-Jones interactions. See the <a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut</em></a> doc page for the definition of Lennard-Jones
|
||||
interactions.</p>
|
||||
<p>The cutoff distance for an interaction between 2 line segments, or
|
||||
between a line segment and a point particle, is calculated from the
|
||||
position of the line segment (its center), not between pairs of
|
||||
individual spheres comprising the line segment. Thus an interaction
|
||||
is either calculated in its entirety or not at all.</p>
|
||||
<p>The set of non-overlapping spherical particles that represent a line
|
||||
segment, for purposes of this pair style, are generated in the
|
||||
following manner. Their size is a function of the line segment length
|
||||
and the specified sigma for that particle type. If a line segment has
|
||||
a length L and is of type I, then the number of spheres N that
|
||||
represent the segment is calculated as N = L/sigma_II, rounded up to
|
||||
an integer value. Thus if L is not evenly divisibly by sigam_II, N is
|
||||
incremented to include one extra sphere. In this case, the spheres
|
||||
must be slightly smaller than sigma_II so as not to overlap, so a new
|
||||
sigma-prime is chosen as the sphere diameter, such that L/N =
|
||||
sigma-prime. Thus the line segment interacts with other segments or
|
||||
point particles as a collection of N spheres of diameter sigma-prime,
|
||||
evenly spaced along the line segment, so as to exactly cover its
|
||||
length.</p>
|
||||
<p>The LJ interaction between 2 spheres on different line segments of
|
||||
types I,J is computed with an arithmetic mixing of the sigma values of
|
||||
the 2 spheres and using the specified epsilon value for I,J atom
|
||||
types. Note that because the sigma values for line segment spheres is
|
||||
computed using only sigma_II values, specific to the line segment’s
|
||||
type, this means that any specified sigma_IJ values (for I != J) are
|
||||
effectively ignored.</p>
|
||||
<p>The set of non-overlapping spherical sub-particles that represent a
|
||||
line segment are generated in the following manner. Their size is a
|
||||
function of the line segment length and the specified sub-particle
|
||||
size for that particle type. If a line segment has a length L and is
|
||||
of type I, then the number of spheres N that represent the segment is
|
||||
calculated as N = L/sizeI, rounded up to an integer value. Thus if L
|
||||
is not evenly divisibly by sizeI, N is incremented to include one
|
||||
extra sphere. The centers of the spheres are spaced equally along the
|
||||
line segment. Imagine N+1 equally-space points, which include the 2
|
||||
end points of the segment. The sphere centers are halfway between
|
||||
each pair of points.</p>
|
||||
<p>The LJ interaction between 2 spheres on different line segments (or a
|
||||
sphere on a line segment and a point particles) is computed with
|
||||
sub-particle epsilon, sigma, and cutoff values that are set by the
|
||||
pair_coeff command, as described below. If the distance bewteen the 2
|
||||
spheres is greater than the sub-particle cutoff, there is no
|
||||
interaction. This means that some pairs of sub-particles on 2 line
|
||||
segments may interact, but others may not.</p>
|
||||
<p>For purposes of creating the neighbor list for pairs of interacting
|
||||
line segments or lines/point particles, a regular particle-particle
|
||||
cutoff is used, as defined by the <em>cutoff</em> setting above in the
|
||||
pair_style command or overridden with an optional argument in the
|
||||
pair_coeff command for a type pair as discussed below. The distance
|
||||
between the centers of 2 line segments, or the center of a line
|
||||
segment and a point particle, must be less than this distance (plus
|
||||
the neighbor skin; see the <a class="reference external" href="neighbor">neighbor</a> command), for the pair
|
||||
of particles to be included in the neighbor list.</p>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">This means that a too-short value for the <em>cutoff</em> setting can
|
||||
exclude a pair of particles from the neighbor list even if pairs of
|
||||
their sub-particle spheres would interact, based on the sub-particle
|
||||
cutoff specified in the pair_coeff command. E.g. sub-particles at the
|
||||
ends of the line segments that are close to each other. Which may not
|
||||
be what you want, since it means the ends of 2 line segments could
|
||||
pass through each other. It is up to you to specify a <em>cutoff</em>
|
||||
setting that is consistent with the length of the line segments you
|
||||
are using and the sub-particle cutoff settings.</p>
|
||||
</div>
|
||||
<p>For style <em>line/lj</em>, the following coefficients must be defined for
|
||||
each pair of atoms types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command
|
||||
each pair of atom types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command
|
||||
as in the examples above, or in the data file or restart files read by
|
||||
the <a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
|
||||
commands:</p>
|
||||
<ul class="simple">
|
||||
<li>sizeI (distance units)</li>
|
||||
<li>sizeJ (distance units)</li>
|
||||
<li>epsilon (energy units)</li>
|
||||
<li>sigma (distance units)</li>
|
||||
<li>subcutoff (distance units)</li>
|
||||
<li>cutoff (distance units)</li>
|
||||
</ul>
|
||||
<p>The last coefficient is optional. If not specified, the global cutoff
|
||||
is used.</p>
|
||||
<p>The <em>sizeI</em> and <em>sizeJ</em> coefficients are the sub-particle sizes for
|
||||
line particles of type I and type J. They are used to define the N
|
||||
sub-particles per segment as described above. These coefficients are
|
||||
actually stored on a per-type basis. Thus if there are multiple
|
||||
pair_coeff commmands that involve type I, as either the first or
|
||||
second atom type, you should use consistent values for sizeI or sizeJ
|
||||
in all of them. If you do not do this, the last value specified for
|
||||
sizeI will apply to all segments of type I. If typeI or typeJ refers
|
||||
to point particles, the corresponding sizeI or sizeJ is ignored; it
|
||||
can be set to 0.0.</p>
|
||||
<p>The <em>epsilon</em>, <em>sigma</em>, and <em>subcutoff</em> coefficients are used to
|
||||
compute an LJ interactions between a pair of sub-particles on 2 line
|
||||
segments (of type I and J), or between a sub particle/point particle
|
||||
pair. As discussed above, the <em>subcutoff</em> and <em>cutoff</em> params are
|
||||
different. The latter is only used for building the neighbor list
|
||||
when the distance between centers of two line segments or one segment
|
||||
and a point particle is calculated.</p>
|
||||
<p>The <em>cutoff</em> coefficient is optional. If not specified, the global
|
||||
cutoff is used.</p>
|
||||
<hr class="docutils" />
|
||||
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
|
|
@ -210,10 +244,8 @@ use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> com
|
|||
more instructions on how to use the accelerated styles effectively.</p>
|
||||
<hr class="docutils" />
|
||||
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
|
||||
<p>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
|
||||
and cutoff distance for all of this pair style can be mixed. The
|
||||
default mix value is <em>geometric</em>. See the “pair_modify” command for
|
||||
details.</p>
|
||||
<p>For atom type pairs I,J and I != J, coeffiecients must be specified.
|
||||
No default mixing rules are used.</p>
|
||||
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
|
||||
shift, table, and tail options.</p>
|
||||
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>.</p>
|
||||
|
|
|
|||
|
|
@ -18,8 +18,9 @@ cutoff = global cutoff for interactions (distance units)
|
|||
[Examples:]
|
||||
|
||||
pair_style line/lj 3.0
|
||||
pair_coeff * * 1.0 1.0
|
||||
pair_coeff 1 1 1.0 1.5 2.5 :pre
|
||||
pair_coeff * * 1.0 1.0 1.0 0.8 1.12
|
||||
pair_coeff 1 2 1.0 2.0 1.0 1.5 1.12 5.0
|
||||
pair_coeff 1 2 1.0 0.0 1.0 1.0 2.5 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
|
|
@ -33,47 +34,80 @@ pairwise sum of N Lennard-Jones interactions. See the "pair_style
|
|||
lj/cut"_pair_lj.html doc page for the definition of Lennard-Jones
|
||||
interactions.
|
||||
|
||||
The cutoff distance for an interaction between 2 line segments, or
|
||||
between a line segment and a point particle, is calculated from the
|
||||
position of the line segment (its center), not between pairs of
|
||||
individual spheres comprising the line segment. Thus an interaction
|
||||
is either calculated in its entirety or not at all.
|
||||
The set of non-overlapping spherical sub-particles that represent a
|
||||
line segment are generated in the following manner. Their size is a
|
||||
function of the line segment length and the specified sub-particle
|
||||
size for that particle type. If a line segment has a length L and is
|
||||
of type I, then the number of spheres N that represent the segment is
|
||||
calculated as N = L/sizeI, rounded up to an integer value. Thus if L
|
||||
is not evenly divisibly by sizeI, N is incremented to include one
|
||||
extra sphere. The centers of the spheres are spaced equally along the
|
||||
line segment. Imagine N+1 equally-space points, which include the 2
|
||||
end points of the segment. The sphere centers are halfway between
|
||||
each pair of points.
|
||||
|
||||
The set of non-overlapping spherical particles that represent a line
|
||||
segment, for purposes of this pair style, are generated in the
|
||||
following manner. Their size is a function of the line segment length
|
||||
and the specified sigma for that particle type. If a line segment has
|
||||
a length L and is of type I, then the number of spheres N that
|
||||
represent the segment is calculated as N = L/sigma_II, rounded up to
|
||||
an integer value. Thus if L is not evenly divisibly by sigam_II, N is
|
||||
incremented to include one extra sphere. In this case, the spheres
|
||||
must be slightly smaller than sigma_II so as not to overlap, so a new
|
||||
sigma-prime is chosen as the sphere diameter, such that L/N =
|
||||
sigma-prime. Thus the line segment interacts with other segments or
|
||||
point particles as a collection of N spheres of diameter sigma-prime,
|
||||
evenly spaced along the line segment, so as to exactly cover its
|
||||
length.
|
||||
The LJ interaction between 2 spheres on different line segments (or a
|
||||
sphere on a line segment and a point particles) is computed with
|
||||
sub-particle epsilon, sigma, and cutoff values that are set by the
|
||||
pair_coeff command, as described below. If the distance bewteen the 2
|
||||
spheres is greater than the sub-particle cutoff, there is no
|
||||
interaction. This means that some pairs of sub-particles on 2 line
|
||||
segments may interact, but others may not.
|
||||
|
||||
The LJ interaction between 2 spheres on different line segments of
|
||||
types I,J is computed with an arithmetic mixing of the sigma values of
|
||||
the 2 spheres and using the specified epsilon value for I,J atom
|
||||
types. Note that because the sigma values for line segment spheres is
|
||||
computed using only sigma_II values, specific to the line segment's
|
||||
type, this means that any specified sigma_IJ values (for I != J) are
|
||||
effectively ignored.
|
||||
For purposes of creating the neighbor list for pairs of interacting
|
||||
line segments or lines/point particles, a regular particle-particle
|
||||
cutoff is used, as defined by the {cutoff} setting above in the
|
||||
pair_style command or overridden with an optional argument in the
|
||||
pair_coeff command for a type pair as discussed below. The distance
|
||||
between the centers of 2 line segments, or the center of a line
|
||||
segment and a point particle, must be less than this distance (plus
|
||||
the neighbor skin; see the "neighbor"_neighbor command), for the pair
|
||||
of particles to be included in the neighbor list.
|
||||
|
||||
NOTE: This means that a too-short value for the {cutoff} setting can
|
||||
exclude a pair of particles from the neighbor list even if pairs of
|
||||
their sub-particle spheres would interact, based on the sub-particle
|
||||
cutoff specified in the pair_coeff command. E.g. sub-particles at the
|
||||
ends of the line segments that are close to each other. Which may not
|
||||
be what you want, since it means the ends of 2 line segments could
|
||||
pass through each other. It is up to you to specify a {cutoff}
|
||||
setting that is consistent with the length of the line segments you
|
||||
are using and the sub-particle cutoff settings.
|
||||
|
||||
For style {line/lj}, the following coefficients must be defined for
|
||||
each pair of atoms types via the "pair_coeff"_pair_coeff.html command
|
||||
each pair of atom types via the "pair_coeff"_pair_coeff.html command
|
||||
as in the examples above, or in the data file or restart files read by
|
||||
the "read_data"_read_data.html or "read_restart"_read_restart.html
|
||||
commands:
|
||||
|
||||
sizeI (distance units)
|
||||
sizeJ (distance units)
|
||||
epsilon (energy units)
|
||||
sigma (distance units)
|
||||
subcutoff (distance units)
|
||||
cutoff (distance units) :ul
|
||||
|
||||
The last coefficient is optional. If not specified, the global cutoff
|
||||
is used.
|
||||
The {sizeI} and {sizeJ} coefficients are the sub-particle sizes for
|
||||
line particles of type I and type J. They are used to define the N
|
||||
sub-particles per segment as described above. These coefficients are
|
||||
actually stored on a per-type basis. Thus if there are multiple
|
||||
pair_coeff commmands that involve type I, as either the first or
|
||||
second atom type, you should use consistent values for sizeI or sizeJ
|
||||
in all of them. If you do not do this, the last value specified for
|
||||
sizeI will apply to all segments of type I. If typeI or typeJ refers
|
||||
to point particles, the corresponding sizeI or sizeJ is ignored; it
|
||||
can be set to 0.0.
|
||||
|
||||
The {epsilon}, {sigma}, and {subcutoff} coefficients are used to
|
||||
compute an LJ interactions between a pair of sub-particles on 2 line
|
||||
segments (of type I and J), or between a sub particle/point particle
|
||||
pair. As discussed above, the {subcutoff} and {cutoff} params are
|
||||
different. The latter is only used for building the neighbor list
|
||||
when the distance between centers of two line segments or one segment
|
||||
and a point particle is calculated.
|
||||
|
||||
The {cutoff} coefficient is optional. If not specified, the global
|
||||
cutoff is used.
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -102,10 +136,8 @@ more instructions on how to use the accelerated styles effectively.
|
|||
|
||||
[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
||||
|
||||
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
|
||||
and cutoff distance for all of this pair style can be mixed. The
|
||||
default mix value is {geometric}. See the "pair_modify" command for
|
||||
details.
|
||||
For atom type pairs I,J and I != J, coeffiecients must be specified.
|
||||
No default mixing rules are used.
|
||||
|
||||
This pair style does not support the "pair_modify"_pair_modify.html
|
||||
shift, table, and tail options.
|
||||
|
|
|
|||
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Reference in New Issue