git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@665 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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@ -24,7 +24,10 @@ certain kinds of LAMMPS simulations.
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4.8 <A HREF = "#4_8">TIP4P water model</A><BR>
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4.9 <A HREF = "#4_9">SPC water model</A><BR>
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4.10 <A HREF = "#4_10">Coupling LAMMPS to other codes</A><BR>
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4.11 <A HREF = "#4_11">Visualizing LAMMPS snapshots</A> <BR>
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4.11 <A HREF = "#4_11">Visualizing LAMMPS snapshots</A><BR>
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4.12 <A HREF = "#4_12">Non-orthogonal simulation boxes</A><BR>
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4.13 <A HREF = "#4_13">NEMD simulations</A><BR>
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4.14 <A HREF = "#4_14">Aspherical particles</A> <BR>
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<P>The example input scripts included in the LAMMPS distribution and
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highlighted in <A HREF = "Section_example.html">this section</A> also show how to
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@ -647,6 +650,145 @@ See the <A HREF = "dump.html">dump</A> command for more information on XTC files
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<HR>
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<A NAME = "4_12"></A><H4>4.12 Non-orthogonal simulation boxes
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</H4>
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<P>By default, LAMMPS uses an orthogonal simulation box to encompass the
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particles. The <A HREF = "boundary.html">boundary</A> command sets the boundary
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conditions of the box (periodic, non-periodic, etc). If the box size
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is xprd by yprd by zprd then the 3 mutually orthogonal edge vectors of
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an orthogonal simulation box are a = (xprd,0,0), b = (0,yprd,0), and c
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= (0,0,zprd).
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</P>
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<P>LAMMPS also allows non-orthogonal simulation boxes (triclinic
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symmetry) to be defined with 3 additional "tilt" parameters which
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change the edge vectors of the simulation box to be a = (xprd,0,0), b
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= (xy,yprd,0), and c = (xz,yz,zprd). The xy, xz, and yz parameters
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can be positive or negative. The simulation box must be periodic in
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both dimensions associated with a tilt factor. For example, if xz !=
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0.0, then the x and z dimensions must be periodic.
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</P>
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<P>To avoid extremely tilted boxes (which would be computationally
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inefficient), no tilt factor can skew the box more than half the
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distance of the parallel box length, which is the 1st dimension in the
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tilt factor (x for xz). For example, if xlo = 2 and xhi = 12, then
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the x box length is 10 and the xy tilt factor must be between -5 and
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5. Similarly, both xz and yz must be between -(xhi-xlo)/2 and
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+(yhi-ylo)/2. Note that this is not a limitation, since if the
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maximum tilt factor is 5 (as in this example), then configurations
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with tilt = ..., -15, -5, 5, 15, 25, ... are all equivalent.
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</P>
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<P>You tell LAMMPS to use a non-orthogonal box when the simulation box is
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defined. This happens in one of 3 ways. If the
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<A HREF = "create_box.html">create_box</A> command is used with a region of style
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<I>prism</I>, then a non-orthogonal domain is setup. See the
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<A HREF = "region.html">region</A> command for details. If the
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<A HREF = "read_data.html">read_data</A> command is used to define the simulation
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box, and the header of the data file contains a line with the "xy xz
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yz" keyword, then a non-orthogonal domain is setup. See the
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<A HREF = "read_data.html">read_data</A> command for details. Finally, if the
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<A HREF = "read_restart.html">read_restart</A> command reads a restart file which
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was written from a simulation using a triclinic box, then a
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non-orthogonal box will be enabled for the restarted simulation.
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</P>
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<P>Note that you can define a non-orthogonal box with all 3 tilt factors
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= 0.0, so that it is initially orthogonal. This is necessary if the
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box will ever become non-orthogonal.
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</P>
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<P>One use of non-orthogonal boxes is to model solid-state crystals with
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triclinic symmetry. The <A HREF = "lattice.html">lattice</A> command can be used
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with non-orthogonal basis vectors to define a lattice that will tile a
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non-orthogonal simulation box via the <A HREF = "create_atoms.html">create_atoms</A>
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command. Note that while the box edge vectors a,b,c cannot be
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arbitrary vectors (e.g. a must be aligned with the x axis), it is
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possible to rotate any crystal's basis vectors so that they meet these
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restrictions.
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</P>
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<P>A second use of non-orthogonal boxes is to shear a bulk solid to study
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the response of the material. The <A HREF = "fix_deform.html">fix deform</A>
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command can be used for this purpose. It allows dynamic control of
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the xy, xz, and yz tilt factors as a simulation runs.
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</P>
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<P>Another use of non-orthogonal boxes is to perform non-equilibrium MD
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(NEMD) simulations, as discussed in the next section.
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</P>
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<HR>
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<A NAME = "4_13"></A><H4>4.13 NEMD simulations
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</H4>
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<P>Non-equilibrium molecular dynamics or NEMD simulations are typically
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used to measure a fluid's rheological properties such as viscosity.
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In LAMMPS, such simulations can be performed by first setting up a
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non-orthogonal simulation box (see the preceeding Howto section).
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</P>
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<P>A shear strain can be applied to the simualation box at a desired
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strain rate by using the <A HREF = "fix_deform.html">fix deform</A> command. The
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<A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A> command can be used to thermostat
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the sheared fluid and integrate the SLLOD equations of motion for the
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system. Fix nvt/sllod uses <A HREF = "compute_temp_deform.html">compute
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temp/deform</A> to compute a thermal temperature
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by subtracting out the streaming velocity of the shearing atoms. The
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velocity profile or other properties of the fluid can be monitored via
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the <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command.
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</P>
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<P>As discussed in the previous section on non-orthogonal simulation
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boxes, the amount of tilt or skew that can be applied is limited by
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LAMMPS for computation efficiency to be 1/2 of the paralell box
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length. However, <A HREF = "fix_deform.html">fix deform</A> can be used to
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continuously strain a box by an arbitrary amount. As discussed in the
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<A HREF = "fix_deform.html">fix deform</A> command, when the tilt reaches a limit,
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the box is re-shaped to the opposite limit which is an equivalent
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tiling of the periodic plane. The strain rate can then continue to
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change as before. In a long NEMD simulation these box re-shaping may
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occur any number of times.
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</P>
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<P>In a NEMD simulation, the "remap" option of <A HREF = "fix_deform.html">fix
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deform</A> should be set to "remap v", since that is what
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<A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A> assumes to generate a velocity
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profile consistent with the applied shear strain rate.
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</P>
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<HR>
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<A NAME = "4_14"></A><H4>4.14 Aspherical particles
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</H4>
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<P>LAMMPS supports ellipsoidal particles via the <A HREF = "atom_style.html">atom_style
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ellipsoid</A> and <A HREF = "shape.html">shape</A> commands. The
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latter defines the 3 axes (diamaters) of a general ellipsoid. The
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<A HREF = "pair_gayberne.html">pair_style gayberne</A> command can be used to define
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a Gay-Berne (GB) potential for how such particles interact with each
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other and with spherical particles. The GB potential is like a
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Lennard-Jones (LJ) potential generalized for ellipsoids interacting in
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an orientiation-dependent manner.
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</P>
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<P>The orientation of ellipsoidal particles is stored as a quaternion.
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See the <A HREF = "set.html">set</A> command for a brief explanation of quaternions
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and how the orientation of such particles can be initialized. The
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data file read by the <A HREF = "read_data.html">read_data</A> command also contains
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quaternions for each atom in the Atoms section if <A HREF = "atom_style.html">atom_style
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ellipsoid</A> is being used. The <A HREF = "compute_temp_asphere.html">compute
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temp/asphere</A> command can be used to
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calculate the temperature of a group of ellipsoidal particles, taking
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account of rotational degrees of freedom. The motion of the particles
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can be integrated via the <A HREF = "fix_nve_asphere.html">fix nve/asphere</A>, <A HREF = "fix_nvt_asphere.html">fix
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nvt/asphere</A>, or <A HREF = "fix_npt_asphere.html">fix
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npt/asphere</A> commands. All of these commands are
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part of the ASPHERE package in LAMMPS.
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</P>
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<P>Computationally, the cost for two ellipsoidal particles to interact is
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30x or more expensive than for 2 LJ particles. Thus if you are
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modeling a system with many spherical particles (e.g. as the solvent),
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then you should insure sphere-sphere interactions are computed with
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the a cheaper potential than GB. This can be done by setting the
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particle's 3 shape parameters to all be equal (a sphere).
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Additionally, the corresponding GB potential coefficients can be set
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so the GB potential will treat the pair of particles as LJ spheres.
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Details are given in the doc page for the <A HREF = "pair_gayberne.html">pair_style
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gayberne</A>. Alternatively, the <A HREF = "pair_hybrid.html">pair_style
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hybrid</A> potential can be used, with the sphere-sphere
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interactions computed by another pair potential, such as <A HREF = "pair_lj.html">pair_style
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lj/cut</A>.
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</P>
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<HR>
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<A NAME = "Cornell"></A>
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