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<CENTER><A HREF = "Section_commands.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_example.html">Next Section</A>
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</CENTER>
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<HR>
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<H3>4. How-to discussions
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</H3>
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<P>The following sections describe what commands can be used to perform
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certain kinds of LAMMPS simulations.
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</P>
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4.1 <A HREF = "#4_1">Restarting a simulation</A><BR>
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4.2 <A HREF = "#4_2">2d simulations</A><BR>
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4.3 <A HREF = "#4_3">CHARMM and AMBER force fields</A><BR>
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4.4 <A HREF = "#4_4">Running multiple simulations from one input script</A><BR>
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4.5 <A HREF = "#4_5">Multi-replica simulations</A><BR>
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4.6 <A HREF = "#4_6">Granular models</A><BR>
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4.7 <A HREF = "#4_7">TIP3P water model</A><BR>
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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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4.12 <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">Extended spherical and aspherical particles</A><BR>
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4.15 <A HREF = "#4_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A><BR>
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4.16 <A HREF = "#4_16">Thermostatting, barostatting and computing temperature</A><BR>
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4.17 <A HREF = "#4_17">Walls</A><BR>
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4.18 <A HREF = "#4_18">Elastic constants</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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setup and run various kinds of problems.
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</P>
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<HR>
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<A NAME = "4_1"></A><H4>4.1 Restarting a simulation
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</H4>
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<P>There are 3 ways to continue a long LAMMPS simulation. Multiple
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<A HREF = "run.html">run</A> commands can be used in the same input script. Each
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run will continue from where the previous run left off. Or binary
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restart files can be saved to disk using the <A HREF = "restart.html">restart</A>
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command. At a later time, these binary files can be read via a
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<A HREF = "read_restart.html">read_restart</A> command in a new script. Or they can
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be converted to text data files and read by a
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<A HREF = "read_data.html">read_data</A> command in a new script. <A HREF = "Section_tools.html">This
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section</A> discusses the <I>restart2data</I> tool that is
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used to perform the conversion.
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</P>
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<P>Here we give examples of 2 scripts that read either a binary restart
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file or a converted data file and then issue a new run command to
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continue where the previous run left off. They illustrate what
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settings must be made in the new script. Details are discussed in the
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documentation for the <A HREF = "read_restart.html">read_restart</A> and
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<A HREF = "read_data.html">read_data</A> commands.
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</P>
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<P>Look at the <I>in.chain</I> input script provided in the <I>bench</I> directory
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of the LAMMPS distribution to see the original script that these 2
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scripts are based on. If that script had the line
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</P>
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<PRE>restart 50 tmp.restart
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</PRE>
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<P>added to it, it would produce 2 binary restart files (tmp.restart.50
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and tmp.restart.100) as it ran.
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</P>
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<P>This script could be used to read the 1st restart file and re-run the
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last 50 timesteps:
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</P>
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<PRE>read_restart tmp.restart.50
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</PRE>
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<PRE>neighbor 0.4 bin
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neigh_modify every 1 delay 1
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</PRE>
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<PRE>fix 1 all nve
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fix 2 all langevin 1.0 1.0 10.0 904297
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</PRE>
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<PRE>timestep 0.012
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</PRE>
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<PRE>run 50
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</PRE>
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<P>Note that the following commands do not need to be repeated because
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their settings are included in the restart file: <I>units, atom_style,
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special_bonds, pair_style, bond_style</I>. However these commands do
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need to be used, since their settings are not in the restart file:
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<I>neighbor, fix, timestep</I>.
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</P>
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<P>If you actually use this script to perform a restarted run, you will
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notice that the thermodynamic data match at step 50 (if you also put a
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"thermo 50" command in the original script), but do not match at step
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100. This is because the <A HREF = "fix_langevin.html">fix langevin</A> command
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uses random numbers in a way that does not allow for perfect restarts.
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</P>
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<P>As an alternate approach, the restart file could be converted to a data
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file using this tool:
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</P>
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<PRE>restart2data tmp.restart.50 tmp.restart.data
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</PRE>
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<P>Then, this script could be used to re-run the last 50 steps:
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</P>
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<PRE>units lj
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atom_style bond
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pair_style lj/cut 1.12
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pair_modify shift yes
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bond_style fene
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special_bonds 0.0 1.0 1.0
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</PRE>
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<PRE>read_data tmp.restart.data
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</PRE>
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<PRE>neighbor 0.4 bin
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neigh_modify every 1 delay 1
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</PRE>
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<PRE>fix 1 all nve
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fix 2 all langevin 1.0 1.0 10.0 904297
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</PRE>
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<PRE>timestep 0.012
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</PRE>
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<PRE>reset_timestep 50
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run 50
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</PRE>
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<P>Note that nearly all the settings specified in the original <I>in.chain</I>
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script must be repeated, except the <I>pair_coeff</I> and <I>bond_coeff</I>
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commands since the new data file lists the force field coefficients.
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Also, the <A HREF = "reset_timestep.html">reset_timestep</A> command is used to tell
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LAMMPS the current timestep. This value is stored in restart files,
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but not in data files.
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</P>
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<HR>
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<A NAME = "4_2"></A><H4>4.2 2d simulations
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</H4>
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<P>Use the <A HREF = "dimension.html">dimension</A> command to specify a 2d simulation.
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</P>
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<P>Make the simulation box periodic in z via the <A HREF = "boundary.html">boundary</A>
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command. This is the default.
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</P>
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<P>If using the <A HREF = "create_box.html">create box</A> command to define a
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simulation box, set the z dimensions narrow, but finite, so that the
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create_atoms command will tile the 3d simulation box with a single z
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plane of atoms - e.g.
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</P>
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<PRE><A HREF = "create_box.html">create box</A> 1 -10 10 -10 10 -0.25 0.25
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</PRE>
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<P>If using the <A HREF = "read_data.html">read data</A> command to read in a file of
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atom coordinates, set the "zlo zhi" values to be finite but narrow,
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similar to the create_box command settings just described. For each
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atom in the file, assign a z coordinate so it falls inside the
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z-boundaries of the box - e.g. 0.0.
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</P>
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<P>Use the <A HREF = "fix_enforce2d.html">fix enforce2d</A> command as the last
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defined fix to insure that the z-components of velocities and forces
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are zeroed out every timestep. The reason to make it the last fix is
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so that any forces induced by other fixes will be zeroed out.
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</P>
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<P>Many of the example input scripts included in the LAMMPS distribution
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are for 2d models.
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</P>
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<P>IMPORTANT NOTE: Some models in LAMMPS treat particles as extended
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spheres, as opposed to point particles. In 2d, the particles will
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still be spheres, not disks, meaning their moment of inertia will be
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the same as in 3d.
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</P>
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<HR>
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<A NAME = "4_3"></A><H4>4.3 CHARMM and AMBER force fields
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</H4>
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<P>There are many different ways to compute forces in the <A HREF = "http://www.scripps.edu/brooks">CHARMM</A>
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and <A HREF = "http://amber.scripps.edu">AMBER</A> molecular dynamics codes, only some of which are
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available as options in LAMMPS. A force field has 2 parts: the
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formulas that define it and the coefficients used for a particular
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system. Here we only discuss formulas implemented in LAMMPS. Setting
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coefficients is done in the input data file via the
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<A HREF = "read_data.html">read_data</A> command or in the input script with
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commands like <A HREF = "pair_coeff.html">pair_coeff</A> or
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<A HREF = "bond_coeff.html">bond_coeff</A>. See <A HREF = "Section_tools.html">this section</A> for
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additional tools that can use CHARMM or AMBER to assign force field
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coefficients and convert their output into LAMMPS input.
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</P>
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<P>See <A HREF = "#MacKerell">(MacKerell)</A> for a description of the CHARMM force
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field. See <A HREF = "#Cornell">(Cornell)</A> for a description of the AMBER force
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field.
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</P>
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<P>These style choices compute force field formulas that are consistent
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with common options in CHARMM or AMBER. See each command's
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documentation for the formula it computes.
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</P>
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<UL><LI><A HREF = "bond_style.html">bond_style</A> harmonic
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<LI><A HREF = "angle_style.html">angle_style</A> charmm
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<LI><A HREF = "dihedral_style.html">dihedral_style</A> charmm
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<LI><A HREF = "pair_style.html">pair_style</A> lj/charmm/coul/charmm
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<LI><A HREF = "pair_style.html">pair_style</A> lj/charmm/coul/charmm/implicit
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<LI><A HREF = "pair_style.html">pair_style</A> lj/charmm/coul/long
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</UL>
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<UL><LI><A HREF = "special_bonds.html">special_bonds</A> charmm
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<LI><A HREF = "special_bonds.html">special_bonds</A> amber
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</UL>
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<HR>
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<A NAME = "4_4"></A><H4>4.4 Running multiple simulations from one input script
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</H4>
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<P>This can be done in several ways. See the documentation for
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individual commands for more details on how these examples work.
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</P>
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<P>If "multiple simulations" means continue a previous simulation for
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more timesteps, then you simply use the <A HREF = "run.html">run</A> command
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multiple times. For example, this script
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</P>
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<PRE>units lj
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atom_style atomic
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read_data data.lj
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run 10000
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run 10000
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run 10000
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run 10000
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run 10000
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</PRE>
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<P>would run 5 successive simulations of the same system for a total of
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50,000 timesteps.
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</P>
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<P>If you wish to run totally different simulations, one after the other,
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the <A HREF = "clear.html">clear</A> command can be used in between them to
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re-initialize LAMMPS. For example, this script
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</P>
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<PRE>units lj
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atom_style atomic
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read_data data.lj
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run 10000
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clear
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units lj
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atom_style atomic
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read_data data.lj.new
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run 10000
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</PRE>
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<P>would run 2 independent simulations, one after the other.
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</P>
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<P>For large numbers of independent simulations, you can use
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<A HREF = "variable.html">variables</A> and the <A HREF = "next.html">next</A> and
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<A HREF = "jump.html">jump</A> commands to loop over the same input script
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multiple times with different settings. For example, this
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script, named in.polymer
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</P>
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<PRE>variable d index run1 run2 run3 run4 run5 run6 run7 run8
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shell cd $d
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read_data data.polymer
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run 10000
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shell cd ..
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clear
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next d
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jump in.polymer
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</PRE>
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<P>would run 8 simulations in different directories, using a data.polymer
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file in each directory. The same concept could be used to run the
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same system at 8 different temperatures, using a temperature variable
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and storing the output in different log and dump files, for example
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</P>
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<PRE>variable a loop 8
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variable t index 0.8 0.85 0.9 0.95 1.0 1.05 1.1 1.15
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log log.$a
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read data.polymer
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velocity all create $t 352839
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fix 1 all nvt $t $t 100.0
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dump 1 all atom 1000 dump.$a
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run 100000
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next t
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next a
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jump in.polymer
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</PRE>
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<P>All of the above examples work whether you are running on 1 or
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multiple processors, but assumed you are running LAMMPS on a single
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partition of processors. LAMMPS can be run on multiple partitions via
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the "-partition" command-line switch as described in <A HREF = "Section_start.html#2_6">this
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section</A> of the manual.
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</P>
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<P>In the last 2 examples, if LAMMPS were run on 3 partitions, the same
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scripts could be used if the "index" and "loop" variables were
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replaced with <I>universe</I>-style variables, as described in the
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<A HREF = "variable.html">variable</A> command. Also, the "next t" and "next a"
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commands would need to be replaced with a single "next a t" command.
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With these modifications, the 8 simulations of each script would run
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on the 3 partitions one after the other until all were finished.
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Initially, 3 simulations would be started simultaneously, one on each
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partition. When one finished, that partition would then start
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the 4th simulation, and so forth, until all 8 were completed.
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</P>
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<HR>
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<A NAME = "4_5"></A><H4>4.5 Multi-replica simulations
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</H4>
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<P>Several commands in LAMMPS run mutli-replica simulations, meaning
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that multiple instances (replicas) of your simulation are run
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simultaneously, with small amounts of data exchanged between replicas
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periodically.
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</P>
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<P>These are the relevant commands:
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</P>
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<UL><LI><A HREF = "neb.html">neb</A> for nudged elastic band calculations
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<LI><A HREF = "prd.html">prd</A> for parallel replica dynamics
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<LI><A HREF = "temper.html">temper</A> for parallel tempering
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</UL>
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<P>NEB is a method for finding transition states and barrier energies.
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PRD is a method for performing accelerated dynamics to find and
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perform infrequent events. Parallel tempering or replica exchange
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runs different replicas at a series of temperature to facilitate
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rare-event sampling.
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</P>
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<P>In all these cases, you must run with one or more processors per
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replica. The processors assigned to each replica are determined at
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run-time by using the <A HREF = "Section_start.html#2_6">-partition command-line
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switch</A> to launch LAMMPS on multiple
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partitions, which in this context are the same as replicas. E.g.
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these commands:
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</P>
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<PRE>mpirun -np 16 lmp_linux -partition 8x2 -in in.temper
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mpirun -np 8 lmp_linux -partition 8x1 -in in.neb
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</PRE>
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<P>would each run 8 replicas, on either 16 or 8 processors. Note the use
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of the <A HREF = "Section_start.html#2_6">-in command-line switch</A> to specify the
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input script which is required when running in multi-replica mode.
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</P>
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<P>Also note that with MPI installed on a machine (e.g. your desktop),
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you can run on more (virtual) processors than you have physical
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processors. Thus the above commands could be run on a
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single-processor (or few-processor) desktop so that you can run
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a multi-replica simulation on more replicas than you have
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physical processors.
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</P>
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<HR>
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<A NAME = "4_6"></A><H4>4.6 Granular models
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</H4>
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<P>Granular system are composed of spherical particles with a diameter,
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as opposed to point particles. This means they have an angular
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velocity and torque can be imparted to them to cause them to rotate.
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</P>
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<P>To run a simulation of a granular model, you will want to use
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the following commands:
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</P>
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<UL><LI><A HREF = "atom_style.html">atom_style</A> granular
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<LI><A HREF = "fix_nve_sphere.html">fix nve/sphere</A>
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<LI><A HREF = "fix_gravity.html">fix gravity</A>
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</UL>
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<P>This compute
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</P>
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<UL><LI><A HREF = "compute_erotate_sphere.html">compute erotate/sphere</A>
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</UL>
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<P>calculates rotational kinetic energy which can be <A HREF = "Section_howto.html#4_15">output with
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thermodynamic info</A>.
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</P>
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<P>Use one of these 3 pair potentials, which compute forces and torques
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between interacting pairs of particles:
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</P>
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<UL><LI><A HREF = "pair_style.html">pair_style</A> gran/history
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<LI><A HREF = "pair_style.html">pair_style</A> gran/no_history
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<LI><A HREF = "pair_style.html">pair_style</A> gran/hertzian
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</UL>
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<P>These commands implement fix options specific to granular systems:
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</P>
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<UL><LI><A HREF = "fix_freeze.html">fix freeze</A>
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<LI><A HREF = "fix_pour.html">fix pour</A>
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<LI><A HREF = "fix_viscous.html">fix viscous</A>
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<LI><A HREF = "fix_wall_gran.html">fix wall/gran</A>
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</UL>
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<P>The fix style <I>freeze</I> zeroes both the force and torque of frozen
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atoms, and should be used for granular system instead of the fix style
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<I>setforce</I>.
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</P>
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<P>For computational efficiency, you can eliminate needless pairwise
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computations between frozen atoms by using this command:
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</P>
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<UL><LI><A HREF = "neigh_modify.html">neigh_modify</A> exclude
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</UL>
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<HR>
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<A NAME = "4_7"></A><H4>4.7 TIP3P water model
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</H4>
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<P>The TIP3P water model as implemented in CHARMM
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<A HREF = "#MacKerell">(MacKerell)</A> specifies a 3-site rigid water molecule with
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charges and Lennard-Jones parameters assigned to each of the 3 atoms.
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In LAMMPS the <A HREF = "fix_shake.html">fix shake</A> command can be used to hold
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the two O-H bonds and the H-O-H angle rigid. A bond style of
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<I>harmonic</I> and an angle style of <I>harmonic</I> or <I>charmm</I> should also be
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used.
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</P>
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<P>These are the additional parameters (in real units) to set for O and H
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atoms and the water molecule to run a rigid TIP3P-CHARMM model with a
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cutoff. The K values can be used if a flexible TIP3P model (without
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fix shake) is desired. If the LJ epsilon and sigma for HH and OH are
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set to 0.0, it corresponds to the original 1983 TIP3P model
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<A HREF = "#Jorgensen">(Jorgensen)</A>.
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</P>
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<P>O mass = 15.9994<BR>
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H mass = 1.008 <BR>
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</P>
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<P>O charge = -0.834<BR>
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H charge = 0.417 <BR>
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</P>
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<P>LJ epsilon of OO = 0.1521<BR>
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LJ sigma of OO = 3.1507<BR>
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|
LJ epsilon of HH = 0.0460<BR>
|
|
LJ sigma of HH = 0.4000<BR>
|
|
LJ epsilon of OH = 0.0836<BR>
|
|
LJ sigma of OH = 1.7753 <BR>
|
|
</P>
|
|
<P>K of OH bond = 450<BR>
|
|
r0 of OH bond = 0.9572 <BR>
|
|
</P>
|
|
<P>K of HOH angle = 55<BR>
|
|
theta of HOH angle = 104.52 <BR>
|
|
</P>
|
|
<P>These are the parameters to use for TIP3P with a long-range Coulombic
|
|
solver (Ewald or PPPM in LAMMPS), see <A HREF = "#Price">(Price)</A> for details:
|
|
</P>
|
|
<P>O mass = 15.9994<BR>
|
|
H mass = 1.008 <BR>
|
|
</P>
|
|
<P>O charge = -0.830<BR>
|
|
H charge = 0.415 <BR>
|
|
</P>
|
|
<P>LJ epsilon of OO = 0.102<BR>
|
|
LJ sigma of OO = 3.188<BR>
|
|
LJ epsilon, sigma of OH, HH = 0.0 <BR>
|
|
</P>
|
|
<P>K of OH bond = 450<BR>
|
|
r0 of OH bond = 0.9572 <BR>
|
|
</P>
|
|
<P>K of HOH angle = 55<BR>
|
|
theta of HOH angle = 104.52 <BR>
|
|
</P>
|
|
<P>Wikipedia also has a nice article on <A HREF = "http://en.wikipedia.org/wiki/Water_model">water
|
|
models</A>.
|
|
</P>
|
|
<HR>
|
|
|
|
<A NAME = "4_8"></A><H4>4.8 TIP4P water model
|
|
</H4>
|
|
<P>The four-point TIP4P rigid water model extends the traditional
|
|
three-point TIP3P model by adding an additional site, usually
|
|
massless, where the charge associated with the oxygen atom is placed.
|
|
This site M is located at a fixed distance away from the oxygen along
|
|
the bisector of the HOH bond angle. A bond style of <I>harmonic</I> and an
|
|
angle style of <I>harmonic</I> or <I>charmm</I> should also be used.
|
|
</P>
|
|
<P>Currently, only a four-point model for long-range Coulombics is
|
|
implemented via the LAMMPS <A HREF = "pair_lj.html">pair style
|
|
lj/cut/coul/long/tip4p</A>. A cutoff version may be added
|
|
the future. For both models, the bond lengths and bond angles should
|
|
be held fixed using the <A HREF = "fix_shake.html">fix shake</A> command.
|
|
</P>
|
|
<P>These are the additional parameters (in real units) to set for O and H
|
|
atoms and the water molecule to run a rigid TIP4P model with a cutoff
|
|
<A HREF = "#Jorgensen">(Jorgensen)</A>. Note that the OM distance is specified in
|
|
the <A HREF = "pair_style.html">pair_style</A> command, not as part of the pair
|
|
coefficients.
|
|
</P>
|
|
<P>O mass = 15.9994<BR>
|
|
H mass = 1.008 <BR>
|
|
</P>
|
|
<P>O charge = -1.040<BR>
|
|
H charge = 0.520 <BR>
|
|
</P>
|
|
<P>r0 of OH bond = 0.9572<BR>
|
|
theta of HOH angle = 104.52 <BR>
|
|
</P>
|
|
<P>OM distance = 0.15 <BR>
|
|
</P>
|
|
<P>LJ epsilon of O-O = 0.1550<BR>
|
|
LJ sigma of O-O = 3.1536<BR>
|
|
LJ epsilon, sigma of OH, HH = 0.0 <BR>
|
|
</P>
|
|
<P>These are the parameters to use for TIP4P with a long-range Coulombic
|
|
solver (Ewald or PPPM in LAMMPS):
|
|
</P>
|
|
<P>O mass = 15.9994<BR>
|
|
H mass = 1.008 <BR>
|
|
</P>
|
|
<P>O charge = -1.0484<BR>
|
|
H charge = 0.5242 <BR>
|
|
</P>
|
|
<P>r0 of OH bond = 0.9572<BR>
|
|
theta of HOH angle = 104.52 <BR>
|
|
</P>
|
|
<P>OM distance = 0.1250 <BR>
|
|
</P>
|
|
<P>LJ epsilon of O-O = 0.16275<BR>
|
|
LJ sigma of O-O = 3.16435<BR>
|
|
LJ epsilon, sigma of OH, HH = 0.0 <BR>
|
|
</P>
|
|
<P>Wikipedia also has a nice article on <A HREF = "http://en.wikipedia.org/wiki/Water_model">water
|
|
models</A>.
|
|
</P>
|
|
<HR>
|
|
|
|
<A NAME = "4_9"></A><H4>4.9 SPC water model
|
|
</H4>
|
|
<P>The SPC water model specifies a 3-site rigid water molecule with
|
|
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
|
|
In LAMMPS the <A HREF = "fix_shake.html">fix shake</A> command can be used to hold
|
|
the two O-H bonds and the H-O-H angle rigid. A bond style of
|
|
<I>harmonic</I> and an angle style of <I>harmonic</I> or <I>charmm</I> should also be
|
|
used.
|
|
</P>
|
|
<P>These are the additional parameters (in real units) to set for O and H
|
|
atoms and the water molecule to run a rigid SPC model.
|
|
</P>
|
|
<P>O mass = 15.9994<BR>
|
|
H mass = 1.008 <BR>
|
|
</P>
|
|
<P>O charge = -0.820<BR>
|
|
H charge = 0.410 <BR>
|
|
</P>
|
|
<P>LJ epsilon of OO = 0.1553<BR>
|
|
LJ sigma of OO = 3.166<BR>
|
|
LJ epsilon, sigma of OH, HH = 0.0 <BR>
|
|
</P>
|
|
<P>r0 of OH bond = 1.0<BR>
|
|
theta of HOH angle = 109.47 <BR>
|
|
</P>
|
|
<P>Note that as originally proposed, the SPC model was run with a 9
|
|
Angstrom cutoff for both LJ and Coulommbic terms. It can also be used
|
|
with long-range Coulombics (Ewald or PPPM in LAMMPS), without changing
|
|
any of the parameters above, though it becomes a different model in
|
|
that mode of usage.
|
|
</P>
|
|
<P>The SPC/E (extended) water model is the same, except
|
|
the partial charge assignemnts change:
|
|
</P>
|
|
<P>O charge = -0.8476<BR>
|
|
H charge = 0.4238 <BR>
|
|
</P>
|
|
<P>See the <A HREF = "#Berendsen">(Berendsen)</A> reference for more details on both
|
|
the SPC and SPC/E models.
|
|
</P>
|
|
<P>Wikipedia also has a nice article on <A HREF = "http://en.wikipedia.org/wiki/Water_model">water
|
|
models</A>.
|
|
</P>
|
|
<HR>
|
|
|
|
<A NAME = "4_10"></A><H4>4.10 Coupling LAMMPS to other codes
|
|
</H4>
|
|
<P>LAMMPS is designed to allow it to be coupled to other codes. For
|
|
example, a quantum mechanics code might compute forces on a subset of
|
|
atoms and pass those forces to LAMMPS. Or a continuum finite element
|
|
(FE) simulation might use atom positions as boundary conditions on FE
|
|
nodal points, compute a FE solution, and return interpolated forces on
|
|
MD atoms.
|
|
</P>
|
|
<P>LAMMPS can be coupled to other codes in at least 3 ways. Each has
|
|
advantages and disadvantages, which you'll have to think about in the
|
|
context of your application.
|
|
</P>
|
|
<P>(1) Define a new <A HREF = "fix.html">fix</A> command that calls the other code. In
|
|
this scenario, LAMMPS is the driver code. During its timestepping,
|
|
the fix is invoked, and can make library calls to the other code,
|
|
which has been linked to LAMMPS as a library. This is the way the
|
|
<A HREF = "http://www.rpi.edu/~anderk5/lab">POEMS</A> package that performs constrained rigid-body motion on
|
|
groups of atoms is hooked to LAMMPS. See the
|
|
<A HREF = "fix_poems.html">fix_poems</A> command for more details. See <A HREF = "Section_modify.html">this
|
|
section</A> of the documentation for info on how to add
|
|
a new fix to LAMMPS.
|
|
</P>
|
|
|
|
|
|
<P>(2) Define a new LAMMPS command that calls the other code. This is
|
|
conceptually similar to method (1), but in this case LAMMPS and the
|
|
other code are on a more equal footing. Note that now the other code
|
|
is not called during the timestepping of a LAMMPS run, but between
|
|
runs. The LAMMPS input script can be used to alternate LAMMPS runs
|
|
with calls to the other code, invoked via the new command. The
|
|
<A HREF = "run.html">run</A> command facilitates this with its <I>every</I> option, which
|
|
makes it easy to run a few steps, invoke the command, run a few steps,
|
|
invoke the command, etc.
|
|
</P>
|
|
<P>In this scenario, the other code can be called as a library, as in
|
|
(1), or it could be a stand-alone code, invoked by a system() call
|
|
made by the command (assuming your parallel machine allows one or more
|
|
processors to start up another program). In the latter case the
|
|
stand-alone code could communicate with LAMMPS thru files that the
|
|
command writes and reads.
|
|
</P>
|
|
<P>See <A HREF = "Section_modify.html">this section</A> of the documentation for how to
|
|
add a new command to LAMMPS.
|
|
</P>
|
|
<P>(3) Use LAMMPS as a library called by another code. In this case the
|
|
other code is the driver and calls LAMMPS as needed. Or a wrapper
|
|
code could link and call both LAMMPS and another code as libraries.
|
|
Again, the <A HREF = "run.html">run</A> command has options that allow it to be
|
|
invoked with minimal overhead (no setup or clean-up) if you wish to do
|
|
multiple short runs, driven by another program.
|
|
</P>
|
|
<P>Examples of driver codes that call LAMMPS as a library are included in
|
|
the "couple" directory of the LAMMPS distribution; see couple/README
|
|
for more details:
|
|
</P>
|
|
<UL><LI>simple: simple driver programs in C++ and C which invoke LAMMPS as a
|
|
library
|
|
|
|
<LI>lammps_quest: coupling of LAMMPS and <A HREF = "http://dft.sandia.gov/Quest">Quest</A>, to run classical
|
|
MD with quantum forces calculated by a density functional code
|
|
|
|
<LI>lammps_spparks: coupling of LAMMPS and <A HREF = "http://www.sandia.gov/~sjplimp/spparks.html">SPPARKS</A>, to couple
|
|
a kinetic Monte Carlo model for grain growth using MD to calculate
|
|
strain induced across grain boundaries
|
|
</UL>
|
|
|
|
|
|
|
|
|
|
<P><A HREF = "Section_start.html#2_4">This section</A> of the documentation describes
|
|
how to build LAMMPS as a library. Once this is done, you can
|
|
interface with LAMMPS either via C++, C, or Fortran (or any other
|
|
language that supports a vanilla C-like interface, e.g. a scripting
|
|
language). For example, from C++ you could create one (or more)
|
|
"instances" of LAMMPS, pass it an input script to process, or execute
|
|
individual commands, all by invoking the correct class methods in
|
|
LAMMPS. From C or Fortran you can make function calls to do the same
|
|
things. Library.cpp and library.h contain such a C interface with the
|
|
functions:
|
|
</P>
|
|
<PRE>void lammps_open(int, char **, MPI_Comm, void **);
|
|
void lammps_close(void *);
|
|
void lammps_file(void *, char *);
|
|
char *lammps_command(void *, char *);
|
|
</PRE>
|
|
<P>The functions contain C++ code you could write in a C++ application
|
|
that was invoking LAMMPS directly. Note that LAMMPS classes are
|
|
defined within a LAMMPS namespace (LAMMPS_NS) if you use them
|
|
from another C++ application.
|
|
</P>
|
|
<P>Two of the routines in library.cpp are of particular note. The
|
|
lammps_open() function initiates LAMMPS and takes an MPI communicator
|
|
as an argument. It returns a pointer to a LAMMPS "object". As with
|
|
C++, the lammps_open() function can be called multiple times, to
|
|
create multiple instances of LAMMPS.
|
|
</P>
|
|
<P>LAMMPS will run on the set of processors in the communicator. This
|
|
means the calling code can run LAMMPS on all or a subset of
|
|
processors. For example, a wrapper script might decide to alternate
|
|
between LAMMPS and another code, allowing them both to run on all the
|
|
processors. Or it might allocate half the processors to LAMMPS and
|
|
half to the other code and run both codes simultaneously before
|
|
syncing them up periodically.
|
|
</P>
|
|
<P>Library.cpp contains a lammps_command() function to which the caller
|
|
passes a single LAMMPS command (a string). Thus the calling code can
|
|
read or generate a series of LAMMPS commands (e.g. an input script)
|
|
one line at a time and pass it thru the library interface to setup a
|
|
problem and then run it.
|
|
</P>
|
|
<P>A few other sample functions are included in library.cpp, but the key
|
|
idea is that you can write any functions you wish to define an
|
|
interface for how your code talks to LAMMPS and add them to
|
|
library.cpp and library.h. The routines you add can access any LAMMPS
|
|
data. The examples/couple directory has example C++ and C codes which
|
|
show how a stand-alone code can link LAMMPS as a library, run LAMMPS
|
|
on a subset of processors, grab data from LAMMPS, change it, and put
|
|
it back into LAMMPS.
|
|
</P>
|
|
<HR>
|
|
|
|
<A NAME = "4_11"></A><H4>4.11 Visualizing LAMMPS snapshots
|
|
</H4>
|
|
<P>LAMMPS itself does not do visualization, but snapshots from LAMMPS
|
|
simulations can be visualized (and analyzed) in a variety of ways.
|
|
</P>
|
|
<P>LAMMPS snapshots are created by the <A HREF = "dump.html">dump</A> command which can
|
|
create files in several formats. The native LAMMPS dump format is a
|
|
text file (see "dump atom" or "dump custom") which can be visualized
|
|
by the <A HREF = "Section_tools.html#xmovie">xmovie</A> program, included with the
|
|
LAMMPS package. This produces simple, fast 2d projections of 3d
|
|
systems, and can be useful for rapid debugging of simulation geometry
|
|
and atom trajectories.
|
|
</P>
|
|
<P>Several programs included with LAMMPS as auxiliary tools can convert
|
|
native LAMMPS dump files to other formats. See the
|
|
<A HREF = "Section_tools.html">Section_tools</A> doc page for details. The first is
|
|
the <A HREF = "Section_tools.html#charmm">ch2lmp tool</A>, which contains a
|
|
lammps2pdb Perl script which converts LAMMPS dump files into PDB
|
|
files. The second is the <A HREF = "Section_tools.html#arc">lmp2arc tool</A> which
|
|
converts LAMMPS dump files into Accelrys' Insight MD program files.
|
|
The third is the <A HREF = "Section_tools.html#cfg">lmp2cfg tool</A> which converts
|
|
LAMMPS dump files into CFG files which can be read into the
|
|
<A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> visualizer.
|
|
</P>
|
|
<P>A Python-based toolkit distributed by our group can read native LAMMPS
|
|
dump files, including custom dump files with additional columns of
|
|
user-specified atom information, and convert them to various formats
|
|
or pipe them into visualization software directly. See the <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py
|
|
WWW site</A> for details. Specifically, Pizza.py can convert
|
|
LAMMPS dump files into PDB, XYZ, <A HREF = "http://www.ensight.com">Ensight</A>, and VTK formats.
|
|
Pizza.py can pipe LAMMPS dump files directly into the Raster3d and
|
|
RasMol visualization programs. Pizza.py has tools that do interactive
|
|
3d OpenGL visualization and one that creates SVG images of dump file
|
|
snapshots.
|
|
</P>
|
|
<P>LAMMPS can create XYZ files directly (via "dump xyz") which is a
|
|
simple text-based file format used by many visualization programs
|
|
including <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A>.
|
|
</P>
|
|
<P>LAMMPS can create DCD files directly (via "dump dcd") which can be
|
|
read by <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> in conjunction with a CHARMM PSF file. Using this
|
|
form of output avoids the need to convert LAMMPS snapshots to PDB
|
|
files. See the <A HREF = "dump.html">dump</A> command for more information on DCD
|
|
files.
|
|
</P>
|
|
<P>LAMMPS can create XTC files directly (via "dump xtc") which is GROMACS
|
|
file format which can also be read by <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> for visualization.
|
|
See the <A HREF = "dump.html">dump</A> command for more information on XTC files.
|
|
</P>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<HR>
|
|
|
|
<A NAME = "4_12"></A><H4>4.12 Non-orthogonal simulation boxes
|
|
</H4>
|
|
<P>By default, LAMMPS uses an orthogonal simulation box to encompass the
|
|
particles. The <A HREF = "boundary.html">boundary</A> command sets the boundary
|
|
conditions of the box (periodic, non-periodic, etc). If the box size
|
|
is xprd by yprd by zprd then the 3 mutually orthogonal edge vectors of
|
|
an orthogonal simulation box are a = (xprd,0,0), b = (0,yprd,0), and c
|
|
= (0,0,zprd).
|
|
</P>
|
|
<P>LAMMPS also allows non-orthogonal simulation boxes (triclinic
|
|
symmetry) to be defined with 3 additional "tilt" parameters which
|
|
change the edge vectors of the simulation box to be a = (xprd,0,0), b
|
|
= (xy,yprd,0), and c = (xz,yz,zprd). The xy, xz, and yz parameters
|
|
can be positive or negative. The simulation box must be periodic in
|
|
both dimensions associated with a tilt factor. For example, if xz !=
|
|
0.0, then the x and z dimensions must be periodic.
|
|
</P>
|
|
<P>To avoid extremely tilted boxes (which would be computationally
|
|
inefficient), no tilt factor can skew the box more than half the
|
|
distance of the parallel box length, which is the 1st dimension in the
|
|
tilt factor (x for xz). For example, if xlo = 2 and xhi = 12, then
|
|
the x box length is 10 and the xy tilt factor must be between -5 and
|
|
5. Similarly, both xz and yz must be between -(xhi-xlo)/2 and
|
|
+(yhi-ylo)/2. Note that this is not a limitation, since if the
|
|
maximum tilt factor is 5 (as in this example), then configurations
|
|
with tilt = ..., -15, -5, 5, 15, 25, ... are all equivalent.
|
|
</P>
|
|
<P>You tell LAMMPS to use a non-orthogonal box when the simulation box is
|
|
defined. This happens in one of 3 ways. If the
|
|
<A HREF = "create_box.html">create_box</A> command is used with a region of style
|
|
<I>prism</I>, then a non-orthogonal domain is setup. See the
|
|
<A HREF = "region.html">region</A> command for details. If the
|
|
<A HREF = "read_data.html">read_data</A> command is used to define the simulation
|
|
box, and the header of the data file contains a line with the "xy xz
|
|
yz" keyword, then a non-orthogonal domain is setup. See the
|
|
<A HREF = "read_data.html">read_data</A> command for details. Finally, if the
|
|
<A HREF = "read_restart.html">read_restart</A> command reads a restart file which
|
|
was written from a simulation using a triclinic box, then a
|
|
non-orthogonal box will be enabled for the restarted simulation.
|
|
</P>
|
|
<P>Note that you can define a non-orthogonal box with all 3 tilt factors
|
|
= 0.0, so that it is initially orthogonal. This is necessary if the
|
|
box will become non-orthogonal. Alternatively, you can use the
|
|
<A HREF = "change_box.html">change_box</A> command to convert a simulation box from
|
|
orthogonal to non-orthogonal and vice versa.
|
|
</P>
|
|
<P>One use of non-orthogonal boxes is to model solid-state crystals with
|
|
triclinic symmetry. The <A HREF = "lattice.html">lattice</A> command can be used
|
|
with non-orthogonal basis vectors to define a lattice that will tile a
|
|
non-orthogonal simulation box via the <A HREF = "create_atoms.html">create_atoms</A>
|
|
command. Note that while the box edge vectors a,b,c cannot be
|
|
arbitrary vectors (e.g. a must be aligned with the x axis), it is
|
|
possible to rotate any crystal's basis vectors so that they meet these
|
|
restrictions.
|
|
</P>
|
|
<P>A second use of non-orthogonal boxes is to shear a bulk solid to study
|
|
the response of the material. The <A HREF = "fix_deform.html">fix deform</A>
|
|
command can be used for this purpose. It allows dynamic control of
|
|
the xy, xz, and yz tilt factors as a simulation runs.
|
|
</P>
|
|
<P>Another use of non-orthogonal boxes is to perform non-equilibrium MD
|
|
(NEMD) simulations, as discussed in the next section.
|
|
</P>
|
|
<HR>
|
|
|
|
<A NAME = "4_13"></A><H4>4.13 NEMD simulations
|
|
</H4>
|
|
<P>Non-equilibrium molecular dynamics or NEMD simulations are typically
|
|
used to measure a fluid's rheological properties such as viscosity.
|
|
In LAMMPS, such simulations can be performed by first setting up a
|
|
non-orthogonal simulation box (see the preceding Howto section).
|
|
</P>
|
|
<P>A shear strain can be applied to the simulation box at a desired
|
|
strain rate by using the <A HREF = "fix_deform.html">fix deform</A> command. The
|
|
<A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A> command can be used to thermostat
|
|
the sheared fluid and integrate the SLLOD equations of motion for the
|
|
system. Fix nvt/sllod uses <A HREF = "compute_temp_deform.html">compute
|
|
temp/deform</A> to compute a thermal temperature
|
|
by subtracting out the streaming velocity of the shearing atoms. The
|
|
velocity profile or other properties of the fluid can be monitored via
|
|
the <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command.
|
|
</P>
|
|
<P>As discussed in the previous section on non-orthogonal simulation
|
|
boxes, the amount of tilt or skew that can be applied is limited by
|
|
LAMMPS for computational efficiency to be 1/2 of the parallel box
|
|
length. However, <A HREF = "fix_deform.html">fix deform</A> can continuously strain
|
|
a box by an arbitrary amount. As discussed in the <A HREF = "fix_deform.html">fix
|
|
deform</A> command, when the tilt value reaches a limit,
|
|
the box is re-shaped to the opposite limit which is an equivalent
|
|
tiling of periodic space. The strain rate can then continue to change
|
|
as before. In a long NEMD simulation these box re-shaping events may
|
|
occur many times.
|
|
</P>
|
|
<P>In a NEMD simulation, the "remap" option of <A HREF = "fix_deform.html">fix
|
|
deform</A> should be set to "remap v", since that is what
|
|
<A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A> assumes to generate a velocity
|
|
profile consistent with the applied shear strain rate.
|
|
</P>
|
|
<P>An alternative method for calculating viscosities is provided via the
|
|
<A HREF = "fix_viscosity.html">fix viscosity</A> command.
|
|
</P>
|
|
<HR>
|
|
|
|
<A NAME = "4_14"></A><H4>4.14 Extended spherical and aspherical particles
|
|
</H4>
|
|
<P>Typical MD models treat atoms or particles as point masses.
|
|
Sometimes, however, it is desirable to have a model with finite-size
|
|
particles such as spherioids or aspherical ellipsoids. The difference
|
|
is that such particles have a moment of inertia, rotational energy,
|
|
and angular momentum. Rotation is induced by torque from interactions
|
|
with other particles.
|
|
</P>
|
|
<P>LAMMPS has several options for running simulations with these kinds of
|
|
particles. The following aspects are discussed in turn:
|
|
</P>
|
|
<UL><LI>atom styles
|
|
<LI>pair potentials
|
|
<LI>time integration
|
|
<LI>computes, thermodynamics, and dump output
|
|
<LI>rigid bodies composed of extended particles
|
|
</UL>
|
|
<H5>Atom styles
|
|
</H5>
|
|
<P>There are 3 <A HREF = "atom_style.html">atom styles</A> that allow for definition of
|
|
finite-size particles: granular, dipole, ellipsoid.
|
|
</P>
|
|
<P>Granular particles are spheriods and each particle can have a unique
|
|
diameter and mass (or density). These particles store an angular
|
|
velocity (omega) and can be acted upon by torque.
|
|
</P>
|
|
<P>Dipolar particles are typically spheriods with a point dipole and each
|
|
particle type has a diamater and mass, set by the <A HREF = "shape.html">shape</A>
|
|
and <A HREF = "mass.html">mass</A> commands. These particles store an angular
|
|
velocity (omega) and can be acted upon by torque. They also store an
|
|
orientation for the point dipole (mu) which has a length set by the
|
|
<A HREF = "dipole.html">dipole</A> command. The <A HREF = "set.html">set</A> command can be used
|
|
to initialize the orientation of dipole moments.
|
|
</P>
|
|
<P>Ellipsoid particles are aspherical. Each particle type has an
|
|
ellipsoidal shape and mass, defined by the <A HREF = "shape.html">shape</A> and
|
|
<A HREF = "mass.html">mass</A> commands. These particles store an angular momentum
|
|
and their orientation (quaternion), and can be acted upon by torque.
|
|
They do not store an angular velocity (omega), which can be in a
|
|
different direction than angular momentum, rather they compute it as
|
|
needed. Ellipsoidal particles can also store a dipole moment if an
|
|
<A HREF = "atom_style.html">atom_style hybrid ellipsoid dipole</A> is used. The
|
|
<A HREF = "set.html">set</A> command can be used to initialize the orientation of
|
|
ellipsoidal particles and has a brief explanation of quaternions.
|
|
</P>
|
|
<P>Note that if one of these atom styles is used (or multiple styles via
|
|
the <A HREF = "atom_style.html">atom_style hybrid</A> command), not all particles in
|
|
the system are required to be finite-size or aspherical. For example,
|
|
if the 3 shape parameters are set to the same value, the particle will
|
|
be a spheroid rather than an ellipsoid. If the 3 shape parameters are
|
|
all set to 0.0 or if the diameter is set to 0.0, it will be a point
|
|
particle. If the dipole moment is set to zero, the particle will not
|
|
have a point dipole associated with it. The pair styles used to
|
|
compute pairwise interactions will typically compute the correct
|
|
interaction in these simplified (cheaper) cases. <A HREF = "pair_hybrid.html">Pair_style
|
|
hybrid</A> can be used to insure the correct
|
|
interactions are computed for the appropriate style of interactions.
|
|
Likewise, using groups to partition particles (ellipsoid versus
|
|
spheroid versus point particles) will allow you to use the appropriate
|
|
time integrators and temperature computations for each class of
|
|
particles. See the doc pages for various commands for details.
|
|
</P>
|
|
<P>Also note that for <A HREF = "dimension.html">2d simulations</A>, finite-size
|
|
spheroids and ellipsoids are still treated as 3d particles, rather
|
|
than as disks or ellipses. This means they have the same moment of
|
|
inertia for a 3d extended object. When their temperature is
|
|
coomputed, the correct degrees of freedom are used for rotation in a
|
|
2d versus 3d system.
|
|
</P>
|
|
<H5>Pair potentials
|
|
</H5>
|
|
<P>When a system with extended particles is defined, the particles will
|
|
only rotate and experience torque if the force field computes such
|
|
interactions. These are the various <A HREF = "pair_style.html">pair styles</A>
|
|
that generate torque:
|
|
</P>
|
|
<UL><LI><A HREF = "pair_gran.html">pair_style gran/history</A>
|
|
<LI><A HREF = "pair_gran.html">pair_style gran/hertzian</A>
|
|
<LI><A HREF = "pair_gran.html">pair_style gran/no_history</A>
|
|
<LI><A HREF = "pair_dipole.html">pair_style dipole/cut</A>
|
|
<LI><A HREF = "pair_gayberne.html">pair_style gayberne</A>
|
|
<LI><A HREF = "pair_resquared.html">pair_style resquared</A>
|
|
<LI><A HREF = "pair_lubricate.html">pair_style lubricate</A>
|
|
</UL>
|
|
<P>The <A HREF = "pair_gran.html">granular pair styles</A> are used with <A HREF = "atom_style.html">atom_style
|
|
granular</A>. The <A HREF = "pair_dipole.html">dipole pair style</A>
|
|
is used with <A HREF = "atom_style.html">atom_style dipole</A>. The
|
|
<A HREF = "pair_gayberne.html">GayBerne</A> and <A HREF = "pair_resquared.html">REsquared</A>
|
|
potentials require particles have a <A HREF = "shape.html">shape</A> and are
|
|
designed for <A HREF = "atom_style.html">ellipsoidal particles</A>. The
|
|
<A HREF = "pair_lubricate.html">lubrication potential</A> requires that particles
|
|
have a <A HREF = "shape.html">shape</A>. It can currently only be used with
|
|
extended spherical particles.
|
|
</P>
|
|
<H5>Time integration
|
|
</H5>
|
|
<P>There are 3 fixes that perform time integration on extended spherical
|
|
particles, meaning the integrators update the rotational orientation
|
|
and angular velocity or angular momentum of the particles:
|
|
</P>
|
|
<UL><LI><A HREF = "fix_nve_sphere.html">fix nve/sphere</A>
|
|
<LI><A HREF = "fix_nvt_sphere.html">fix nvt/sphere</A>
|
|
<LI><A HREF = "fix_npt_sphere.html">fix npt/sphere</A>
|
|
</UL>
|
|
<P>Likewise, there are 3 fixes that perform time integration on extended
|
|
aspherical particles:
|
|
</P>
|
|
<UL><LI><A HREF = "fix_nve_asphere.html">fix nve/asphere</A>
|
|
<LI><A HREF = "fix_nvt_asphere.html">fix nvt/asphere</A>
|
|
<LI><A HREF = "fix_npt_asphere.html">fix npt/asphere</A>
|
|
</UL>
|
|
<P>The advantage of these fixes is that those which thermostat the
|
|
particles include the rotational degrees of freedom in the temperature
|
|
calculation and thermostatting. Other thermostats can be used with
|
|
fix nve/sphere or fix nve/asphere, such as fix langevin or fix
|
|
temp/berendsen, but those thermostats only operate on the
|
|
translational kinetic energy of the extended particles.
|
|
</P>
|
|
<P>Note that for mixtures of point and extended particles, you should
|
|
only use these integration fixes on <A HREF = "group.html">groups</A> which contain
|
|
extended particles.
|
|
</P>
|
|
<H5>Computes, thermodynamics, and dump output
|
|
</H5>
|
|
<P>There are 4 computes that calculate the temperature or rotational energy
|
|
of extended spherical or aspherical particles:
|
|
</P>
|
|
<UL><LI><A HREF = "compute_temp_sphere.html">compute temp/sphere</A>
|
|
<LI><A HREF = "compute_temp_asphere.html">compute temp/asphere</A>
|
|
<LI><A HREF = "compute_erotate_sphere.html">compute erotate/sphere</A>
|
|
<LI><A HREF = "compute_erotate_asphere.html">compute erotate/asphere</A>
|
|
</UL>
|
|
<P>These include rotational degrees of freedom in their computation. If
|
|
you wish the thermodynamic output of temperature or pressure to use
|
|
one of these computes (e.g. for a system entirely composed of extended
|
|
particles), then the compute can be defined and the
|
|
<A HREF = "thermo_modify.html">thermo_modify</A> command used. Note that by
|
|
default thermodynamic quantities will be calculated with a temperature
|
|
that only includes translational degrees of freedom. See the
|
|
<A HREF = "thermo_style.html">thermo_style</A> command for details.
|
|
</P>
|
|
<P>The <A HREF = "dump.html">dump custom</A> command can output various attributes of
|
|
extended particles, including the dipole moment (mu), the angular
|
|
velocity (omega), the angular momentum (angmom), the quaternion
|
|
(quat), and the torque (tq) on the particle.
|
|
</P>
|
|
<H5>Rigid bodies composed of extended particles
|
|
</H5>
|
|
<P>The <A HREF = "fix_rigid.html">fix rigid</A> command treats a collection of
|
|
particles as a rigid body, computes its inertia tensor, sums the total
|
|
force and torque on the rigid body each timestep due to forces on its
|
|
constituent particles, and integrates the motion of the rigid body.
|
|
</P>
|
|
<P>(NOTE: the feature described in the following paragraph has not yet
|
|
been released. It will be soon.)
|
|
</P>
|
|
<P>If any of the constituent particles of a rigid body are extended
|
|
particles (spheroids or ellipsoids), then their contribution to the
|
|
inertia tensor of the body is different than if they were point
|
|
particles. This means the rotational dynamics of the rigid body will
|
|
be different. Thus a model of a dimer is different if the dimer
|
|
consists of two point masses versus two extended sphereoids, even if
|
|
the two particles have the same mass. Extended particles that
|
|
experience torque due to their interaction with other particles will
|
|
also impart that torque to a rigid body they are part of.
|
|
</P>
|
|
<P>See the "fix rigid" command for example of complex rigid-body models
|
|
it is possible to define in LAMMPS.
|
|
</P>
|
|
<P>Note that the <A HREF = "fix_shake.html">fix shake</A> command can also be used to
|
|
treat 2, 3, or 4 particles as a rigid body, but it always assumes the
|
|
particles are point masses.
|
|
</P>
|
|
<HR>
|
|
|
|
<A NAME = "4_15"></A><H4>4.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables)
|
|
</H4>
|
|
<P>There are four basic kinds of LAMMPS output:
|
|
</P>
|
|
<UL><LI><A HREF = "thermo_style.html">Thermodynamic output</A>, which is a list
|
|
of quantities printed every few timesteps to the screen and logfile.
|
|
|
|
<LI><A HREF = "dump.html">Dump files</A>, which contain snapshots of atoms and various
|
|
per-atom values and are written at a specified frequency.
|
|
|
|
<LI>Certain fixes can output user-specified quantities to files: <A HREF = "fix_ave_time.html">fix
|
|
ave/time</A> for time averaging, <A HREF = "fix_ave_spatial.html">fix
|
|
ave/spatial</A> for spatial averaging, and <A HREF = "fix_print.html">fix
|
|
print</A> for single-line output of
|
|
<A HREF = "variable.html">variables</A>. Fix print can also output to the
|
|
screen.
|
|
|
|
<LI><A HREF = "restart.html">Restart files</A>.
|
|
</UL>
|
|
<P>A simulation prints one set of thermodynamic output and (optionally)
|
|
restart files. It can generate any number of dump files and fix
|
|
output files, depending on what <A HREF = "dump.html">dump</A> and <A HREF = "fix.html">fix</A>
|
|
commands you specify.
|
|
</P>
|
|
<P>As discussed below, LAMMPS gives you a variety of ways to determine
|
|
what quantities are computed and printed when the thermodynamics,
|
|
dump, or fix commands listed above perform output. Throughout this
|
|
discussion, note that users can also <A HREF = "Section_modify.html">add their own computes and fixes
|
|
to LAMMPS</A> which can then generate values that can
|
|
then be output with these commands.
|
|
</P>
|
|
<P>The following sub-sections discuss different LAMMPS command related
|
|
to output and the kind of data they operate on and produce:
|
|
</P>
|
|
<UL><LI><A HREF = "#global">Global/per-atom/local data</A>
|
|
<LI><A HREF = "#scalar">Scalar/vector/array data</A>
|
|
<LI><A HREF = "#thermo">Thermodynamic output</A>
|
|
<LI><A HREF = "#dump">Dump file output</A>
|
|
<LI><A HREF = "#fixoutput">Fixes that write output files</A>
|
|
<LI><A HREF = "#computeoutput">Computes that process output quantities</A>
|
|
<LI><A HREF = "#fixoutput">Fixes that process output quantities</A>
|
|
<LI><A HREF = "#compute">Computes that generate values to output</A>
|
|
<LI><A HREF = "#fix">Fixes that generate values to output</A>
|
|
<LI><A HREF = "#variable">Variables that generate values to output</A>
|
|
<LI><A HREF = "#table">Summary table of output options and data flow between commands</A>
|
|
</UL>
|
|
<H5><A NAME = "global"></A>Global/per-atom/local data
|
|
</H5>
|
|
<P>Various output-related commands work with three different styles of
|
|
data: global, per-atom, or local. A global datum is one or more
|
|
system-wide values, e.g. the temperature of the system. A per-atom
|
|
datum is one or more values per atom, e.g. the kinetic energy of each
|
|
atom. Local datums are calculated by each processor based on the
|
|
atoms it owns, but there may be zero or more per atom, e.g. a list of
|
|
bond distances.
|
|
</P>
|
|
<H5><A NAME = "scalar"></A>Scalar/vector/array data
|
|
</H5>
|
|
<P>Global, per-atom, and local datums can each come in three kinds: a
|
|
single scalar value, a vector of values, or a 2d array of values. The
|
|
doc page for a "compute" or "fix" or "variable" that generates data
|
|
will specify both the style and kind of data it produces, e.g. a
|
|
per-atom vector.
|
|
</P>
|
|
<P>When a quantity is accessed, as in many of the output commands
|
|
discussed below, it can be referenced via the following bracket
|
|
notation, where ID in this case is the ID of a compute. The leading
|
|
"c_" would be replaced by "f_" for a fix, or "v_" for a variable:
|
|
</P>
|
|
<DIV ALIGN=center><TABLE BORDER=1 >
|
|
<TR><TD >c_ID </TD><TD > entire scalar, vector, or array</TD></TR>
|
|
<TR><TD >c_ID[I] </TD><TD > one element of vector, one column of array</TD></TR>
|
|
<TR><TD >c_ID[I][J] </TD><TD > one element of array
|
|
</TD></TR></TABLE></DIV>
|
|
|
|
<P>In other words, using one bracket reduces the dimension of the data
|
|
once (vector -> scalar, array -> vector). Using two brackets reduces
|
|
the dimension twice (array -> scalar). Thus a command that uses
|
|
scalar values as input can typically also process elements of a vector
|
|
or array.
|
|
</P>
|
|
<H5><A NAME = "thermo"></A>Thermodynamic output
|
|
</H5>
|
|
<P>The frequency and format of thermodynamic output is set by the
|
|
<A HREF = "thermo.html">thermo</A>, <A HREF = "thermo_style.html">thermo_style</A>, and
|
|
<A HREF = "thermo_modify.html">thermo_modify</A> commands. The
|
|
<A HREF = "thermo_style.html">thermo_style</A> command also specifies what values
|
|
are calculated and written out. Pre-defined keywords can be specified
|
|
(e.g. press, etotal, etc). Three additional kinds of keywords can
|
|
also be specified (c_ID, f_ID, v_name), where a <A HREF = "compute.html">compute</A>
|
|
or <A HREF = "fix.html">fix</A> or <A HREF = "variable.html">variable</A> provides the value to be
|
|
output. In each case, the compute, fix, or variable must generate
|
|
global values for input to the <A HREF = "dump.html">thermo_style custom</A>
|
|
command.
|
|
</P>
|
|
<H5><A NAME = "dump"></A>Dump file output
|
|
</H5>
|
|
<P>Dump file output is specified by the <A HREF = "dump.html">dump</A> and
|
|
<A HREF = "dump_modify.html">dump_modify</A> commands. There are several
|
|
pre-defined formats (dump atom, dump xtc, etc).
|
|
</P>
|
|
<P>There is also a <A HREF = "dump.html">dump custom</A> format where the user
|
|
specifies what values are output with each atom. Pre-defined atom
|
|
attributes can be specified (id, x, fx, etc). Three additional kinds
|
|
of keywords can also be specified (c_ID, f_ID, v_name), where a
|
|
<A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A> or <A HREF = "variable.html">variable</A>
|
|
provides the values to be output. In each case, the compute, fix, or
|
|
variable must generate per-atom values for input to the <A HREF = "dump.html">dump
|
|
custom</A> command.
|
|
</P>
|
|
<P>There is also a <A HREF = "dump.html">dump local</A> format where the user specifies
|
|
what local values to output. A pre-defined index keyword can be
|
|
specified to enumuerate the local values. Two additional kinds of
|
|
keywords can also be specified (c_ID, f_ID), where a
|
|
<A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A> or <A HREF = "variable.html">variable</A>
|
|
provides the values to be output. In each case, the compute or fix
|
|
must generate local values for input to the <A HREF = "dump.html">dump local</A>
|
|
command.
|
|
</P>
|
|
<H5><A NAME = "fixoutput"></A>Fixes that write output files
|
|
</H5>
|
|
<P>Sevarl fixes take various quantities as input and can write output
|
|
files: <A HREF = "fix_ave_time.html">fix ave/time</A>, <A HREF = "fix_ave_spatial.html">fix
|
|
ave/spatial</A>, <A HREF = "fix_ave_histo.html">fix ave/histo</A>,
|
|
<A HREF = "fix_ave_correlate.html">fix ave/correlate</A>, and <A HREF = "fix_print.html">fix
|
|
print</A>.
|
|
</P>
|
|
<P>The <A HREF = "fix_ave_time.html">fix ave/time</A> command enables direct output to
|
|
a file and/or time-averaging of global scalars or vectors. The user
|
|
specifies one or more quantities as input. These can be global
|
|
<A HREF = "compute.html">compute</A> values, global <A HREF = "fix.html">fix</A> values, or
|
|
<A HREF = "variable.html">variables</A> of any style except the atom style which
|
|
produces per-atom values. Since a variable can refer to keywords used
|
|
by the <A HREF = "thermo_style.html">thermo_style custom</A> command (like temp or
|
|
press) and individual per-atom values, a wide variety of quantities
|
|
can be time averaged and/or output in this way. If the inputs are one
|
|
or more scalar values, then the fix generate a global scalar or vector
|
|
of output. If the inputs are one or more vector values, then the fix
|
|
generates a global vector or array of output. The time-averaged
|
|
output of this fix can also be used as input to other output commands.
|
|
</P>
|
|
<P>The <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command enables direct
|
|
output to a file of spatial-averaged per-atom quantities like those
|
|
output in dump files, within 1d layers of the simulation box. The
|
|
per-atom quantities can be atom density (mass or number) or atom
|
|
attributes such as position, velocity, force. They can also be
|
|
per-atom quantities calculated by a <A HREF = "compute.html">compute</A>, by a
|
|
<A HREF = "fix.html">fix</A>, or by an atom-style <A HREF = "variable.html">variable</A>. The
|
|
spatial-averaged output of this fix can also be used as input to other
|
|
output commands.
|
|
</P>
|
|
<P>The <A HREF = "fix_ave_histo.html">fix ave/histo</A> command enables direct output
|
|
to a file of histogrammed quantities, which can be global or per-atom
|
|
or local quantities. The histogram output of this fix can also be
|
|
used as input to other output commands.
|
|
</P>
|
|
<P>The <A HREF = "fix_ave_histo.html">fix ave/correlate</A> command enables direct
|
|
output to a file of time-correlated quantities, which can be global
|
|
scalars. The correlation matrix output of this fix can also be used
|
|
as input to other output commands.
|
|
</P>
|
|
<P>The <A HREF = "fix_print.html">fix print</A> command can generate a line of output
|
|
written to the screen and log file or to a separate file, periodically
|
|
during a running simulation. The line can contain one or more
|
|
<A HREF = "variable.html">variable</A> values for any style variable except the atom
|
|
style). As explained above, variables themselves can contain
|
|
references to global values generated by <A HREF = "thermo_style.html">thermodynamic
|
|
keywords</A>, <A HREF = "compute.html">computes</A>,
|
|
<A HREF = "fix.html">fixes</A>, or other <A HREF = "variable.html">variables</A>, or to per-atom
|
|
values for a specific atom. Thus the <A HREF = "fix_print.html">fix print</A>
|
|
command is a means to output a wide variety of quantities separate
|
|
from normal thermodynamic or dump file output.
|
|
</P>
|
|
<H5><A NAME = "computeoutput"></A>Computes that process output quantities
|
|
</H5>
|
|
<P>The <A HREF = "compute_reduce.html">compute reduce</A> and <A HREF = "compute_reduce.html">compute
|
|
reduce/region</A> commands take one or more per-atom
|
|
or local vector quantities as inputs and "reduce" them (sum, min, max,
|
|
ave) to scalar quantities. These are produced as output values which
|
|
can be used as input to other output commands.
|
|
</P>
|
|
<P>The <A HREF = "compute_property_atom.html">compute property/atom</A> command takes a
|
|
list of one or more pre-defined atom attributes (id, x, fx, etc) and
|
|
stores the values in a per-atom vector or array. These are produced
|
|
as output values which can be used as input to other output commands.
|
|
The list of atom attributes is the same as for the <A HREF = "dump.html">dump
|
|
custom</A> command.
|
|
</P>
|
|
<P>The <A HREF = "compute_property_local.html">compute property/local</A> command takes
|
|
a list of one or more pre-defined local attributes (bond info, angle
|
|
info, etc) and stores the values in a local vector or array. These
|
|
are produced as output values which can be used as input to other
|
|
output commands.
|
|
</P>
|
|
<H5><A NAME = "fixoutput"></A>Fixes that process output quantities
|
|
</H5>
|
|
<P>The <A HREF = "fix_ave_atom.html">fix ave/atom</A> command performs time-averaging
|
|
of per-atom vectors. The per-atom quantities can be atom attributes
|
|
such as position, velocity, force. They can also be per-atom
|
|
quantities calculated by a <A HREF = "compute.html">compute</A>, by a
|
|
<A HREF = "fix.html">fix</A>, or by an atom-style <A HREF = "variable.html">variable</A>. The
|
|
time-averaged per-atom output of this fix can be used as input to
|
|
other output commands.
|
|
</P>
|
|
<P>The <A HREF = "fix_store_state.html">fix store/state</A> command can archive one or
|
|
more per-atom attributes at a particular time, so that the old values
|
|
can be used in a future calculation or output. The list of atom
|
|
attributes is the same as for the <A HREF = "dump.html">dump custom</A> command,
|
|
including per-atom quantities calculated by a <A HREF = "compute.html">compute</A>,
|
|
by a <A HREF = "fix.html">fix</A>, or by an atom-style <A HREF = "variable.html">variable</A>.
|
|
The output of this fix can be used as input to other output commands.
|
|
</P>
|
|
<H5><A NAME = "compute"></A>Computes that generate values to output
|
|
</H5>
|
|
<P>Every <A HREF = "compute.html">compute</A> in LAMMPS produces either global or
|
|
per-atom or local values. The values can be scalars or vectors or
|
|
arrays of data. These values can be output using the other commands
|
|
described in this section. The doc page for each compute command
|
|
describes what it produces. Computes that produce per-atom or local
|
|
values have the word "atom" or "local" in their style name. Computes
|
|
without the word "atom" or "local" produce global values.
|
|
</P>
|
|
<H5><A NAME = "fix"></A>Fixes that generate values to output
|
|
</H5>
|
|
<P>Some <A HREF = "fix.html">fixes</A> in LAMMPS produces either global or per-atom or
|
|
local values which can be accessed by other commands. The values can
|
|
be scalars or vectors or arrays of data. These values can be output
|
|
using the other commands described in this section. The doc page for
|
|
each fix command tells whether it produces any output quantities and
|
|
describes them.
|
|
</P>
|
|
<H5><A NAME = "variable"></A>Variables that generate values to output
|
|
</H5>
|
|
<P>Every <A HREF = "variable.html">variables</A> defined in an input script generates
|
|
either a global scalar value or a per-atom vector (only atom-style
|
|
variables) when it is accessed. The formulas used to define equal-
|
|
and atom-style variables can contain references to the thermodynamic
|
|
keywords and to global and per-atom data generated by computes, fixes,
|
|
and other variables. The values generated by variables can be output
|
|
using the other commands described in this section.
|
|
</P>
|
|
<H5><A NAME = "table"></A>Summary table of output options and data flow between commands
|
|
</H5>
|
|
<P>This table summarizes the various commands that can be used for
|
|
generating output from LAMMPS. Each command produces output data of
|
|
some kind and/or writes data to a file. Most of the commands can take
|
|
data from other commands as input. Thus you can link many of these
|
|
commands together in pipeline form, where data produced by one command
|
|
is used as input to another command and eventually written to the
|
|
screen or to a file. Note that to hook two commands together the
|
|
output and input data types must match, e.g. global/per-atom/local
|
|
data and scalar/vector/array data.
|
|
</P>
|
|
<P>Also note that, as described above, when a command takes a scalar as
|
|
input, that could be an element of a vector or array. Likewise a
|
|
vector input could be a column of an array.
|
|
</P>
|
|
<DIV ALIGN=center><TABLE BORDER=1 >
|
|
<TR><TD >Command</TD><TD > Input</TD><TD > Output</TD><TD ></TD></TR>
|
|
<TR><TD ><A HREF = "thermo_style.html">thermo_style custom</A></TD><TD > global scalars</TD><TD > screen, log file</TD><TD ></TD></TR>
|
|
<TR><TD ><A HREF = "dump.html">dump custom</A></TD><TD > per-atom vectors</TD><TD > dump file</TD><TD ></TD></TR>
|
|
<TR><TD ><A HREF = "dump.html">dump local</A></TD><TD > local vectors</TD><TD > dump file</TD><TD ></TD></TR>
|
|
<TR><TD ><A HREF = "fix_print.html">fix print</A></TD><TD > global scalar from variable</TD><TD > screen, file</TD><TD ></TD></TR>
|
|
<TR><TD ><A HREF = "print.html">print</A></TD><TD > global scalar from variable</TD><TD > screen</TD><TD ></TD></TR>
|
|
<TR><TD ><A HREF = "compute.html">computes</A></TD><TD > N/A</TD><TD > global/per-atom/local scalar/vector/array</TD><TD ></TD></TR>
|
|
<TR><TD ><A HREF = "fix.html">fixes</A></TD><TD > N/A</TD><TD > global/per-atom/local scalar/vector/array</TD><TD ></TD></TR>
|
|
<TR><TD ><A HREF = "variable.html">variables</A></TD><TD > global scalars, per-atom vectors</TD><TD > global scalar, per-atom vector</TD><TD ></TD></TR>
|
|
<TR><TD ><A HREF = "compute_reduce.html">compute reduce</A></TD><TD > per-atom/local vectors</TD><TD > global scalar/vector</TD><TD ></TD></TR>
|
|
<TR><TD ><A HREF = "compute_property_atom.html">compute property/atom</A></TD><TD > per-atom vectors</TD><TD > per-atom vector/array</TD><TD ></TD></TR>
|
|
<TR><TD ><A HREF = "compute_property_local.html">compute property/local</A></TD><TD > local vectors</TD><TD > local vector/array</TD><TD ></TD></TR>
|
|
<TR><TD ><A HREF = "fix_ave_atom.html">fix ave/atom</A></TD><TD > per-atom vectors</TD><TD > per-atom vector/array</TD><TD ></TD></TR>
|
|
<TR><TD ><A HREF = "fix_ave_time.html">fix ave/time</A></TD><TD > global scalars/vectors</TD><TD > global scalar/vector/array, file</TD><TD ></TD></TR>
|
|
<TR><TD ><A HREF = "fix_ave_spatial.html">fix ave/spatial</A></TD><TD > per-atom vectors</TD><TD > global array, file</TD><TD ></TD></TR>
|
|
<TR><TD ><A HREF = "fix_ave_histo.html">fix ave/histo</A></TD><TD > global/per-atom/local scalars and vectors</TD><TD > global array, file</TD><TD ></TD></TR>
|
|
<TR><TD ><A HREF = "fix_ave_correlate.html">fix ave/correlate</A></TD><TD > global scalars</TD><TD > global array, file</TD><TD ></TD></TR>
|
|
<TR><TD ><A HREF = "fix_store_state.html">fix store/state</A></TD><TD > per-atom vectors</TD><TD > per-atom vector/array</TD><TD ></TD></TR>
|
|
<TR><TD >
|
|
</TD></TR></TABLE></DIV>
|
|
|
|
<HR>
|
|
|
|
<A NAME = "4_16"></A><H4>4.16 Thermostatting, barostatting, and computing temperature
|
|
</H4>
|
|
<P>Thermostatting means controlling the temperature of particles in an MD
|
|
simulation. Barostatting means controlling the pressure. Since the
|
|
pressure includes a kinetic component due to particle velocities, both
|
|
these operations require calculation of the temperature. Typically a
|
|
target temperature (T) and/or pressure (P) is specified by the user,
|
|
and the thermostat or barostat attempts to equilibrate the system to
|
|
the requested T and/or P.
|
|
</P>
|
|
<P>Temperature is computed as kinetic energy divided by some number of
|
|
degrees of freedom (and the Boltzmann constant). Since kinetic energy
|
|
is a function of particle velocity, there is often a need to
|
|
distinguish between a particle's advection velocity (due to some
|
|
aggregate motiion of particles) and its thermal velocity. The sum of
|
|
the two is the particle's total velocity, but the latter is often what
|
|
is wanted to compute a temperature.
|
|
</P>
|
|
<P>LAMMPS has several options for computing temperatures, any of which
|
|
can be used in thermostatting and barostatting. These <A HREF = "compute.html">compute
|
|
commands</A> calculate temperature, and the <A HREF = "compute_pressure.html">compute
|
|
pressure</A> command calculates pressure.
|
|
</P>
|
|
<UL><LI><A HREF = "compute_temp.html">compute temp</A>
|
|
<LI><A HREF = "compute_temp_sphere.html">compute temp/sphere</A>
|
|
<LI><A HREF = "compute_temp_asphere.html">compute temp/asphere</A>
|
|
<LI><A HREF = "compute_temp_com.html">compute temp/com</A>
|
|
<LI><A HREF = "compute_temp_deform.html">compute temp/deform</A>
|
|
<LI><A HREF = "compute_temp_partial.html">compute temp/partial</A>
|
|
<LI><A HREF = "compute_temp_profile.html">compute temp/profile</A>
|
|
<LI><A HREF = "compute_temp_ramp.html">compute temp/ramp</A>
|
|
<LI><A HREF = "compute_temp_region.html">compute temp/region</A>
|
|
</UL>
|
|
<P>All but the first 3 calculate velocity biases (i.e. advection
|
|
velocities) that are removed when computing the thermal temperature.
|
|
<A HREF = "compute_temp_sphere.html">Compute temp/sphere</A> and <A HREF = "compute_temp_asphere.html">compute
|
|
temp/asphere</A> compute kinetic energy for
|
|
extended particles that includes rotational degrees of freedom. They
|
|
both allow, as an extra argument, which is another temperature compute
|
|
that subtracts a velocity bias. This allows the translational
|
|
velocity of extended spherical or aspherical particles to be adjusted
|
|
in prescribed ways.
|
|
</P>
|
|
<P>Thermostatting in LAMMPS is performed by <A HREF = "fix.html">fixes</A>, or in one
|
|
case by a pair style. Four thermostatting fixes are currently
|
|
available: Nose-Hoover (nvt), Berendsen, Langevin, and direct
|
|
rescaling (temp/rescale). Dissipative particle dynamics (DPD)
|
|
thermostatting can be invoked via the <I>dpd/tstat</I> pair style:
|
|
</P>
|
|
<UL><LI><A HREF = "fix_nh.html">fix nvt</A>
|
|
<LI><A HREF = "fix_nvt_sphere.html">fix nvt/sphere</A>
|
|
<LI><A HREF = "fix_nvt_asphere.html">fix nvt/asphere</A>
|
|
<LI><A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A>
|
|
<LI><A HREF = "fix_temp_berendsen.html">fix temp/berendsen</A>
|
|
<LI><A HREF = "fix_langevin.html">fix langevin</A>
|
|
<LI><A HREF = "fix_temp_rescale.html">fix temp/rescale</A>
|
|
<LI><A HREF = "pair_dpd.html">pair_style dpd/tstat</A>
|
|
</UL>
|
|
<P><A HREF = "fix_nh.html">Fix nvt</A> only thermostats the translational velocity of
|
|
particles. <A HREF = "fix_nvt_sllod.html">Fix nvt/sllod</A> also does this, except
|
|
that it subtracts out a velocity bias due to a deforming box and
|
|
integrates the SLLOD equations of motion. See the <A HREF = "#4_13">NEMD
|
|
simulations</A> section of this page for further details. <A HREF = "fix_nvt_sphere.html">Fix
|
|
nvt/sphere</A> and <A HREF = "fix_nvt_asphere.html">fix
|
|
nvt/asphere</A> thermostat not only translation
|
|
velocities but also rotational velocities for spherical and aspherical
|
|
particles.
|
|
</P>
|
|
<P>DPD thermostatting alters pairwise interactions in a manner analagous
|
|
to the per-particle thermostatting of <A HREF = "fix_langevin.html">fix
|
|
langevin</A>.
|
|
</P>
|
|
<P>Any of the thermostatting fixes can use temperature computes that
|
|
remove bias for two purposes: (a) computing the current temperature to
|
|
compare to the requested target temperature, and (b) adjusting only
|
|
the thermal temperature component of the particle's velocities. See
|
|
the doc pages for the individual fixes and for the
|
|
<A HREF = "fix_modify.html">fix_modify</A> command for instructions on how to assign
|
|
a temperature compute to a thermostatting fix. For example, you can
|
|
apply a thermostat to only the x and z components of velocity by using
|
|
it in conjunction with <A HREF = "compute_temp_partial.html">compute
|
|
temp/partial</A>.
|
|
</P>
|
|
<P>IMPORTANT NOTE: Only the nvt fixes perform time integration, meaning
|
|
they update the velocities and positions of particles due to forces
|
|
and velocities respectively. The other thermostat fixes only adjust
|
|
velocities; they do NOT perform time integration updates. Thus they
|
|
should be used in conjunction with a constant NVE integration fix such
|
|
as these:
|
|
</P>
|
|
<UL><LI><A HREF = "fix_nve.html">fix nve</A>
|
|
<LI><A HREF = "fix_nve_sphere.html">fix nve/sphere</A>
|
|
<LI><A HREF = "fix_nve_asphere.html">fix nve/asphere</A>
|
|
</UL>
|
|
<P>Barostatting in LAMMPS is also performed by <A HREF = "fix.html">fixes</A>. Two
|
|
barosttating methods are currently available: Nose-Hoover (npt and
|
|
nph) and Berendsen:
|
|
</P>
|
|
<UL><LI><A HREF = "fix_nh.html">fix npt</A>
|
|
<LI><A HREF = "fix_npt_sphere.html">fix npt/sphere</A>
|
|
<LI><A HREF = "fix_npt_asphere.html">fix npt/asphere</A>
|
|
<LI><A HREF = "fix_nh.html">fix nph</A>
|
|
<LI><A HREF = "fix_press_berendsen.html">fix press/berendsen</A>
|
|
</UL>
|
|
<P>The <A HREF = "fix_nh.html">fix npt</A> commands include a Nose-Hoover thermostat
|
|
and barostat. <A HREF = "fix_nh.html">Fix nph</A> is just a Nose/Hoover barostat;
|
|
it does no thermostatting. Both <A HREF = "fix_nh.html">fix nph</A> and <A HREF = "fix_press_berendsen.html">fix
|
|
press/bernendsen</A> can be used in conjunction
|
|
with any of the thermostatting fixes.
|
|
</P>
|
|
<P>As with the thermostats, <A HREF = "fix_nh.html">fix npt</A> and <A HREF = "fix_nh.html">fix
|
|
nph</A> only use translational motion of the particles in
|
|
computing T and P and performing thermo/barostatting. <A HREF = "fix_npt_sphere.html">Fix
|
|
npt/sphere</A> and <A HREF = "fix_npt_asphere.html">fix
|
|
npt/asphere</A> thermo/barostat using not only
|
|
translation velocities but also rotational velocities for spherical
|
|
and aspherical particles.
|
|
</P>
|
|
<P>All of the barostatting fixes use the <A HREF = "compute_pressure.html">compute
|
|
pressure</A> compute to calculate a current
|
|
pressure. By default, this compute is created with a simple <A HREF = "compute_temp.html">compute
|
|
temp</A> (see the last argument of the <A HREF = "compute_pressure.html">compute
|
|
pressure</A> command), which is used to calculated
|
|
the kinetic componenet of the pressure. The barostatting fixes can
|
|
also use temperature computes that remove bias for the purpose of
|
|
computing the kinetic componenet which contributes to the current
|
|
pressure. See the doc pages for the individual fixes and for the
|
|
<A HREF = "fix_modify.html">fix_modify</A> command for instructions on how to assign
|
|
a temperature or pressure compute to a barostatting fix.
|
|
</P>
|
|
<P>IMPORTANT NOTE: As with the thermostats, the Nose/Hoover methods (<A HREF = "fix_nh.html">fix
|
|
npt</A> and <A HREF = "fix_nh.html">fix nph</A>) perform time
|
|
integration. <A HREF = "fix_press_berendsen.html">Fix press/berendsen</A> does NOT,
|
|
so it should be used with one of the constant NVE fixes or with one of
|
|
the NVT fixes.
|
|
</P>
|
|
<P>Finally, thermodynamic output, which can be setup via the
|
|
<A HREF = "thermo_style.html">thermo_style</A> command, often includes temperature
|
|
and pressure values. As explained on the doc page for the
|
|
<A HREF = "thermo_style.html">thermo_style</A> command, the default T and P are
|
|
setup by the thermo command itself. They are NOT the ones associated
|
|
with any thermostatting or barostatting fix you have defined or with
|
|
any compute that calculates a temperature or pressure. Thus if you
|
|
want to view these values of T and P, you need to specify them
|
|
explicitly via a <A HREF = "thermo_style.html">thermo_style custom</A> command. Or
|
|
you can use the <A HREF = "thermo_modify.html">thermo_modify</A> command to
|
|
re-define what temperature or pressure compute is used for default
|
|
thermodynamic output.
|
|
</P>
|
|
<HR>
|
|
|
|
<A NAME = "4_17"></A><H4>4.17 Walls
|
|
</H4>
|
|
<P>Walls in an MD simulation are typically used to bound particle motion,
|
|
i.e. to serve as a boundary condition.
|
|
</P>
|
|
<P>Walls in LAMMPS can be of rough (made of particles) or idealized
|
|
surfaces. Ideal walls can be smooth, generating forces only in the
|
|
normal direction, or frictional, generating forces also in the
|
|
tangential direction.
|
|
</P>
|
|
<P>Rough walls, built of particles, can be created in various ways. The
|
|
particles themselves can be generated like any other particle, via the
|
|
<A HREF = "lattice.html">lattice</A> and <A HREF = "create_atoms.html">create_atoms</A> commands,
|
|
or read in via the <A HREF = "read_data.html">read_data</A> command.
|
|
</P>
|
|
<P>Their motion can be constrained by many different commands, so that
|
|
they do not move at all, move together as a group at constant velocity
|
|
or in response to a net force acting on them, move in a prescribed
|
|
fashion (e.g. rotate around a point), etc. Note that if a time
|
|
integration fix like <A HREF = "fix_nve.html">fix nve</A> or <A HREF = "fix_nh.html">fix nvt</A>
|
|
is not used with the group that contains wall particles, their
|
|
positions and velocities will not be updated.
|
|
</P>
|
|
<UL><LI><A HREF = "fix_aveforce.html">fix aveforce</A> - set force on particles to average value, so they move together
|
|
<LI><A HREF = "fix_setforce.html">fix setforce</A> - set force on particles to a value, e.g. 0.0
|
|
<LI><A HREF = "fix_freeze.html">fix freeze</A> - freeze particles for use as granular walls
|
|
<LI><A HREF = "fix_nve_noforce.html">fix nve/noforce</A> - advect particles by their velocity, but without force
|
|
<LI><A HREF = "fix_move.html">fix move</A> - prescribe motion of particles by a linear velocity, oscillation, rotation, variable
|
|
</UL>
|
|
<P>The <A HREF = "fix_move.html">fix move</A> command offers the most generality, since
|
|
the motion of individual particles can be specified with
|
|
<A HREF = "variable.html">variable</A> formula which depends on time and/or the
|
|
particle position.
|
|
</P>
|
|
<P>For rough walls, it may be useful to turn off pairwise interactions
|
|
between wall particles via the <A HREF = "neigh_modify.html">neigh_modify
|
|
exclude</A> command.
|
|
</P>
|
|
<P>Rough walls can also be created by specifying frozen particles that do
|
|
not move and do not interact with mobile particles, and then tethering
|
|
other particles to the fixed particles, via a <A HREF = "bond_style.html">bond</A>.
|
|
The bonded particles do interact with other mobile particles.
|
|
</P>
|
|
<P>Idealized walls can be specified via several fix commands. <A HREF = "fix_wall_gran.html">Fix
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|
wall/gran</A> creates frictional walls for use with
|
|
granular particles; all the other commands create smooth walls.
|
|
</P>
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|
<UL><LI><A HREF = "fix_wall_reflect.html">fix wall/reflect</A> - reflective flat walls
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|
<LI><A HREF = "fix_wall.html">fix wall/lj93</A> - flat walls, with Lennard-Jones 9/3 potential
|
|
<LI><A HREF = "fix_wall.html">fix wall/lj126</A> - flat walls, with Lennard-Jones 12/6 potential
|
|
<LI><A HREF = "fix_wall.html">fix wall/colloid</A> - flat walls, with <A HREF = "pair_colloid.html">pair_style colloid</A> potential
|
|
<LI><A HREF = "fix_wall.html">fix wall/harmonic</A> - flat walls, with repulsive harmonic spring potential
|
|
<LI><A HREF = "fix_wall_region.html">fix wall/region</A> - use region surface as wall
|
|
<LI><A HREF = "fix_wall_gran.html">fix wall/gran</A> - flat or curved walls with <A HREF = "pair_gran.html">pair_style granular</A> potential
|
|
</UL>
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|
<P>The <I>lj93</I>, <I>lj126</I>, <I>colloid</I>, and <I>harmonic</I> styles all allow the
|
|
flat walls to move with a constant velocity, or oscillate in time.
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|
The <A HREF = "fix_wall_region.html">fix wall/region</A> command offers the most
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|
generality, since the region surface is treated as a wall, and the
|
|
geometry of the region can be a simple primitive volume (e.g. a
|
|
sphere, or cube, or plane), or a complex volume made from the union
|
|
and intersection of primitive volumes. <A HREF = "region.html">Regions</A> can also
|
|
specify a volume "interior" or "exterior" to the specified primitive
|
|
shape or <I>union</I> or <I>intersection</I>. <A HREF = "region.html">Regions</A> can also be
|
|
"dynamic" meaning they move with constant velocity, oscillate, or
|
|
rotate.
|
|
</P>
|
|
<P>The only frictional idealized walls currently in LAMMPS are flat or
|
|
curved surfaces specified by the <A HREF = "fix_wall_gran.html">fix wall/gran</A>
|
|
command. At some point we plan to allow regoin surfaces to be used as
|
|
frictional walls, as well as triangulated surfaces.
|
|
</P>
|
|
<HR>
|
|
|
|
<A NAME = "4_18"></A><H4>4.18 Elastic constants
|
|
</H4>
|
|
<P>Elastic constants characterize the stiffness of a material. The formal
|
|
definition is provided by the linear relation that holds between the
|
|
stress and strain tensors in the limit of infinitesimal deformation.
|
|
In tensor notation, this is expressed as s_ij = C_ijkl * e_kl, where
|
|
the repeated indices imply summation. s_ij are the elements of the
|
|
symmetric stress tensor. e_kl are the elements of the symmetric strain
|
|
tensor. C_ijkl are the elements of the fourth rank tensor of elastic
|
|
constants. In three dimensions, this tensor has 3^4=81 elements. Using
|
|
Voigt notation, the tensor can be written as a 6x6 matrix, where C_ij
|
|
is now the derivative of s_i w.r.t. e_j. Because s_i is itself a
|
|
derivative w.r.t. e_i, it follows that C_ij is also symmetric, with at
|
|
most 6*5/2 = 21 distinct elements.
|
|
</P>
|
|
<P>At zero temperature, it is easy to estimate these derivatives by
|
|
deforming the cell in one of the six directions using the command
|
|
<A HREF = "displace_box.html">displace_box</A> and measuring the change in the
|
|
stress tensor. A general-purpose script that does this is given in the
|
|
examples/elastic directory described in <A HREF = "Section_example.html">this
|
|
section</A>.
|
|
</P>
|
|
<P>Calculating elastic constants at finite temperature is more
|
|
challenging, because it is necessary to run a simulation that perfoms
|
|
time averages of differential properties. One way to do this is to
|
|
measure the change in average stress tensor in an NVT simulations when
|
|
the cell volume undergoes a finite deformation. In order to balance
|
|
the systematic and statistical errors in this method, the magnitude of
|
|
the deformation must be chosen judiciously, and care must be taken to
|
|
fully equilibrate the deformed cell before sampling the stress
|
|
tensor. Another approach is to sample the triclinic cell fluctuations
|
|
that occur in an NPT simulation. This method can also be slow to
|
|
converge and requires careful post-processing <A HREF = "#Shinoda">(Shinoda)</A>
|
|
</P>
|
|
<HR>
|
|
|
|
<HR>
|
|
|
|
<A NAME = "Berendsen"></A>
|
|
|
|
<P><B>(Berendsen)</B> Berendsen, Grigera, Straatsma, J Phys Chem, 91,
|
|
6269-6271 (1987).
|
|
</P>
|
|
<A NAME = "Cornell"></A>
|
|
|
|
<P><B>(Cornell)</B> Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
|
|
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
|
|
</P>
|
|
<A NAME = "Horn"></A>
|
|
|
|
<P><B>(Horn)</B> Horn, Swope, Pitera, Madura, Dick, Hura, and Head-Gordon,
|
|
J Chem Phys, 120, 9665 (2004).
|
|
</P>
|
|
<A NAME = "MacKerell"></A>
|
|
|
|
<P><B>(MacKerell)</B> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
|
|
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
|
|
</P>
|
|
<A NAME = "Jorgensen"></A>
|
|
|
|
<P><B>(Jorgensen)</B> Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
|
|
Phys, 79, 926 (1983).
|
|
</P>
|
|
<A NAME = "Price"></A>
|
|
|
|
<P><B>(Price)</B> Price and Brooks, J Chem Phys, 121, 10096 (2004).
|
|
</P>
|
|
<A NAME = "Shinoda"></A>
|
|
|
|
<P><B>(Shinoda)</B> Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
|
|
</P>
|
|
</HTML>
|