forked from lijiext/lammps
164 lines
6.1 KiB
HTML
164 lines
6.1 KiB
HTML
<HTML>
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<CENTER><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>
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<HR>
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<H3>fix external command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID group-ID external mode args
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>external = style name of this fix command
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<LI>mode = <I>pf/callback</I> or <I>pf/array</I>
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<PRE> <I>pf/callback</I> args = Ncall Napply
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Ncall = make callback every Ncall steps
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Napply = apply callback forces every Napply steps
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<I>pf/array</I> args = Napply
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Napply = apply array forces every Napply steps
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>fix 1 all external pf/callback 1 1
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fix 1 all external pf/callback 100 1
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fix 1 all external pf/array 10
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>This fix allows external programs that are running LAMMPS through its
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<A HREF = "Section_howto.html#howto_19">library interface</A> to modify certain
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LAMMPS properties on specific timesteps, similar to the way other
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fixes do. The external driver can be a <A HREF = "Section_howto.html#howto_19">C/C++ or Fortran
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program</A> or a <A HREF = "Section_python.html">Python
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script</A>.
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</P>
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<HR>
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<P>If mode is <I>pf/callback</I> then the fix will make a callback every
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<I>Ncall</I> timesteps or minimization iterations to the external program.
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The external program computes forces on atoms by setting values in an
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array owned by the fix. The fix then adds these forces to each atom
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in the group, once every <I>Napply</I> steps, similar to the way the <A HREF = "fix_addforce.html">fix
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addforce</A> command works. Note that if <I>Ncall</I> >
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<I>Napply</I>, the force values produced by one callback will persist, and
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be used multiple times to update atom forces.
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</P>
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<P>The callback function "foo" is invoked by the fix as:
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</P>
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<PRE>foo(void *ptr, bigint timestep, int nlocal, int *ids, double **x, double **fexternal);
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</PRE>
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<P>The arguments are as follows:
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</P>
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<UL><LI>ptr = pointer provided by and simply passed back to external driver
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<LI>timestep = current LAMMPS timestep
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<LI>nlocal = # of atoms on this processor
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<LI>ids = list of atom IDs on this processor
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<LI>x = coordinates of atoms on this processor
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<LI>fexternal = forces to add to atoms on this processor
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</UL>
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<P>Note that timestep is a "bigint" which is defined in src/lmptype.h,
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typically as a 64-bit integer.
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</P>
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<P>Fexternal are the forces returned by the driver program.
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</P>
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<P>The fix has a set_callback() method which the external driver can call
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to pass a pointer to its foo() function. See the
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couple/lammps_quest/lmpqst.cpp file in the LAMMPS distribution for an
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example of how this is done. This sample application performs
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classical MD using quantum forces computed by a density functional
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code <A HREF = "http://dft.sandia.gov/Quest">Quest</A>.
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</P>
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<HR>
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<P>If mode is <I>pf/array</I> then the fix simply stores force values in an
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array. The fix adds these forces to each atom in the group, once
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every <I>Napply</I> steps, similar to the way the <A HREF = "fix_addforce.html">fix
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addforce</A> command works.
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</P>
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<P>The name of the public force array provided by the FixExternal
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class is
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</P>
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<PRE>double **fexternal;
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</PRE>
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<P>It is allocated by the FixExternal class as an (N,3) array where N is
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the number of atoms owned by a processor. The 3 corresponds to the
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fx, fy, fz components of force.
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</P>
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<P>It is up to the external program to set the values in this array to
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the desired quantities, as often as desired. For example, the driver
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program might perform an MD run in stages of 1000 timesteps each. In
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between calls to the LAMMPS <A HREF = "run.html">run</A> command, it could retrieve
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atom coordinates from LAMMPS, compute forces, set values in fexternal,
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etc.
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</P>
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<HR>
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<P>To use this fix during energy minimization, the energy corresponding
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to the added forces must also be set so as to be consistent with the
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added forces. Otherwise the minimization will not converge correctly.
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</P>
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<P>This can be done from the external driver by calling this public
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method of the FixExternal class:
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</P>
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<PRE>void set_energy(double eng);
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</PRE>
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<P>where eng is the potential energy. Eng is an extensive quantity,
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meaning it should be the sum over per-atom energies of all affected
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atoms. It should also be provided in <A HREF = "units.html">energy units</A>
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consistent with the simulation. See the details below for how to
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insure this energy setting is used appropriately in a minimization.
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</P>
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<HR>
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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</P>
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<P>No information about this fix is written to <A HREF = "restart.html">binary restart
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files</A>.
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</P>
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<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
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fix to add the potential "energy" set by the external driver to the
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system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
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output</A>. This is a fictitious quantity but is
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needed so that the <A HREF = "minimize.html">minimize</A> command can include the
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forces added by this fix in a consistent manner. I.e. there is a
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decrease in potential energy when atoms move in the direction of the
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added force.
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</P>
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<P>This fix computes a global scalar which can be accessed by various
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<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
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potential energy discussed above. The scalar stored by this fix
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is "extensive".
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</P>
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<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
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the <A HREF = "run.html">run</A> command.
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</P>
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<P>The forces due to this fix are imposed during an energy minimization,
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invoked by the <A HREF = "minimize.html">minimize</A> command.
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</P>
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<P>IMPORTANT NOTE: If you want the fictitious potential energy associated
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with the added forces to be included in the total potential energy of
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the system (the quantity being minimized), you MUST enable the
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<A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for this fix.
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</P>
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<P><B>Restrictions:</B> none
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</P>
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<P><B>Related commands:</B> none
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</P>
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<P><B>Default:</B> none
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</P>
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</HTML>
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