fix external command¶
Syntax¶
fix ID group-ID external mode args
- ID, group-ID are documented in fix command
- external = style name of this fix command
- mode = pf/callback or pf/array
pf/callback args = Ncall Napply Ncall = make callback every Ncall steps Napply = apply callback forces every Napply steps pf/array args = Napply Napply = apply array forces every Napply steps
Examples¶
fix 1 all external pf/callback 1 1
fix 1 all external pf/callback 100 1
fix 1 all external pf/array 10
Description¶
This fix allows external programs that are running LIGGGHTS(R)-PUBLIC through its library interface to modify certain LIGGGHTS(R)-PUBLIC properties on specific timesteps, similar to the way other fixes do. The external driver can be a C/C++ or Fortran program or a Python script.
If mode is pf/callback then the fix will make a callback every Ncall timesteps or minimization iterations to the external program. The external program computes forces on atoms by setting values in an array owned by the fix. The fix then adds these forces to each atom in the group, once every Napply steps, similar to the way the fix addforce command works. Note that if Ncall > Napply, the force values produced by one callback will persist, and be used multiple times to update atom forces.
The callback function “foo” is invoked by the fix as:
foo(void *ptr, bigint timestep, int nlocal, int *ids, double **x, double **fexternal);
The arguments are as follows:
- ptr = pointer provided by and simply passed back to external driver
- timestep = current LIGGGHTS(R)-PUBLIC timestep
- nlocal = # of atoms on this processor
- ids = list of atom IDs on this processor
- x = coordinates of atoms on this processor
- fexternal = forces to add to atoms on this processor
Note that timestep is a “bigint” which is defined in src/lmptype.h, typically as a 64-bit integer.
Fexternal are the forces returned by the driver program.
The fix has a set_callback() method which the external driver can call to pass a pointer to its foo() function. See the couple/lammps_quest/lmpqst.cpp file in the LIGGGHTS(R)-PUBLIC distribution for an example of how this is done. This sample application performs classical MD using quantum forces computed by a density functional code Quest.
If mode is pf/array then the fix simply stores force values in an array. The fix adds these forces to each atom in the group, once every Napply steps, similar to the way the fix addforce command works.
The name of the public force array provided by the FixExternal class is
double **fexternal;
It is allocated by the FixExternal class as an (N,3) array where N is the number of atoms owned by a processor. The 3 corresponds to the fx, fy, fz components of force.
It is up to the external program to set the values in this array to the desired quantities, as often as desired. For example, the driver program might perform an MD run in stages of 1000 timesteps each. In between calls to the LIGGGHTS(R)-PUBLIC run command, it could retrieve atom coordinates from LIGGGHTS(R)-PUBLIC, compute forces, set values in fexternal, etc.
To use this fix during energy minimization, the energy corresponding to the added forces must also be set so as to be consistent with the added forces. Otherwise the minimization will not converge correctly.
This can be done from the external driver by calling this public method of the FixExternal class:
void set_energy(double eng);
where eng is the potential energy. Eng is an extensive quantity, meaning it should be the sum over per-atom energies of all affected atoms. It should also be provided in energy units consistent with the simulation. See the details below for how to insure this energy setting is used appropriately in a minimization.
Restart, fix_modify, output, run start/stop, minimize info¶
No information about this fix is written to binary restart files.
The fix_modify energy option is supported by this
fix to add the potential “energy” set by the external driver to the
system’s potential energy as part of thermodynamic output. This is a fictitious quantity but is
needed so that the minimize command can include the
forces added by this fix in a consistent manner. I.e. there is a
decrease in potential energy when atoms move in the direction of the
added force.
This fix computes a global scalar which can be accessed by various output commands. The scalar is the potential energy discussed above. The scalar stored by this fix is “extensive”.
No parameter of this fix can be used with the start/stop keywords of the run command.
The forces due to this fix are imposed during an energy minimization,
invoked by the minimize command.
Warning
If you want the fictitious potential energy associated with the added forces to be included in the total potential energy of the system (the quantity being minimized), you MUST enable the fix_modify energy option for this fix.