4.8.7. Writing a new fix style — LAMMPS documentation

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# 4.8.7. Writing a new fix style

Writing fix styles is a flexible way of extending LAMMPS. Users can implement many things using fixes. Some fix styles are only used internally to support compute styles or pair styles:

- change particles attributes (positions, velocities, forces, etc.). Examples: `FixNVE`, `FixFreeze`.

- read or write data. Example: `FixRestart`.

- adding or modifying properties due to geometry. Example: `FixWall`.

- interacting with other subsystems or external code: Examples: `FixTTM`, `FixExternal`, `FixMDI`

- saving information for analysis or future use (previous positions, for instance). Examples: `FixAveTime`, `FixStoreState`.

All fixes are derived from the `Fix` base class and must have a constructor with the signature: `FixPrintVel(class LAMMPS *, int, char **)`.

Every fix must be registered in LAMMPS by writing the following lines of code in the header before include guards:

    #ifdef FIX_CLASS
    // clang-format off
    FixStyle(print/vel,FixPrintVel);
    // clang-format on
    #else
    /* the definition of the FixPrintVel class comes here */
    ...
    #endif

Where `print/vel` is the style name of your fix in the input script and `FixPrintVel` is the name of the class. The header file would be called `fix_print_vel.h` and the implementation file `fix_print_vel.cpp`. These conventions allow LAMMPS to automatically integrate it into the executable when compiling and associate your new fix class with the designated keyword when it parses the input script.

Let’s write a simple fix which will print the average velocity at the end of each timestep. First of all, implement a constructor:

    FixPrintVel::FixPrintVel(LAMMPS *lmp, int narg, char **arg)
    : Fix(lmp, narg, arg)
    {
      if (narg < 4) utils::missing_cmd_args(FLERR, "fix print/vel", error);

      nevery = utils::inumeric(FLERR,arg[3],false,lmp);
      if (nevery <= 0)
        error->all(FLERR,"Illegal fix print/vel nevery value: {}", nevery);
    }

In the constructor you should parse the fix arguments which are specified in the script. All fixes have pretty much the same syntax: `fix <fix-ID> <fix group> <fix name> <fix arguments ...>`. The first 3 parameters are parsed by Fix base class constructor, while `<fix arguments>` should be parsed by you. In our case, we need to specify how often we want to print an average velocity. For instance, once in 50 timesteps: `fix 1 print/vel 50`. There is a special variable in the Fix class called `nevery` which specifies how often the method `end_of_step()` is called. Thus all we need to do is just set it up.

The next method we need to implement is `setmask()`:

    int FixPrintVel::setmask()
    {
      int mask = 0;
      mask |= FixConst::END_OF_STEP;
      return mask;
    }

Here the we specify which methods of the fix should be called during execution of a timestep. The constant `END_OF_STEP` corresponds to the `end_of_step()` method.

    void FixPrintVel::end_of_step()
    {
      // for add3, scale3
      using namespace MathExtra;

      double** v = atom->v;
      int nlocal = atom->nlocal;
      double localAvgVel[4]; // 4th element for particles count
      memset(localAvgVel, 0, 4 * sizeof(double));
      for (int particleInd = 0; particleInd < nlocal; ++particleInd) {
        add3(localAvgVel, v[particleInd], localAvgVel);
      }
      localAvgVel[3] = nlocal;
      double globalAvgVel[4];
      memset(globalAvgVel, 0, 4 * sizeof(double));
      MPI_Allreduce(localAvgVel, globalAvgVel, 4, MPI_DOUBLE, MPI_SUM, world);
      scale3(1.0 / globalAvgVel[3], globalAvgVel);
      if ((comm->me == 0) && screen) {
        utils::print(screen, "{}, {}, {}\n",
                     globalAvgVel[0], globalAvgVel[1], globalAvgVel[2]);
      }
    }

In the code above, we use MathExtra routines defined in `math_extra.h`. There are bunch of math functions to work with arrays of doubles as with math vectors. It is also important to note that LAMMPS code should always assume to be run in parallel and that atom data is thus distributed across the MPI ranks. Thus you can only process data from local atoms directly and need to use MPI library calls to combine or exchange data. For serial execution, LAMMPS comes bundled with the MPI STUBS library that contains the MPI library function calls in dummy versions that only work for a single MPI rank.

In this code we use an instance of Atom class. This object is stored in the Pointers class (see `pointers.h`) which is the base class of the Fix base class. This object contains references to various class instances (the original instances are created and held by the LAMMPS class) with all global information about the simulation system. Data from the Pointers class is available to all classes inherited from it using protected inheritance. Hence when you write you own class, which is going to use LAMMPS data, don’t forget to inherit from Pointers or pass a Pointer to it to all functions that need access. When writing fixes we inherit from class Fix which is inherited from Pointers so there is no need to inherit from it directly.

The code above computes average velocity for all particles in the simulation. Yet you have one unused parameter in fix call from the script: `group_name`. This parameter specifies the group of atoms used in the fix. So we should compute the average for all particles in the simulation only if `group_name == "all"`, but it can be any group. The group membership information of an atom is contained in the mask property of an atom and the bit corresponding to a given group is stored in the groupbit variable which is defined in Fix base class:

    for (int i = 0; i < nlocal; ++i) {
      if (atom->mask[i] & groupbit) {
      // Do all job here
      }
    }

Class Atom encapsulates atoms positions, velocities, forces, etc. Users can access them using the particle index. Note, that particle indexes are usually changed every few timesteps because of neighbor list rebuilds and spatial sorting (to improve cache efficiency).

Let us consider another Fix example: We want to have a fix which stores atoms position from the previous time step in your fix. The local atoms indexes may not be valid on the next iteration. In order to handle this situation there are several methods which should be implemented:

- `double memory_usage()`: return how much memory the fix uses (optional)

- `void grow_arrays(int)`: do reallocation of the per-particle arrays in your fix

- `void copy_arrays(int i, int j, int delflag)`: copy i-th per-particle information to j-th particle position. Used when atom sorting is performed. if delflag is set and atom j owns a body, move the body information to atom i.

- `void set_arrays(int i)`: sets i-th particle related information to zero

Note, that if your class implements these methods, it must add calls of add_callback and delete_callback to the constructor and destructor. Since we want to store positions of atoms from the previous timestep, we need to add `double** xold` to the header file. Than add allocation code to the constructor:

    FixSavePos::FixSavePos(LAMMPS *lmp, int narg, char **arg), xold(nullptr)
    {
    //...
      memory->create(xold, atom->nmax, 3, "FixSavePos:x");
      atom->add_callback(0);
    }

    FixSavePos::~FixSavePos() {
      atom->delete_callback(id, 0);
      memory->destroy(xold);
    }

Implement the aforementioned methods:

    double FixSavePos::memory_usage()
    {
      int nmax = atom->nmax;
      double bytes = 0.0;
      bytes += nmax * 3 * sizeof(double);
      return bytes;
    }

    void FixSavePos::grow_arrays(int nmax)
    {
      memory->grow(xold, nmax, 3, "FixSavePos:xold");
    }

    void FixSavePos::copy_arrays(int i, int j, int delflag)
    {
      memcpy(xold[j], xold[i], sizeof(double) * 3);
    }

    void FixSavePos::set_arrays(int i)
    {
      memset(xold[i], 0, sizeof(double) * 3);
    }

    int FixSavePos::pack_exchange(int i, double *buf)
    {
      int m = 0;
      buf[m++] = xold[i][0];
      buf[m++] = xold[i][1];
      buf[m++] = xold[i][2];

      return m;
    }

    int FixSavePos::unpack_exchange(int nlocal, double *buf)
    {
      int m = 0;
      xold[nlocal][0] = buf[m++];
      xold[nlocal][1] = buf[m++];
      xold[nlocal][2] = buf[m++];

      return m;
    }

Now, a little bit about memory allocation. We use the Memory class which is just a bunch of template functions for allocating 1D and 2D arrays. So you need to add include `memory.h` to have access to them.

Finally, if you need to write/read some global information used in your fix to the restart file, you might do it by setting the flag `restart_global = 1` in the constructor and implementing methods `void write_restart(FILE *fp)` and `void restart(char *buf)`. If, in addition, you want to write the per-atom property to restart files then these additional settings and functions are needed:

- a fix flag indicating this needs to be set `restart_peratom = 1;`

- `atom->add_callback()` and `atom->delete_callback()` must be called a second time with the final argument set to 1 instead of 0 (indicating restart processing instead of per-atom data memory management).

- the functions `void pack_restart(int i, double *buf)` and `void unpack_restart(int nlocal, int nth)` need to be implemented