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4.8. Notes for developers and code maintainers

This section documents how some of the code functionality within LAMMPS works at a conceptual level. Comments on code in source files typically document what a variable stores, what a small section of code does, or what a function does and its input/outputs. The topics on this page are intended to document code functionality at a higher level.

Available topics are:


4.8.1. Reading and parsing of text and text files

It is frequently required for a class in LAMMPS to read in additional data from a file, e.g. potential parameters from a potential file for manybody potentials. LAMMPS provides several custom classes and convenience functions to simplify the process. They offer the following benefits:

  • better code reuse and fewer lines of code needed to implement reading and parsing data from a file

  • better detection of format errors, incompatible data, and better error messages

  • exit with an error message instead of silently converting only part of the text to a number or returning a 0 on unrecognized text and thus reading incorrect values

  • re-entrant code through avoiding global static variables (as used by strtok())

  • transparent support for translating unsupported UTF-8 characters to their ASCII equivalents (the text-to-value conversion functions only accept ASCII characters)

In most cases (e.g. potential files) the same data is needed on all MPI ranks. Then it is best to do the reading and parsing only on MPI rank 0, and communicate the data later with one or more MPI_Bcast() calls. For reading generic text and potential parameter files the custom classes TextFileReader and PotentialFileReader are available. They allow reading the file as individual lines for which they can return a tokenizer class (see below) for parsing the line. Or they can return blocks of numbers as a vector directly. The documentation on File reader classes contains an example for a typical case.

When reading per-atom data, the data on each line of the file usually needs to include an atom ID so it can be associated with a particular atom. In that case the data can be read in multi-line chunks and broadcast to all MPI ranks with utils::read_lines_from_file(). Those chunks are then split into lines, parsed, and applied only to atoms the MPI rank “owns”.

For splitting a string (incrementally) into words and optionally converting those to numbers, the Tokenizer and ValueTokenizer can be used. Those provide a superset of the functionality of strtok() from the C-library and the latter also includes conversion to different types. Any errors while processing the string in those classes will result in an exception, which can be caught and the error processed as needed. Unlike the C-library functions atoi(), atof(), strtol(), or strtod() the conversion will check if the converted text is a valid integer or floating point number and will not silently return an unexpected or incorrect value. For example, atoi() will return 12 when converting “12.5”, while the ValueTokenizer class will throw an InvalidIntegerException if ValueTokenizer::next_int() is called on the same string.

4.8.2. Requesting and accessing neighbor lists

LAMMPS uses Verlet-style neighbor lists to avoid having to loop over all pairs of all atoms when computing pairwise properties with a cutoff (e.g. pairwise forces or radial distribution functions). There are three main algorithms that can be selected by the neighbor command: bin (the default, uses binning to achieve linear scaling with system size), nsq (without binning, quadratic scaling), multi (with binning, optimized for varying cutoffs or polydisperse granular particles). In addition to how the neighbor lists are constructed a number of different variants of neighbor lists need to be created (e.g. “full” or “half”) for different purposes and styles and those may be required in every time step (“perpetual”) or on some steps (“occasional”).

The neighbor list creation is managed by the Neighbor class. Individual classes can obtain a neighbor list by creating an instance of a NeighRequest class which is stored in a list inside the Neighbor class. The Neighbor class will then analyze the various requests and apply optimizations where neighbor lists that have the same settings will be created only once and then copied, or a list may be constructed by processing a neighbor list from a different request that is a superset of the requested list. The neighbor list build is then processed in parallel.

The most commonly required neighbor list is a so-called “half” neighbor list, where each pair of atoms is listed only once (except when the newton command setting for pair is off; in that case pairs straddling sub-domains or periodic boundaries will be listed twice). Thus these are the default settings when a neighbor list request is created in:

void Pair::init_style()
{
  neighbor->add_request(this);
}

void Pair::init_list(int /*id*/, NeighList *ptr)
{
  list = ptr;
}

The this pointer argument is required so the neighbor list code can access the requesting class instance to store the assembled neighbor list with that instance by calling its init_list() member function. The optional second argument (omitted here) contains a bitmask of flags that determines the kind of neighbor list requested. The default value used here asks for a perpetual “half” neighbor list.

Non-default values of the second argument need to be used to adjust a neighbor list request to the specific needs of a style an additional request flag is needed. The tersoff pair style, for example, needs a “full” neighbor list:

void PairTersoff::init_style()
{
  // [...]
  neighbor->add_request(this, NeighConst::REQ_FULL);
}

When a pair style supports r-RESPA time integration with different cutoff regions, the request flag may depend on the corresponding r-RESPA settings. Here an example from pair style lj/cut:

void PairLJCut::init_style()
{
  int list_style = NeighConst::REQ_DEFAULT;

  if (update->whichflag == 1 && utils::strmatch(update->integrate_style, "^respa")) {
    auto respa = (Respa *) update->integrate;
    if (respa->level_inner >= 0) list_style = NeighConst::REQ_RESPA_INOUT;
    if (respa->level_middle >= 0) list_style = NeighConst::REQ_RESPA_ALL;
  }
  neighbor->add_request(this, list_style);
  // [...]
}

Granular pair styles need neighbor lists based on particle sizes and not cutoff and also may require to have the list of previous neighbors available (“history”). For example with:

if (use_history) neighbor->add_request(this, NeighConst::REQ_SIZE | NeighConst::REQ_HISTORY);
else neighbor->add_request(this, NeighConst::REQ_SIZE);

In case a class would need to make multiple neighbor list requests with different settings each request can set an id which is then used in the corresponding init_list() function to assign it to the suitable pointer variable. This is done for example by the pair style meam:

void PairMEAM::init_style()
{
// [...]
  neighbor->add_request(this, NeighConst::REQ_FULL)->set_id(1);
  neighbor->add_request(this)->set_id(2);
}
void PairMEAM::init_list(int id, NeighList *ptr)
{
  if (id == 1) listfull = ptr;
  else if (id == 2) listhalf = ptr;
}

Fixes may require a neighbor list that is only build occasionally (or just once) and this can also be indicated by a flag. As an example here is the request from the FixPeriNeigh class which is created internally by Peridynamics pair styles:

neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);

It is also possible to request a neighbor list that uses a different cutoff than what is usually inferred from the pair style settings (largest cutoff of all pair styles plus neighbor list skin). The following is used in the compute rdf command implementation:

if (cutflag)
  neighbor->add_request(this, NeighConst::REQ_OCCASIONAL)->set_cutoff(mycutneigh);
else
  neighbor->add_request(this, NeighConst::REQ_OCCASIONAL);

The neighbor list request function has a slightly different set of arguments when created by a command style. In this case the neighbor list is always an occasional neighbor list, so that flag is not needed. However for printing the neighbor list summary the name of the requesting command should be set. Below is the request from the delete atoms command:

neighbor->add_request(this, "delete_atoms", NeighConst::REQ_FULL);

4.8.3. Fix contributions to instantaneous energy, virial, and cumulative energy

Fixes can calculate contributions to the instantaneous energy and/or virial of the system, both in a global and peratom sense. Fixes that perform thermostatting or barostatting can calculate the cumulative energy they add to or subtract from the system, which is accessed by the ecouple and econserve thermodynamic keywords. This subsection explains how both work and what flags to set in a new fix to enable this functionality.

Let’s start with thermostatting and barostatting fixes. Examples are the fix langevin and fix npt commands. Here is what the fix needs to do:

  • Set the variable ecouple_flag = 1 in the constructor. Also set scalar_flag = 1, extscalar = 1, and global_freq to a timestep increment which matches how often the fix is invoked.

  • Implement a compute_scalar() method that returns the cumulative energy added or subtracted by the fix, e.g. by rescaling the velocity of atoms. The sign convention is that subtracted energy is positive, added energy is negative. This must be the total energy added to the entire system, i.e. an “extensive” quantity, not a per-atom energy. Cumulative means the summed energy since the fix was instantiated, even across multiple runs. This is because the energy is used by the econserve thermodynamic keyword to check that the fix is conserving the total energy of the system, i.e. potential energy + kinetic energy + coupling energy = a constant.

And here is how the code operates:

  • The Modify class makes a list of all fixes that set ecouple_flag = 1.

  • The thermo_style custom command defines ecouple and econserve keywords.

  • These keywords sum the energy contributions from all the ecouple_flag = 1 fixes by invoking the energy_couple() method in the Modify class, which calls the compute_scalar() method of each fix in the list.


Next, here is how a fix contributes to the instantaneous energy and virial of the system. First, it sets any or all of these flags to a value of 1 in their constructor:

  • energy_global_flag to contribute to global energy, example: fix indent

  • energy_peratom_flag to contribute to peratom energy, fix cmap

  • virial_global_flag to contribute to global virial, example: fix wall

  • virial_peratom_flag to contribute to peratom virial, example: fix wall

The fix must also do the following:

  • For global energy, implement a compute_scalar() method that returns the energy added or subtracted on this timestep. Here the sign convention is that added energy is positive, subtracted energy is negative.

  • For peratom energy, invoke the ev_init(eflag,vflag) function each time the fix is invoked, which initializes per-atom energy storage. The value of eflag may need to be stored from an earlier call to the fix during the same timestep. See how the fix cmap command does this in src/MOLECULE/fix_cmap.cpp. When an energy for one or more atoms is calculated, invoke the ev_tally() function to tally the contribution to each atom. Both the ev_init() and ev_tally() methods are in the parent Fix class.

  • For global and/or peratom virial, invoke the v_init(vflag) function each time the fix is invoked, which initializes virial storage. When forces on one or more atoms are calculated, invoke the v_tally() function to tally the contribution. Both the v_init() and v_tally() methods are in the parent Fix class. Note that there are several variants of v_tally(); choose the one appropriate to your fix.

Note

The ev_init() and ev_tally() methods also account for global and peratom virial contributions. Thus you do not need to invoke the v_init() and v_tally() methods, if the fix also calculates peratom energies.

The fix must also specify whether (by default) to include or exclude these contributions to the global/peratom energy/virial of the system. For the fix to include the contributions, set either of both of these variables in the constructor:

  • thermo_energy = 1, for global and peratom energy

  • thermo_virial = 1, for global and peratom virial

Note that these variables are zeroed in fix.cpp. Thus if you don’t set the variables, the contributions will be excluded (by default)

However, the user has ultimate control over whether to include or exclude the contributions of the fix via the fix modify command:

  • fix modify energy yes to include global and peratom energy contributions

  • fix modify virial yes to include global and peratom virial contributions

If the fix contributes to any of the global/peratom energy/virial values for the system, it should be explained on the fix doc page, along with the default values for the energy yes/no and virial yes/no settings of the fix modify command.

Finally, these 4 contributions are included in the output of 4 computes:

These computes invoke a method of the Modify class to include contributions from fixes that have the corresponding flags set, e.g. energy_peratom_flag and thermo_energy for compute pe/atom.

Note that each compute has an optional keyword to either include or exclude all contributions from fixes. Also note that compute pe and compute pressure are what is used (by default) by thermodynamic output to calculate values for its pe and press keywords.

4.8.4. KSpace PPPM FFT grids

The various KSpace PPPM styles in LAMMPS use FFTs to solve Poisson’s equation. This subsection describes:

  • how FFT grids are defined

  • how they are decomposed across processors

  • how they are indexed by each processor

  • how particle charge and electric field values are mapped to/from the grid

An FFT grid cell is a 3d volume; grid points are corners of a grid cell and the code stores values assigned to grid points in vectors or 3d arrays. A global 3d FFT grid has points indexed 0 to N-1 inclusive in each dimension.

Each processor owns two subsets of the grid, each subset is brick-shaped. Depending on how it is used, these subsets are allocated as a 1d vector or 3d array. Either way, the ordering of values within contiguous memory x fastest, then y, z slowest.

For the 3d decomposition of the grid, the global grid is partitioned into bricks that correspond to the sub-domains of the simulation box that each processor owns. Often, this is a regular 3d array (Px by Py by Pz) of bricks, where P = number of processors = Px * Py * Pz. More generally it can be a tiled decomposition, where each processor owns a brick and the union of all the bricks is the global grid. Tiled decompositions are produced by load balancing with the RCB algorithm; see the balance rcb command.

For the FFT decompostion of the grid, each processor owns a brick that spans the entire x dimension of the grid while the y and z dimensions are partitioned as a regular 2d array (P1 by P2), where P = P1 * P2.

The following indices store the inclusive bounds of the brick a processor owns, within the global grid:

nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in = 3d decomposition brick
nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft = FFT decomposition brick
nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out = 3d decomposition brick + ghost cells

The in and fft indices are from 0 to N-1 inclusive in each dimension, where N is the grid size.

The out indices index an array which stores the in subset of the grid plus ghost cells that surround it. These indices can thus be < 0 or >= N.

The number of ghost cells a processor owns in each of the 6 directions is a function of:

neighbor skin distance (since atoms can move outside a proc subdomain)
qdist = offset or charge from atom due to TIP4P fictitious charge
order = mapping stencil size
shift = factor used when order is an even number (see below)

Here is an explanation of how the PPPM variables order, nlower / nupper, shift, and OFFSET work. They are the relevant variables that determine how atom charge is mapped to grid points and how field values are mapped from grid points to atoms:

order = # of nearby grid points in each dim that atom charge/field are mapped to/from
nlower,nupper = extent of stencil around the grid point an atom is assigned to
OFFSET = large integer added/subtracted when mapping to avoid int(-0.75) = 0 when -1 is the desired result

The particle_map() method assigns each atom to a grid point.

If order is even, say 4:

atom is assigned to grid point to its left (in each dim)
shift = OFFSET
nlower = -1, nupper = 2, which are offsets from assigned grid point
window of mapping grid pts is thus 2 grid points to left of atom, 2 to right

If order is odd, say 5:

atom is assigned to left/right grid pt it is closest to (in each dim)
shift = OFFSET + 0.5
nlower = 2, nupper = 2
if point is in left half of cell, then window of affected grid pts is 3 grid points to left of atom, 2 to right
if point is in right half of cell, then window of affected grid pts is 2 grid points to left of atom, 3 to right

These settings apply to each dimension, so that if order = 5, an atom’s charge is mapped to 125 grid points that surround the atom.