4.5. 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.
4.5.1. 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.
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.
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:
global energy in compute pe
peratom energy in compute pe/atom
global virial in compute pressure
peratom virial in compute stress/atom
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.
4.5.2. 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.
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.
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
fft indices are from 0 to N-1 inclusive in each
dimension, where N is the grid size.
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
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.