finish example

examples/fix_external.jl

@@ -15,14 +15,39 @@ command(lmp, "boundary p p p")
 command(lmp, "region cell block 0 $x_hi 0 $y_hi 0 $z_hi units box")
 command(lmp, "create_box 1 cell")
 
+# Use `pair_style zero` to create neighbor list for `julia_lj`
+cutoff = 2.5
+command(lmp, "pair_style zero $cutoff")
+command(lmp, "pair_coeff * *")
 command(lmp, "fix julia_lj all external pf/callback 1 1")
 
-# Register external fix
-lj = LAMMPS.FixExternal(lmp, "julia_lj") do fix, timestep, nlocal, ids, x, fexternal
-    @info "julia lj called" timestep nlocal
-    LAMMPS.energy_global!(fix, 0.0)
+const coefficients = Dict(
+    1 => Dict(
+        1 => [48.0, 24.0, 4.0,4.0]
+    )
+)
+
+function compute_force(rsq, itype, jtype)
+    coeff = coefficients[itype][jtype]
+    r2inv  = 1.0/rsq
+    r6inv  = r2inv^3
+    lj1 = coeff[1]
+    lj2 = coeff[2]
+    return (r6inv * (lj1*r6inv - lj2))*r2inv
+end
+
+function compute_energy(rsq, itype, jtype)
+    coeff = coefficients[itype][jtype]
+    r2inv  = 1.0/rsq
+    r6inv  = r2inv^3
+    lj3 = coeff[3]
+    lj4 = coeff[4]
+    return (r6inv * (lj3*r6inv - lj4))
 end
 
+# Register external fix
+lj = LAMMPS.PairExternal(lmp, "julia_lj", "zero", compute_force, compute_energy, cutoff)
+
 # Setup atoms
 natoms = 10
 command(lmp, "create_atoms 1 random $natoms 1 NULL")

src/LAMMPS.jl

@@ -300,6 +300,39 @@ function gather_atoms(lmp::LMP, name, T, count)
     return data
 end
 
+function pair_neighbor_list(lmp, name, exact, nsub, request)
+    idx = API.lammps_find_pair_neighlist(lmp, name, exact, nsub, request)
+    if idx == -1
+        error("Could not find neighbor list for pair $(name)")
+    end
+    return idx
+end
+
+function fix_neighbor_list(lmp, name, request)
+    idx = API.lammps_find_fix_neighlist(lmp, name, request)
+    if idx == -1
+        error("Could not find neighbor list for fix $(name)")
+    end
+    return idx
+end
+
+
+"""
+    neighbors(lmb::LMP, idx, element)
+
+Given a neighbor list `idx` and the element therein,
+return the atom index, and it's neigbors.
+"""
+function neighbors(lmp, idx, element)
+    r_iatom = Ref{Cint}()
+    r_numneigh = Ref{Cint}()
+    r_neighbors = Ref{Ptr{Cint}}(0)
+
+    API.lammps_neighlist_element_neighbors(lmp, idx, element - 1, r_iatom, r_numneigh, r_neighbors)
+
+    return r_iatom[], Base.unsafe_wrap(Array, r_neighbors[], r_numneigh[]; own = false)
+end
+
 include("external.jl")
 
 end # module

src/external.jl

@@ -25,9 +25,14 @@ FixExternal(callback, lmp::LMP, name::String) = FixExternal(lmp::LMP, name::Stri
 
 function fix_external_callback(ctx::Ptr{Cvoid}, timestep::Int64, nlocal::Cint, ids::Ptr{Cint}, x::Ptr{Ptr{Float64}}, fexternal::Ptr{Ptr{Float64}})
     fix = Base.unsafe_pointer_to_objref(ctx)::FixExternal
+    nlocal = Int(nlocal)
+
+    @debug "Calling fix_external_callback on" fix timestep nlocal
+    shape = (nlocal, 3)
+    x = unsafe_wrap(x, shape)
+    fexternal = unsafe_wrap(fexternal, shape)
+    ids = unsafe_wrap(ids, (nlocal,))
 
-    @debug "Calling fix_external_callback on" fix timestep ids x fexternal
-    # TODO wrap as arrays
     fix.callback(fix, timestep, nlocal, ids, x, fexternal)
     return nothing
 end
@@ -36,7 +41,57 @@ function energy_global!(fix::FixExternal, energy)
     API.lammps_fix_external_set_energy_global(fix.lmp, fix.name, energy)
 end
 
+function neighbor_list(fix::FixExternal, request)
+    fix_neighbor_list(fix.lmp, fix.name, request)
+end
+
 # TODO
 # virial_global!
 # function virial_global!(fix::FixExternal, )
 
+function PairExternal(lmp, name, neigh_name, compute_force, compute_energy, cut_global)
+    cutsq = cut_global^2
+    FixExternal(lmp, name) do fix, timestep, nlocal, ids, x, fexternal
+        # Full neighbor list
+        idx = pair_neighbor_list(fix.lmp, neigh_name, 1, 0, 0)
+        nelements = API.lammps_neighlist_num_elements(fix.lmp, idx)
+
+        type = LAMMPS.extract_atom(lmp, "type")
+
+        # zero-out fexternal (noticed some undef memory)
+        fexternal .= 0
+
+        for ii in 1:nelements
+            iatom, neigh = LAMMPS.neighbors(lmp, idx, ii)
+            iatom += 1 # 1-based indexing
+            xtmp, ytmp, ztmp = view(x, :, iatom) # TODO SArray?
+            itype = type[iatom]
+            for jj in 1:length(neigh)
+                jatom = neigh[jj] + 1
+                delx = xtmp - x[1, jatom]
+                dely = ytmp - x[2, jatom]
+                delz = ztmp = x[3, jatom]
+                jtype = type[jatom]
+
+                rsq = delx*delx + dely*dely + delz*delz;
+
+                if rsq < cutsq
+                    fpair = compute_force(rsq, itype, jtype)
+
+                    fexternal[1, iatom] += delx*fpair
+                    fexternal[2, iatom] += dely*fpair
+                    fexternal[3, iatom] += delz*fpair
+                    if jatom <= nlocal # newton_pair
+                        fexternal[1, jatom] -= delx*fpair
+                        fexternal[2, jatom] -= dely*fpair
+                        fexternal[3, jatom] -= delz*fpair
+                    end
+
+                    # todo call compute_energy
+                    # TODO eflag 
+                    # TODO evflag
+                end
+            end
+        end
+    end
+end