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b/examples/cuda/Project.toml new file mode 100644 index 0000000..b2be155 --- /dev/null +++ b/examples/cuda/Project.toml @@ -0,0 +1,4 @@ +[deps] +ArraysOfArrays = "65a8f2f4-9b39-5baf-92e2-a9cc46fdf018" +CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" +LAMMPS = "ee2e13b9-eee9-4449-aafa-cfa6a2dbe14d" diff --git a/examples/fix_external.jl b/examples/fix_external.jl new file mode 100644 index 0000000..27210e5 --- /dev/null +++ b/examples/fix_external.jl @@ -0,0 +1,65 @@ +using LAMMPS + +lmp = LMP() + +command(lmp, "units lj") +command(lmp, "atom_style atomic") +command(lmp, "atom_modify map array sort 0 0") +command(lmp, "box tilt large") + +# Setup box +x_hi = 10.0 +y_hi = 10.0 +z_hi = 10.0 +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") + +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") +command(lmp, "mass 1 1.0") + +# (x,y,z), natoms +# positions = rand(3, 10) .* 5 +positions = [4.4955289268519625 3.3999909266656836 4.420245465344918 2.3923580632470216 1.9933183377321746 2.3367019702697096 0.014668174434679937 4.5978923623562356 2.9389893820585025 4.800351333939365; 4.523573662784505 3.1582899538900304 2.5562765646443 3.199496583966941 4.891026316235915 4.689641854106464 2.7591724192198575 0.7491156338926308 1.258994308308421 2.0419941687773937; 2.256261603545908 0.694847945108647 4.058244561946366 3.044596885569421 2.60225212714946 4.0030490608195555 0.9941423774290642 1.8076536961230087 1.9712395260164222 1.2705916409499818] + +LAMMPS.API.lammps_scatter_atoms(lmp, "x", 1, 3, positions) + +command(lmp, "run 0") + +# extract forces +forces = extract_atom(lmp, "f") diff --git a/examples/fix_external_cuda.jl b/examples/fix_external_cuda.jl new file mode 100644 index 0000000..da06082 --- /dev/null +++ b/examples/fix_external_cuda.jl @@ -0,0 +1,161 @@ +using LAMMPS +using CUDA +using Adapt +using ArraysOfArrays + +lmp = LMP() + +command(lmp, "units lj") +command(lmp, "atom_style atomic") +command(lmp, "atom_modify map array sort 0 0") +command(lmp, "box tilt large") + +# Setup box +x_hi = 10.0 +y_hi = 10.0 +z_hi = 10.0 +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_cuda all external pf/callback 1 1") + +struct Potential{Coeff} + coefficients::Coeff +end + +function compute_force(p::Potential, rsq, itype, jtype) + coeff = p.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(p::Potential, rsq, itype, jtype) + coeff = p.coefficients[itype][jtype] + r2inv = 1.0/rsq + r6inv = r2inv^3 + lj3 = coeff[3] + lj4 = coeff[4] + return (r6inv * (lj3*r6inv - lj4)) +end + +const NEIGHMASK = 0x3FFFFFFF +const SBBITS = 30 +sbmask(atom) = (atom >> SBBITS) & 3 +const special_lj = CuArray([1.0, 0.0, 0.0 ,0.0]) + +LAMMPS.FixExternal(lmp, "julia_lj_cuda") do fix, timestep, nlocal, ids, x, fexternal + # Full neighbor list + idx = LAMMPS.pair_neighbor_list(fix.lmp, "zero", 1, 0, 0) + nelements = LAMMPS.API.lammps_neighlist_num_elements(fix.lmp, idx) + + potential = Potential((((48.0, 24.0, 4.0, 4.0),),)) + cutsq::Float64 = cutoff^2 + + # TODO how to obtain in fix + eflag = false + evflag = false + + newton_pair = LAMMPS.extract_setting(fix.lmp, "newton_pair") == 1 + # special_lj = extract_global(fix.lmp, "special_lj") + + type = LAMMPS.extract_atom(lmp, "type") + + # zero-out fexternal (noticed some undef memory) + fexternal .= 0 + + energies = CUDA.zeros(nlocal) + cu_fexternal = adapt(CuArray, fexternal) + cu_x = adapt(CuArray, x) + cu_type = adapt(CuArray, type) + + neighbors_array = VectorOfArrays{Int64, 2}() + ilist = Vector{Int64}() + + # Copy neighbor_list to Julia datastructure + for ii in 1:nelements + # local atom index (i.e. in the range [0, nlocal + nghost) + iatom, neigh = LAMMPS.neighbors(lmp, idx, ii) + push!(neighbors_array, reshape(neigh, (1, length(neigh)))) + push!(ilist, iatom) + end + neighbors_array = adapt(CuArray, neighbors_array) + ilist = adapt(CuArray, ilist) + + function kernel(potential, x, fexternal, energies, ilist, neighbors, cutsq, nlocal, type, special_lj) + ii = threadIdx().x + iatom = ilist[ii] + neighs = neighbors[ii] + + iatom += 1 # 1-based indexing + xtmp = x[1, iatom] + ytmp = x[2, iatom] + ztmp = x[3, iatom] + + itype = type[iatom] + + for jatom in neighs + factor_lj = special_lj[sbmask(jatom) + 1] + jatom &= NEIGHMASK + jatom += 1 # 1-based indexing + + 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 = factor_lj * compute_force(potential, rsq, itype, jtype) + + if iatom <= nlocal + CUDA.@atomic fexternal[1, iatom] += delx*fpair + CUDA.@atomic fexternal[2, iatom] += dely*fpair + CUDA.@atomic fexternal[3, iatom] += delz*fpair + if jatom <= nlocal || newton_pair + CUDA.@atomic fexternal[1, jatom] -= delx*fpair + CUDA.@atomic fexternal[2, jatom] -= dely*fpair + CUDA.@atomic fexternal[3, jatom] -= delz*fpair + end + energies[iatom] += compute_energy(potential, rsq, itype, jtype) + end + end + end + return nothing + end + + @cuda threads=nlocal kernel(potential, cu_x, cu_fexternal, energies, + ilist, neighbors_array, + cutsq, nlocal, cu_type, special_lj) + + copyto!(fexternal, cu_fexternal) # TODO async + total_energy = sum(energies) + energies = Array(energies) + + LAMMPS.API.lammps_fix_external_set_energy_peratom(fix.lmp, fix.name, energies) + LAMMPS.energy_global!(fix, total_energy) +end + +# Setup atoms +natoms = 10 +command(lmp, "create_atoms 1 random $natoms 1 NULL") +command(lmp, "mass 1 1.0") + +# (x,y,z), natoms +# positions = rand(3, 10) .* 5 +positions = [4.4955289268519625 3.3999909266656836 4.420245465344918 2.3923580632470216 1.9933183377321746 2.3367019702697096 0.014668174434679937 4.5978923623562356 2.9389893820585025 4.800351333939365; 4.523573662784505 3.1582899538900304 2.5562765646443 3.199496583966941 4.891026316235915 4.689641854106464 2.7591724192198575 0.7491156338926308 1.258994308308421 2.0419941687773937; 2.256261603545908 0.694847945108647 4.058244561946366 3.044596885569421 2.60225212714946 4.0030490608195555 0.9941423774290642 1.8076536961230087 1.9712395260164222 1.2705916409499818] + +LAMMPS.API.lammps_scatter_atoms(lmp, "x", 1, 3, positions) + +command(lmp, "run 0") + +# extract forces +forces = extract_atom(lmp, "f") diff --git a/src/LAMMPS.jl b/src/LAMMPS.jl index a9620d5..49c89ad 100644 --- a/src/LAMMPS.jl +++ b/src/LAMMPS.jl @@ -49,6 +49,7 @@ end mutable struct LMP @atomic handle::Ptr{Cvoid} + external_fixes::Dict{String, Any} function LMP(args::Vector{String}=String[], comm::Union{Nothing, MPI.Comm}=nothing) if !isempty(args) @@ -67,7 +68,7 @@ mutable struct LMP end end - this = new(handle) + this = new(handle, Dict{String, Any}()) finalizer(close!, this) return this end @@ -82,8 +83,10 @@ Shutdown an LMP instance. function close!(lmp::LMP) handle = @atomicswap lmp.handle = C_NULL if handle !== C_NULL - API.lammps_close(handle) + empty!(lmp.external_fixes) + API.lammps_close(handle) end + return nothing end function LMP(f::Function, args=String[], comm=nothing) @@ -154,6 +157,7 @@ end function extract_global(lmp::LMP, name, dtype=nothing) if dtype === nothing dtype = API.lammps_extract_global_datatype(lmp, name) + dtype == -1 && error("Could not find dataype for global $name") end dtype = API._LMP_DATATYPE_CONST(dtype) type = dtype2type(dtype) @@ -198,6 +202,7 @@ function extract_atom(lmp::LMP, name, if dtype === nothing dtype = API.lammps_extract_atom_datatype(lmp, name) + dtype == -1 && error("Could not find dataype for atom $name") dtype = API._LMP_DATATYPE_CONST(dtype) end @@ -361,6 +366,12 @@ function extract_variable(lmp::LMP, name::String, group=nothing) end end +function extract_setting(lmp, name) + val = API.lammps_extract_setting(lmp, name) + val == -1 && error("Could not find setting $name") + return val +end + function gather_atoms(lmp::LMP, name, T, count) if T === Int32 dtype = 0 @@ -376,4 +387,39 @@ 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 diff --git a/src/api.jl b/src/api.jl index 578439b..41dd51d 100644 --- a/src/api.jl +++ b/src/api.jl @@ -389,6 +389,10 @@ function lammps_flush_buffers(ptr) ccall((:lammps_flush_buffers, liblammps), Cvoid, (Ptr{Cvoid},), ptr) end +function lammps_fix_external_set_energy_peratom(handle, id, eng) + ccall((:lammps_fix_external_set_energy_peratom, liblammps), Cvoid, (Ptr{Cvoid}, Ptr{Cchar}, Ptr{Cdouble}), handle, id, eng) +end + function lammps_free(ptr) ccall((:lammps_free, liblammps), Cvoid, (Ptr{Cvoid},), ptr) end diff --git a/src/external.jl b/src/external.jl new file mode 100644 index 0000000..58bbd5c --- /dev/null +++ b/src/external.jl @@ -0,0 +1,116 @@ +function fix_external_callback end + +mutable struct FixExternal + lmp::LMP + name::String + callback + + function FixExternal(lmp::LMP, name::String, callback) + if haskey(lmp.external_fixes, name) + error("FixExternal has already been registered with $name") + end + + this = new(lmp, name, callback) + lmp.external_fixes[name] = this # preserves pair globally + + ctx = Base.pointer_from_objref(this) + callback = @cfunction(fix_external_callback, Cvoid, (Ptr{Cvoid}, Int64, Cint, Ptr{Cint}, Ptr{Ptr{Float64}}, Ptr{Ptr{Float64}})) + API.lammps_set_fix_external_callback(lmp, name, callback, ctx) + + return this + end +end + +FixExternal(callback, lmp::LMP, name::String) = FixExternal(lmp::LMP, name::String, callback) + +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,)) + + fix.callback(fix, timestep, nlocal, ids, x, fexternal) + return nothing +end + +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, ) + +const NEIGHMASK = 0x3FFFFFFF +const SBBITS = 30 +sbmask(atom) = (atom >> SBBITS) & 3 +const special_lj = [1.0, 0.0, 0.0 ,0.0] + +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) + + # TODO how to obtain in fix + eflag = false + evflag = false + + newton_pair = extract_setting(fix.lmp, "newton_pair") == 1 + # special_lj = extract_global(fix.lmp, "special_lj") + + type = LAMMPS.extract_atom(lmp, "type") + + # zero-out fexternal (noticed some undef memory) + fexternal .= 0 + + energies = zeros(nlocal) + + for ii in 1:nelements + # local atom index (i.e. in the range [0, nlocal + nghost) + 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] + factor_lj = special_lj[sbmask(jatom) + 1] + jatom &= NEIGHMASK + jatom += 1 # 1-based indexing + + 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 = factor_lj * compute_force(rsq, itype, jtype) + + if iatom <= nlocal + 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 + energies[iatom] += compute_energy(rsq, itype, jtype) + end + end + end + end + API.lammps_fix_external_set_energy_peratom(fix.lmp, fix.name, energies) + energy_global!(fix, sum(energies)) + end +end diff --git a/test/external_pair.jl b/test/external_pair.jl new file mode 100644 index 0000000..9fb18ce --- /dev/null +++ b/test/external_pair.jl @@ -0,0 +1,72 @@ +using LAMMPS +using Test + +lmp_native = LMP() +lmp_julia = LMP() + +for lmp in (lmp_native, lmp_julia) + command(lmp, "units lj") + command(lmp, "atom_style atomic") + command(lmp, "atom_modify map array sort 0 0") + command(lmp, "box tilt large") + + # Setup box + command(lmp, "boundary p p p") + command(lmp, "region cell block 0 10.0 0 10.0 0 10.0 units box") + command(lmp, "create_box 1 cell") +end + +cutoff = 2.5 +command(lmp_julia, "pair_style zero $cutoff") +command(lmp_julia, "pair_coeff * *") +command(lmp_julia, "fix julia_lj all external pf/callback 1 1") + +command(lmp_native, "pair_style lj/cut $cutoff") +command(lmp_native, "pair_coeff * * 1 1") + +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, "julia_lj", "zero", compute_force, compute_energy, cutoff) + +# Setup atoms +natoms = 10 +positions = rand(3, 10) .* 5 +for lmp in (lmp_native, lmp_julia) + command(lmp, "create_atoms 1 random $natoms 1 NULL") + command(lmp, "mass 1 1.0") + + LAMMPS.API.lammps_scatter_atoms(lmp, "x", 1, 3, positions) + + command(lmp, "run 0") +end + +# extract forces +forces_native = extract_atom(lmp_native, "f") +forces_julia = extract_atom(lmp_julia, "f") + +@testset "External Pair" begin + @test forces_native == forces_julia +end diff --git a/test/runtests.jl b/test/runtests.jl index 73b319a..96a76c9 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -13,6 +13,16 @@ LMP(["-screen", "none"]) do lmp @test_throws ErrorException command(lmp, "nonsense") end + +function f() + lmp = LMP(["-screen", "none"]) + @test LAMMPS.version(lmp) >= 0 + command(lmp, "clear") + @test_throws ErrorException command(lmp, "nonsense") + LAMMPS.close!(lmp) +end + + @testset "Variables" begin LMP(["-screen", "none"]) do lmp command(lmp, "box tilt large") @@ -42,3 +52,20 @@ end MPI.mpiexec() do mpiexec @test success(pipeline(`$mpiexec -n 2 $(Base.julia_cmd()) mpitest.jl`, stderr=stderr, stdout=stdout)) end + +LMP(["-screen", "none"]) do lmp + called = Ref(false) + command(lmp, "boundary p p p") + command(lmp, "region cell block 0 1 0 1 0 1 units box") + command(lmp, "create_box 1 cell") + command(lmp, "fix julia all external pf/callback 1 1") + LAMMPS.FixExternal(lmp, "julia") do fix, timestep, nlocal, ids, x, fexternal + LAMMPS.energy_global!(fix, 0.0) + called[] = true + end + command(lmp, "mass 1 1.0") + command(lmp, "run 0") + @test called[] == true +end + +include("external_pair.jl")