def __init__(self, comm: Comm):
self.comm = comm
self.v: pk.View2D[pk.double] = t_v(0, 3)
self.mass: pk.View1D[pk.double] = t_mass(0)
self.type: pk.View1D[pk.int32] = t_type(0)
self.N_local: int = 0
# Reduction result
self.T: float = 0.0
def __init__(self, s: System, comm_depth: float):
super().__init__(s, comm_depth)
# copied from System
self.domain_x: float = 0.0
self.domain_y: float = 0.0
self.domain_z: float = 0.0
self.sub_domain_x: float = 0.0
self.sub_domain_y: float = 0.0
self.sub_domain_z: float = 0.0
self.sub_domain_hi_x: float = 0.0
self.sub_domain_hi_y: float = 0.0
self.sub_domain_hi_z: float = 0.0
self.sub_domain_lo_x: float = 0.0
self.sub_domain_lo_y: float = 0.0
self.sub_domain_lo_z: float = 0.0
self.x: pk.View2D[pk.double] = t_x(0, 3)
self.v: pk.View2D[pk.double] = t_v(0, 3)
self.f: pk.View2D[pk.double] = t_f(0, 3)
self.id: pk.View1D[pk.int32] = t_id(0)
self.type: pk.View1D[pk.int32] = t_type(0)
self.q: pk.View1D[pk.double] = t_q(0)
self.mass: pk.View1D[pk.double] = t_mass(0)
# copied from Comm
self.comm_depth: float = comm_depth
print("CommSerial")
self.pack_count: pk.View1D[pk.int32] = pk.View([1], pk.int32)
self.pack_indicies_all: pk.View2D[pk.int32] = pk.View(
[6, 0], pk.int32, layout=pk.Layout.LayoutRight)
self.num_ghost: List[int] = [0] * 6
self.ghost_offsets: List[int] = [0] * 6
self.phase: int = 0
# Assign
self.workunit_id: int = 0
# Needed for translation to succeed
self.N_local: int = 0
self.nparticles: int = 0
self.update_threads: int = 0
self.force_threads: int = 0
self.N_ghost: int = 0
self.pack_indicies: pk.View1D[pk.int32] = self.pack_indicies_all[0, :]
self.ghost_offsets: pk.View1D[pk.int32] = pk.View([6], pk.int32)
def compute(self, system: System) -> float:
self.v = system.v
self.mass = system.mass
self.type = system.type
self.N_local = system.N_local
pk.execute(pk.ExecutionSpace.Default, self)
self.v = t_v(0, 3)
self.mass = t_mass(0)
self.type = t_type(0)
factor: float = 0.5 * system.mvv2e
self.comm.reduce_float(self.KE, 1)
return self.KE * factor
def __init__(self):
self.N: int = 0
self.N_max: int = 0
self.N_local: int = 0
self.N_ghost: int = 0
self.ntypes: int = 1
self.x = t_x(0, 3, pk.double)
self.v = t_v(0, 3, pk.double)
self.f = t_f(0, 3, pk.double)
self.id = t_id(0, pk.int32)
self.type = t_type(0, pk.int32)
self.q = t_q(0, pk.double)
self.mass = t_mass(0, pk.double)
self.domain_x: float = 0.0
self.domain_y: float = 0.0
self.domain_z: float = 0.0
self.sub_domain_x: float = 0.0
self.sub_domain_y: float = 0.0
self.sub_domain_z: float = 0.0
self.sub_domain_hi_x: float = 0.0
self.sub_domain_hi_y: float = 0.0
self.sub_domain_hi_z: float = 0.0
self.sub_domain_lo_x: float = 0.0
self.sub_domain_lo_y: float = 0.0
self.sub_domain_lo_z: float = 0.0
self.mvv2e: float = 0.0
self.boltz: float = 0.0
self.dt: float = 0.0
self.do_print: bool = True
self.print_lammps: bool = False
def check_lammps_command(self, line: int) -> None:
known: bool = False
if self.input_data.words[line][0] == "":
known = True
command: str = self.input_data.words[line][0]
if "#" in command:
known = True
if command == "variable":
if self.system.do_print:
print("LAMMPS-Command:"
" 'variable' keyword is not supported in ExaMiniMD")
if command == "units":
unit: str = self.input_data.words[line][1]
if unit == "metal":
known = True
self.units = Units.UNITS_METAL.value
self.system.boltz = 8.617343e-5
self.system.mvv2e = 1.0364269e-4
self.system.dt = 0.001
elif unit == "real":
known = True
self.units = Units.UNITS_REAL.value
self.system.boltz = 0.0019872067
self.system.mvv2e = 48.88821291 * 48.88821291
if not self.timestepflag:
self.system.dt = 1.0
elif unit == "lj":
known = True
self.units = Units.UNITS_LJ.value
self.system.boltz = 1.0
self.system.mvv2e = 1.0
if not self.timestepflag:
self.system.dt = 0.005
else:
if self.system.do_print:
print("LAMMPS-Command: 'units' command only supports"
" 'real' and 'lj' in ExaMiniMD")
if command == "atom_style":
style: str = self.input_data.words[line][1]
if style == "atomic":
known = True
else:
if self.system.do_print:
print("LAMMPS-Command: 'atom_style' command only"
" supports 'atomic' in ExaMiniMD")
if command == "lattice":
lattice: str = self.input_data.words[line][1]
if lattice == "sc":
known = True
self.lattice_style = LatticeType.LATTICE_SC.value
self.lattice_constant = float(self.input_data.words[line][2])
elif lattice == "fcc":
known = True
self.lattice_style = LatticeType.LATTICE_FCC.value
self.lattice_constant = (
4.0 / float(self.input_data.words[line][2]))**(1.0 / 3.0)
else:
if self.system.do_print:
print("LAMMPS-Command: 'lattice' command only supports"
" 'sc' and 'fcc' in ExaMiniMD")
if self.input_data.words[line][3] == "origin":
self.lattice_offset_x = float(self.input_data.words[line][4])
self.lattice_offset_y = float(self.input_data.words[line][5])
self.lattice_offset_z = float(self.input_data.words[line][6])
if command == "region":
region: str = self.input_data.words[line][2]
if region == "block":
known = True
box: List[int] = [0] * 6
box[0] = int(self.input_data.words[line][3])
box[1] = int(self.input_data.words[line][4])
box[2] = int(self.input_data.words[line][5])
box[3] = int(self.input_data.words[line][6])
box[4] = int(self.input_data.words[line][7])
box[5] = int(self.input_data.words[line][8])
if box[0] != 0 or box[2] != 0 or box[4] != 0:
if self.system.do_print:
print("Error: LAMMPS-Command: region only allows for"
" boxes with 0,0,0 offset")
self.lattice_nx = box[1]
self.lattice_ny = box[3]
self.lattice_nz = box[5]
else:
if self.system.do_print:
print("LAMMPS-Command: 'region' command only supports"
" 'block' option in ExaMiniMD")
if command == "create_box":
known = True
self.system.ntypes = int(self.input_data.words[line][1])
self.system.mass = t_mass(self.system.ntypes)
if command == "create_atoms":
known = True
if command == "mass":
known = True
mass_type: int = int(self.input_data.words[line][1]) - 1
mass: float = float(self.input_data.words[line][2])
self.system.mass[mass_type] = mass
if command == "pair_style":
pair_style: str = self.input_data.words[line][1]
if pair_style == "lj/cut/idial":
known = True
self.force_type = ForceType.FORCE_LJ_IDIAL.value
self.force_cutoff = float(self.input_data.words[line][2])
self.force_line = line
elif pair_style == "lj/cut":
known = True
self.force_type = ForceType.FORCE_LJ.value
self.force_cutoff = float(self.input_data.words[line][2])
self.force_line = line
if pair_style == "snap":
known = True
self.force_type = ForceType.FORCE_SNAP.value
self.force_cutoff = 4.73442
self.force_line = line
if self.system.do_print and not known:
print("LAMMPS-Command: 'pair_style' command only supports"
" 'lj/cut', 'lj/cut/idial', and 'snap' style"
" in ExaMiniMD")
if command == "pair_coeff":
known = True
n_coeff_lines: int = self.force_coeff_lines.extent(0)
self.force_coeff_lines.resize(0, n_coeff_lines + 1)
self.force_coeff_lines[n_coeff_lines] = line
n_coeff_lines += 1
if command == "velocity":
known = True
if self.input_data.words[line][1] != "all":
if self.system.do_print:
print("Error: LAMMPS-Command: 'velocity' command can only"
" be applied to 'all'")
if self.input_data.words[line][2] != "create":
if self.system.do_print:
print("Error: LAMMPS-Command: 'velocity' command can only"
" be used with option 'create'")
self.temperature_target = float(self.input_data.words[line][3])
self.temperature_seed = int(self.input_data.words[line][4])
if command == "neighbor":
known = True
self.neighbor_skin = float(self.input_data.words[line][1])
if command == "neigh_modify":
known = True
for i in range(1, self.input_data.words_per_line - 1):
if self.input_data.words[line][i] == "every":
self.comm_exchange_rate = int(
self.input_data.words[line][i + 1])
if command == "fix":
if self.input_data.words[line][3] == "nve":
known = True
self.integrator_type = IntegratorType.INTEGRATOR_NVE.value
else:
if self.system.do_print:
print("LAMMPS-Command: 'fix' command only supports"
" 'nve' style in ExaMiniMD")
if command == "run":
known = True
self.nsteps = int(self.input_data.words[line][1])
if command == "thermo":
known = True
self.thermo_rate = int(self.input_data.words[line][1])
if command == "timestep":
known = True
self.system.dt = float(self.input_data.words[line][1])
self.timestepflag = True
if command == "newton":
known = True
newton: str = self.input_data.words[line][1]
if newton == "on":
self.comm_newton = 1
elif newton == "off":
self.comm_newton = 0
else:
if self.system.do_print:
print("LAMMPS-Command: 'newton' must be followed by"
" 'on' or 'off'")
if command == "":
known = True
if not known and self.system.do_print:
print("ERROR: unknown keyword")
self.input_data.print_line(line)