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Diffstat (limited to 'Exec/Langmuir/python/Langmuir.py')
| -rwxr-xr-x | Exec/Langmuir/python/Langmuir.py | 550 |
1 files changed, 550 insertions, 0 deletions
diff --git a/Exec/Langmuir/python/Langmuir.py b/Exec/Langmuir/python/Langmuir.py new file mode 100755 index 000000000..9bc1ff7e7 --- /dev/null +++ b/Exec/Langmuir/python/Langmuir.py @@ -0,0 +1,550 @@ +#!/usr/bin/env python + +import sys +import ctypes +from ctypes.util import find_library +import numpy as np +from numpy.ctypeslib import ndpointer +import matplotlib.pyplot as plt + +libwarpx = ctypes.CDLL("libwarpx.so") +libc = ctypes.CDLL(find_library('c')) + +# some useful data structures and typenames +class Particle(ctypes.Structure): + _fields_ = [('x', ctypes.c_double), + ('y', ctypes.c_double), + ('z', ctypes.c_double), + ('id', ctypes.c_int), + ('cpu', ctypes.c_int)] + + +p_dtype = np.dtype([('x', 'f8'), ('y', 'f8'), ('z', 'f8'), + ('id', 'i4'), ('cpu', 'i4')]) + +c_double_p = ctypes.POINTER(ctypes.c_double) +LP_c_char = ctypes.POINTER(ctypes.c_char) +LP_LP_c_char = ctypes.POINTER(LP_c_char) + +# from where do I import these? this might only work for CPython... +PyBuf_READ = 0x100 +PyBUF_WRITE = 0x200 + +# this is a function for converting a ctypes pointer to a numpy array +def array1d_from_pointer(pointer, dtype, size): + if sys.version_info.major >= 3: + buffer_from_memory = ctypes.pythonapi.PyMemoryView_FromMemory + buffer_from_memory.argtypes = (ctypes.c_void_p, ctypes.c_int, ctypes.c_int) + buffer_from_memory.restype = ctypes.py_object + buf = buffer_from_memory(pointer, dtype.itemsize*size, PyBUF_WRITE) + else: + buffer_from_memory = ctypes.pythonapi.PyBuffer_FromReadWriteMemory + buffer_from_memory.restype = ctypes.py_object + buf = buffer_from_memory(pointer, dtype.itemsize*size) + return np.frombuffer(buf, dtype=dtype, count=size) + + +# set the arg and return types of the wrapped functions +f = libwarpx.amrex_init +f.argtypes = (ctypes.c_int, LP_LP_c_char) + +f = libwarpx.warpx_getParticleStructs +f.restype = ctypes.POINTER(ctypes.POINTER(Particle)) + +f = libwarpx.warpx_getParticleArrays +f.restype = ctypes.POINTER(c_double_p) + +f = libwarpx.warpx_getEfield +f.restype = ctypes.POINTER(c_double_p) + +f = libwarpx.warpx_getBfield +f.restype = ctypes.POINTER(c_double_p) + +f = libwarpx.warpx_getCurrentDensity +f.restype = ctypes.POINTER(c_double_p) + +f = libwarpx.warpx_addNParticles +f.argtypes = (ctypes.c_int, ctypes.c_int, + ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), + ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), + ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), + ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), + ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), + ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), + ctypes.c_int, + ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"), + ctypes.c_int) + +def initialize(): + ''' + + Initialize WarpX and AMReX. Must be called before + doing anything else. + + ''' + + # convert command line args to pass into amrex + argc = len(sys.argv) + argv = (LP_c_char * (argc+1))() + for i, arg in enumerate(sys.argv): + enc_arg = arg.encode('utf-8') + argv[i] = ctypes.create_string_buffer(enc_arg) + + libwarpx.amrex_init(argc, argv) + libwarpx.warpx_init() + + +def finalize(): + ''' + + Call finalize for WarpX and AMReX. Must be called at + the end of your script. + + ''' + libwarpx.warpx_finalize() + libwarpx.amrex_finalize() + + +def evolve(num_steps=-1): + ''' + + Evolve the simulation for num_steps steps. If num_steps=-1, + the simulation will be run until the end as specified in the + inputs file. + + Parameters + ---------- + + num_steps: int, the number of steps to take + + ''' + + libwarpx.warpx_evolve(num_steps); + +def add_particles(species_number, N, + x, y, z, ux, uy, uz, nattr, attr, unique_particles): + ''' + + A function for adding particles to the WarpX simulation. + + Parameters + ---------- + + species_number : the species to add the particle to + N : the number of particles + x, y, z : numpy arrays of the particle positions + ux, uy, uz : numpy arrays of the particle momenta + nattr : the number of particle attributes to add + attr : a 2D numpy array with the particle attributes + unique_particles : whether the particles are unique or duplicated on + several processes + + ''' + libwarpx.warpx_addNParticles(species_number, N, + x, y, z, ux, uy, uz, + nattr, attr, unique_particles) + +def get_particle_structs(species_number): + ''' + + This returns a list of numpy arrays containing the particle struct data + on each tile for this process. The particle data is represented as a structured + numpy array and contains the particle 'x', 'y', 'z', 'id', and 'cpu'. + + The data for the numpy arrays are not copied, but share the underlying + memory buffer with WarpX. The numpy arrays are fully writeable. + + Parameters + ---------- + + species_number : the species id that the data will be returned for + + Returns + ------- + + A List of numpy arrays. + + ''' + + particles_per_tile = ctypes.POINTER(ctypes.c_int)() + num_tiles = ctypes.c_int(0) + data = libwarpx.warpx_getParticleStructs(species_number, + ctypes.byref(num_tiles), + ctypes.byref(particles_per_tile)) + + particle_data = [] + for i in range(num_tiles.value): + arr = array1d_from_pointer(data[i], p_dtype, particles_per_tile[i]) + particle_data.append(arr) + + libc.free(particles_per_tile) + libc.free(data) + return particle_data + + +def get_particle_arrays(species_number, comp): + ''' + + This returns a list of numpy arrays containing the particle array data + on each tile for this process. + + The data for the numpy arrays are not copied, but share the underlying + memory buffer with WarpX. The numpy arrays are fully writeable. + + Parameters + ---------- + + species_number : the species id that the data will be returned for + comp : the component of the array data that will be returned. + + Returns + ------- + + A List of numpy arrays. + + ''' + + particles_per_tile = ctypes.POINTER(ctypes.c_int)() + num_tiles = ctypes.c_int(0) + data = libwarpx.warpx_getParticleArrays(species_number, comp, + ctypes.byref(num_tiles), + ctypes.byref(particles_per_tile)) + + particle_data = [] + for i in range(num_tiles.value): + arr = np.ctypeslib.as_array(data[i], (particles_per_tile[i],)) + arr.setflags(write=1) + particle_data.append(arr) + + libc.free(particles_per_tile) + libc.free(data) + return particle_data + + +def get_particle_x(species_number): + ''' + + Return a list of numpy arrays containing the particle 'x' + positions on each tile. + + ''' + structs = get_particle_structs(species_number) + return [struct['x'] for struct in structs] + + +def get_particle_y(species_number): + ''' + + Return a list of numpy arrays containing the particle 'y' + positions on each tile. + + ''' + structs = get_particle_structs(species_number) + return [struct['y'] for struct in structs] + + +def get_particle_z(species_number): + ''' + + Return a list of numpy arrays containing the particle 'z' + positions on each tile. + + ''' + structs = get_particle_structs(species_number) + return [struct['z'] for struct in structs] + + +def get_particle_id(species_number): + ''' + + Return a list of numpy arrays containing the particle 'z' + positions on each tile. + + ''' + structs = get_particle_structs(species_number) + return [struct['id'] for struct in structs] + + +def get_particle_cpu(species_number): + ''' + + Return a list of numpy arrays containing the particle 'z' + positions on each tile. + + ''' + structs = get_particle_structs(species_number) + return [struct['cpu'] for struct in structs] + + +def get_particle_weight(species_number): + ''' + + Return a list of numpy arrays containing the particle + weight on each tile. + + ''' + + return get_particle_arrays(species_number, 0) + + +def get_particle_ux(species_number): + ''' + + Return a list of numpy arrays containing the particle + x momentum on each tile. + + ''' + + return get_particle_arrays(species_number, 1) + + +def get_particle_uy(species_number): + ''' + + Return a list of numpy arrays containing the particle + y momentum on each tile. + + ''' + + return get_particle_arrays(species_number, 2) + + +def get_particle_uz(species_number): + ''' + + Return a list of numpy arrays containing the particle + z momentum on each tile. + + ''' + + return get_particle_arrays(species_number, 3) + + +def get_particle_Ex(species_number): + ''' + + Return a list of numpy arrays containing the particle + x electric field on each tile. + + ''' + + return get_particle_arrays(species_number, 4) + + +def get_particle_Ey(species_number): + ''' + + Return a list of numpy arrays containing the particle + y electric field on each tile. + + ''' + + return get_particle_arrays(species_number, 5) + + +def get_particle_Ez(species_number): + ''' + + Return a list of numpy arrays containing the particle + z electric field on each tile. + + ''' + + return get_particle_arrays(species_number, 6) + + +def get_particle_Bx(species_number): + ''' + + Return a list of numpy arrays containing the particle + x magnetic field on each tile. + + ''' + + return get_particle_arrays(species_number, 7) + + +def get_particle_By(species_number): + ''' + + Return a list of numpy arrays containing the particle + y magnetic field on each tile. + + ''' + + return get_particle_arrays(species_number, 8) + + +def get_particle_Bz(species_number): + ''' + + Return a list of numpy arrays containing the particle + z magnetic field on each tile. + + ''' + + return get_particle_arrays(species_number, 9) + + +def get_mesh_electric_field(level, direction, include_ghosts=True): + ''' + + This returns a list of numpy arrays containing the mesh electric field + data on each grid for this process. + + The data for the numpy arrays are not copied, but share the underlying + memory buffer with WarpX. The numpy arrays are fully writeable. + + Parameters + ---------- + + level : the AMR level to get the data for + direction : the component of the data you want + include_ghosts : whether to include ghost zones or not + + Returns + ------- + + A List of numpy arrays. + + ''' + + assert(level == 0) + + shapes = ctypes.POINTER(ctypes.c_int)() + size = ctypes.c_int(0) + ngrow = ctypes.c_int(0) + data = libwarpx.warpx_getEfield(level, direction, + ctypes.byref(size), ctypes.byref(ngrow), + ctypes.byref(shapes)) + ng = ngrow.value + grid_data = [] + for i in range(size.value): + shape=(shapes[3*i+0], shapes[3*i+1], shapes[3*i+2]) + arr = np.ctypeslib.as_array(data[i], shape) + arr.setflags(write=1) + if include_ghosts: + grid_data.append(arr) + else: + grid_data.append(arr[ng:-ng,ng:-ng,ng:-ng]) + + libc.free(shapes) + libc.free(data) + return grid_data + + +def get_mesh_magnetic_field(level, direction, include_ghosts=True): + ''' + + This returns a list of numpy arrays containing the mesh magnetic field + data on each grid for this process. + + The data for the numpy arrays are not copied, but share the underlying + memory buffer with WarpX. The numpy arrays are fully writeable. + + Parameters + ---------- + + level : the AMR level to get the data for + direction : the component of the data you want + include_ghosts : whether to include ghost zones or not + + Returns + ------- + + A List of numpy arrays. + + ''' + + assert(level == 0) + + shapes = ctypes.POINTER(ctypes.c_int)() + size = ctypes.c_int(0) + ngrow = ctypes.c_int(0) + data = libwarpx.warpx_getBfield(level, direction, + ctypes.byref(size), ctypes.byref(ngrow), + ctypes.byref(shapes)) + ng = ngrow.value + grid_data = [] + for i in range(size.value): + shape=(shapes[3*i+0], shapes[3*i+1], shapes[3*i+2]) + arr = np.ctypeslib.as_array(data[i], shape) + arr.setflags(write=1) + if include_ghosts: + grid_data.append(arr) + else: + grid_data.append(arr[ng:-ng,ng:-ng,ng:-ng]) + + libc.free(shapes) + libc.free(data) + return grid_data + + +def get_mesh_current_density(level, direction, include_ghosts=True): + ''' + + This returns a list of numpy arrays containing the mesh current density + data on each grid for this process. + + The data for the numpy arrays are not copied, but share the underlying + memory buffer with WarpX. The numpy arrays are fully writeable. + + Parameters + ---------- + + level : the AMR level to get the data for + direction : the component of the data you want + include_ghosts : whether to include ghost zones or not + + Returns + ------- + + A List of numpy arrays. + + ''' + + assert(level == 0) + + shapes = ctypes.POINTER(ctypes.c_int)() + size = ctypes.c_int(0) + ngrow = ctypes.c_int(0) + data = libwarpx.warpx_getCurrentDensity(level, direction, + ctypes.byref(size), ctypes.byref(ngrow), + ctypes.byref(shapes)) + ng = ngrow.value + grid_data = [] + for i in range(size.value): + shape=(shapes[3*i+0], shapes[3*i+1], shapes[3*i+2]) + arr = np.ctypeslib.as_array(data[i], shape) + arr.setflags(write=1) + if include_ghosts: + grid_data.append(arr) + else: + grid_data.append(arr[ng:-ng,ng:-ng,ng:-ng]) + + libc.free(shapes) + libc.free(data) + return grid_data + + +# here begins the actual simulation script +initialize() + +# run for ten time steps +evolve(10) + +x = get_particle_x(0) +y = get_particle_y(0) +plt.plot(x[0], y[0], '.') +plt.savefig("particles.png") + +# this returns a list of numpy arrays that hold the magnetic field +# data in the x-direction on each grid for level 0 +grid_data = get_mesh_magnetic_field(0, 0, False) + +# plot a slice through the second grid +plt.clf() +plt.pcolormesh(grid_data[1][9,:,:]) +plt.savefig("field.png") + +finalize() |
