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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,209 +0,0 @@ | ||
| import os | ||
|
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| import numpy as np | ||
|
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| from yt.funcs import mylog | ||
| from yt.geometry.selection_routines import GridSelector | ||
|
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| def parse_orion_sinks(fn): | ||
| r""" | ||
| Orion sink particles are stored in text files. This function | ||
| is for figuring what particle fields are present based on the | ||
| number of entries per line in the \*.sink file. | ||
| """ | ||
|
|
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| # Figure out the format of the particle file | ||
| with open(fn) as f: | ||
| lines = f.readlines() | ||
|
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| try: | ||
| line = lines[1] | ||
| except IndexError: | ||
| # a particle file exists, but there is only one line, | ||
| # so no sinks have been created yet. | ||
| index = {} | ||
| return index | ||
|
|
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| # The basic fields that all sink particles have | ||
| index = { | ||
| "particle_mass": 0, | ||
| "particle_position_x": 1, | ||
| "particle_position_y": 2, | ||
| "particle_position_z": 3, | ||
| "particle_momentum_x": 4, | ||
| "particle_momentum_y": 5, | ||
| "particle_momentum_z": 6, | ||
| "particle_angmomen_x": 7, | ||
| "particle_angmomen_y": 8, | ||
| "particle_angmomen_z": 9, | ||
| "particle_id": -1, | ||
| } | ||
|
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| if len(line.strip().split()) == 11: | ||
| # these are vanilla sinks, do nothing | ||
| pass | ||
|
|
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| elif len(line.strip().split()) == 17: | ||
| # these are old-style stars, add stellar model parameters | ||
| index["particle_mlast"] = 10 | ||
| index["particle_r"] = 11 | ||
| index["particle_mdeut"] = 12 | ||
| index["particle_n"] = 13 | ||
| index["particle_mdot"] = 14 | ||
| index["particle_burnstate"] = 15 | ||
|
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| elif len(line.strip().split()) == 18 or len(line.strip().split()) == 19: | ||
| # these are the newer style, add luminosity as well | ||
| index["particle_mlast"] = 10 | ||
| index["particle_r"] = 11 | ||
| index["particle_mdeut"] = 12 | ||
| index["particle_n"] = 13 | ||
| index["particle_mdot"] = 14 | ||
| index["particle_burnstate"] = 15 | ||
| index["particle_luminosity"] = 16 | ||
| else: | ||
| # give a warning if none of the above apply: | ||
| mylog.warning("Warning - could not figure out particle output file") | ||
| mylog.warning("These results could be nonsense!") | ||
|
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| return index | ||
|
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|
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| class BoxlibParticleSelectionMixin: | ||
| def _read_particle_selection(self, chunks, selector, fields): | ||
| rv = {} | ||
| chunks = list(chunks) | ||
|
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| if isinstance(selector, GridSelector): | ||
|
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| if not (len(chunks) == len(chunks[0].objs) == 1): | ||
| raise RuntimeError | ||
|
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| grid = chunks[0].objs[0] | ||
|
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| for ftype, fname in fields: | ||
| rv[ftype, fname] = self._read_particles(grid, fname) | ||
|
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| return rv | ||
|
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| rv = {f: np.array([]) for f in fields} | ||
| for chunk in chunks: | ||
| for grid in chunk.objs: | ||
| for ftype, fname in fields: | ||
| data = self._read_particles(grid, fname) | ||
| rv[ftype, fname] = np.concatenate((data, rv[ftype, fname])) | ||
| return rv | ||
|
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|
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| class BoxlibReadParticleFileMixin: | ||
| def _read_particle_file(self, fn): | ||
| """actually reads the orion particle data file itself.""" | ||
| if not os.path.exists(fn): | ||
| return | ||
| with open(fn) as f: | ||
| lines = f.readlines() | ||
| self.num_stars = int(lines[0].strip()[0]) | ||
| for num, line in enumerate(lines[1:]): | ||
| particle_position_x = float(line.split(" ")[1]) | ||
| particle_position_y = float(line.split(" ")[2]) | ||
| particle_position_z = float(line.split(" ")[3]) | ||
| coord = [particle_position_x, particle_position_y, particle_position_z] | ||
| # for each particle, determine which grids contain it | ||
| # copied from object_finding_mixin.py | ||
| mask = np.ones(self.num_grids) | ||
| for i in range(len(coord)): | ||
| np.choose( | ||
| np.greater(self.grid_left_edge.d[:, i], coord[i]), | ||
| (mask, 0), | ||
| mask, | ||
| ) | ||
| np.choose( | ||
| np.greater(self.grid_right_edge.d[:, i], coord[i]), | ||
| (0, mask), | ||
| mask, | ||
| ) | ||
| ind = np.where(mask == 1) | ||
| selected_grids = self.grids[ind] | ||
| # in orion, particles always live on the finest level. | ||
| # so, we want to assign the particle to the finest of | ||
| # the grids we just found | ||
| if len(selected_grids) != 0: | ||
| grid = sorted(selected_grids, key=lambda grid: grid.Level)[-1] | ||
| ind = np.where(self.grids == grid)[0][0] | ||
| self.grid_particle_count[ind] += 1 | ||
| self.grids[ind].NumberOfParticles += 1 | ||
|
|
||
| # store the position in the particle file for fast access. | ||
| try: | ||
| self.grids[ind]._particle_line_numbers.append(num + 1) | ||
| except AttributeError: | ||
| self.grids[ind]._particle_line_numbers = [num + 1] | ||
| return True | ||
|
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||
|
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| class BoxlibSetupParticleFieldsMixin: | ||
| def setup_particle_fields(self, ptype): | ||
| def _get_vel(axis): | ||
| def velocity(field, data): | ||
| return ( | ||
| data[(ptype, f"particle_momentum_{axis}")] | ||
| / data[(ptype, "particle_mass")] | ||
| ) | ||
|
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| return velocity | ||
|
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| for ax in "xyz": | ||
| self.add_field( | ||
| (ptype, f"particle_velocity_{ax}"), | ||
| sampling_type="particle", | ||
| function=_get_vel(ax), | ||
| units="code_length/code_time", | ||
| ) | ||
|
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| super().setup_particle_fields(ptype) | ||
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| class IOHandlerParticlesBoxlibMixin: | ||
| def _read_particles(self, grid, field): | ||
| """ | ||
| parses the Orion Star Particle text files | ||
| """ | ||
|
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| particles = [] | ||
|
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| if grid.NumberOfParticles == 0: | ||
| return np.array(particles) | ||
|
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| def read(line, field): | ||
| entry = line.strip().split(" ")[self.particle_field_index[field]] | ||
| return float(entry) | ||
|
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| try: | ||
| lines = self._cached_lines | ||
| for num in grid._particle_line_numbers: | ||
| line = lines[num] | ||
| particles.append(read(line, field)) | ||
| return np.array(particles) | ||
| except AttributeError: | ||
| fn = self.particle_filename | ||
| with open(fn) as f: | ||
| lines = f.readlines() | ||
| self._cached_lines = lines | ||
| for num in grid._particle_line_numbers: | ||
| line = lines[num] | ||
| particles.append(read(line, field)) | ||
| return np.array(particles) | ||
|
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| _particle_field_index = None | ||
|
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| @property | ||
| def particle_field_index(self): | ||
| if self._particle_field_index: | ||
| return self._particle_field_index | ||
|
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| index = parse_orion_sinks(self.particle_filename) | ||
|
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| self._particle_field_index = index | ||
| return self._particle_field_index | ||
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