Mercurial > repos > astroteam > crbeam_astro_tool

annotate crbeam.py @ 0:f40d05521dca draft default tip

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planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
author astroteam
date Fri, 25 Apr 2025 19:33:20 +0000
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f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
astroteam
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diff changeset
1 import subprocess
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
astroteam
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2 import sys
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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3 import tempfile
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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4 from os import makedirs, path
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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5 from os.path import join
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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6
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7 import numpy as np
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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8
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9
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10 class objdict(dict):
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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11 def __getattr__(self, name):
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12 if name in self:
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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13 return self[name]
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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14 else:
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15 raise AttributeError("No such attribute: " + name)
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16
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17 def __setattr__(self, name, value):
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18 self[name] = value
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19
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20 def __delattr__(self, name):
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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21 if name in self:
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22 del self[name]
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23 else:
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24 raise AttributeError("No such attribute: " + name)
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25
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26
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27 class CRbeam(object):
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28 default_parameters = dict(
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29 nparticles=10000,
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30 z=0.1,
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31 emax=1e13,
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32 emin=1e7,
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33 emin_source=None, # if None, emin is used
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34 primary="photon",
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35 EGMF=0.0,
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36 lmaxEGMF=5,
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37 lminEGMF=0.05,
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38 background=12,
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39 )
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40
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41 particles = dict(
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42 electron=0, positron=1, photon=2, gamma=2, neutron=9, proton=10
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43 )
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44
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45 prog_name = "crbeam"
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46
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47 # Here we always use fixed power law E^{-1} for MC and then adjust weights for the events if needed
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48 power_law = 1
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49
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50 def __init__(self, **kwargs):
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51 self._step = 0
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52 self._cache = None
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53 self._size_per_step = 100
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54 p = objdict(self.default_parameters)
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55 p.update(kwargs)
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56 if p.emin_source is None:
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57 p.emin_source = p.emin
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58
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59 self._cache_name_prefix = (
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60 f"{p.primary}_z{p.z}_E_{p.emin:g}_{p.emax:g}_{p.background}"
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61 )
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62 if p.emin_source < p.emax:
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63 self._cache_name_prefix += (
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64 f"_pow{self.power_law}_Emin{p.emin_source:g}"
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65 )
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66 if p.EGMF > 0:
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67 self._cache_name_prefix += (
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68 f"_B{p.EGMF:g}_turbL{p.lminEGMF}-{p.lmaxEGMF}"
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69 )
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70
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71 self._cache_name_prefix += "_N"
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72
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73 self._output_dir = self._cache_name_prefix + f"{p.nparticles}"
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74
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75 p.primary = self.particles[p.primary]
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76
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77 self.p = p
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78
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79 @property
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80 def output_dir(self):
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81 return self._output_dir
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82
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83 @property
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84 def cache(self):
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85 from cache import CRbeamCache
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86
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87 if self._cache is None:
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88 self._cache = CRbeamCache()
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89 return self._cache
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90
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91 @property
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92 def command(self):
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93 result = f"{self.prog_name} "
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94 result += " ".join(
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95 [f"--{key} {value}" for key, value in self.p.items()]
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96 )
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97 result += " --output " + self.output_dir
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98 power = 1 if self.p.emin_source < self.p.emax else -1000
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99 result += f" --power {power}"
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100 if self.p.EGMF > 0:
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101 # use turbulent magnetic field with unique random orientation for all particles
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102 result += " -mft -mfr"
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103 return result
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104
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105 @property
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106 def output_path(self):
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107 return join(self.output_dir, "z0")
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108
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109 def run(self, force_overwrite):
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110 command_suffix = ""
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111 if force_overwrite:
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112 command_suffix = " --overwrite"
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113 if path.isdir(self.output_path) and not force_overwrite:
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114 return
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115 logs_dir = "logs"
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116 makedirs(logs_dir, exist_ok=True)
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117 log_file = f"{logs_dir}/{self.output_dir}.log"
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118 with tempfile.NamedTemporaryFile() as script_file:
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119 with open(script_file.name, "wt") as out_script:
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120 print("#!/bin/bash", file=out_script)
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121 print(
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122 self.command + command_suffix,
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123 "2>&1 1>" + log_file,
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124 file=out_script,
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125 )
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126 subprocess.run(["bash", script_file.name])
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127 return log_file
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128
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129 def run_cached(self, overwrite_local_cache=False):
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130 import shutil
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131
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132 output_root = self.output_dir
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133 if path.isdir(output_root):
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134 if not overwrite_local_cache:
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135 return self.output_path
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136 shutil.rmtree(output_root)
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137
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138 size = self.cache.get_cache_size(self._cache_name_prefix)
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139 print("s3 data size: ", size)
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140 skip_paths = []
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141 makedirs(self.output_path, exist_ok=False)
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142 if size < self.p.nparticles:
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143 try:
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144 self.p.nparticles = self.p.nparticles - size
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145 self.run(force_overwrite=True)
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146 skip_paths.append(self.upload_cache())
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147 finally:
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148 self.p.nparticles = self.p.nparticles + size
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149 else:
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150 self.p.nparticles = size
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151
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152 if size > 0: # append results from s3 cache to the local cach file
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153 self.cache.load_results(
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154 self.output_path + "/photon",
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155 self._cache_name_prefix,
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156 skip_paths=skip_paths,
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157 )
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158
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159 return self.output_path
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160
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161 def start_multistage_run(self, overwrite_local_cache=False, n_steps=10):
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162 """
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163 Initialize environment for running different parts of simulation in subsiquent calls of simulation_step
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164 This function is useful if we show progress by running code in different jupyter cells
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165 :param overwrite_local_cache: remove local cache
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166 :param n_steps: number intermediate steps
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167 :return: True if further simulation is needed, False if data is already available
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168 """
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169 import shutil
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170
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171 output_root = self.output_dir
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172 if path.isdir(output_root):
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173 if not overwrite_local_cache:
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174 return False
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175 shutil.rmtree(output_root)
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176
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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177 size = self.cache.get_cache_size(self._cache_name_prefix)
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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178 print("s3 data size: ", size)
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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179 if size >= self.p.nparticles:
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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180 makedirs(self.output_path, exist_ok=False)
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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181 self.cache.load_results(
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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182 self.output_path + "/photon", self._cache_name_prefix
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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183 )
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184 self.p.nparticles = size
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185 return False
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186 self.p.nparticles = self.p.nparticles - size
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187 self._size_per_step = max(
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188 100, int(np.ceil((self.p.nparticles) / n_steps))
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189 )
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190 self._step = 0
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191 return True
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192
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193 def simulation_step(self):
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194 size = self._size_per_step * self._step
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195 target_nparticles = self.p.nparticles
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196 if size >= target_nparticles:
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197 return False
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198 save_output_dir = self._output_dir
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199 try:
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200 adjusted_size_per_step = min(
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201 self._size_per_step, target_nparticles - size
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202 )
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203 self.p.nparticles = adjusted_size_per_step
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204 self._step += 1
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205 self._output_dir = f"{self._output_dir}_step{self._step}"
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206 self.run(force_overwrite=True)
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207 finally:
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208 self.p.nparticles = target_nparticles
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209 self._output_dir = save_output_dir
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210
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211 return size + adjusted_size_per_step < target_nparticles
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212
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213 def end_multistep_run(self):
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214 makedirs(self.output_path, exist_ok=False)
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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215 with tempfile.NamedTemporaryFile() as script_file:
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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216 with open(script_file.name, "wt") as task:
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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217 print(
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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218 f"cat {self.output_dir}_step*/z0/photon >"
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219 f" {self.output_path}/photon",
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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220 file=task,
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221 )
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222 subprocess.run(["bash", script_file.name])
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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223 try:
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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224 skip_paths = [self.upload_cache()]
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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225 self.cache.load_results(
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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226 self.output_path + "/photon",
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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227 self._cache_name_prefix,
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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228 skip_paths=skip_paths,
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229 )
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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230 self.p.nparticles = self.cache.get_cache_size(
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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231 self._cache_name_prefix
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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232 )
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233 except Exception as ex:
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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234 print(ex, file=sys.stderr)
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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235 return self.output_path
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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236
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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237 def upload_cache(self):
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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238 source_file = self.output_path + "/photon"
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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239 if not path.isfile(source_file):
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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240 if path.isdir(self.output_path):
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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241 print("empty result")
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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242 return None
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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243 else:
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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244 assert False, "result dir not found"
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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245 obj_name = self._cache_name_prefix + f"{self.p.nparticles}"
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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246 print("saving", source_file, "to s3 as", obj_name)
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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247 return self.cache.save(obj_name, source_file)
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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248
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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249 def remove_cache(self):
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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250 from cache import CRbeamCache
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251
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252 c = CRbeamCache()
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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253 prefix = (
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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254 self._cache_name_prefix
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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255 ) # todo: use metadata when metadata reading is implemented
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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256 c.detete_results(prefix)