Include all the stupid tools required for BORG analysis and plotting

python_sample/gen_2lpt_asmooth.py

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+import os
+import h5py as h5
+import numpy as np
+import cosmotool as ct
+import icgen as bic
+import icgen.cosmogrowth as cg
+import sys
+import argparse
+
+ADAPT_SMOOTH="/home/bergeron1NS/lavaux/Software/cosmotool/build/sample/simple3DFilter"
+cosmo={'omega_M_0':0.3175, 'h':0.6711}
+cosmo['omega_lambda_0']=1-cosmo['omega_M_0']
+cosmo['omega_k_0'] = 0
+cosmo['omega_B_0']=0.049
+cosmo['SIGMA8']=0.8344
+cosmo['ns']=0.9624
+N0=256
+
+doSimulation=True
+
+astart=1.
+
+parser=argparse.ArgumentParser(description="Generate CIC density from 2LPT")
+parser.add_argument('--start', type=int, required=True)
+parser.add_argument('--end', type=int, required=True)
+parser.add_argument('--step', type=int, required=True)
+parser.add_argument('--base', type=str, required=True)
+parser.add_argument('--N', type=int, default=256)
+parser.add_argument('--output', type=str, default="fields_%d.h5")
+parser.add_argument('--supersample', type=int, default=1)
+args = parser.parse_args()
+
+
+
+for i in xrange(args.start, args.end, args.step):
+  print i
+
+  pos,vel,density,N,L,_ = bic.run_generation("%s/initial_density_%d.dat" % (args.base,i), 0.001, astart, 
+                                           cosmo, supersample=args.supersample, do_lpt2=True)
+
+  q = pos + vel
+
+  with h5.File("particles.h5", mode="w") as f:
+    f.create_dataset("particles", data=np.array(q).transpose())
+  
+  os.system(ADAPT_SMOOTH + " %s %lg %lg %d %lg %lg %lg" % ("particles.h5", 3000000, L, args.N, 0, 0, 0))
+  os.rename("fields.h5", args.output % i)