unpack=True,
skiprows=2)
# mass, radius, velx, dens, temp, entr, ye = np.loadtxt(file2, usecols=(1, 0, 7, 2, 3, 6, 9),unpack=True,skiprows=11)
print(mass[-1] / 1.989e33)
# Define mass grid
n = 42
start_M = 1.49
end_M = 1.9
mass_grid = np.linspace(start_M, end_M, n)
print(mass_grid[-1])
# Get FLASH simulation data
path = "/home/zac/projects/data/stir/run_12.0/output/stir2_14may19_s12.0_alpha1.25"
myFiles = simfiles.FlashOutputFiles(path)
print(myFiles.dirname)
myChkfiles = myFiles.chkFilePaths()
files = [chkfiles for chkfiles in myChkfiles]
print("first checkpoint:", files[0])
print("last checkpoint:", files[-1])
print("datfile:", myFiles.datfile)
defVar = hdf5file.FLASH1dFile(files[-1]).loadDefindedVariables()
simTime = (lambda simFile: simFile.simulationTime)
time = singlerun.CCSN1dRun(path).chkfileloop(simTime)
table = [None] * (len(defVar))
output = []
out_time = []
out_rad = []
def setup(dir_path):
#path = "/mnt/research/SNAPhU/STIR/run_ps/"
#path = "./trial_test/step0"
paramFile = os.path.join(dir_path, "positions.txt")
param = np.loadtxt(paramFile, delimiter=",")
if len(param.shape) == 0 or len(param.shape) == 1:
param = np.reshape(param, (1, -1))
alphaL = param[:, 1]
dneut = param[:, 2]
dye = param[:, 3]
deint = param[:, 4]
detrb = param[:, 5]
#alphaL = (0.0, 0.2, 0.4, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.4)
#alphaD = (0.3333333333, 0.666666666)
runname = "mcmcPS"
restart = False
mcmcRun = "1"
i = 1
#for (a,b) in [(a,b) for a in alphaL for b in alphaD]:
for k in range(len(alphaL)):
a = alphaL[k]
b = dneut[k]
c = dye[k]
d = deint[k]
e = detrb[k]
# counter for file names
#mass = (9.0,9.25,9.5,9.75,10.0,10.25,10.5,10.75,11.0,11.25,11.5,11.75,12.0,12.25,12.5,12.75,13.0, \
# 13.1,13.2,13.3,13.4,13.5,13.6,13.7,13.8,13.9, \
# 14.0,14.1,14.2,14.3,14.4,14.5,14.6,14.7,14.8,14.9, \
# 15.0,15.1,15.2,15.3,15.4,15.5,15.6,15.7,15.8,15.9, \
# 16.0,16.1,16.2,16.3,16.4,16.5,16.6,16.7,16.8,16.9, \
# 17.0,17.1,17.2,17.3,17.4,17.5,17.6,17.7,17.8,17.9, \
# 18.0,18.1,18.2,18.3,18.4,18.5,18.6,18.7,18.8,18.9, \
# 19.0,19.1,19.2,19.3,19.4,19.5,19.6,19.7,19.8,19.9, \
# 20.0,20.1,20.2,20.3,20.4,20.5,20.6,20.7,20.8,20.9, \
# 21.0,21.1,21.2,21.3,21.4,21.5,21.6,21.7,21.8,21.9, \
# 22.0,22.1,22.2,22.3,22.4,22.5,22.6,22.7,22.8,22.9, \
# 23.0,23.1,24.0,25.0,26.0,27.0,28.0,29.0, \
# 30.0,31,32,33,35,40,45,50,55,60,70,80,100,120)
mass = [20.0]
path1 = "run_" + runname + "_" + str(i) # Sets the name of the run.
dir_loc = os.path.join(dir_path, path1)
if not os.path.isdir(dir_loc): # returns true if a directory exists.
os.makedirs(dir_loc) # Creates a run directory if it doesn't exist
mlt_filename = "run.mlt"
mlt_path = os.path.join(dir_loc, mlt_filename)
#print("fullpath = "+str(fullpath))
# ----------------------------------------
# This loop writes the bash script to run
# the simulations.
# ----------------------------------------
with open(mlt_path, "w+") as file:
file.write("#!/bin/bash -login\n")
file.write("\n")
file.write("### define resources needed:\n")
file.write("### walltime - how long you expect the job to run\n")
file.write("#PBS -l walltime=10:00:00\n")
file.write("\n")
file.write(
"### nodes:ppn - how many nodes & cores per node (ppn) that you require\n"
)
file.write("#PBS -l nodes=1:ppn=2,feature=intel16\n")
file.write("\n")
file.write("### mem: amount of memory that the job will need\n")
file.write("#PBS -l mem=4gb\n")
file.write("#PBS -A ptg\n") # Can Theo and I use this?
file.write("###Batch job\n")
# file.write("#PBS -t 1-138\n") # Will have to edit this
file.write(
"### you can give your job a name for easier identification\n")
file.write("#PBS -N param_study_" + str(k + 1) + "\n")
file.write("\n")
file.write("### load necessary modules, e.g.\n")
file.write("module purge\n")
file.write("module load Intel/16.3\n")
file.write("module load OpenMPI/2.0.1\n")
file.write("module load HDF5/1.8.18\n")
file.write("\n")
file.write(
"### change to the working directory where your code is located\n"
)
# --- Change this On Runtime ---
#file.write("cd /mnt/research/SNAPhU/STIR/run_ps/"+path1+"/output${PBS_ARRAYID}\n")
file.write("cd " + str(dir_loc) + "/output\n")
file.write("\n")
file.write("### call your executable\n")
file.write("mpirun -np 2 flash4 \n")
## Copy FLASH executable to run directory once, then symlink to m directories
#dest = os.path.join(path1,"flash4")
#if os.path.isfile(dest):
# print('file exists')
# os.remove(dest)
## Source for flash executable:
#src = "/mnt/research/SNAPhU/STIR/run_sukhbold/flash4_1f31289"
#shutil.copy(src,dest)
# --- Do We Need This? ---
# I think that we do not need loops over mass.
# Creates output files labelled by mass.
outfull = ""
for m in mass:
#path = "output"#+str(mass.index(m)+1) # We don't need so many
dest1 = os.path.join(dir_path, path1)
if not os.path.isdir(dest1):
os.makedirs(dest1)
out = "output"
outfull = os.path.join(dest1, out)
if not os.path.isdir(outfull):
os.makedirs(outfull)
## Now make symlinks to copied executable
#src = "/mnt/research/SNAPhU/STIR/run_ps/flash4_1f31289" #change this once in HPC
src = "/mnt/research/SNAPhU/STIR/run_sukhbold/flash4_jul3"
dest = os.path.join(outfull, "flash4")
if os.path.isfile(dest):
os.remove(dest)
os.symlink(src, dest)
print(dest)
## EOS table
dest = os.path.join(outfull, "SFHo.h5")
if os.path.isfile(dest):
print('file exists')
os.remove(dest)
os.mkdir(os.path.join(outfull, "sim_output"))
## Source for eos table:
src = "/mnt/research/SNAPhU/Tables/SFHo.h5"
os.symlink(src, dest)
dest = os.path.join(outfull, "NuLib_SFHo.h5")
if os.path.isfile(dest):
print('file exists')
os.remove(dest)
## Source for opacity table:
src = "/mnt/research/SNAPhU/Tables/NuLib_SFHo_noweakrates_rho82_temp65_ye60_ng12_ns3_Itemp65_Ieta61_version1.0_20170719.h5"
os.symlink(src, dest)
dest = os.path.join(outfull, "mesa20_SFHo_GREP_15.82ms_12.flash")
if os.path.isfile(dest):
print('file exists')
os.remove(dest)
## Source for progenitor:
src = os.path.join("/mnt/research/SNAPhU/Progenitors2",
"mesa20_SFHo_GREP_15.82ms_12.flash")
os.symlink(src, dest)
path2 = outfull
if restart:
path2 = os.path.join(
path, "stir_" + runname + "_s" + str(m) + "_alpha" + str(a))
myFiles = simfiles.FlashOutputFiles(path)
myChkfiles = myFiles.chkFilePaths()
files = [chkfiles for chkfiles in myChkfiles]
print("last checkpoint:" + str(files[-1]))
refile = files[-1]
refile = refile[-4:]
par_filename = "flash.par"
par_path = os.path.join(outfull, par_filename)
#print("fullpath2 = "+str(fullpath2))
# ----------------------------------------
# Write the flash.par file
# ----------------------------------------
with open(par_path, "w") as file:
file.write("# Parameters file for 1D M1 Core Collapse with MLT\n")
file.write("basenm = \"run_" + runname + "_" +
str(i) + "\"\n")
if restart:
file.write("restart = .true.\n")
file.write("checkpointFileNumber = " + str(refile) + "\n")
else:
file.write("restart = .false.\n")
file.write("checkpointFileNumber = 0000 \n")
file.write("plotFileNumber = 0\n")
file.write("output_directory = \"sim_output\"\n")
file.write("\n")
file.write("# IO\n")
file.write("wr_integrals_freq = 20\n")
file.write("checkpointFileIntervalStep = 0\n")
file.write("checkpointFileIntervalTime = 0.01\n")
file.write("plotFileIntervalStep = 0\n")
file.write("plotFileIntervalTime = 0.00\n")
file.write("particleFileIntervalTime = 0.000\n")
file.write("wall_clock_time_limit = 86000\n")
file.write("\n")
file.write("#particles\n")
file.write("useparticles = .false.\n")
file.write("pt_dtfactor = 0.5\n")
file.write("pt_numR = 200\n")
file.write("pt_numT = 160\n")
file.write("pt_numP = 1\n")
file.write("\n")
file.write(
"pt_initialRMin = 1.97d8 #unique to every progenitor and t_init, center around region of interest\n"
)
file.write(
"pt_initialRMax = 7.0d8 #unique to every progenitor and t_init, center around region of interest\n"
)
file.write("pt_initialCTMin = -1.0d0\n")
file.write("pt_initialCTMax = 1.0d0\n")
file.write("pt_initialPMin = 0.0d0\n")
file.write("pt_initialPMax = 6.2831853072d0\n")
file.write("pt_maxPerProc = 32000\n")
file.write("\n")
file.write("# Time\n")
file.write("tinitial = 0.005\n")
file.write("tmax = 0.135\n"
) # May need to change
file.write("nend = 1000000000\n")
file.write("#nend = 1\n")
file.write("tstep_change_factor = 1.05\n")
file.write("dtinit = 1.E-8\n")
file.write("dtmax = 1.E5\n")
file.write("dtmin = 1.E-20\n")
file.write("useHPCC = .true.\n")
file.write("\n")
file.write("# Domain\n")
file.write("geometry = \"spherical\"\n")
file.write("xmin = 0.0\n")
if (m == 9.0 or m == 9.25):
file.write("xmax = 1.3e9\n")
else:
file.write("xmax = 1e9\n")
file.write("xl_boundary_type = \"reflect\"\n")
file.write("xr_boundary_type = \"user\"\n")
file.write("\n")
file.write("# Grid/Refinement\n")
file.write("nblockx = 8\n")
file.write("nblocky = 1\n")
file.write("nblockz = 1\n")
file.write("\n")
file.write("gr_lrefineMaxRedDoByLogR = .true.\n")
file.write("gr_angularResolution = 0.4\n")
file.write("lrefine_max = 9\n")
file.write("lrefine_min = 1\n")
file.write("refine_var_1 = \"dens\"\n")
file.write("refine_var_2 = \"pres\"\n")
file.write("refine_var_3 = \"none\"\n")
file.write("refine_var_4 = \"none\"\n")
file.write("refine_cutoff_1 = 0.8\n")
file.write("refine_cutoff_2 = 0.8\n")
file.write("refine_cutoff_3 = 0.8\n")
file.write("refine_cutoff_4 = 0.8\n")
file.write("\n")
file.write("# Simulation\n")
file.write("model_file = \"mesa20_SFHo_GREP_15.82ms_12.flash\"\n")
file.write("#rnd_seed = 1000\n")
file.write("#rnd_scale = 0.001\n")
file.write("nsub = 4\n")
file.write("vel_mult = 1.0\n")
file.write("ener_exp = 0.0\n")
file.write("r_exp_max = 0.0\n")
file.write("r_exp_min = 0.0\n")
file.write(
"mass_loss = 1.0e-4 # Solar masses per year\n"
)
file.write("vel_wind = 1.0e4 # cm/s\n")
file.write("use_PnotT = .FALSE.\n")
file.write("rot_a = 8.0e7\n")
file.write("rot_omega = 0.\n")
file.write("use_perturb = .false.\n")
file.write("mag_e = 1.0e18\n")
file.write("perturb_radMax = 2.4e8\n")
file.write("perturb_radMin = 1.82952e8\n")
file.write("perturb_nodes = 5\n")
file.write("perturb_mag = 0.2\n")
file.write("mri_refine = .false.\n")
file.write("mri_time = 0.0\n")
file.write("alwaysRefineShock = .false.\n")
file.write("\n")
file.write("# Hydro\n")
file.write("useHydro = .TRUE.\n")
file.write("cfl = 0.5\n")
file.write("interpol_order = 2\n")
file.write("updateHydroFluxes = .TRUE.\n")
file.write("eintSwitch = 0.0 # Always use Etot\n")
file.write("#convertToConsvdForMeshCalls = .false.\n")
file.write("#converttoconsvdinmeshinterp = .false.\n")
file.write("\n")
file.write(
"## SWITCHES SPECIFIC TO THE UNSPLIT HYDRO SOLVER ##\n"
)
file.write("# I. INTERPOLATION SCHEME:\n")
file.write(
"order = 3 # Interpolation order (first/second/third/fifth order)\n"
)
file.write(
"slopeLimiter = \"hybrid\" # Slope limiters (minmod, mc, vanLeer, hybrid, limited)\n"
)
file.write(
"LimitedSlopeBeta= 1. # Slope parameter for the \"limited\" slope by Toro\n"
)
file.write(
"charLimiting = .true. # Characteristic limiting vs.Primitive limiting\n"
)
file.write("\n")
file.write(
"use_avisc = .true. # use artificial viscosity (originally for PPM)\n"
)
file.write(
"cvisc = 0.2 # coefficient for artificial viscosity\n"
)
file.write(
"use_flattening = .true. # use flattening (dissipative) (originally for PPM)\n"
)
file.write(
"use_steepening = .false. # use contact steepening (originally for PPM)\n"
)
file.write(
"use_upwindTVD = .false. # use upwind biased TVD slope for PPM (need nguard=6)\n"
)
file.write("flux_correct = .true.\n")
file.write("\n")
file.write("# II. RIEMANN SOLVERS:\n")
file.write(
"RiemannSolver = \"HLLC\" # Roe, HLL, HLLC, LLF, Marquina\n"
)
file.write(
"entropy = .false. # Entropy fix for the Roe solver\n"
)
file.write("EOSforRiemann = .true.\n")
file.write("use_hybridRiemann = .true.\n")
file.write("\n")
file.write("# III. STRONG SHOCK HANDELING SCHEME:\n")
file.write(
"shockDetect = .true. # Shock Detect for numerical stability\n"
)
file.write("shockLowerCFL = .false.\n")
file.write("\n")
file.write(
"## -------------------------------------------------------------##\n"
)
file.write("\n")
file.write("# Gravity\n")
file.write("useGravity = .true.\n")
file.write("updateGravity = .TRUE.\n")
file.write("grav_boundary_type = \"isolated\"\n")
file.write("mpole_3daxisymmetry = .false.\n")
file.write("mpole_dumpMoments = .FALSE.\n")
file.write("mpole_PrintRadialInfo = .false.\n")
file.write("mpole_IgnoreInnerZone = .false.\n")
file.write("mpole_lmax = 0\n")
file.write("mpole_ZoneRadiusFraction_1 = 1.0\n")
file.write("mpole_ZoneExponent_1 = 0.005\n")
file.write("mpole_ZoneScalar_1 = 0.5\n")
file.write("mpole_ZoneType_1 = \"logarithmic\"\n")
file.write("point_mass = 0.0\n")
file.write("point_mass_rsoft = 0.e0\n")
file.write("use_gravHalfUpdate = .TRUE.\n")
file.write("use_gravConsv = .FALSE.\n")
file.write("use_gravPotUpdate = .FALSE.\n")
file.write("mpole_useEffectivePot = .true.\n")
file.write("mpole_EffPotNum = 1000\n")
file.write("\n")
file.write("# Hole\n")
file.write("useHole = .FALSE.\n")
file.write("hole_radius = 90e5 #2.0e8\n")
file.write(
"hole_bnd = 1 #diode=0, reflect=1, outflow=2\n")
file.write("hole_time = 0.0 #3.0\n")
file.write("hole_vel = 0.0 #1.0e7\n")
file.write("\n")
file.write("# Nuclear Burning\n")
file.write("#useBurn = .FALSE.\n")
file.write("#useBurnTable = .FALSE.\n")
file.write("#burnUpdateEint = .FALSE.\n")
file.write("#enucDtFactor = 1.e30\n")
file.write("#nuclearDensMax = 1.0E14\n")
file.write("#nuclearDensMin = 1.0E-10\n")
file.write("#nuclearNI56Max = 1.0\n")
file.write("#nuclearTempMax = 1.0E12\n")
file.write("#nuclearTempMin = 1.1E8\n")
file.write("#odeStepper = 1\n")
file.write("#algebra = 2\n")
file.write("#useShockBurn = .FALSE.\n")
file.write("\n")
file.write("#MLT\n")
file.write("useMLT = .true.\n")
file.write("mlt_alphaL = " + str(a) + "\n")
file.write("mlt_Dneut = " + str(b) + "\n")
file.write("mlt_Dye = " + str(c) + "\n")
file.write("mlt_Deint = " + str(d) + "\n")
file.write("mlt_Detrb = " + str(e) + "\n")
file.write("\n")
file.write("# EOS\n")
file.write("eos_file = \"./SFHo.h5\"\n")
file.write("eosMode = \"dens_ie\"\n")
file.write("eosModeInit = \"dens_temp\"\n")
file.write("#eos_coulombAbort = .true.\n")
file.write("#eos_coulombMult = 0.0\n")
file.write("#eos_forceConstantInput = .false.\n")
file.write("#eos_maxNewton = 50\n")
file.write("#eos_singleSpeciesA = 1.00\n")
file.write("#eos_singleSpeciesZ = 1.00\n")
file.write("#eos_tolerance = 1.e-8\n")
file.write("gamma = 1.2\n")
file.write("#eos_table_tmax = 50.\n")
file.write("\n")
file.write("# Deleptonization\n")
file.write("useDeleptonize = .false.\n")
file.write("delep_Enu = 10.0 # MeV\n")
file.write("delep_rhoOne = 3.0e7 #3.0e7\n")
file.write("delep_rhoTwo = 2.0e13 #2.0e13\n")
file.write("delep_rhoThree = 2.0e14 \n")
file.write("delep_yOne = 0.5\n")
file.write("delep_yTwo = 0.278 #0.278\n")
file.write("delep_yc = 0.035 #0.035\n")
file.write("bounceTime = 0.0 #0.248\n")
file.write("postBounce = .true.\n")
file.write("useEntr = .true.\n")
file.write("\n")
file.write("# RadTrans/M1\n")
file.write("rt_useRadTrans = .true.\n")
file.write(
"rt_NumGroups = 12 #must match m1_groups used in setup\n"
)
file.write("rt_opacTable = \"./NuLib_SFHo.h5\"\n")
file.write("rt_dtFactor = 0.3d0\n")
file.write("rt_fluxCorrect = .false. \n")
file.write("rt_rkTime = .false. \n")
file.write("rt_doVel = .true.\n")
file.write("rt_pushFac = 1.0d0\n")
file.write("\n")
file.write("# Neutrino Heating/Cooling\n")
file.write("useHeat = .false.\n")
file.write("Lneut = 2.2e52\n")
file.write("Tneut = 4.0 #MeV\n")
file.write("heatTimeFac = 1.0e4\n")
file.write("useHalfState = .false.\n")
file.write("\n")
file.write("# EnergyDeposition - Jets\n")
file.write("useEnergyDeposition = .FALSE.\n")
file.write("#jetAngleN = 0.52\n")
file.write("#jetAngleS = 0.52\n")
file.write("#jetAccN = 5.0e10\n")
file.write("#jetAccS = 1.0e10\n")
file.write("#jetTimeN = 2.0\n")
file.write("#jetTimeS = 0.0\n")
file.write("#jetRad = 4.0e8\n")
file.write("#heat_fact = 1.0\n")
file.write("\n")
file.write("# Small numbers\n")
file.write("smallt = 1.2e8\n")
file.write("smlrho = 1.1e3\n")
file.write("smallp = 1.E-20\n")
file.write("smalle = 1.E1\n")
file.write("\n")
file.write("smallu = 1.E-10\n")
file.write("smallx = 1.E-100\n")
file.write("small = 1.E-100\n")
i = i + 1