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isochrone_suites7.py
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#!/usr/bin/env python
import numpy as np
import subprocess
import sys
import codecs
import re as re
import shutil
import os
import sys, os, time
from subprocess import Popen, list2cmdline
PKG_DIR = os.path.abspath(os.path.dirname(__file__))
head = PKG_DIR.split(PKG_DIR.split('dsep3')[1])[0]
sys.path.append(head+'/pysep/')
import generate_prems7 as GP
# solar_ML = 1.9258 ##new as of 4/5/17
# Zsolar=0.019
# Ysolar=0.28
# aFe=0.0
###########################################################################################
def cpu_count():
''' Returns the number of CPUs in the system
'''
num = 1
if sys.platform == 'win32':
try:
num = int(os.environ['NUMBER_OF_PROCESSORS'])
except (ValueError, KeyError):
pass
elif sys.platform == 'darwin':
try:
num = int(os.popen('sysctl -n hw.ncpu').read())
except ValueError:
pass
else:
try:
num = os.sysconf('SC_NPROCESSORS_ONLN')
except (ValueError, OSError, AttributeError):
pass
print "number of threads available: ", num
return num
def exec_commands(cmds):
''' Exec commands in parallel in multiple process
(as much as we have CPU)
'''
if not cmds: return # empty list
def done(p):
return p.poll() is not None
def success(p):
return p.returncode == 0
def fail():
sys.exit(1)
max_task = cpu_count()
processes = []
while True:
while cmds and len(processes) < max_task:
task = cmds.pop()
#task = task + ""
print list2cmdline(task)
processes.append(Popen( task , stdout=subprocess.PIPE,stderr=subprocess.STDOUT, shell=True ))
for p in processes:
if done(p):
print "process ", p, " believes it has concluded successfully...."
if success(p):
processes.remove(p)
else:
print "process ", p, "has failed"
#fail()
pass
if not processes and not cmds:
break
else:
time.sleep(0.05)
def format(number):
number=float(number)
f=("%.3f"%number)
return f
#####################################################################################
def update_cont(cont_file, CMIXLA, Z, Y,NMOD, *args, **kwargs):
endage=float(kwargs.get('endage',-4.7))
#which_comp=str(kwargs.get('which_comp','LMC'))
head = str(kwargs.get('head', ''))
# if which_comp=='LMC':
# comp_str='mjoyce'
# else:
# comp_str='mjoyce'
asteroseismic=bool(kwargs.get('asteroseismic',False))
cont=open(cont_file,"w")
# def strip_DSEP_header(in_file, outfn, *args, **kwargs):
# mjoyce_common.py: n = int(kwargs.get('n', 14))
Z_solar=0.019
X = 1.00-float(Y)-float(Z)
print >> cont, " $CONTROL"
print >> cont, " DESCRIP(1)='[Fe/H]=0.0'"
print >> cont, " DESCRIP(2)='mjoyce_on_LMC' "
print >> cont, ""
print >> cont, " NUMRUN=2"
print >> cont, ""
print >> cont, " KINDRN(1)=2"
print >> cont, " LFIRST(1)=.TRUE."
print >> cont, " NMODLS(1)=2"
print >> cont, " CMIXLA(1)="+str(CMIXLA)+"D0"
print >> cont, " RSCLX(1)="+str(X)+"D0"
print >> cont, " RSCLZ(1)="+str(Z)+"D0"
print >> cont, ""
print >> cont, " KINDRN(2)=1"
print >> cont, " LFIRST(2)=.FALSE."
print >> cont, " NMODLS(2)= " + str(int(NMOD))
print >> cont, " CMIXLA(2)="+str(float(CMIXLA))+"D0"
print >> cont, " ENDAGE(2)="+str(endage)+"D9"
print >> cont, ""
print >> cont, " LOPAL95=.TRUE."
print >> cont, " FO95COBIN='"+ head +"/opac/OPAL/OPAL_GS98.bin'"
print >> cont, ""
print >> cont, " LALEX95=.TRUE."
print >> cont, " ZALEX="+str(Z)+"D0"
print >> cont, ""
print >> cont, " MIX='GS98'"
print >> cont, " IAFE=0"
if asteroseismic:
print >> cont, ""
print >> cont, " LPULSE=.TRUE."
print >> cont, ""
print >> cont, " LZAMS=.FALSE."
print >> cont, " LHB=.FALSE."
print >> cont, " LTRACK=.TRUE."
print >> cont, " LISO=.TRUE."
print >> cont, " LCORR=.TRUE."
print >> cont, " LRWSH=.FALSE."
print >> cont, ""
print >> cont, " OPECALEX(1)='"+ head +"/opac/ferg04/gs98.0.tron'"
print >> cont, " OPECALEX(2)='"+ head +"/opac/ferg04/gs98.1.tron'"
print >> cont, " OPECALEX(3)='"+ head +"/opac/ferg04/gs98.2.tron'"
print >> cont, " OPECALEX(4)='"+ head +"/opac/ferg04/gs98.35.tron'"
print >> cont, " OPECALEX(5)='"+ head +"/opac/ferg04/gs98.5.tron'"
print >> cont, " OPECALEX(6)='"+ head +"/opac/ferg04/gs98.7.tron'"
print >> cont, " OPECALEX(7)='"+ head +"/opac/ferg04/gs98.8.tron'"
print >> cont, " OPECALEX(8)='"+ head +"/opac/ferg04/gs98.9.tron'"
print >> cont, ""
print >> cont, " $END"
cont.close()
return 0
cont.close()
return 0
def update_phys(phys_file_name,atm,eta_D,ovs, FREEOS, *args, **kwargs):
asteroseismic=bool(kwargs.get('asteroseismic',False))
phys=open(phys_file_name,"w")
print >> phys, "$PHYSICS"
print >> phys, " KTTAU=" +str(int(atm))
print >> phys, ""
print >> phys, " LDIFY = .TRUE."
print >> phys, " LDIFZ=.TRUE."
print >> phys, " LTHOUL=.TRUE."
print >> phys, " LTHOULFIT = .FALSE."
print >> phys, " FGRY = " +str(eta_D)+"D0"
print >> phys, " FGRZ = "+str(eta_D)+"D0"
print >> phys, " DT_GS = 0.1D0 "
print >> phys, " XMIN = 1.0D-3 "
print >> phys, " YMIN = 1.0D-3 "
print >> phys, " GRTOL = 2.0D-7 "
print >> phys, " NITER_GS = 10 "
print >> phys, " ILAMBDA = 4"
print >> phys, ""
print >> phys, " LNEWS=.TRUE."
print >> phys, " LSNU=.TRUE."
print >> phys, ""
print >> phys, " NITER1=2"
print >> phys, " NITER2=40"
print >> phys, " NITER3=0"
print >> phys, " NITER4=0"
print >> phys, ""
print >> phys, " LSEMIC=.FALSE. "
print >> phys, " DPENV=1.00"
print >> phys, " LOVSTC=.TRUE. "
print >> phys, " ALPHAC=" + str(ovs)
print >> phys, " LOVSTE=.TRUE. "
print >> phys, " LOVSTM=.FALSE. "
print >> phys, ""
print >> phys, " LEXCOM=.FALSE. "
print >> phys, ""
print >> phys, " LENVG=.TRUE. "
print >> phys, " ATMSTP=0.0050 "
print >> phys, " ENVSTP=0.0050 "
print >> phys, ""
print >> phys, " LCOREL=.TRUE."
print >> phys, " LHAFT=.TRUE."
print >> phys, " LNULOS1=.TRUE."
print >> phys, " LNULOS2=.TRUE."
print >> phys, ""
print >> phys, " LROT=.FALSE."
print >> phys, ""
print >> phys, " LFREE_EOS=."+str(FREEOS)+ "."
print >> phys, " IEOS=1,101,0"
print >> phys, " LOPALE=.FALSE."
print >> phys, " LDH=.TRUE. "
print >> phys, " ETADH0 = -1.0D0"
print >> phys, " ETADH1 = 1.0D0 "
print >> phys, ""
print >> phys, " LCORE=.FALSE. "
print >> phys, " FCORE=1.0"
print >> phys, " MCORE=1 "
print >> phys, ""
print >> phys, " LNEWCP=.FALSE. "
print >> phys, " ANEWCP=' ' "
print >> phys, " ATMP='REL' "
print >> phys, " XNEWCP=13 "
print >> phys, ""
print >> phys, " FCORR0=0.8D0 "
print >> phys, " FCORRI=0.1D0 "
print >> phys, ""
print >> phys, " LNEW0=.FALSE."
print >> phys, " TRIDT=1.0D-3"
print >> phys, " TRIDL=8.0D-3 "
print >> phys, " "
print >> phys, " ATMERR=1.0D-5 "
print >> phys, " ATMMAX=0.05D0 "
print >> phys, " ATMMIN=0.015D0 "
print >> phys, " ATMBEG=0.015D0"
print >> phys, " ATMD0=1.0D-10 "
print >> phys, " ENVERR=1.0D-5 "
print >> phys, " ENVMAX=0.05D0 "
print >> phys, " ENVMIN=0.015D0 "
print >> phys, " ENVBEG=0.015D0 "
print >> phys, " STOLR0=1.0D-7 "
print >> phys, " IMAX=11 "
print >> phys, " NUSE=7 "
print >> phys, " "
if asteroseismic:
print(r"\n\nWARNING! Asteroseismic tolerances in use!!!!\n\n")
print >> phys, " HTOLER(1,1)=6.0D-6"
print >> phys, " HTOLER(2,1)=4.5D-6 "
print >> phys, " HTOLER(3,1)=3.0D-6 "
print >> phys, " HTOLER(4,1)=9.0D-6 "
print >> phys, " HTOLER(5,1)=3.0D-6 "
else:
print("---------------------------- STANDARD TOLERANCES IN USE ----------------------------")
print >> phys, " HTOLER(1,1)=6.0D-5"
print >> phys, " HTOLER(2,1)=4.5D-5 "
print >> phys, " HTOLER(3,1)=3.0D-5 "
print >> phys, " HTOLER(4,1)=9.0D-5 "
print >> phys, " HTOLER(5,1)=3.0D-5 "
print >> phys, " HTOLER(1,2)=9.0D4"
print >> phys, " HTOLER(2,2)=5.0D4 "
print >> phys, " HTOLER(3,2)=5.0D4 "
print >> phys, " HTOLER(4,2)=5.0D10"
print >> phys, " HTOLER(5,2)=2.5D-6"
print >> phys, " "
print >> phys, " SHELLTOL(1)=1.0D-10"
print >> phys, " SHELLTOL(2)=1.0D-2"
print >> phys, " SHELLTOL(3)=5.0D-2"
print >> phys, " SHELLTOL(4)=1.0D0 "
print >> phys, " SHELLTOL(5)=1.0D0 "
print >> phys, " SHELLTOL(6)=1.0D0 "
print >> phys, " SHELLTOL(7)=0.0D0"
print >> phys, " "
print >> phys, " SHELLTOL(8)=1.0D-2 "
print >> phys, " SHELLTOL(9)=1.0D-2 "
print >> phys, " SHELLTOL(10)=1.0D-2"
print >> phys, " SHELLTOL(11)=1.0D-2 "
print >> phys, " "
print >> phys, " SHELLTOL(12)=0.1D0"
print >> phys, " "
print >> phys, " ATIME(1)=1.0D-4"
print >> phys, " ATIME(2)=1.0D-3 "
print >> phys, " ATIME(3)=3.0D-2 "
print >> phys, " ATIME(4)=2.0D-2"
print >> phys, " ATIME(5)=3.0D-2 "
print >> phys, " ATIME(6)=1.5D-3"
print >> phys, " ATIME(7)=1.0D-1 "
print >> phys, " ATIME(8)=2.0D-2"
print >> phys, " ATIME(9)=2.0D-2 "
print >> phys, " ATIME(10)=2.0D-2 "
print >> phys, " ATIME(11)=2.0D-2"
print >> phys, " ATIME(13)=1.05d0"
print >> phys, " LPTIME=.TRUE. "
print >> phys, " "
print >> phys, " TCUT(1)=6.5D0 "
print >> phys, " TCUT(2)=6.5D0 "
print >> phys, " TCUT(3)=6.82D0 "
print >> phys, " TCUT(4)=7.73D0 "
print >> phys, " TCUT(5)=7.5D0 "
print >> phys, " TSCUT=6.0D0 "
print >> phys, " TENV0=3.0D0 "
print >> phys, " TENV1=9.0D0 "
print >> phys, " TGCUT=6.9D0 "
print >> phys, " "
print >> phys, " OPTOL=1.0D-8"
print >> phys, " CMIN = 1.0D-20"
print >> phys, " ABSTOL = 1.0D-6"
print >> phys, " RELTOL = 1.0D-5"
print >> phys, " KEMMAX = 50"
print >> phys, " "
print >> phys, " CLSUN = 3.828D33"
print >> phys, " CRSUN=6.957D10"
print >> phys, " "
print >> phys, " SStandard=0.997543,1.02913,1.03704,0.965517,1.47273,0.478916,1.12766,1.0,1.0/"
print >> phys, " ,1.0,1.0,1.0,1.0,1.0,1.01083,0.876543,1.075,0.625,1.21795"
print >> phys, " "
print >> phys, " $END"
phys.close()
return
def update_shell(run_file,prems_model_dir,input_model,phys_file_name,cont_file_name, *arg, **kwargs):
#run_file, input_model, output_iso_name, prems_dir
which_comp=str(kwargs.get('which_comp',''))
head = str(kwargs.get('head', ''))
output_dir=str(kwargs.get('output_dir',''))
#print "(loc 2 ) prems_model_dir: ", prems_model_dir
print "inpute model (update_shell): ", input_model
asteroseismic=bool(kwargs.get('asteroseismic',False))
if which_comp!='Erika':
comp_str='meridith'
else:
comp_str='mjoyce'
phys_file_piece=str(phys_file_name).split('.nml')[0].split('/nml/')[1]
cont_file_piece=str(cont_file_name).split('.nml')[0].split('/nml/')[1]
run=open(run_file,"w")
print >> run, "# ! /bin/bash"
print >> run, "# this file executes dsep3"
### special cases for badly configured computers:
if which_comp == 'LMC':
print >> run, "LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/free_eos-2.2.1/install_dir/lib"
elif which_comp== 'Marsha':
print >> run, "#"
elif which_comp=="Erika":
print >> run, "export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/meridith/free_eos-2.2.1/lib"
print >> run, "LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/free_eos-2.2.1/lib"
print >> run, "ldd /home/meridith/dsep3/dsepX/dsepX"
### everything else
else:
print >> run, "export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:"+head+"/free_eos-2.2.1/lib"
print >> run, "LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/free_eos-2.2.1/lib"
print >> run, "ldd "+head+"/dsepX/dsepX"
print >> run, ""
print >> run, "local=$HOME/dsep3"
print >> run, "nml=$local/nml"
print >> run, "out=$local/out"
print >> run, "prog=$local/dsepX"
print >> run, "zams=$local/zams"
print >> run, "prems=$local/prems"
print >> run, "opac=$local/opac"
print >> run, "atm=$local/surfBC"
print >> run, "opal=$opac/OPAL"
print >> run, "phx=$opac/phoenix"
print >> run, "bcphx=$atm/phoenix/GS98"
print >> run, "bckur=$atm/atmk"
print >> run, "out_meridith=$local/run/out_meridith/"+output_dir
print >> run, ""
print >> run, "outname="+str(input_model)
print >> run, ""
print >> run, "rm fort.*"
print >> run, " ln -s $nml/"+str(phys_file_piece)+".nml fort.13"
print >> run, " ln -s $nml/"+str(cont_file_piece)+".nml fort.14"
print >> run,""
print >> run, "# input opacities/boundry conditions; Fergson low T specified in CONTROL nml"
print >> run, " ln -s $opac/FERMI.TAB fort.15"
print >> run, " ln -s $bckur/atmk1990p00.tab fort.38"
print >> run, " ln -s $opal/GS98hz fort.48"
print >> run, "# Phoenix boundary conditions, code picks correct Z, multipe ones "
print >> run, "# to allow for correct BC when rescaling"
print >> run, " ln -s $bcphx/z_p0d0.afe_p0d0.dat fort.95"
print >> run, " ln -s $bcphx/z_m0d5.afe_p0d0.dat fort.96"
print >> run, " ln -s $bcphx/z_m0d7.afe_p0d0.dat fort.97"
print >> run, " ln -s $bcphx/z_m1d0.afe_p0d0.dat fort.98"
print >> run, " ln -s $bcphx/z_m1d5.afe_p0d0.dat fort.99"
print >> run, ""
print >> run, "# input model"
print >> run, " ln -s $prems/"+str(prems_model_dir)+"/"+str(input_model)+" fort.12"
print >> run, ""
print >> run, "# output"
print >> run, " ln -s $out_meridith$outname.track fort.19"
print >> run, " ln -s $out$outname.short fort.20"
print >> run, " ln -s $out_meridith$outname.iso fort.37"
print >> run, " ln -s $out_meridith$outname.last fort.11"
print >> run, ""
if asteroseismic:
print >> run, "ln -s $out_meridith$outname.fpmod fort.24"
print >> run, "ln -s $out_meridith$outname.fpenv fort.25"
print >> run, "ln -s $out_meridith$outname.fpatm fort.26"
print >> run, ""
print >> run, "time $prog/dsepX"
run.close()
#subprocess.call('chmod +x '+run_file,shell=True)
return
def make_prems_models(mstar,amlt,zin,yin, *args, **kwargs):
###### THIS DOES NOT CARE ABOUT OVERSHOOT, MIXING EFFICIENCY, ATMOSPHERE, ETC
###### THIS IS JUST A PILE OF GAS
###### THIS ONLY CARES ABOUT COMPOSITION
which_comp=str(kwargs.get('which_comp',''))
head = str(kwargs.get('head', ''))
if which_comp=='Erika':
mname='meridith'
else:
mname='mjoyce'
#config=int(kwargs.get('config',True))
model_ID_head = str(kwargs.get('model_ID_head', ''))
model_dir= str(kwargs.get('model_dir', ''))
#print "(loc 6) model_dir:", model_dir
aFe=float(kwargs.get('aFe',0.0))
starting_mass=int(float(mstar)*1000.)
interval=5#100
ending_mass=int(float(mstar)*1000.) + interval
print_zin=('%1.3f'%float(zin))
print_yin=('%1.2f'%float(yin))
print_mlt=('%1.3f'%float(amlt))
model_ID=str(kwargs.get('model_ID',model_ID_head+"."+print_mlt+'.Z'+print_zin+'.Y'+print_yin))
#print "loc 10 model_ID", model_ID
#print "value of head (loc 1): ", head
GP.make_prems_model(amlt, zin, yin, aFe, starting_mass, ending_mass, model_dir, interval, model_ID,\
which_comp=which_comp, head=head)
return
def make_solar_prems_model(tag, amlt, zin, yin, *args, **kwargs):
###### THIS DOES NOT CARE ABOUT OVERSHOOT, MIXING EFFICIENCY, ATMOSPHERE, ETC
###### THIS IS JUST A PILE OF GAS
###### THIS ONLY CARES ABOUT COMPOSITION
which_comp=str(kwargs.get('which_comp',''))
if which_comp=='LMC':
mname='mjoyce'
else:
mname='meridith'
mstar=1.0
aFe=0.0
model_dir= str(kwargs.get('model_dir', 'solar_calibrations'))
model_ID=tag+'.solar.MIX_'+ ('%1.5f'%amlt)+'.Y_'+('%1.3f'%yin) +'.Z_'+('%1.4f'%zin)
make_prems_models(mstar,amlt,zin,yin,model_ID=model_ID,model_dir=model_dir, which_comp=which_comp, path=head)
return
def do_run(mstar,amlt,zin,yin, shell_file, cont_file,phys_file,\
run_dir, atm, eta_D,ovs, FREEOS, *args, **kwargs):
###################
#
# kwargs
#
###################
which_comp=str(kwargs.get('which_comp',''))
NMOD=int(kwargs.get('NMOD',9999))
endage=float(kwargs.get('endage',-4.7))
model_ID_head = str(kwargs.get('model_ID_head', ''))
prems_model_dir= str(kwargs.get('prems_model_dir', ''))
head = str(kwargs.get('head', ''))
output_dir =str(kwargs.get('output_dir', ''))
asteroseismic=bool(kwargs.get('asteroseismic',False))
print "using:\n", cont_file, "\n", shell_file, "\n"
mstar=100.*float(mstar)
mstar=('%1.1f'%mstar)
print_zin=('%1.3f'%float(zin))
print_yin=('%1.2f'%float(yin))
print_mlt=('%1.3f'%float(amlt))
model_ID=str(kwargs.get('model_ID',model_ID_head+"."+print_mlt+'.Z'+print_zin+'.Y'+print_yin))
if float(mstar) < 100.0:
out_iso_name ="m0"+str(mstar)+"."+model_ID
else:
out_iso_name = "m"+str(mstar)+"."+model_ID
update_phys(phys_file ,atm, eta_D, ovs, FREEOS)
update_cont(cont_file, amlt, zin, yin, NMOD,\
endage=endage, which_comp=which_comp,
asteroseismic=asteroseismic, head=head)
update_shell(shell_file,prems_model_dir,out_iso_name,\
phys_file, cont_file,which_comp=which_comp,\
output_dir=output_dir,asteroseismic=asteroseismic,\
head=head)
subprocess.call("pwd", shell=True)
subprocess.call("bash "+shell_file, shell=True)
print r"\n\do_run terminated successfully"
return
def make_input_prems_sets(mhead,mixing_lengths,yins,zins,*args, **kwargs):
which_comp=str(kwargs.get('which_comp',''))
if which_comp=='LMC':
mname='mjoyce'
else:
mname='meridith'
CMIXLA_list=np.array(mixing_lengths)
Zsolar_list=np.array(zins)
helium_list=np.array(yins)
for k in range(len(Zsolar_list)):
Zsolar=Zsolar_list[k]
for i in range(len(CMIXLA_list)):
CMIXLA=CMIXLA_list[i]
for j in range(len(helium_list)):
He=helium_list[j]
make_solar_prems_model(mhead,CMIXLA,Zsolar,He, model_dir='solar_calibrations',which_comp=which_comp)
return
def solar_calibrate(mhead,run_dir,mixing_lengths,yins,zins, atm, eta_D, ovs,*args,**kwargs):
which_comp=str(kwargs.get('which_comp',''))
if which_comp!='Erika':
mname='mjoyce'
else:
mname='meridith'
mstar=1.0
FREEOS="FALSE"
endage=4.603
try:
run_dir_piece=run_dir.split('/home/'+mname+'/dsep3/')[1].split('/')[0]
except IndexError:
run_dir_piece=run_dir
cont_file='/home/'+mname+'/dsep3/nml/cont_solar_'+run_dir_piece+'.nml'
shell_file='/home/'+mname+'/dsep3/'+run_dir+'/run_solar_'+run_dir_piece+'.sh'
phys_file='/home/'+mname+'/dsep3/nml/phys_solar_'+run_dir_piece+'.nml'
CMIXLA_list=np.array(mixing_lengths)
Zsolar_list=np.array(zins)
helium_list=np.array(yins)
for k in range(len(Zsolar_list)):
Zsolar=Zsolar_list[k]
for i in range(len(CMIXLA_list)):
CMIXLA=CMIXLA_list[i]
for j in range(len(helium_list)):
He=helium_list[j]
model_ID=mhead+'.solar.MIX_'+ ('%1.5f'%CMIXLA)+'.Y_'+('%1.3f'%He) +'.Z_'+('%1.4f'%Zsolar)
do_run(mstar,CMIXLA,Zsolar,He, shell_file, cont_file,phys_file, run_dir,atm, eta_D,ovs, FREEOS,\
endage=endage, prems_model_dir='solar_calibrations',output_dir='solarCalibrate',model_ID=model_ID, which_comp=which_comp)
return 0
def set_par(tag):
tag = str(tag)
if tag =='ttau':
atm,eta_D,ovs=0,1.0,0
elif tag =='ks':
atm,eta_D,ovs=1.0,1.0,0
elif tag =='0p5':
atm,eta_D,ovs=0.0,0.5,0
elif tag =='1p5':
atm,eta_D,ovs=0.0,1.5,0
elif tag =='1p5ovs':
atm,eta_D,ovs=0.0,1.5,0.1
else:
print "tag type unknown!"
sys.exit()
return atm,eta_D,ovs