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genetools.py
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genetools.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import sys
import glob
import math
import numpy as npy
import efittools
import read_iterdb
from ParIO import *
from momlib import *
from fieldlib import *
from finite_differences import *
from read_write_geometry import *
from scipy.interpolate import interp1d
def create_k_grid(x_grid):
#Developed by Ehab Hassan on 2019-04-28
nx = npy.size(x_grid)
dx = min(npy.diff(x_grid))
dKx = 2.0*npy.pi/nx/dx
iKx = npy.zeros(nx)
for ix in range(nx):
if ix<=int(nx/2)-1:
iKx[ix] = ix*dx
elif ix>=int(nx/2):
iKx[ix] =-(nx-ix)*dx
return npy.fft.fftshift(iKx)
def findall(inlist,item):
#Developed by Ehab Hassan on 2019-03-28
inds = []
for i,character in enumerate(inlist):
if character==item: inds.append(i)
return inds
def str2bool(vin):
#Developed by Ehab Hassan on 2019-03-28
return (vin.strip()).lower() in ('t','.t.','true','.true.')
def read_parameters(paramfpath):
#Developed by Ehab Hassan on 2019-02-07
#Modified by Ehab Hassan on 2019-03-09
if "parameters_" in paramfpath.strip():
paramflist=[paramfpath.strip()]
elif "parameters.dat" in paramfpath.strip():
paramflist=[paramfpath.strip()]
elif "nrg_" in paramfpath.strip():
paramflist=[paramfpath.strip()[:-8]+'parameters_'+paramfpath.strip()[-4:]]
else:
if paramfpath[-1] != "/": paramfpath+="/"
if os.path.isfile(paramfpath+"parameters_0001"):
paramflist = sorted(glob.glob(paramfpath+"parameters_*"))
else:
paramflist = sorted(glob.glob(paramfpath+"parameters.dat"))
geneparam = {'filepath':paramfpath}
for fid in range(len(paramflist)):
if not os.path.isfile(paramflist[fid]):
print('FATAL in read_parameters:')
print(paramflist[fid]+' FILE NOT FOUND. Exit!'); sys.exit()
ofh = open(paramflist[fid],'r')
lines = ofh.readlines()
ofh.close()
nspecs = 1
for line in lines:
pkeys = geneparam.keys()
if line[0] == '&':
pkey = line[1:].strip()
if pkey == 'species':
pkey += str(nspecs)
nspecs += 1
if pkey not in pkeys: geneparam[pkey] = {}
elif line.strip() in ['/', '!','']:
continue
else:
skeys = geneparam[pkey].keys()
items = (line.strip()).split('=')
skey = items[0].strip()
if pkey == "parallelization":
if skey not in skeys:
geneparam[pkey][skey] = int(items[1])
elif type(geneparam[pkey][skey]) == list:
geneparam[pkey][skey].append(int(items[1]))
else:
if geneparam[pkey][skey] != int(items[1]):
geneparam[pkey][skey] = [geneparam[pkey][skey],int(items[1])]
elif pkey == "units":
if skey not in skeys:
geneparam[pkey][skey] = float(items[1])
elif type(geneparam[pkey][skey]) == list:
geneparam[pkey][skey].append(float(items[1]))
else:
if abs(geneparam[pkey][skey]-float(items[1])) >= 1.0e-9:
geneparam[pkey][skey] = [geneparam[pkey][skey],float(items[1])]
elif pkey == "bdgrid":
if skey not in skeys:
geneparam[pkey][skey] = str2bool(items[1])
elif type(geneparam[pkey][skey]) == list:
geneparam[pkey][skey].append(str2bool(items[1]))
else:
if geneparam[pkey][skey] != str2bool(items[1]):
geneparam[pkey][skey] = [geneparam[pkey][skey],str2bool(items[1])]
elif pkey == "box":
if skey not in skeys:
if skey in ['lx','lx_a','x0','kymin','lv','lw','kx_center']:
geneparam[pkey][skey] = float(items[1])
elif skey in ['adapt_lx','adapt_ly']:
geneparam[pkey][skey] = bool(items[1])
elif skey in ['mu_grid_type']:
geneparam[pkey][skey] = str(items[1])
else:
geneparam[pkey][skey] = int(items[1])
elif type(geneparam[pkey][skey]) == list:
if skey in ['lx','lx_a','x0','kymin','lv','lw','kx_center']:
geneparam[pkey][skey].append(float(items[1]))
elif skey in ['adapt_lx','adapt_ly']:
geneparam[pkey][skey].append(str2bool(items[1]))
elif skey in ['mu_grid_type']:
geneparam[pkey][skey].append(str(items[1]))
else:
geneparam[pkey][skey].append(int(items[1]))
else:
if skey in ['lx','lx_a','x0','kymin','lv','lw','kx_center']:
if geneparam[pkey][skey] != float(items[1]):
geneparam[pkey][skey] = [geneparam[pkey][skey],float(items[1])]
elif skey in ['adapt_lx','adapt_ly']:
if geneparam[pkey][skey] != str2bool(items[1]):
geneparam[pkey][skey] = [geneparam[pkey][skey],str2bool(items[1])]
elif skey in ['mu_grid_type']:
if geneparam[pkey][skey] != str(items[1]):
geneparam[pkey][skey] = [geneparam[pkey][skey],str(items[1])]
else:
if geneparam[pkey][skey] != int(items[1]):
geneparam[pkey][skey] = [geneparam[pkey][skey],int(items[1])]
elif pkey == "in_out":
if skey not in skeys:
if skey in ['iterdb_time']:
geneparam[pkey][skey] = float(items[1])
elif skey in ['diagdir','chptdir','iterdb_file']:
geneparam[pkey][skey] = items[1].strip()[1:-1]
elif skey in ['write_std','read_checkpoint','write_checkpoint','write_h5','chpt_read_h5','chpt_write_h5','chpt_read_hac','chpt_write_hac','many_chpts']:
geneparam[pkey][skey] = str2bool(items[1])
else:
geneparam[pkey][skey] = int(items[1])
elif type(geneparam[pkey][skey]) == list:
if skey in ['iterdb_time']:
geneparam[pkey][skey].append(float(items[1]))
elif skey in ['diagdir','chptdir','iterdb_file']:
geneparam[pkey][skey].append(items[1].strip()[1:-1])
elif skey in ['write_std','read_checkpoint','write_checkpoint','write_h5','chpt_read_h5','chpt_write_h5','chpt_read_hac','chpt_write_hac','many_chpts']:
geneparam[pkey][skey].append(str2bool(items[1]))
else:
geneparam[pkey][skey].append(int(items[1]))
else:
if skey in ['iterdb_time']:
if geneparam[pkey][skey] != float(items[1]):
geneparam[pkey][skey] = [geneparam[pkey][skey],float(items[1])]
elif skey in ['diagdir','chptdir','iterdb_file']:
if geneparam[pkey][skey] != items[1].strip()[1:-1]:
geneparam[pkey][skey] = [geneparam[pkey][skey],items[1].strip()[1:-1]]
elif skey in ['write_std','read_checkpoint','write_checkpoint','write_h5','chpt_read_h5','chpt_write_h5','chpt_read_hac','chpt_write_hac','many_chpts']:
if geneparam[pkey][skey] != str2bool(items[1]):
geneparam[pkey][skey] = [geneparam[pkey][skey],str2bool(items[1])]
else:
if geneparam[pkey][skey] != int(items[1]):
geneparam[pkey][skey] = [geneparam[pkey][skey],int(items[1])]
elif "species" in pkey:
if skey not in skeys:
if skey in ['omn','omt','mass','temp','dens']:
geneparam[pkey][skey] = float(items[1])
elif skey in ['charge','prof_type']:
geneparam[pkey][skey] = int(float(items[1]))
elif skey in ['passive']:
geneparam[pkey][skey] = str2bool(items[1])
elif skey in ['name']:
geneparam[pkey][skey] = items[1].strip()[1:-1]
elif type(geneparam[pkey][skey]) == list:
if skey in ['omn','omt','mass','temp','dens']:
geneparam[pkey][skey].append(float(items[1]))
elif skey in ['charge','prof_type']:
geneparam[pkey][skey].append(int(float(items[1])))
elif skey in ['passive']:
geneparam[pkey][skey].append(str2bool(items[1]))
elif skey in ['name']:
geneparam[pkey][skey].append(items[1].strip()[1:-1])
else:
if skey in ['omn','omt','mass','temp','dens']:
if geneparam[pkey][skey] != float(items[1]):
geneparam[pkey][skey] = [geneparam[pkey][skey],float(items[1])]
elif skey in ['charge','prof_type']:
if geneparam[pkey][skey] != int(float(items[1])):
geneparam[pkey][skey] = [geneparam[pkey][skey],int(items[1])]
elif skey in ['passive']:
if geneparam[pkey][skey] != str2bool(items[1]):
geneparam[pkey][skey] = [geneparam[pkey][skey],str2bool(items[1])]
elif skey in ['name']:
if geneparam[pkey][skey] != items[1].strip()[1:-1]:
geneparam[pkey][skey] = [geneparam[pkey][skey],items[1].strip()[1:-1]]
elif pkey == "geometry":
if skey not in skeys:
if skey in ['norm_flux_projection','mag_prof']:
geneparam[pkey][skey] = str2bool(items[1])
elif skey in ['magn_geometry','geomdir','geomfile','x_def','dpdx_term']:
geneparam[pkey][skey] = items[1].strip()[1:-1]
else:
try: #in case for the miller geometry
geneparam[pkey][skey] = float(items[1])
except:
pass
elif type(geneparam[pkey][skey]) == list:
if skey in ['norm_flux_projection','mag_prof']:
geneparam[pkey][skey].append(str2bool(items[1]))
elif skey in ['magn_geometry','geomdir','geomfile','x_def','dpdx_term']:
geneparam[pkey][skey].append(items[1].strip()[1:-1])
else:
geneparam[pkey][skey].append(float(items[1]))
else:
if skey in ['norm_flux_projection','mag_prof']:
if geneparam[pkey][skey] != str2bool(items[1]):
geneparam[pkey][skey] = [geneparam[pkey][skey],str2bool(items[1])]
elif skey in ['magn_geometry','geomdir','geomfile','x_def','dpdx_term']:
if geneparam[pkey][skey] != items[1].strip()[1:-1]:
geneparam[pkey][skey] = [geneparam[pkey][skey],items[1].strip()[1:-1]]
else:
if geneparam[pkey][skey] != float(items[1]):
geneparam[pkey][skey] = [geneparam[pkey][skey],float(items[1])]
elif pkey == "external_contr":
if skey not in skeys:
if skey in ['with_coriolis','with_centrifugal','with_comoving_other']:
geneparam[pkey][skey] = str2bool(items[1])
elif skey in ['kxind_phi_ext','kxind_omn_ext','kxind_omt_ext','kxind_apar_ext','phase_phi_ext','phase_omn_ext','phase_omt_ext','phase_apar_ext']:
geneparam[pkey][skey] = int(items[1])
else:
geneparam[pkey][skey] = float(items[1])
elif type(geneparam[pkey][skey]) == list:
if skey in ['with_coriolis','with_centrifugal','with_comoving_other']:
geneparam[pkey][skey].append(str2bool(items[1]))
elif skey in ['kxind_phi_ext','kxind_omn_ext','kxind_omt_ext','kxind_apar_ext','phase_phi_ext','phase_omn_ext','phase_omt_ext','phase_apar_ext']:
geneparam[pkey][skey].append(int(items[1]))
else:
geneparam[pkey][skey].append(float(items[1]))
else:
if skey in ['with_coriolis','with_centrifugal','with_comoving_other']:
if geneparam[pkey][skey] != str2bool(items[1]):
geneparam[pkey][skey] = [geneparam[pkey][skey],str2bool(items[1])]
elif skey in ['kxind_phi_ext','kxind_omn_ext','kxind_omt_ext','kxind_apar_ext','phase_phi_ext','phase_omn_ext','phase_omt_ext','phase_apar_ext']:
if geneparam[pkey][skey] != int(items[1]):
geneparam[pkey][skey] = [geneparam[pkey][skey],int(items[1])]
else:
if geneparam[pkey][skey] != float(items[1]):
geneparam[pkey][skey] = [geneparam[pkey][skey],float(items[1])]
elif pkey == "nonlocal_x":
if skey not in skeys:
if skey in ['rad_bc_type','lpow_krook','upow_krook','psource_type','ck_filter_type','lckpow_krook','uckpow_krook']:
geneparam[pkey][skey] = int(items[1])
elif skey in ['buffer_on_ky0','explicit_buffer','shifted_metric','drive_buffer','ga_spatial_var']:
geneparam[pkey][skey] = str2bool(items[1])
else:
geneparam[pkey][skey] = float(items[1])
elif type(geneparam[pkey][skey]) == list:
if skey in ['rad_bc_type','lpow_krook','upow_krook','psource_type','ck_filter_type','lckpow_krook','uckpow_krook']:
geneparam[pkey][skey].append(int(items[1]))
elif skey in ['buffer_on_ky0','explicit_buffer','shifted_metric','drive_buffer','ga_spatial_var']:
geneparam[pkey][skey].append(str2bool(items[1]))
else:
geneparam[pkey][skey].append(float(items[1]))
else:
if skey in ['rad_bc_type','lpow_krook','upow_krook','psource_type','ck_filter_type','lckpow_krook','uckpow_krook']:
if geneparam[pkey][skey] != int(items[1]):
geneparam[pkey][skey] = [geneparam[pkey][skey],int(items[1])]
elif skey in ['buffer_on_ky0','explicit_buffer','shifted_metric','drive_buffer','ga_spatial_var']:
if geneparam[pkey][skey] != str2bool(items[1]):
geneparam[pkey][skey] = [geneparam[pkey][skey],str2bool(items[1])]
else:
if geneparam[pkey][skey] != float(items[1]):
geneparam[pkey][skey] = [geneparam[pkey][skey],float(items[1])]
elif pkey == "info":
#print(skeys)
if skey not in skeys:
if skey in ['lx']:
geneparam[pkey][skey] = float(items[1])
elif skey in ['nu_ei']:
geneparam[pkey][skey] = float(items[1])
elif pkey == "general":
if skey not in skeys:
if skey in ['antenna_type','perf_tsteps','hyp_z_order','hyp_y_order','hyp_x_order','ev_max_it','n_ev','timelim','ntimesteps']:
geneparam[pkey][skey] = int(items[1])
elif skey in ['ntimesteps']:
geneparam[pkey][skey] = long(items[1])
elif skey in ['nonlinear','hypz_compensation','x_local','calc_dt','include_f0_contr','bpar','delzonal','delzonal_fields','arakawa_zv','check qn gradients']:
geneparam[pkey][skey] = str2bool(items[1])
elif skey in ['hyp_z_with_dz_prefactor','hyp_v_with_dv_prefactor']:
geneparam[pkey][skey] = str2bool(items[1])
elif skey in ['comp_type','timescheme','coll_split_scheme','which_ev','init_cond','collision_op','coll_cons_model']:
geneparam[pkey][skey] = items[1].strip()[1:-1]
elif skey in ['lv_antenna_freq','lv_antenna_initamp','lv_antenna_amp','ev_shift']:
try:
geneparam[pkey][skey] = complex(items[1])
except:
geneparam[pkey][skey] = 0.+0.j
elif skey in ['perf_vec']:
geneparam[pkey][skey] = tuple([int(item) for item in items[1].split()])
elif skey in ['lv_antenna_modes']:
try:
geneparam[pkey][skey].append(items[1])
except ValueError:
geneparam[pkey][skey] = [items[1]]
elif skey in ['taumfn']:
geneparam[pkey][skey] = 0
else:
geneparam[pkey][skey] = float(items[1])
elif type(geneparam[pkey][skey]) == list:
if skey in ['antenna_type','perf_tsteps','hyp_z_order','hyp_y_order','hyp_x_order','ev_max_it','n_ev','timelim','ntimesteps']:
geneparam[pkey][skey].append(int(items[1]))
elif skey in ['ntimesteps']:
geneparam[pkey][skey].append(long(items[1]))
elif skey in ['nonlinear','hypz_compensation','x_local','calc_dt','include_f0_contr','bpar','delzonal','delzonal_fields','arakawa_zv','check qn gradients']:
geneparam[pkey][skey].append(str2bool(items[1]))
elif skey in ['hyp_z_with_dz_prefactor','hyp_v_with_dv_prefactor']:
geneparam[pkey][skey].append(str2bool(items[1]))
elif skey in ['comp_type','timescheme','coll_split_scheme','which_ev','init_cond','collision_op','coll_cons_model']:
geneparam[pkey][skey].append(items[1].strip()[1:-1])
elif skey in ['lv_antenna_freq','lv_antenna_initamp','lv_antenna_amp','ev_shift']:
geneparam[pkey][skey].append(complex(items[1]))
elif skey in ['perf_vec']:
geneparam[pkey][skey].append(tuple([int(item) for item in items[1].split()]))
elif skey in ['lv_antenna_modes']:
continue
else:
geneparam[pkey][skey].append(float(items[1]))
else:
if skey in ['antenna_type','perf_tsteps','hyp_z_order','hyp_y_order','hyp_x_order','ev_max_it','n_ev','timelim','ntimesteps']:
if geneparam[pkey][skey] != int(items[1]):
geneparam[pkey][skey] = [geneparam[pkey][skey],int(items[1])]
elif skey in ['ntimesteps']:
if geneparam[pkey][skey] != long(items[1]):
geneparam[pkey][skey] = [geneparam[pkey][skey],long(items[1])]
elif skey in ['nonlinear','hypz_compensation','x_local','calc_dt','include_f0_contr','bpar','delzonal','delzonal_fields','arakawa_zv','check qn gradients']:
if geneparam[pkey][skey] != str2bool(items[1]):
geneparam[pkey][skey] = [geneparam[pkey][skey],str2bool(items[1])]
elif skey in ['hyp_z_with_dz_prefactor','hyp_v_with_dv_prefactor']:
if geneparam[pkey][skey] != str2bool(items[1]):
geneparam[pkey][skey] = [geneparam[pkey][skey],str2bool(items[1])]
elif skey in ['comp_type','timescheme','coll_split_scheme','which_ev','init_cond','collision_op','coll_cons_model']:
if geneparam[pkey][skey] != items[1].strip()[1:-1]:
geneparam[pkey][skey] = [geneparam[pkey][skey],items[1].strip()[1:-1]]
elif skey in ['lv_antenna_freq','lv_antenna_initamp','lv_antenna_amp','ev_shift']:
if geneparam[pkey][skey] != complex(items[1]):
geneparam[pkey][skey] = [geneparam[pkey][skey],complex(items[1])]
elif skey in ['perf_vec']:
perf_vec_list = tuple([int(item) for item in items[1].split()])
if geneparam[pkey][skey] != perf_vec_list:
geneparam[pkey][skey] = [geneparam[pkey][skey],perf_vec_list]
elif skey in ['lv_antenna_modes']:
continue
else:
if geneparam[pkey][skey] != float(items[1]):
geneparam[pkey][skey] = [geneparam[pkey][skey],float(items[1])]
return geneparam
def read_nrg(nrgfpath,nspecs=0,parameters={},normalized=True):
#Developed by Ehab Hassan on 2019-03-12
if "nrg_" in nrgfpath.strip():
nrgflist=[nrgfpath.strip()]
parameters = read_parameters(nrgflist[0][:-8]+'parameters'+nrgflist[0][-5:])
elif "nrg.dat" in nrgfpath.strip():
nrgflist=[nrgfpath.strip()]
parameters = read_parameters(nrgflist[0][:-7]+'parameters'+nrgflist[0][-4:])
else:
if nrgfpath[-1] != "/": nrgfpath+="/"
nrgflist = sorted(glob.glob(nrgfpath+"nrg_*"))
if nrgflist==[]:
nrgflist = sorted(glob.glob(nrgfpath+"nrg.*"))
if "nrg_" in nrgflist[0]:
parameters = read_parameters(nrgflist[0][:-8]+'parameters'+nrgflist[0][-5:])
elif "nrg.dat" in nrgflist[0]:
parameters = read_parameters(nrgflist[0][:-7]+'parameters'+nrgflist[0][-4:])
nspecs = parameters['box']['n_spec']
specstype = []
for ispec in range(1,nspecs+1):
specname = 'species'+str(ispec)
specstype.append(parameters[specname]['name'])
if not normalized:
units = units_conversion(parameters=parameters)
nrgdata = {}
for inrgf in nrgflist:
if not os.path.isfile(inrgf):
print(inrgf+' FILE NOT FOUND. Exit!'); sys.exit()
inrgfkey = inrgf
nrgdata[inrgfkey] = {}
nrgfhand = open(inrgf,'r')
nrgdata[inrgfkey]['time']=npy.empty(0,dtype=float)
for ispecs in specstype:
nrgdata[inrgfkey][ispecs]={}
nrgdata[inrgfkey][ispecs]['n']=npy.empty(0,dtype=float)
nrgdata[inrgfkey][ispecs]['upara']=npy.empty(0,dtype=float)
nrgdata[inrgfkey][ispecs]['Tpara']=npy.empty(0,dtype=float)
nrgdata[inrgfkey][ispecs]['Tperp']=npy.empty(0,dtype=float)
nrgdata[inrgfkey][ispecs]['PFluxes']=npy.empty(0,dtype=float)
nrgdata[inrgfkey][ispecs]['PFluxem']=npy.empty(0,dtype=float)
nrgdata[inrgfkey][ispecs]['HFluxes']=npy.empty(0,dtype=float)
nrgdata[inrgfkey][ispecs]['HFluxem']=npy.empty(0,dtype=float)
nrgdata[inrgfkey][ispecs]['Viscoses']=npy.empty(0,dtype=float)
nrgdata[inrgfkey][ispecs]['Viscosem']=npy.empty(0,dtype=float)
while True:
try:
ctime = float(nrgfhand.readline())
#if not normalized:
# ctime*=(units['Lref']/units['cref'])
nrgdata[inrgfkey]['time']=npy.append(nrgdata[inrgfkey]['time'],ctime)
for ispecs in specstype:
linedata = nrgfhand.readline().split()
specdata = [float(item) for item in linedata]
if len(specdata)==0:
nrgdata[inrgfkey]['time'] = npy.delete(nrgdata[inrgfkey]['time'],-1)
ntimes = npy.size(nrgdata[inrgfkey]['time'])
specsid = specstype.index(ispecs)
if npy.size(nrgdata[inrgfkey][ispecs]['n']) > ntimes:
for specind in range(specid):
npy.delete(nrgdata[inrgfkey][spectype[specind]]['n'],-1)
npy.delete(nrgdata[inrgfkey][spectype[specind]]['upara'],-1)
npy.delete(nrgdata[inrgfkey][spectype[specind]]['Tpara'],-1)
npy.delete(nrgdata[inrgfkey][spectype[specind]]['Tperp'],-1)
npy.delete(nrgdata[inrgfkey][spectype[specind]]['PFluxes'],-1)
npy.delete(nrgdata[inrgfkey][spectype[specind]]['PFluxem'],-1)
npy.delete(nrgdata[inrgfkey][spectype[specind]]['HFluxes'],-1)
npy.delete(nrgdata[inrgfkey][spectype[specind]]['HFluxem'],-1)
npy.delete(nrgdata[inrgfkey][spectype[specind]]['Viscoses'],-1)
npy.delete(nrgdata[inrgfkey][spectype[specind]]['Viscosem'],-1)
break
if not normalized:
specdata[0]*=(units['nref']*units['rhostar'])**2
specdata[1]*=(units['vref']*units['rhostar'])**2
specdata[2]*=(units['Tref']*units['rhostar'])**2
specdata[3]*=(units['Tref']*units['rhostar'])**2
specdata[4]*=(units['Ggb'])
specdata[5]*=(units['Ggb'])
specdata[6]*=(units['Qgb'])
specdata[7]*=(units['Qgb'])
specdata[8]*=(units['Pgb'])
specdata[9]*=(units['Pgb'])
nrgdata[inrgfkey][ispecs]['n']=npy.append(nrgdata[inrgfkey][ispecs]['n'],specdata[0])
nrgdata[inrgfkey][ispecs]['upara']=npy.append(nrgdata[inrgfkey][ispecs]['upara'],specdata[1])
nrgdata[inrgfkey][ispecs]['Tpara']=npy.append(nrgdata[inrgfkey][ispecs]['Tpara'],specdata[2])
nrgdata[inrgfkey][ispecs]['Tperp']=npy.append(nrgdata[inrgfkey][ispecs]['Tperp'],specdata[3])
nrgdata[inrgfkey][ispecs]['PFluxes']=npy.append(nrgdata[inrgfkey][ispecs]['PFluxes'],specdata[4])
nrgdata[inrgfkey][ispecs]['PFluxem']=npy.append(nrgdata[inrgfkey][ispecs]['PFluxem'],specdata[5])
nrgdata[inrgfkey][ispecs]['HFluxes']=npy.append(nrgdata[inrgfkey][ispecs]['HFluxes'],specdata[6])
nrgdata[inrgfkey][ispecs]['HFluxem']=npy.append(nrgdata[inrgfkey][ispecs]['HFluxem'],specdata[7])
nrgdata[inrgfkey][ispecs]['Viscoses']=npy.append(nrgdata[inrgfkey][ispecs]['Viscoses'],specdata[8])
nrgdata[inrgfkey][ispecs]['Viscosem']=npy.append(nrgdata[inrgfkey][ispecs]['Viscosem'],specdata[9])
except ValueError:
break
nrgfhand.close()
return nrgdata
def read_neoclass(neoclassfpath,nspecs=0,parameters={},normalized=True):
#Developed by Ehab Hassan on 2019-03-12
neoclassfpath = neoclassfpath.strip()
if "neoclass.dat" in neoclassfpath[-13:]:
neoclassflist=[neoclassfpath]
parameters = read_parameters(neoclassflist[0][:-12]+'parameters'+neoclassflist[0][-4:])
elif "neoclass_" in neoclassfpath[-13:]:
neoclassflist=[neoclassfpath]
parameters = read_parameters(neoclassflist[0][:-13]+'parameters'+neoclassflist[0][-5:])
else:
if neoclassfpath[-1] != "/": neoclassfpath+="/"
neoclassflist = sorted(glob(neoclassfpath+"neoclass_*"))
if neoclassflist==[]:
neoclassflist = sorted(glob.glob(neoclassfpath+"neoclass.*"))
if "neoclass.dat" in neoclassflist[0][-13:]:
parameters = read_parameters(neoclassflist[0][:-12]+'parameters'+neoclassflist[0][-4:])
elif "neoclass_" in neoclassflist[0][-13:]:
parameters = read_parameters(neoclassflist[0][:-13]+'parameters'+neoclassflist[0][-5:])
nspecs = parameters['box']['n_spec']
specstype = []
for ispec in range(1,nspecs+1):
specname = 'species'+str(ispec)
specstype.append(parameters[specname]['name'])
if not normalized:
units = units_conversion(parameters=parameters)
neoclassdata = {}
for ineoclassf in neoclassflist:
if not os.path.isfile(ineoclassf):
print(ineoclassf+' FILE NOT FOUND. Exit!'); sys.exit()
ineoclassfkey = ineoclassf
neoclassdata[ineoclassfkey] = {}
neoclassfhand = open(ineoclassf,'r')
pagetitle = neoclassfhand.readline()
neoclassdata[ineoclassfkey]['time']=npy.empty(0,dtype=float)
for ispecs in specstype:
neoclassdata[ineoclassfkey][ispecs]={}
neoclassdata[ineoclassfkey][ispecs]['PFlux']=npy.empty(0,dtype=float)
neoclassdata[ineoclassfkey][ispecs]['HFlux']=npy.empty(0,dtype=float)
neoclassdata[ineoclassfkey][ispecs]['Viscos']=npy.empty(0,dtype=float)
neoclassdata[ineoclassfkey][ispecs]['JBS']=npy.empty(0,dtype=float)
while True:
try:
ctime = float(neoclassfhand.readline())
if not normalized:
ctime*=(units['Lref']/units['cref'])
neoclassdata[ineoclassfkey]['time']=npy.append(neoclassdata[ineoclassfkey]['time'],ctime)
for ispecs in specstype:
linedata = neoclassfhand.readline().split()
specdata = [float(item) for item in linedata]
if len(specdata)==0:
neoclassdata[ineoclassfkey]['time'] = npy.delete(neoclassdata[ineoclassfkey]['time'],-1)
ntimes = npy.size(neoclassdata[ineoclassfkey]['time'])
specsid = specstype.index(ispecs)
if npy.size(neoclassdata[ineoclassfkey][ispecs]['PFlux']) > ntimes:
for specind in range(specid):
npy.delete(neoclassdata[ineoclassfkey][spectype[specind]]['PFlux'],-1)
npy.delete(neoclassdata[ineoclassfkey][spectype[specind]]['HFlux'],-1)
npy.delete(neoclassdata[ineoclassfkey][spectype[specind]]['Viscos'],-1)
npy.delete(neoclassdata[ineoclassfkey][spectype[specind]]['JBS'],-1)
break
if not normalized:
specdata[0]*=(units['Ggb'])
specdata[1]*=(units['Qgb'])
specdata[2]*=(units['Pgb'])
specdata[3]*=(units['nref']*units['cref']*units['Bref']*units['rhostar'])
neoclassdata[ineoclassfkey][ispecs]['PFlux']=npy.append(neoclassdata[ineoclassfkey][ispecs]['PFlux'],specdata[0])
neoclassdata[ineoclassfkey][ispecs]['HFlux']=npy.append(neoclassdata[ineoclassfkey][ispecs]['HFlux'],specdata[1])
neoclassdata[ineoclassfkey][ispecs]['Viscos']=npy.append(neoclassdata[ineoclassfkey][ispecs]['Viscos'],specdata[2])
neoclassdata[ineoclassfkey][ispecs]['JBS']=npy.append(neoclassdata[ineoclassfkey][ispecs]['JBS'],specdata[3])
except ValueError:
break
neoclassfhand.close()
return neoclassdata
def read_scanfile(scanfpath):
#Developed by Ehab Hassan on 2019-02-01
if "scan.log" not in scanfpath:
if scanfpath[-1] != "/": scanfpath += "/"
else:
scanfpath = scanfpath[0:-8]
if not os.path.isfile(scanfpath+'scan.log'):
print('FATAL in read_scanfile:')
print(scanfpath+'scan.log FILE NOT FOUND. Exit!'); sys.exit()
ofh = open(scanfpath+'scan.log','r')
lines = ofh.readlines()
ofh.close()
scandata = {'scanpath':scanfpath}
hlist = lines[0].split('|')[1:]
vlist = []
for ihead in hlist:
vlist.append(ihead.split()[0])
nrecs = npy.size(lines)-1
vscan = npy.zeros((len(vlist),nrecs))
gamma = npy.zeros(nrecs)
omega = npy.zeros(nrecs)
for irec in range(nrecs):
line = lines[irec+1].split('|')
for ivar in range(1,len(vlist)+1):
vscan[ivar-1,irec] = float(line[ivar])
gamma[irec] = float(line[-1].split()[0])
omega[irec] = float(line[-1].split()[1])
scandata['gamma'] = gamma
scandata['omega'] = omega
for ivar in range(len(vlist)):
scandata[vlist[ivar]] = vscan[ivar,:]
return scandata
def read_omega(omegafpath):
#Developed by Ehab Hassan on 2019-03-13
if "omega" in omegafpath.strip():
omegaflist=[omegafpath.strip()]
else:
if omegafpath[-1] != "/": omegafpath+="/"
omegaflist = sorted(glob.glob(omegafpath+"omega*"))
kymin = []
gamma = []
omega = []
for iomegaf in omegaflist:
if not os.path.isfile(iomegaf):
print('FATAL in read_omega:')
print(iomegaf+' FILE NOT FOUND. Exit!'); sys.exit()
recvr = npy.genfromtxt(iomegaf)
kymin.append(float(recvr[0]))
gamma.append(float(recvr[1]))
omega.append(float(recvr[2]))
omegadata = {'kymin':npy.array(kymin),'gamma':npy.array(gamma),'omega':npy.array(omega)}
return omegadata
def omega_to_hz(genefpath):
#Developed by Ehab Hassan on 2019-05-16
if "omega" in genefpath.strip():
omegaflist=[genefpath.strip()]
else:
if genefpath[-1] != "/": genefpath+="/"
omegaflist = sorted(glob.glob(genefpath+"omega*"))
kymin = []
frequency = []
for iomegaf in omegaflist:
if not os.path.isfile(iomegaf):
raise IOError('FATAL: '+iomegaf+' FILE NOT FOUND. Exit!')
if 'dat' in iomegaf:
if not os.path.isfile(iomegaf[:-9]+'parameters.dat'):
raise IOError('FATAL: '+iomegaf[:-9]+'parameters.dat FILE NOT FOUND. Exit!')
iparamf = iomegaf[:-9]+'parameters.dat'
else:
if not os.path.isfile(iomegaf[:-10]+'parameters'+iomegaf[-5:]):
raise IOError('FATAL: '+iomegaf[:-10]+'parameters'+iomegaf[-5:]+' FILE NOT FOUND. Exit!')
iparamf = iomegaf[:-10]+'parameters'+iomegaf[-5:]
paramdata = read_parameters(iparamf)
omegadata = read_omega(iomegaf)
Cs = npy.sqrt(paramdata['units']['Tref']*1000.0*1.602e-19/paramdata['units']['mref']/1.6726e-27)
omegaref = Cs/paramdata['units']['Lref']
kymin.append(omegadata['kymin'][omegaflist.index(iomegaf)])
frequency.append(omegadata['omega'][omegaflist.index(iomegaf)]*omegaref/2.0/npy.pi)
return kymin,frequency
def my_corr_func_complex(v1,v2,time,show_plot=False,v1eqv2=True):
#Developed by David Hatch on ????-??-??
dt=time[1]-time[0]
N=len(time)
cfunc=npy.zeros(N,dtype='complex')
for i in range(N):
i0=i+1
cfunc[-i0]=npy.sum(npy.conj(v1[-i0:])*v2[:i0])
tau=npy.arange(N)
tau=tau*dt
if v1eqv2:
cfunc=npy.real(cfunc)
max_corr=max(npy.abs(cfunc))
corr_time=0.0
i=0
while corr_time==0.0:
if (abs(cfunc[i])-max_corr/npy.e) > 0.0 and \
(abs(cfunc[i+1])-max_corr/npy.e) <= 0.0:
slope=(cfunc[i+1]-cfunc[i])/(tau[i+1]-tau[i])
zero=cfunc[i]-slope*tau[i]
corr_time=(max_corr/npy.e-zero)/slope
i+=1
neg_loc = 10000.0
i=0
while neg_loc==10000.0 and i < N:
if cfunc[i] < 0.0:
neg_loc = tau[i]
i+=1
if neg_loc < corr_time:
print ("WARNING: neg_loc < corr_time")
corr_time = neg_loc
if show_plot:
plt.plot(tau,cfunc,'x-')
ax=plt.axis()
plt.vlines(corr_time,ax[2],ax[3])
plt.show()
return cfunc,tau,corr_time
def read_mom(momfpath,specs='',timeslot=-1):
#Developed by Ehab Hassan on 2019-03-15
if "mom_"+specs in momfpath.strip():
momflist=[momfpath.strip()]
else:
if momfpath[-1] != "/": momfpath+="/"
momflist = sorted(glob.glob(momfpath+"mom_%s*" % specs))
momdata = {}
for imomf in momflist:
if not os.path.isfile(imomf):
print('FATAL in read_mom:')
print(imomf+' FILE NOT FOUND. Exit!'); sys.exit()
momdata[imomf] = {}
par0 = Parameters()
par0.Read_Pars(imomf[:-10]+"parameters_"+imomf[-4:])
pars = par0.pardict
mom = momfile(imomf,pars)
mom.set_time(mom.tmom[timeslot])
momdata[imomf]['dens'] = mom.dens()[:,:,:]
momdata[imomf]['tpar'] = mom.tpar()[:,:,:]
momdata[imomf]['tperp'] = mom.tperp()[:,:,:]
momdata[imomf]['qpar'] = mom.qpar()[:,:,:]
momdata[imomf]['qperp'] = mom.qperp()[:,:,:]
momdata[imomf]['upar'] = mom.upar()[:,:,:]
#nx = int(mom.pars['nx0'])
#nky = int(mom.pars['nky0'])
#nz = int(mom.pars['nz0'])
#dz = 2.0/nz
#if 'lx_a' in mom.pars:
# xgrid = npy.arange(nx)/float(nx-1)*float(mom.pars['lx_a']) + float(mom.pars['x0']) - float(mom.pars['lx_a'])/2.0
#else:
# xgrid = npy.arange(nx)/float(nx-1)*float(mom.pars['lx']) - float(mom.pars['lx'])/2.0
#zgrid = npy.arange(nz)/float(nz-1)*(2.0-dz)-1.0
#momdata[imomf]['xgrid'] = xgrid
#momdata[imomf]['zgrid'] = xgrid
return momdata
def read_field(fieldfpath,timeslot=None,fieldfmt=None):
#Developed by Ehab Hassan on 2019-03-13
'''
fieldfmt argument takes three choices:
fieldfmt = 'original' returns the fields as read from file
fieldfmt = 'local-central' returns the fields at the central point
fieldfmt = 'local-flatten' returns the fields flattened over all dimensions
fieldfmt = 'global-modes' returns the fields and the global modes
'''
fieldfmttypes = ['local-central','local-flatten','global-modes','global-flatten']
if fieldfmt not in fieldfmttypes: fieldfmt = 'original'
if "field" in fieldfpath.strip():
fieldflist=[fieldfpath.strip()]
else:
if fieldfpath[-1] != "/": fieldfpath+="/"
fieldflist = sorted(glob.glob(fieldfpath+"field*"))
fielddata={}
for ifieldf in fieldflist:
if not os.path.isfile(ifieldf):
print('FATAL in read_field:')
print(ifieldf+' FILE NOT FOUND. Exit!'); sys.exit()
fielddata[ifieldf] = {}
par0 = Parameters()
if 'field.dat' in ifieldf:
par0.Read_Pars(ifieldf[:-9]+"parameters"+ifieldf[-4:])
else:
par0.Read_Pars(ifieldf[:-10]+"parameters"+ifieldf[-5:])
pars = par0.pardict
field = fieldfile(ifieldf,pars)
if timeslot == None: t_ind = -1
else: t_ind = timeslot
field.set_time(field.tfld[t_ind])
if 'x_local' in pars:
if pars['x_local'].lower() in ['t','true']:
x_local = True
else:
x_local = False
else:
x_local = True
if fieldfmt=='original':
phi = field.phi()
apar = field.apar()
zgrid = npy.arange(field.nx*field.nz)/float(field.nx*field.nz-1)*float(2.0*field.nx-(2.0/field.nz))-float(field.nx)
fielddata[ifieldf]['t'] = field.tfld
fielddata[ifieldf]['nx'] = field.nx
fielddata[ifieldf]['ny'] = field.ny
fielddata[ifieldf]['nz'] = field.nz
fielddata[ifieldf]['phi'] = phi
fielddata[ifieldf]['apar'] = apar
fielddata[ifieldf]['zgrid'] = zgrid
fielddata[ifieldf]['nfields'] = field.nfields
elif fieldfmt in fieldfmttypes:
phi3d = field.phi()
apar3d = field.apar()
if x_local:
if fieldfmt=='local-central': nx = 1
elif fieldfmt=='local-flatten': nx = field.nx
ny = field.ny
nz = field.nz
phi = npy.zeros(nx*nz,dtype='complex128')
apar = npy.zeros(nx*nz,dtype='complex128')
zgrid = npy.arange(nx*nz)/float(nx*nz-1)*(2.0*nx-(2.0/nz))-nx
if 'n0_global' in pars:
n0_global = int(pars['n0_global'])
q0 = float(pars['q0'])
phase = -npy.e**(-2.0*npy.pi*(0.0+1.0J)*n0_global*q0)
else:
shat = float(pars['shat'])
kymin = float(pars['kymin'])
lx = float(pars['lx'])
phase = -npy.e**(-npy.pi*(0.0+1.0J)*shat*kymin*lx)
shatsgn = int(npy.sign(float(pars['shat'])))
for iy in range(ny):
for ix in range(int(int(nx/2))):
phi[(ix+int(nx/2))*nz:(ix+int(nx/2)+1)*nz]=phi3d[:,iy,ix*shatsgn]*phase**ix
if ix < int(nx/2):
phi[(int(nx/2)-ix-1)*nz:(int(nx/2)-ix)*nz]=phi3d[:,iy,-(ix+1)*shatsgn]*phase**(-(ix+1))
if int(field.nfields)>1 and float(pars['beta'])!=0:
apar[(ix+int(nx/2))*nz:(ix+int(nx/2)+1)*nz]=apar3d[:,iy,ix*shatsgn]*phase**ix
if ix < int(nx/2):
apar[(int(nx/2)-ix-1)*nz:(int(nx/2)-ix)*nz]=apar3d[:,iy,-(ix+1)*shatsgn]*phase**(-(ix+1))
fielddata[ifieldf]['t'] = field.tfld
fielddata[ifieldf]['nx'] = field.nx
fielddata[ifieldf]['ny'] = field.ny
fielddata[ifieldf]['nz'] = field.nz
fielddata[ifieldf]['phi'] = phi
fielddata[ifieldf]['apar'] = apar
fielddata[ifieldf]['zgrid'] = zgrid
fielddata[ifieldf]['nfields'] = field.nfields
elif not x_local:
gpars,geometry = read_geometry_global(ifieldf[:-10]+pars['magn_geometry'][1:-1]+'_'+ifieldf[-4:])
n0_global = int(pars['n0_global'])
q = geometry['q']
phase = 2.0*npy.pi*(0.0+1.0J)*n0_global*q
nx = field.nx
ny = field.ny
nz = field.nz
zgrid = npy.arange(nz)/float(nz-1)*(2.0-(2.0/nz))-1.0
if 'lx_a' in field.pars:
xgrid = npy.arange(nx)/float(nx-1)*float(pars['lx_a'])+float(pars['x0'])-float(pars['lx_a'])/2.0
else:
xgrid = npy.arange(nx)/float(nx-1)*float(pars['lx'])-float(pars['lx'])/2.0
phi = npy.empty((nz+4,ny,nx),dtype = 'complex128')
phi[2:-2,:,:] = phi3d
#phi[2:-2,:,:] = phi3d*float(pars['rhostar'])
for iy in range(ny):
for ix in range(nx):
phi[-2,iy,ix] = phi[ 2,iy,ix]*npy.exp(-phase[ix])
phi[-1,iy,ix] = phi[ 3,iy,ix]*npy.exp(-phase[ix])
phi[ 0,iy,ix] = phi[-4,iy,ix]*npy.exp( phase[ix])
phi[ 1,iy,ix] = phi[-3,iy,ix]*npy.exp( phase[ix])
if field.nfields>1:
apar = npy.empty((nz,ny,nx),dtype = 'complex128')
apar = apar3d
# apar = apar3d*float(pars['rhostar'])
fielddata[ifieldf]['t'] = field.tfld
fielddata[ifieldf]['nx'] = field.nx
fielddata[ifieldf]['ny'] = field.ny
fielddata[ifieldf]['nz'] = field.nz
fielddata[ifieldf]['phi'] = phi
fielddata[ifieldf]['apar'] = apar
fielddata[ifieldf]['xgrid'] = xgrid
fielddata[ifieldf]['zgrid'] = zgrid
fielddata[ifieldf]['nfields'] = field.nfields
if fieldfmt=='global-flatten':
phix = npy.empty(nx*(nz+4),dtype = 'complex128')
if field.nfields>1:
aparx = npy.empty(nx*nz,dtype = 'complex128')
if 'n0_global' in pars:
n0_global = int(pars['n0_global'])
q0 = float(gpars['q0'])
phase = -npy.e**(-2.0*npy.pi*(0.0+1.0J)*n0_global*q0)
else:
shat = float(pars['shat'])
kymin = float(pars['kymin'])
lx = float(pars['lx'])
phase = -npy.e**(-npy.pi*(0.0+1.0J)*shat*kymin*lx)
shatsgn = int(npy.sign(float(gpars['shat'])))
for iy in range(ny):
for ix in range(int(int(nx/2))):
phix[(ix+int(nx/2))*(nz+4):(ix+int(nx/2)+1)*(nz+4)]=phi[:,iy,ix*shatsgn]*phase**ix
if ix < int(nx/2):
phix[(int(nx/2)-ix-1)*(nz+4):(int(nx/2)-ix)*(nz+4)]=phi[:,iy,-(ix+1)*shatsgn]*phase**(-(ix+1))
if int(field.nfields)>1 and float(pars['beta'])!=0:
aparx[(ix+int(nx/2))*nz:(ix+int(nx/2)+1)*nz]=apar[:,iy,ix*shatsgn]*phase**ix
if ix < int(nx/2):
aparx[(int(nx/2)-ix-1)*nz:(int(nx/2)-ix)*nz]=apar[:,iy,-(ix+1)*shatsgn]*phase**(-(ix+1))
fielddata[ifieldf]['phi'] = phix
fielddata[ifieldf]['apar'] = aparx
elif fieldfmt=='global-modes':
min_mode = math.ceil( npy.min(q)*n0_global)
max_mode = math.floor(npy.max(q)*n0_global)
mode_aray = npy.arange(min_mode,max_mode+1)
mode_zgrid = npy.arange(max_mode*20)/float(max_mode*20)*2.0-1.0
n_mode_zgrid = npy.size(mode_zgrid)
phi_theta = npy.empty((n_mode_zgrid,ny,nx),dtype = 'complex128')
phi_modes = npy.empty((n_mode_zgrid,ny,nx),dtype = 'complex128')
if field.nfields>1:
apar_theta = npy.empty((n_mode_zgrid,ny,nx),dtype = 'complex128')
apar_modes = npy.zeros((n_mode_zgrid,ny,nx),dtype = 'complex128')
zgridx = npy.arange(nz+4)/float(nz+4-1)*(2.0+3.0*(2.0/nz))-(1.0+2.0*(2.0/nz))
for iy in range(ny):
for ix in range(nx):
phi_theta[:,iy,ix] = interp(zgridx,npy.real(phi[:,iy,ix]),mode_zgrid)
phi_theta[:,iy,ix] = phi_theta[:,iy,ix]*npy.exp(phase[ix]*mode_zgrid)
phi_modes[:,iy,ix] = npy.fft.fft(phi_theta[:,iy,ix])
if field.nfields>1:
apar_theta[:,iy,ix] = interp(zgrid,npy.real(apar[:,iy,ix]),mode_zgrid)
apar_theta[:,iy,ix] = apar_theta[:,iy,ix]*npy.exp(phase[ix]*mode_zgrid)
apar_modes[:,iy,ix] = npy.fft.fft(apar_theta[:,iy,ix])
fielddata[ifieldf]['zgridx'] = zgridx
fielddata[ifieldf]['phi_theta'] = phi_theta
fielddata[ifieldf]['phi_modes'] = phi_modes
fielddata[ifieldf]['apar_theta'] = apar_theta
fielddata[ifieldf]['apar_modes'] = apar_modes
return fielddata
def field_info(field,param={}):
#Developed by Ehab Hassan on 2019-03-14
for ifieldf in field:
if not param.keys():
param = read_parameters(ifieldf[:-10]+"parameters_"+ifieldf[-4:])
if 'x_local' in param['general'].keys():
if param['general']['x_local']:
x_local = True
else:
x_local = False
else:
x_local = True
if x_local:
nx = field[ifieldf]['nx']
ny = field[ifieldf]['ny']
nz = field[ifieldf]['nz']
phi = field[ifieldf]['phi']
apar = field[ifieldf]['apar']
nfields = field[ifieldf]['nfields']
zgrid = npy.arange(nx*nz)/float(nx*nz-1)*(2.0*nx-(2.0/nz))-nx
if 'n0_global' in param['box']:
phase = -npy.e**(-2.0*npy.pi*(0.0+1.0J)*param['box']['n0_global']*param['geometry']['q0'])
else:
phase = -npy.e**(-npy.pi*(0.0+1.0J)*param['geometry']['shat']*param['box']['kymin']*param['box']['lx'])
phi1d = npy.zeros(nx*nz,dtype='complex128')
apar1d = npy.zeros(nx*nz,dtype='complex128')
shatsgn = int(npy.sign(param['geometry']['shat']))
for i in range(int(int(nx/2))):
phi1d[(i+int(nx/2))*nz:(i+int(nx/2)+1)*nz]=phi[:,0,i*shatsgn]*phase**i
if i < int(nx/2):
phi1d[(int(nx/2)-i-1)*nz:(int(nx/2)-i)*nz]=phi[:,0,-(i+1)*shatsgn]*phase**(-(i+1))
if int(nfields)>1:
apar1d[(i+int(nx/2))*nz:(i+int(nx/2)+1)*nz]=apar[:,0,i*shatsgn]*phase**i
if i < int(nx/2):
apar1d[(int(nx/2)-i-1)*nz:(int(nx/2)-i)*nz]=apar[:,0,-(i+1)*shatsgn]*phase**(-(i+1))
phi = phi1d/phi[int(nz/2),0,0]
apar = apar1d/apar[int(nz/2),0,0]
field_info = {}
field_info['phi'] = phi
field_info['apar']= apar