def WriteMP3dFile(self, aqui, listEsp, Tbase, Etemps, opt, parmk=None):
self.interpreter = MtInterpreter(self.model, opt)
aqui.createZoneTransient()
self.zoneTransient = aqui.getZoneTransient()
self.tlist = self.zoneTransient['tlist']
[aL, aT, aZ, rf] = zip(*Tbase['Transp'])[1]
self.WriteNamFile(opt, rf)
if opt in ['MT3D', 'SEAWAT']: self.mcomp = self.ncomp = 1
else:
self.mcomp, self.ncomp, self.anySol = listEsp['mcomp'], listEsp[
'ncomp'], listEsp['anySol']
if opt in ['MT3D', 'SEAWAT']:
l = 'T' # transport que traceur
trans = self.model.Aquifere.getZoneTransient()['Transport']
if opt == 'SEAWAT':
self.WriteVdfFile()
if opt == 'PHT3D':
self.WritePht3dFile(aqui, Tbase, listEsp, parmk)
self.WritePhreeqc(aqui, Tbase, listEsp)
trans = self.model.Aquifere.getZoneTransient()['PHT3D']
for n in ['btn', 'adv', 'dsp']:
self.writeFile(n, opt)
if len(trans) > 0: self.writeFile('ssm', opt)
## self.WriteBtnFile(aqui,Tbase,listEsp,Etemps,opt);
## self.WriteAdvFile(Tbase,opt);
## self.WriteDspFile(aqui,Tbase,opt);
## self.WriteSsmFile(aqui,Tbase,listEsp,Etemps,opt);
self.WriteGcgFile(Tbase, opt)
if rf > 1:
self.WriteRctFile(aqui, Tbase, listEsp,
opt) # case with retardation
if self.model.getDualPoro() and opt == 'PHT3D':
self.WriteRct1File(aqui, Tbase, listEsp,
opt) # dual porosity exists
return
def WriteMP3dFile(self, aqui,listEsp,Tbase,Etemps,opt,parmk=None):
self.interpreter=MtInterpreter(self.model,opt)
aqui.createZoneTransient();
self.zoneTransient = aqui.getZoneTransient()
self.tlist=self.zoneTransient['tlist']
[aL,aT,aZ,rf] = zip(*Tbase['Transp'])[1]
self.WriteNamFile(opt,rf)
if opt in ['MT3D','SEAWAT']:self.mcomp=self.ncomp=1
else :
self.mcomp,self.ncomp,self.anySol=listEsp['mcomp'],listEsp['ncomp'],listEsp['anySol']
if opt in ['MT3D','SEAWAT']:
l='T' # transport que traceur
trans=self.model.Aquifere.getZoneTransient()['Transport']
if opt=='SEAWAT':
self.WriteVdfFile()
if opt=='PHT3D':
self.WritePht3dFile(aqui,Tbase,listEsp,parmk)
self.WritePhreeqc(aqui,Tbase,listEsp);
trans=self.model.Aquifere.getZoneTransient()['PHT3D']
for n in ['btn','adv','dsp']: self.writeFile(n,opt)
if len(trans)>0: self.writeFile('ssm',opt)
## self.WriteBtnFile(aqui,Tbase,listEsp,Etemps,opt);
## self.WriteAdvFile(Tbase,opt);
## self.WriteDspFile(aqui,Tbase,opt);
## self.WriteSsmFile(aqui,Tbase,listEsp,Etemps,opt);
self.WriteGcgFile(Tbase,opt);
if rf>1: self.WriteRctFile(aqui,Tbase,listEsp,opt) # case with retardation
if self.model.getDualPoro() and opt=='PHT3D':
self.WriteRct1File(aqui,Tbase,listEsp,opt) # dual porosity exists
return
class MP3dWriter:
def __init__(self, model, path, name):
self.model, self.gui = model, model.gui
self.pPath, self.pName = path, name
self.fullPath = path + os.sep + name
self.ncomp, self.mcomp = 1, 1
def CreateFile(self, extension, mode):
filename = self.pPath + os.sep + extension
file_descriptor = open(filename, mode)
return file_descriptor
def WriteMP3dFile(self, aqui, listEsp, Tbase, Etemps, opt, parmk=None):
self.interpreter = MtInterpreter(self.model, opt)
aqui.createZoneTransient()
self.zoneTransient = aqui.getZoneTransient()
self.tlist = self.zoneTransient['tlist']
[aL, aT, aZ, rf] = zip(*Tbase['Transp'])[1]
self.WriteNamFile(opt, rf)
if opt in ['MT3D', 'SEAWAT']: self.mcomp = self.ncomp = 1
else:
self.mcomp, self.ncomp, self.anySol = listEsp['mcomp'], listEsp[
'ncomp'], listEsp['anySol']
if opt in ['MT3D', 'SEAWAT']:
l = 'T' # transport que traceur
trans = self.model.Aquifere.getZoneTransient()['Transport']
if opt == 'SEAWAT':
self.WriteVdfFile()
if opt == 'PHT3D':
self.WritePht3dFile(aqui, Tbase, listEsp, parmk)
self.WritePhreeqc(aqui, Tbase, listEsp)
trans = self.model.Aquifere.getZoneTransient()['PHT3D']
for n in ['btn', 'adv', 'dsp']:
self.writeFile(n, opt)
if len(trans) > 0: self.writeFile('ssm', opt)
## self.WriteBtnFile(aqui,Tbase,listEsp,Etemps,opt);
## self.WriteAdvFile(Tbase,opt);
## self.WriteDspFile(aqui,Tbase,opt);
## self.WriteSsmFile(aqui,Tbase,listEsp,Etemps,opt);
self.WriteGcgFile(Tbase, opt)
if rf > 1:
self.WriteRctFile(aqui, Tbase, listEsp,
opt) # case with retardation
if self.model.getDualPoro() and opt == 'PHT3D':
self.WriteRct1File(aqui, Tbase, listEsp,
opt) # dual porosity exists
return
def WriteNamFile(self, opt, rf):
f1 = self.CreateFile(opt + '.nam', 'w')
f1.write('List 7 ' + opt + '.out\n')
if opt == 'SEAWAT':
f2 = open(self.fullPath + '.nam', 'r')
f2.readline()
for ll in f2:
f1.write(ll)
f2.close()
else:
f1.write('FTL 66 ' + self.pName + '.flo\n')
f1.write('BTN 31 ' + opt + 'btn.dat\n ADV 32 ' + opt +
'adv.dat\n')
f1.write('DSP 33 ' + opt + 'dsp.dat\n SSM 34 ' + opt +
'ssm.dat\n')
f1.write('GCG 35 ' + opt + 'gcg.dat\n')
if opt == 'PHT3D':
f1.write('PHC 64 ' + opt + '_ph.dat\n')
if rf > 1 or self.model.getDualPoro():
f1.write('RCT 36 ' + opt + 'rct.dat\n')
f1.close()
#*********************** generic file writer ****************
def writeFile(self, name, opt):
"""to write any modflow file.
reads the keyword file and prints all keywords by types : param (0D)
vector (1D) array (2D). types are found by (dim1,dim2).."""
f1 = open(self.pPath + os.sep + opt + name + '.dat', 'w')
ptslist, arrlist = [], []
n1 = Mkey.groups.keys()
#print n1,name
for n in n1:
if n.split('.')[1] == name: llist = Mkey.groups[n]
for ll in llist:
cond = Mkey.lines[ll]['cond']
#print 'mflw 1',cond,self.testCondition(cond)
if self.testCondition(cond) == False: continue
kwlist = Mkey.lines[ll]['kw']
kw0 = kwlist[0].split('(')[0]
ktyp = Mkey.lines[ll]['type']
#print 'mtw',kw0,ktyp
if ktyp in ['arr', 'vec', 'xarr']:
arr, aname = self.interpreter.getArray(kw0)
if ktyp == 'vec': # a vector
self.writeVecMT3D(arr, f1)
exec('self.' + kw0 + '=' + str(arr[0]))
elif ktyp == 'string': # a string to print
s = self.interpreter.getParm(kw0)
f1.write(s)
#exec('self.'+kw0+'='+s[:2])
elif ktyp == 'arr': # one array
self.writeBlockMT3D(arr, f1, aname)
elif ktyp == 'xarr': # several arrays
for i in range(len(arr)):
self.writeBlockMT3D(arr[i], f1, aname[i])
elif ktyp == 'parr': # one variable, p arrays: one for each period
nper = self.interpreter.getNper()
for ip in range(nper):
arr = self.interpreter.getArrayPeriod(kw0, ip)
arrlist.append(arr)
elif ktyp == 'nvec2': # list of periods or others
vlist = []
for k in kwlist:
a = k.split('(')
b, c = self.interpreter.getArray(a[0])
vlist.append(b)
nlines = len(vlist[0])
s = ''
for j in range(nlines):
for ik in range(3):
val = vlist[ik][j]
s += str(val)[:9].ljust(9) + ' ' #' %9.3e'%val#
s += '\n'
for ik in range(3, 7):
val = vlist[ik][j]
s += str(val)[:9].ljust(9) + ' ' #' %9.3e'%val #
s += '\n'
f1.write(s)
elif ktyp == 'npoints': # points on the grid stored in alist (for ssm)
nper = self.interpreter.getNper()
print 'opt', opt
for ip in range(nper):
plist = self.interpreter.getPointsPer(opt, ip)
il, ir, ic, typ, v = plist
s = str(len(il)) + '\n'
#print len(il),len(ir),len(ic),len(typ),len(v)
for i in range(len(il)):
s += str(il[i] + 1).ljust(10) + str(ir[i] + 1).ljust(
10) + str(ic[i] + 1).ljust(10)
if opt == 'MT3D':
s += '%9.3e ' % float(v[i]) + str(
typ[i]).rjust(9) + '\n'
elif opt == 'PHT3D':
s += ' 0.' + str(
typ[i]).ljust(10) + v[i] + '\n'
ptslist.append(s)
else: # classical parameters
for k in kwlist:
val = str(self.interpreter.getParm(k))
try:
int(val)
exec('self.' + k + '=' + val) #
except ValueError:
if val[0] != '#':
exec('self.' + k + '=\'' + val + '\'')
if val != ' ': f1.write(val[:9].ljust(9) + ' ')
if val != ' ': f1.write('\n')
if len(arrlist) + len(
ptslist
) > 0: # write the variables by period saved in a list previously
nper = self.interpreter.getNper()
for ip in range(nper):
if len(arrlist) > ip:
if type(arrlist[ip]) == type(
[5, 6]): # case of recharge with several species
f1.write('1 \n')
for j in range(len(arrlist[ip])):
self.writeMatMT3D(arrlist[ip][j], f1)
else:
f1.write('1 \n')
self.writeMatMT3D(arrlist[ip], f1)
if len(ptslist) > ip: f1.write(ptslist[ip])
print 'print ' + name + ' done'
f1.close()
#**************** test condition **********************
def testCondition(self, cond):
""" test if the condition is satisfied"""
a = True
if cond != '':
if len(cond.split('and')) > 1:
c1 = cond.split('and')
c2 = '(self.' + c1[0].strip() + ')'
for i in range(1, len(c1)):
c2 += ' and (self.' + c1[i].strip() + ')'
elif len(cond.split('or')) > 1:
c1 = cond.split('or')
c2 = '(self.' + c1[0] + ')'
for i in range(1, len(c1)):
c2 += ' or (self.' + c1[i].strip() + ')'
else:
c2 = 'self.' + cond
exec('a=' + c2)
#print 'cond',c2,a;
if a or cond == '': return True
return False
#************************ writeture du fichier GCG ***********************************
def WriteGcgFile(self, Tbase, opt):
f1 = self.CreateFile(opt + 'gcg.dat', 'w')
it, mxiter, isolve, ncrs, accl, cclose, iprgcg = zip(
*Tbase['Solver'])[1]
f1.write('%9i %9i %9i %9i\n' %
(int(it), int(mxiter), int(isolve), int(ncrs)))
f1.write('%9i %9.4e %9i\n' % (accl, cclose, int(iprgcg)))
f1.close() #fermer le fichier gcg
#*************************** write RCT file for sorption *********************
def WriteRctFile(self, aqui, Tbase, listE, opt):
""" writes an RCT file in case of retardation """
f1 = self.CreateFile(opt + 'rct.dat', 'w')
nrow = int(aqui.getFullGrid()['ny'])
nlay = aqui.getNbCouches()
if aqui.getDim() in ['Xsection', 'Radial']: nlay = nrow
[aL, aT, aZ, rf] = zip(*Tbase['Transp'])[1]
Isothm, Ireact, Irctop, Igetsc = 1, 0, 2, 0
f1.write('%9i %9i %9i %9i\n' % (Isothm, Ireact, Irctop, Igetsc))
# Rec 2 : Rohb (2b and 2c not used here)
poro = obj2matBlock(aqui, 'Porosite')
rhob = 2650. * (1. - poro)
#print nlay,shape(poro),shape(rhob)
for l in range(nlay):
self.writeMatMT3D(rhob[l] * self.radfact, f1,
'Rhob') # rhob matric(ncol,nrow) en kg/m3
# line E3 sorption (isothm>0)
Kd = (float(rf) - 1.) * poro / rhob
for l in range(nlay):
self.writeMatMT3D(Kd[l], f1, 'Kd')
# line E4 2nd sorption coeff not used here
for l in range(nlay):
f1.write(' 0 0.0 \n')
f1.close()
#*************************** write RCT file for 2domain *********************
def WriteRct1File(self, aqui, Tbase, listE, opt):
""" writes an RCT file in case of double porosity"""
f1 = self.CreateFile(opt + 'rct.dat', 'w')
nlay = aqui.getNbCouches()
if aqui.getDim() in ['Xsection', 'Radial']:
nlay = nrow
nrow = 1
# Rec1 : Isothm, Ireact, Irctop, IGetsc Irctop 0
# 2domain : Isothm : 5 dual domain( no sorption), igetsc>0 : initial conc read here
Isothm, Ireact, Irctop, Igetsc = 5, 0, 1, 1
f1.write('%9i %9i %9i %9i\n' % (Isothm, Ireact, Irctop, Igetsc))
# Rec 2 : Rohb do not enter if isothm=5
# Rec3 Prsty2 only for dual domain (isothm 5 or 6)
# the porosity matrix comes from Pht3D immobile solutions, line Imm_poro
opt1 = opt * 1
if opt == 'MT3D': opt1 = 'Transport'
mS = obj2matBlockNb(aqui, opt1, 'zon')
m0 = mS[0] * 0
imm_s = Tbase['Immobile']['Solutions']
ie = imm_s['rows'].index('Imm_poro')
for l in range(nlay):
poro = m0 + float(imm_s['data'][ie][1]) # data[1] backgrd
for s in range(self.nsol - 1):
poro[abs(mS[l]) / 1000 == s + 1] = float(imm_s['data'][ie][s +
2])
self.writeMatMT3D(poro, f1, 'Poro')
# Rec4 : if Igetsc>0 initial conc in immob phase for each species
# run along the Chemistry to find the species for whic conc are needed
short = ['k', 'i', 'kim', 'p', 'e', 's', 'kp']
ntot = 0
div = [1000, 1000, 1000, 100, 10, 100, 1]
lon = ['Solutions'] * 3
lon.extend(['Phases', 'Exchange', 'Surface', 'Phases'])
for ik in range(len(short)):
l0 = listE[short[ik]] # list of species present in chemistry
for esp in l0:
if esp in ['Imm_poro', 'Transf_coeff']: continue
kw = lon[ik]
imm = Tbase['Immobile'][kw].copy()
ntot += 1
ie = imm['rows'].index(esp)
#print 'mtpht rct',kw,esp,ie
for l in range(nlay):
cnc = m0 + float(imm['data'][ie][1])
#print imm['data'][ie][1]
nsp = len(imm['cols']) - 1
for s in range(
nsp -
1): # to find the place where BC is true solution
cnc[abs(mS[l]) / div[ik] == s + 1] = float(
imm['data'][ie][s + 2])
self.writeMatMT3D(cnc, f1, esp)
# Rec 5 sorption1 (each species)
for i in range(ntot):
f1.write(' 0 0.0 \n')
# Rec6 sorption 2, here mass transfer coeff for all species
ie = imm_s['rows'].index('Transf_coeff')
for i in range(ntot):
for l in range(nlay):
tcoeff = m0 + float(imm_s['data'][ie][1]) # data[1] backgrd
for s in range(
self.nsol -
1): # to find the place where BC is true solution
tcoeff[abs(mS[l]) / 1000 == s + 1] = float(
imm_s['data'][ie][s + 2])
self.writeMatMT3D(tcoeff, f1, 'Transf Coeff')
#REc7 RC1 parm for fisrt order deg1
for i in range(ntot):
f1.write(' 0 0.0 \n')
#REc8 RC2 parm for fisrt order deg 2
for i in range(ntot):
f1.write(' 0 0.0 \n')
f1.close()
#********************************* Ecire fichier VDF for Seawat ********************
def WriteVdfFile(self):
f1 = self.CreateFile('Seawatvdf.dat', 'w')
## 1. MTDNCONC MFNADVFD NSWTCPL IWTABLE
## Mtdconc=0 density specified =n dens calculated from n species
## MFNADVFD=2 centre in sapce, ><2 upstream weigthed
## NSWTCPL max number of non linear iterations if 0 or 1 explicit coupling
## iwtable : 0 water table correction not applied, >0 applied
Mtdnconc, Mfnadvdf, Nswtcpl, Iwtable = 1, 1, 1, 0
f1.write(' %9i %9i %9i %9i Mtdnconc Mfnadvdf Nswtcpl Iwtable \n' %
(Mtdnconc, Mfnadvdf, Nswtcpl, Iwtable))
## 2. DENSEMIN DENSEMAX min an dmax density if 0 not limitation
Densemin, Densemax = 0, 0
f1.write(' %9i %9i DENSEMIN DENSEMAX \n' % (Densemin, Densemax))
## If NSWTCPL is greater than 1, then read item 3.
## 3. DNSCRIT convergene criterion difference in density
Dnscrit = 1e-3
if Nswtcpl > 1: f1.write(' %9.4e \n' % Dnscrit)
## 4. DENSEREF DENSESLP
Denseref, Denseslp = 1000., .7143 # Care in kg/m3, slp for freash and sea water
f1.write(' %9i %9i DENSEREF DENSESLP \n' % (Denseref, Denseslp))
## 5. FIRSTDT ength of first time step
Firstdt = 1e-3
f1.write(' %9.4e \n' % Firstdt)
## FOR EACH STRESS PERIOD (read items 6 and 7 only if MTDNCONC = 0)
## 6. INDENSE if<0 val of dense reused form prev tstep
## =0 Dense=ref >=1 dense read from item 7 =2 read from 7 but as conc
## Read item 7 only if INDENSE is greater than zero
## 7. [DENSE(NCOL,NROW)] – U2DREL
## Item 7 is read for each layer in the grid.
nper = len(self.tlist)
Indense = -1
for ip in range(nper):
if Mtdnconc == 0: f1.write(' %9i %9i INDENSE \n' % Indense)
f1.close()
#********************************* Ecire fichier Pht3d ********************
def WritePht3dFile(self, aqui, Tbase, listE, parmk):
f1 = self.CreateFile('PHT3D_ph.dat', 'w')
#PH1 Record: OS TMP_LOC RED_MOD TEMP ASBIN EPS_AQU EPS_PH PACK_SZ
# OS 1 iterative, 2 sequential. que 2 implemente
# TMP_LOC : 0 writere dans temp, 1 : writere sur dir local
# REd mode : 0 pH pe vairables, 1 : pe fixe, 2 : pH et pe fixes (plus rapide)
# TEmp temperature, ASBIN : 0 : writeture fich binaire, 1 :ascii
# eps_aqu et eps_ph : si 0 calcul partout
# pack_sz : taille des paquets pour phreeqc 4000 chiffre OK
temp = Tbase['PHparm'][0][1]
os0, tmp, fix0, asbin, eps0, eps1, pack = 2, 1, 0, 0, 1e-10, .001, 2000
f1.write('%9i %9i %9i %9.1f %9i %9.1e %9.5f %9i\n' %
(os0, tmp, fix0, temp, asbin, eps0, eps1, pack))
dcharge = Tbase['PHparm'][1][1]
f1.write('%9i\n' % dcharge) # PH2 v2 diif de charge admissibe
# determiner le noimbre d'esp cinetiques et en faire la liste
nInorg = len(listE['i'])
#+len(self.lists);
nKmob = len(listE['k'])
nKimob = len(listE['kim'])
nMinx = len(listE['p'])
nExch = len(listE['e'])
f1.write('%9i\n' % (nInorg)) # PH3 nb compose inorganiques
f1.write('%9i\n' % (nMinx)) # PH4 nb mineraux
f1.write('%9i %9i\n' %
(nExch, 0)) # PH5 nb ech ions, 0 je sais pas pourquoi
# PH6 surface complexation
nSurf = len(listE['s'])
f1.write('%9i\n' % nSurf)
#PH7 Record: NR_MOB_KIN NR_MIN_KIN NR_SURF_KIN NR_IMOB_KIN
# nb especes cinetiques mobiles, minerales, surfaces et substeps pour plus tard
nKsurf, nKmin = 0, len(listE['kp'])
f1.write('%9i %9i %9i %9i\n' % (nKmob, nKmin, nKsurf, nKimob))
# PH8 : NR_OUTP_SPEC (complexes) PR_ALKALINITY_FLAG (futur)
f1.write('%9i %9i\n' % (0, 0))
## nb unites inutile car pht3d considere que tout est en jour
Chem = Tbase['Chemistry']
if Chem.has_key('Rates'):
rates = Chem['Rates']
for nom in listE['k']:
iek = rates['rows'].index(nom)
f1.write(nom + '%5i \n ' % (parmk[nom])) #param k
for ip in range(parmk[nom]):
f1.write('%9.5e \n' % float(rates['data'][iek][ip + 2]))
f1.write('-formula ' + rates['data'][iek][-1] +
'\n') # formula
#for n in self.lists: f1.write(n+' \n') # species
optsu = Tbase['PHparm'][2][1]
for n in listE['i']:
add = ''
if optsu.strip() == n: add = ' charge'
f1.write(n.replace('(+', '(') + add +
'\n') # que reac isntant et AE, pH pe
# kinetic immobile
if Chem.has_key('Rates'):
rates = Chem['Rates']
for nom in listE['kim']:
iek = rates['rows'].index(nom)
f1.write(nom + '%5i \n ' % (parmk[nom])) #param k
for ip in range(parmk[nom]):
f1.write('%9.5e \n' % float(rates['data'][iek][ip + 2]))
f1.write('-formula ' + rates['data'][iek][-1] +
'\n') # formula
for p in listE['p']:
ip = Chem['Phases']['rows'].index(p)
f1.write(p + ' ' + str(Chem['Phases']['data'][ip][1]) +
' \n') # phase name + SI backgrd
for n in listE['e']:
f1.write(n + ' -1 \n') # exchanger
if Chem.has_key('Surface'): # surface
su = Chem['Surface']
l = len(su['cols'])
for esp in listE['s']:
st = esp
ies = su['rows'].index(esp)
for i in range(l - 2, l):
st += ' ' + str(su['data'][ies][i])
f1.write(st + ' \n')
optsu = Tbase['PHparm'][3][1]
if optsu in ['no_edl', 'diffuse_layer']:
f1.write('-' + optsu + '\n')
if Chem.has_key('Kinetic_Minerals'):
kp = Chem['Kinetic_Minerals']
for nom in listE['kp']:
iek = kp['rows'].index(nom)
f1.write(nom + '%5i \n ' % (parmk[nom])) #param k
for ip in range(parmk[nom]):
f1.write('%9.5e \n' % float(kp['data'][iek][ip + 1]))
f1.close()
# ''''''''''''''''''''''''''''''' fonction writeMatMT3D '''''''''''''''''''''''''''
def writeVecMT3D(self, v, f1, name=' '):
l = len(v)
a = str(type(v[0]))
if a[13:16] == 'int': typ = 'I'
else: typ = 'G'
if amin(v) == amax(v):
f1.write(' 0 %7.3e #' % (amin(v)) + name + '\n')
return
if typ == 'I':
fmt = ' 100 1 (' + str(l) + 'I' + str(ln) + ')'
else:
fmt = ' 100 1.0 (' + str(l) + 'G12.4)'
f1.write(fmt)
f1.write('\n')
if typ == 'I': fmt = '%' + str(ln) + 'i'
else: fmt = '%+11.4e '
for i in range(l):
f1.write(fmt % v[i])
f1.write('\n')
def writeMatMT3D(self, m, f1, name=' '):
if len(shape(m)) <= 1: return self.writeVecMT3D(m, f1, name)
[l, c] = shape(m)
ln = 3
a = str(type(m[0, 0]))
if a[13:16] == 'int': typ = 'I'
else: typ = 'G'
if amin(amin(m)) == amax(amax(m)):
if typ == 'I':
f1.write(' 0 %8i #' % (amin(amin(m))) + name[:6] +
'\n')
else:
f1.write(' 0 %7.3e #' % (amin(amin(m))) + name[:6] +
'\n')
return
if typ == 'I':
fmt = ' 100 1 (' + str(c) + 'I' + str(ln) + ')'
else:
fmt = ' 100 1.0 (' + str(c) + 'G12.4) #' + name[:6]
f1.write(fmt + '\n')
if typ == 'I': fmt = '%' + str(ln) + 'i'
else: fmt = '%11.4e '
for i in range(l - 1, -1, -1):
for j in range(c):
f1.write(fmt % m[i][j])
f1.write('\n')
def writeBlockMT3D(self, m, f1, name=' '):
if len(shape(m)) == 3:
nlay, a, b = shape(m)
for l in range(nlay):
self.writeMatMT3D(m[l], f1, name)
else:
self.writeMatMT3D(m, f1, name)
def WritePhreeqc(self, aqui, Tbase, listE):
"""this routine writes a phreeqc file where all solutions are written in
phreqc format to be able to test their equilibrium before running pht3d
1. tabke background, then cycle through pht3d zones
2. get the solution number, phase number...it does not take rates
3 write them in phreeqc format"""
f1 = self.CreateFile('solutions.phrq', 'w')
f1.write('Database ' + self.pPath + '\pht3d_datab.dat \n')
zones = aqui.getZoneList('PHT3D')
nzone = len(zones)
for i in range(nzone):
z = zones[i]
val = z.getVal()
if type(val) == type([5]):
val = int(val[0].split()[1]) #case of transient chemistry
else:
val = int(val)
f1.write('Solution ' + str(i) + ' \n units mol/L \n')
solu = Tbase['Chemistry']['Solutions']
nsol = val / 1000
for esp in listE['i']: # go through phase list
ie = solu['rows'].index(esp)
#print esp,phases['rows'],ip,phases['data'][ip] # index of the phase
conc = solu['data'][ie][nsol +
1] #backgr concentration of species
f1.write(esp + ' ' + str(conc) + '\n')
f1.write('Equilibrium_Phases ' + str(i) + '\n')
phases = Tbase['Chemistry']['Phases']
nphas = mod(val, 1000) / 100
for esp in listE['p']: # go through phase list
ip = phases['rows'].index(esp)
#print esp,phases['rows'],ip,phases['data'][ip] # index of the phase
IS, conc = phases['data'][ip][
nphas * 2 + 1:nphas * 2 +
3] #backgr SI and concentration of phase
f1.write(esp + ' ' + str(IS) + ' ' + str(conc) + '\n')
f1.write('end \n')
f1.close()
class MP3dWriter:
def __init__(self, model, path, name):
self.model,self.gui = model, model.gui
self.pPath,self.pName = path,name;
self.fullPath = path + os.sep + name
self.ncomp, self.mcomp= 1,1
def CreateFile(self, extension, mode):
filename = self.pPath + os.sep+extension
file_descriptor = open(filename, mode)
return file_descriptor
def WriteMP3dFile(self, aqui,listEsp,Tbase,Etemps,opt,parmk=None):
self.interpreter=MtInterpreter(self.model,opt)
aqui.createZoneTransient();
self.zoneTransient = aqui.getZoneTransient()
self.tlist=self.zoneTransient['tlist']
[aL,aT,aZ,rf] = zip(*Tbase['Transp'])[1]
self.WriteNamFile(opt,rf)
if opt in ['MT3D','SEAWAT']:self.mcomp=self.ncomp=1
else :
self.mcomp,self.ncomp,self.anySol=listEsp['mcomp'],listEsp['ncomp'],listEsp['anySol']
if opt in ['MT3D','SEAWAT']:
l='T' # transport que traceur
trans=self.model.Aquifere.getZoneTransient()['Transport']
if opt=='SEAWAT':
self.WriteVdfFile()
if opt=='PHT3D':
self.WritePht3dFile(aqui,Tbase,listEsp,parmk)
self.WritePhreeqc(aqui,Tbase,listEsp);
trans=self.model.Aquifere.getZoneTransient()['PHT3D']
for n in ['btn','adv','dsp']: self.writeFile(n,opt)
if len(trans)>0: self.writeFile('ssm',opt)
## self.WriteBtnFile(aqui,Tbase,listEsp,Etemps,opt);
## self.WriteAdvFile(Tbase,opt);
## self.WriteDspFile(aqui,Tbase,opt);
## self.WriteSsmFile(aqui,Tbase,listEsp,Etemps,opt);
self.WriteGcgFile(Tbase,opt);
if rf>1: self.WriteRctFile(aqui,Tbase,listEsp,opt) # case with retardation
if self.model.getDualPoro() and opt=='PHT3D':
self.WriteRct1File(aqui,Tbase,listEsp,opt) # dual porosity exists
return
def WriteNamFile(self,opt,rf):
f1 = self.CreateFile(opt+'.nam','w');
f1.write('List 7 '+opt+'.out\n')
if opt=='SEAWAT':
f2=open(self.fullPath+'.nam','r');f2.readline()
for ll in f2: f1.write(ll)
f2.close()
else : f1.write('FTL 66 '+self.pName+'.flo\n')
f1.write('BTN 31 '+opt+'btn.dat\n ADV 32 '+opt+'adv.dat\n')
f1.write('DSP 33 '+opt+'dsp.dat\n SSM 34 '+opt+'ssm.dat\n')
f1.write('GCG 35 '+opt+'gcg.dat\n')
if opt=='PHT3D':
f1.write('PHC 64 '+opt+'_ph.dat\n')
if rf>1 or self.model.getDualPoro():
f1.write('RCT 36 '+opt+'rct.dat\n')
f1.close()
#*********************** generic file writer ****************
def writeFile(self,name,opt):
"""to write any modflow file.
reads the keyword file and prints all keywords by types : param (0D)
vector (1D) array (2D). types are found by (dim1,dim2).."""
f1=open(self.pPath +os.sep+opt+ name+'.dat','w');
ptslist,arrlist=[],[]
n1=Mkey.groups.keys();#print n1,name
for n in n1:
if n.split('.')[1]==name: llist=Mkey.groups[n]
for ll in llist:
cond=Mkey.lines[ll]['cond'];#print 'mflw 1',cond,self.testCondition(cond)
if self.testCondition(cond)==False :continue
kwlist=Mkey.lines[ll]['kw'];kw0=kwlist[0].split('(')[0]
ktyp=Mkey.lines[ll]['type'];#print 'mtw',kw0,ktyp
if ktyp in ['arr','vec','xarr']: arr,aname=self.interpreter.getArray(kw0)
if ktyp=='vec': # a vector
self.writeVecMT3D(arr,f1)
exec('self.'+kw0+'='+str(arr[0]))
elif ktyp=='string': # a string to print
s=self.interpreter.getParm(kw0);f1.write(s)
#exec('self.'+kw0+'='+s[:2])
elif ktyp=='arr': # one array
self.writeBlockMT3D(arr,f1,aname)
elif ktyp=='xarr': # several arrays
for i in range(len(arr)): self.writeBlockMT3D(arr[i],f1,aname[i])
elif ktyp=='parr': # one variable, p arrays: one for each period
nper=self.interpreter.getNper()
for ip in range(nper):
arr=self.interpreter.getArrayPeriod(kw0,ip)
arrlist.append(arr)
elif ktyp=='nvec2': # list of periods or others
vlist=[]
for k in kwlist:
a=k.split('(')
b,c=self.interpreter.getArray(a[0]);vlist.append(b)
nlines=len(vlist[0]);s=''
for j in range(nlines):
for ik in range(3):
val=vlist[ik][j];s+=str(val)[:9].ljust(9)+' ' #' %9.3e'%val#
s+='\n'
for ik in range(3,7):
val=vlist[ik][j];s+=str(val)[:9].ljust(9)+' ' #' %9.3e'%val #
s+='\n'
f1.write(s)
elif ktyp=='npoints': # points on the grid stored in alist (for ssm)
nper=self.interpreter.getNper();print 'opt',opt
for ip in range(nper):
plist=self.interpreter.getPointsPer(opt,ip)
il,ir,ic,typ,v=plist;s=str(len(il))+'\n'
#print len(il),len(ir),len(ic),len(typ),len(v)
for i in range(len(il)):
s+=str(il[i]+1).ljust(10)+str(ir[i]+1).ljust(10)+str(ic[i]+1).ljust(10)
if opt=='MT3D': s+='%9.3e '%float(v[i])+str(typ[i]).rjust(9)+'\n'
elif opt=='PHT3D': s+=' 0.'+str(typ[i]).ljust(10)+v[i]+'\n'
ptslist.append(s)
else : # classical parameters
for k in kwlist:
val=str(self.interpreter.getParm(k));
try : int(val); exec('self.'+k+'='+val) #
except ValueError:
if val[0]!='#' : exec('self.'+k+'=\''+val+'\'')
if val!=' ': f1.write(val[:9].ljust(9)+' ')
if val!=' ': f1.write('\n')
if len(arrlist)+len(ptslist)>0: # write the variables by period saved in a list previously
nper=self.interpreter.getNper()
for ip in range(nper):
if len(arrlist)>ip:
if type(arrlist[ip])==type([5,6]): # case of recharge with several species
f1.write('1 \n');
for j in range(len(arrlist[ip])): self.writeMatMT3D(arrlist[ip][j],f1)
else: f1.write('1 \n');self.writeMatMT3D(arrlist[ip],f1)
if len(ptslist)>ip: f1.write(ptslist[ip])
print 'print '+name+' done'
f1.close()
#**************** test condition **********************
def testCondition(self,cond):
""" test if the condition is satisfied"""
a=True
if cond!='':
if len(cond.split('and'))>1:
c1=cond.split('and'); c2='(self.'+c1[0].strip()+')'
for i in range(1,len(c1)): c2+=' and (self.'+c1[i].strip()+')'
elif len(cond.split('or'))>1:
c1=cond.split('or'); c2='(self.'+c1[0]+')'
for i in range(1,len(c1)): c2+=' or (self.'+c1[i].strip()+')'
else : c2='self.'+cond
exec('a='+c2);#print 'cond',c2,a;
if a or cond=='': return True
return False
#************************ writeture du fichier GCG ***********************************
def WriteGcgFile(self, Tbase,opt):
f1 = self.CreateFile(opt+'gcg.dat','w')
it, mxiter, isolve, ncrs, accl, cclose, iprgcg = zip(*Tbase['Solver'])[1]
f1.write('%9i %9i %9i %9i\n' %(int(it),int(mxiter),int(isolve),int(ncrs)))
f1.write('%9i %9.4e %9i\n' %(accl,cclose,int(iprgcg)))
f1.close() #fermer le fichier gcg
#*************************** write RCT file for sorption *********************
def WriteRctFile(self,aqui,Tbase,listE,opt):
""" writes an RCT file in case of retardation """
f1 = self.CreateFile(opt+'rct.dat','w')
nrow = int(aqui.getFullGrid()['ny'])
nlay = aqui.getNbCouches()
if aqui.getDim() in ['Xsection','Radial']: nlay=nrow
[aL,aT,aZ,rf] = zip(*Tbase['Transp'])[1]
Isothm, Ireact,Irctop, Igetsc = 1,0,2,0
f1.write('%9i %9i %9i %9i\n' %(Isothm, Ireact,Irctop, Igetsc))
# Rec 2 : Rohb (2b and 2c not used here)
poro = obj2matBlock(aqui,'Porosite');rhob = 2650.*(1.-poro);#print nlay,shape(poro),shape(rhob)
for l in range(nlay):
self.writeMatMT3D(rhob[l]*self.radfact,f1,'Rhob') # rhob matric(ncol,nrow) en kg/m3
# line E3 sorption (isothm>0)
Kd = (float(rf)-1.)*poro/rhob
for l in range(nlay):
self.writeMatMT3D(Kd[l],f1,'Kd')
# line E4 2nd sorption coeff not used here
for l in range(nlay): f1.write(' 0 0.0 \n')
f1.close()
#*************************** write RCT file for 2domain *********************
def WriteRct1File(self,aqui,Tbase,listE,opt):
""" writes an RCT file in case of double porosity"""
f1 = self.CreateFile(opt+'rct.dat','w')
nlay = aqui.getNbCouches()
if aqui.getDim() in ['Xsection','Radial']:
nlay=nrow;nrow=1
# Rec1 : Isothm, Ireact, Irctop, IGetsc Irctop 0
# 2domain : Isothm : 5 dual domain( no sorption), igetsc>0 : initial conc read here
Isothm, Ireact,Irctop, Igetsc = 5,0,1,1
f1.write('%9i %9i %9i %9i\n' %(Isothm, Ireact,Irctop, Igetsc))
# Rec 2 : Rohb do not enter if isothm=5
# Rec3 Prsty2 only for dual domain (isothm 5 or 6)
# the porosity matrix comes from Pht3D immobile solutions, line Imm_poro
opt1=opt*1;
if opt=='MT3D':opt1='Transport'
mS=obj2matBlockNb(aqui,opt1,'zon');
m0=mS[0]*0;imm_s=Tbase['Immobile']['Solutions']
ie=imm_s['rows'].index('Imm_poro');
for l in range(nlay):
poro=m0+float(imm_s['data'][ie][1]) # data[1] backgrd
for s in range(self.nsol-1):
poro[abs(mS[l])/1000==s+1]=float(imm_s['data'][ie][s+2])
self.writeMatMT3D(poro,f1,'Poro')
# Rec4 : if Igetsc>0 initial conc in immob phase for each species
# run along the Chemistry to find the species for whic conc are needed
short=['k','i','kim','p','e','s','kp'];ntot=0
div=[1000,1000,1000,100,10,100,1]
lon=['Solutions']*3;lon.extend(['Phases','Exchange','Surface','Phases'])
for ik in range(len(short)):
l0=listE[short[ik]] # list of species present in chemistry
for esp in l0:
if esp in ['Imm_poro','Transf_coeff']: continue
kw=lon[ik];imm=Tbase['Immobile'][kw].copy();ntot+=1
ie=imm['rows'].index(esp);#print 'mtpht rct',kw,esp,ie
for l in range(nlay):
cnc=m0+float(imm['data'][ie][1]);#print imm['data'][ie][1]
nsp=len(imm['cols'])-1
for s in range(nsp-1): # to find the place where BC is true solution
cnc[abs(mS[l])/div[ik]==s+1]=float(imm['data'][ie][s+2])
self.writeMatMT3D(cnc,f1,esp)
# Rec 5 sorption1 (each species)
for i in range(ntot): f1.write(' 0 0.0 \n')
# Rec6 sorption 2, here mass transfer coeff for all species
ie=imm_s['rows'].index('Transf_coeff');
for i in range(ntot):
for l in range(nlay):
tcoeff=m0+float(imm_s['data'][ie][1]) # data[1] backgrd
for s in range(self.nsol-1): # to find the place where BC is true solution
tcoeff[abs(mS[l])/1000==s+1]=float(imm_s['data'][ie][s+2])
self.writeMatMT3D(tcoeff,f1,'Transf Coeff')
#REc7 RC1 parm for fisrt order deg1
for i in range(ntot): f1.write(' 0 0.0 \n')
#REc8 RC2 parm for fisrt order deg 2
for i in range(ntot): f1.write(' 0 0.0 \n')
f1.close()
#********************************* Ecire fichier VDF for Seawat ********************
def WriteVdfFile(self):
f1 = self.CreateFile('Seawatvdf.dat','w')
## 1. MTDNCONC MFNADVFD NSWTCPL IWTABLE
## Mtdconc=0 density specified =n dens calculated from n species
## MFNADVFD=2 centre in sapce, ><2 upstream weigthed
## NSWTCPL max number of non linear iterations if 0 or 1 explicit coupling
## iwtable : 0 water table correction not applied, >0 applied
Mtdnconc,Mfnadvdf,Nswtcpl,Iwtable=1,1,1,0
f1.write(' %9i %9i %9i %9i Mtdnconc Mfnadvdf Nswtcpl Iwtable \n' %(Mtdnconc,Mfnadvdf,Nswtcpl,Iwtable))
## 2. DENSEMIN DENSEMAX min an dmax density if 0 not limitation
Densemin,Densemax=0,0
f1.write(' %9i %9i DENSEMIN DENSEMAX \n' %(Densemin,Densemax))
## If NSWTCPL is greater than 1, then read item 3.
## 3. DNSCRIT convergene criterion difference in density
Dnscrit=1e-3
if Nswtcpl>1: f1.write(' %9.4e \n' %Dnscrit)
## 4. DENSEREF DENSESLP
Denseref,Denseslp=1000.,.7143 # Care in kg/m3, slp for freash and sea water
f1.write(' %9i %9i DENSEREF DENSESLP \n' %(Denseref,Denseslp))
## 5. FIRSTDT ength of first time step
Firstdt=1e-3
f1.write(' %9.4e \n' %Firstdt)
## FOR EACH STRESS PERIOD (read items 6 and 7 only if MTDNCONC = 0)
## 6. INDENSE if<0 val of dense reused form prev tstep
## =0 Dense=ref >=1 dense read from item 7 =2 read from 7 but as conc
## Read item 7 only if INDENSE is greater than zero
## 7. [DENSE(NCOL,NROW)] – U2DREL
## Item 7 is read for each layer in the grid.
nper=len(self.tlist);Indense=-1
for ip in range(nper):
if Mtdnconc==0: f1.write(' %9i %9i INDENSE \n' %Indense)
f1.close()
#********************************* Ecire fichier Pht3d ********************
def WritePht3dFile(self,aqui,Tbase,listE,parmk):
f1 = self.CreateFile('PHT3D_ph.dat','w')
#PH1 Record: OS TMP_LOC RED_MOD TEMP ASBIN EPS_AQU EPS_PH PACK_SZ
# OS 1 iterative, 2 sequential. que 2 implemente
# TMP_LOC : 0 writere dans temp, 1 : writere sur dir local
# REd mode : 0 pH pe vairables, 1 : pe fixe, 2 : pH et pe fixes (plus rapide)
# TEmp temperature, ASBIN : 0 : writeture fich binaire, 1 :ascii
# eps_aqu et eps_ph : si 0 calcul partout
# pack_sz : taille des paquets pour phreeqc 4000 chiffre OK
temp=Tbase['PHparm'][0][1]
os0, tmp, fix0, asbin, eps0, eps1, pack = 2,1,0,0,1e-10,.001,2000
f1.write('%9i %9i %9i %9.1f %9i %9.1e %9.5f %9i\n' %(os0,tmp,fix0,temp,asbin,eps0,eps1,pack))
dcharge=Tbase['PHparm'][1][1]
f1.write('%9i\n' %dcharge)# PH2 v2 diif de charge admissibe
# determiner le noimbre d'esp cinetiques et en faire la liste
nInorg=len(listE['i']); #+len(self.lists);
nKmob = len(listE['k']);nKimob = len(listE['kim']);
nMinx= len(listE['p']);nExch=len(listE['e'])
f1.write('%9i\n' %(nInorg))# PH3 nb compose inorganiques
f1.write('%9i\n' %(nMinx))# PH4 nb mineraux
f1.write('%9i %9i\n' %(nExch, 0))# PH5 nb ech ions, 0 je sais pas pourquoi
# PH6 surface complexation
nSurf=len(listE['s']);f1.write('%9i\n' %nSurf)
#PH7 Record: NR_MOB_KIN NR_MIN_KIN NR_SURF_KIN NR_IMOB_KIN
# nb especes cinetiques mobiles, minerales, surfaces et substeps pour plus tard
nKsurf,nKmin = 0,len(listE['kp'])
f1.write('%9i %9i %9i %9i\n' %(nKmob, nKmin, nKsurf, nKimob))
# PH8 : NR_OUTP_SPEC (complexes) PR_ALKALINITY_FLAG (futur)
f1.write('%9i %9i\n' %(0,0))
## nb unites inutile car pht3d considere que tout est en jour
Chem=Tbase['Chemistry']
if Chem.has_key('Rates'):
rates=Chem['Rates'];
for nom in listE['k']:
iek = rates['rows'].index(nom);
f1.write(nom+'%5i \n '%(parmk[nom])) #param k
for ip in range(parmk[nom]):
f1.write('%9.5e \n' %float(rates['data'][iek][ip+2]))
f1.write('-formula '+rates['data'][iek][-1] +'\n') # formula
#for n in self.lists: f1.write(n+' \n') # species
optsu=Tbase['PHparm'][2][1];
for n in listE['i']:
add='';
if optsu.strip()==n: add=' charge'
f1.write(n.replace('(+','(')+add+'\n') # que reac isntant et AE, pH pe
# kinetic immobile
if Chem.has_key('Rates'):
rates=Chem['Rates'];
for nom in listE['kim']:
iek = rates['rows'].index(nom);
f1.write(nom+'%5i \n '%(parmk[nom])) #param k
for ip in range(parmk[nom]):
f1.write('%9.5e \n' %float(rates['data'][iek][ip+2]))
f1.write('-formula '+rates['data'][iek][-1] +'\n') # formula
for p in listE['p']:
ip=Chem['Phases']['rows'].index(p)
f1.write(p+' '+str(Chem['Phases']['data'][ip][1])+' \n') # phase name + SI backgrd
for n in listE['e']: f1.write(n+' -1 \n') # exchanger
if Chem.has_key('Surface'): # surface
su=Chem['Surface'];l=len(su['cols'])
for esp in listE['s']:
st=esp;ies=su['rows'].index(esp)
for i in range(l-2,l): st+=' '+str(su['data'][ies][i])
f1.write(st+' \n')
optsu=Tbase['PHparm'][3][1]
if optsu in ['no_edl','diffuse_layer']: f1.write('-'+optsu+'\n')
if Chem.has_key('Kinetic_Minerals'):
kp=Chem['Kinetic_Minerals']
for nom in listE['kp']:
iek = kp['rows'].index(nom);
f1.write(nom+'%5i \n '%(parmk[nom])) #param k
for ip in range(parmk[nom]):
f1.write('%9.5e \n' %float(kp['data'][iek][ip+1]))
f1.close()
# ''''''''''''''''''''''''''''''' fonction writeMatMT3D '''''''''''''''''''''''''''
def writeVecMT3D(self, v, f1, name=' '):
l = len(v);a=str(type(v[0]))
if a[13:16]=='int': typ='I'
else : typ='G'
if amin(v)==amax(v):
f1.write(' 0 %7.3e #'%(amin(v)) +name+'\n')
return
if typ=='I': fmt=' 100 1 ('+str(l)+'I'+str(ln)+')'
else : fmt=' 100 1.0 ('+str(l)+'G12.4)'
f1.write(fmt)
f1.write('\n')
if typ=='I': fmt='%'+str(ln)+'i'
else : fmt='%+11.4e '
for i in range(l):
f1.write(fmt %v[i])
f1.write('\n')
def writeMatMT3D(self,m,f1,name=' '):
if len(shape(m))<=1: return self.writeVecMT3D(m,f1,name)
[l,c] = shape(m);ln=3;a=str(type(m[0,0]))
if a[13:16]=='int': typ='I'
else : typ='G'
if amin(amin(m))==amax(amax(m)):
if typ=='I':f1.write(' 0 %8i #'%(amin(amin(m))) +name[:6]+'\n' )
else:f1.write(' 0 %7.3e #' %(amin(amin(m))) +name[:6]+'\n' )
return
if typ=='I': fmt=' 100 1 ('+str(c)+'I'+str(ln)+')'
else : fmt=' 100 1.0 ('+str(c)+'G12.4) #'+name[:6]
f1.write(fmt+'\n')
if typ=='I': fmt='%'+str(ln)+'i'
else : fmt='%11.4e '
for i in range(l-1,-1,-1):
for j in range(c):
f1.write(fmt %m[i][j])
f1.write('\n')
def writeBlockMT3D(self,m,f1,name=' '):
if len(shape(m))==3:
nlay,a,b=shape(m)
for l in range(nlay): self.writeMatMT3D(m[l],f1,name)
else : self.writeMatMT3D(m,f1,name)
def WritePhreeqc(self,aqui,Tbase,listE):
"""this routine writes a phreeqc file where all solutions are written in
phreqc format to be able to test their equilibrium before running pht3d
1. tabke background, then cycle through pht3d zones
2. get the solution number, phase number...it does not take rates
3 write them in phreeqc format"""
f1 = self.CreateFile('solutions.phrq','w')
f1.write('Database '+self.pPath+'\pht3d_datab.dat \n')
zones=aqui.getZoneList('PHT3D')
nzone=len(zones)
for i in range(nzone):
z=zones[i];val=z.getVal()
if type(val)==type([5]): val=int(val[0].split()[1]) #case of transient chemistry
else : val=int(val)
f1.write('Solution '+str(i)+' \n units mol/L \n')
solu=Tbase['Chemistry']['Solutions'];
nsol=val/1000
for esp in listE['i']: # go through phase list
ie=solu['rows'].index(esp);#print esp,phases['rows'],ip,phases['data'][ip] # index of the phase
conc=solu['data'][ie][nsol+1] #backgr concentration of species
f1.write(esp+' '+str(conc)+'\n')
f1.write('Equilibrium_Phases '+str(i)+'\n')
phases=Tbase['Chemistry']['Phases'];
nphas=mod(val,1000)/100
for esp in listE['p']: # go through phase list
ip=phases['rows'].index(esp);#print esp,phases['rows'],ip,phases['data'][ip] # index of the phase
IS,conc=phases['data'][ip][nphas*2+1:nphas*2+3] #backgr SI and concentration of phase
f1.write(esp+' '+str(IS)+' '+str(conc)+'\n')
f1.write('end \n')
f1.close()
