# self.T,self.debye,self.cats = T,debye,N.array(cats,dtype='int')
# initialise a phonon bath with debye damping
#cats=range(16)
#phl = phbath(T+dT/2,cats,hwcut,200,mdrun.dt,mdrun.nmd,ml=100)
#phl.gmem()
#mdrun.AddBath(phl)
#cats: python index of system atoms that are connecting to the left phonon bath
cats = range(mdrun.syslist[0], mdrun.syslist[0] + 5)
cats = [0, 1, 2, 3, 4]
print cats
phl = phbath(T + dT / 2,
cats,
hwcut,
200,
mdrun.dt,
mdrun.nmd,
ml=100,
sig=eph.SigL,
gwl=eph.wl)
phl.gmem()
mdrun.AddBath(phl)
#print phl.kernel.shape
#PP.plot(phl.noise[:,0])
#PP.savefig("noise_left.pdf",format="pdf")
#PP.close()
#PP.plot([N.trace(a) for a in phl.kernel])
#PP.savefig("friction_left.pdf",format="pdf")
#PP.close()
###ecats=range(13)
###eb = ebath(ecats,T,test.dt,test.nmd,wmax=1.0,nw=500,bias=eV,efric=eph.efric,exim=eph.xim,exip=eph.xip)
###test.AddBath(eb)
#eb.genoi()
#PP.plot(eb.noise[:,0])
#PP.show()
#----------------------------------------------------
#---------------------------------------------------------------------------------
# left phonon bath
#---------------------------------------------------------------------------------
# def __init__(self,T,cats,debye,nw,dt=None,nmd=None,ml=None,mcof=2.0,gamma=None,gwl=None,K00=None,K01=None,V01=None):
# self.T,self.debye,self.cats = T,debye,N.array(cats,dtype='int')
# initialise a phonon bath with debye damping
cats = range(16)
phl = phbath(T + dT / 2, cats, hwcut, 200, test.dt, test.nmd, ml=100)
phl.gmem()
test.AddBath(phl)
#print phl.kernel.shape
#PP.plot(phl.noise[:,0])
#PP.savefig("noise_left.pdf",format="pdf")
#PP.close()
#PP.plot([N.trace(a) for a in phl.kernel])
#PP.savefig("friction_left.pdf",format="pdf")
#PP.close()
#print "memory length: %s\n"%test.ml
#print phl.ml
#---------------------------------------------------------------------------------
eb = ebath(ecats,T,test.dt,test.nmd,wmax=1.0,nw=500,bias=eV,efric=eph.efric,exim=eph.xim,exip=eph.xip)
test.AddBath(eb)
#eb.genoi()
#PP.plot(eb.noise[:,0])
#PP.show()
#----------------------------------------------------
#---------------------------------------------------------------------------------
# left phonon bath
#---------------------------------------------------------------------------------
# def __init__(self,T,cats,debye,nw,dt=None,nmd=None,ml=None,mcof=2.0,gamma=None,gwl=None,K00=None,K01=None,V01=None):
# self.T,self.debye,self.cats = T,debye,N.array(cats,dtype='int')
# initialise a phonon bath with debye damping
phl = phbath(T+dT/2,[0,1,2,3,4],hwcut,200,test.dt,test.nmd,ml=100,sig=eph.SigL,gwl=eph.wl)
phl.gmem()
test.AddBath(phl)
#print phl.kernel.shape
#PP.plot(phl.noise[:,0])
#PP.savefig("noise_left.pdf",format="pdf")
#PP.close()
#PP.plot([N.trace(a) for a in phl.kernel])
#PP.savefig("friction_left.pdf",format="pdf")
#PP.close()
#print "memory length: %s\n"%test.ml
#print phl.ml
#---------------------------------------------------------------------------------
#eph.hwcut=0.22
##eph.hwcut=0.5
eph.T = 500 #3500
eph.dT = 0 #.1*2*eph.T #60
#print 'dt',eph.dt
#eph.dt=0.5/(0.658211814201041) # from fs to JT units
eph.dt = eph.dt # 0.5->0.05 fs due to hydrogen!
#print 'dt',eph.dt
eph.eta_ad = 0.005 #.01#0.000000001#
phl = phbath(eph.T + eph.dT / 2,
range(eph.NA_L),
eph.hwcut / 2,
eph.nw,
eph.dt,
eph.nmd,
ml=eph.nmemL,
sig=eph.SigL,
gwl=eph.E,
eta_ad=eph.eta_ad,
classical=False,
zpmotion=True) ##sig=eph.SigL,gwl=eph.wl)
phl.gmem()
#phl.gnoi()
phr = phbath(eph.T - eph.dT / 2,
range(eph.NA_R) - eph.NA_R,
eph.hwcut / 2,
eph.nw,
eph.dt,
eph.nmd,
ml=eph.nmemR,
sig=eph.SigR,
