def __init__(self, InitJson):
self.type = InitJson['proj']['type']
self.logFile = InitJson['proj']['logFile']
self.outFile = InitJson['proj']['outFile']
self.nsys = int(InitJson['syst']['nsys'])
self.nmod = int(InitJson['syst']['nmod'])
self.npsd = int(InitJson['bath']['npsd'])
self.iniSite = int(InitJson['prop']['iniSite'])
self.nmax = int(InitJson['prop']['nmax'])
self.lmax = int(InitJson['prop']['lmax'])
self.tolr = float(InitJson['prop']['toler'])
self.nstep = int(InitJson['prop']['nstep'])
self.nchk = int(InitJson['prop']['nchk'])
self.dt = float(InitJson['prop']['dt'])
self.tem = float(InitJson['bath']['tem'])
self.nper = self.npsd + 1
if self.temUnit == 'K':
self.tem *= kt2au
elif self.temUnit == 'cm-1':
self.tem *= cm2au
self.nind = self.nmod * self.nper
self.hams, self.qmds = syst.init()
self.etal, self.etar, self.etaa, self.expn, self.wres = bath.init()
def __init__(self, InitJson):
self.type = InitJson["proj"]["type"]
self.logFile = InitJson["proj"]["logFile"]
self.outFile = InitJson["proj"]["outFile"]
self.nsys = int(InitJson["syst"]["nsys"])
self.nmod = int(InitJson["syst"]["nmod"])
self.npsd = int(InitJson["bath"]["npsd"])
self.iniSite = int(InitJson["prop"]["iniSite"])
self.nmax = int(InitJson["prop"]["nmax"])
self.lmax = int(InitJson["prop"]["lmax"])
self.tolr = float(InitJson["prop"]["toler"])
self.nstep = int(InitJson["prop"]["nstep"])
self.nchk = int(InitJson["prop"]["nchk"])
self.dt = float(InitJson["prop"]["dt"])
self.tem = float(InitJson["bath"]["tem"])
self.nper = self.npsd + 1
if self.temUnit == "K":
self.tem *= kt2au
elif self.temUnit == "cm-1":
self.tem *= cm2au
self.nind = self.nmod * self.nper
self.hams, self.qmds = syst.init()
self.etal, self.etar, self.etaa, self.expn, self.wres = bath.init()
import bath
if __name__ == '__main__':
with open('_default.json') as f:
ini = json.load(f)
# syst
hams = np.zeros((2, 2), dtype=complex)
hams[0, 0] = hams[0, 1] = hams[1, 0] = 1.0
hams[1, 1] = -1.0
qmds = np.zeros((1, 2, 2), dtype=complex)
qmds[0, 0, 0] = 1.0
qmds[0, 1, 1] = -1.0
dips = np.zeros((2, 2), dtype=complex)
syst.init(ini['syst'], hams, qmds, dips)
# bath
ini['bath']['temp'] = 1.0
ini['bath']['jsdr'] = [{'lams': 1.0, 'omgs': 5.0, 'gams': 1.0}]
ini['bath']['nmod'] = qmds.shape[0]
ini['bath']['pade'] = 2
ini['bath']['npsd'] = 1
bath.init(ini['bath'])
# hidx
ini['hidx']['lmax'] = 15
ini['hidx']['nmax'] = 30000
ini['hidx']['ferr'] = 2.0e-6
with open('input.json', 'w') as f:
def main ():
with open('morse.json','r') as f:
d = json.load(f)
ie = d['ie']
ne = ie+1
modes = d['modes']
gxy = d['gxy']
for m in modes:
m['m0'] *= am2au
m['ri'] /= au2ar
m['rf'] /= au2ar
m['re'] /= au2ar
vmn = [[v*cm2au for v in colv] for colv in gxy]
n_list = np.array([m['nr'] for m in modes])
ndim = np.prod(n_list)
nmod = len(modes)
cum_prod = np.zeros(nmod,dtype=int)
cum_prod[0] = modes[nmod-1]['nr']
for i in xrange(1,nmod):
cum_prod[i] = cum_prod[i-1]*modes[nmod-i-1]['nr']
with open('wavetrun.dat','r') as f:
wavefunc=np.loadtxt(f)
with open('energr.dat','r') as f:
energies=np.loadtxt(f)
qmod = []
hami = []
dipo = []
dip2 = []
for imod in xrange(nmod):
m = modes[imod]
q = np.empty(ndim,dtype=float)
d = np.empty(ndim,dtype=float)
d2= np.empty(ndim,dtype=float)
for i in xrange(ndim):
i_list = decode(i,cum_prod,nmod)
d[i] = m['ri']+i_list[imod]*(m['rf']-m['ri'])/m['nr']
d2[i]= (d[i]-m['re'])*(d[i]-m['re'])
q[i] = m['q2']*(d[i]-m['re'])*(d[i]-m['re'])/2+m['q1']*(d[i]-m['re'])
qwave = np.array([[q[i]*wavefunc[i,j] for j in xrange(ne)] for i in xrange(ndim)])
dwave = np.array([[d[i]*wavefunc[i,j] for j in xrange(ne)] for i in xrange(ndim)])
d2wave= np.array([[d2[i]*wavefunc[i,j] for j in xrange(ne)] for i in xrange(ndim)])
qmod.append(np.dot(wavefunc.T,qwave) )
dipo.append(np.dot(wavefunc.T,dwave) )
dip2.append(np.dot(wavefunc.T,d2wave))
#test new geninput
ini={
"syst": {
"hamsFile": "inp_hams.mat",
"qmdsFile": "inp_qmds.mat",
"dipsFile": "inp_dips.mat"
},
"bath": {
"npsd": 1,
"pade": 2,
"temp": 300.0,
"modeFile": "inp_mode.mat",
"etalFile": "inp_etal.mat",
"etarFile": "inp_etar.mat",
"etaaFile": "inp_etaa.mat",
"expnFile": "inp_expn.mat",
"bdipFile": "inp_bdip.mat",
"delrFile": "inp_delr.mat"
},
"hidx": {
"lmax": 5,
"nmax": 5000,
"ferr": 2.0e-7,
"expnFile": "inp_expn.mat"
}
}
qmds = np.array(qmod)*(1.0+0.0J)
hams = np.diag(np.array(energies))*(1.0+0.0J)
syst.init(ini['syst'],hams,qmds)
mutot = np.empty(ne,dtype=float)
pitot = np.empty(ne,dtype=float)
qutot = np.empty(ne,dtype=float)
for imod in xrange(nmod):
mutot=mutot+modes[imod]['d1']*dipo[imod]+modes[imod]['d2']*dip2[imod]
# bath
print ("temperature is K\n",ini['bath']['temp'])
ini['bath']['temp'] *= kt2au
ini['bath']['jomg'] = []
for m in modes:
lamd = m['jdru'][0]['lamd']*cm2au
gamd = m['jdru'][0]['gamd']*cm2au
drupara ={
'jdru': [(lamd,gamd)],
}
ini['bath']['jomg'].append(drupara)
ini['bath']['amod'] = ['dru' for i in xrange(nmod)]
ini['bath']['fmod'] = [0.0 for i in xrange(nmod)]
ini['bath']['nmod'] = qmds.shape[0]
bath.init (ini['bath'])
jsonInit = {"deom":ini,
"rhot": {
"dt": 0.005,
"nk": 10,
"nt": 2000,
"inistate": 0
},
}
with open('input.json','w') as f:
json.dump(jsonInit,f,indent=4)
import bath
if __name__ == '__main__':
with open('_default.json') as f:
ini = json.load(f)
# syst
hams = np.zeros((2,2),dtype=complex)
hams[0,0] = hams[0,1] = hams[1,0] = 1.0
hams[1,1] = -1.0
qmds = np.zeros((1,2,2),dtype=complex)
qmds[0,0,0] = 1.0
qmds[0,1,1] = -1.0
dips = np.zeros((2,2),dtype=complex)
syst.init (ini['syst'],hams,qmds,dips)
# bath
ini['bath']['temp'] = 1.0
ini['bath']['jsdr'] = [{'lams':1.0,'omgs':5.0,'gams':1.0}]
ini['bath']['nmod'] = qmds.shape[0]
ini['bath']['pade'] = 2
ini['bath']['npsd'] = 1
bath.init (ini['bath'])
# hidx
ini['hidx']['lmax'] = 15
ini['hidx']['nmax'] = 30000
ini['hidx']['ferr'] = 2.0e-6
with open('input.json','w') as f: