def do_command_file(args):
"""Report on the content of a file
"""
qr.printlog("Checking file info", loglevel=1)
#
# File name
#
if args.fname:
fname = args.fname[0]
qr.printlog("File name: " + fname, loglevel=1)
try:
check = qr.check_parcel(fname)
qr.printlog("Object type: " + check["class_name"], loglevel=1)
if check["class_name"] == "builtins.list":
prcl = qr.load_parcel(fname)
qr.printlog("List length: " + str(len(prcl)), loglevel=1)
types = []
for el in prcl:
tp = type(prcl[0])
if tp not in types:
types.append(tp)
qr.printlog("Element types: " + str(types), loglevel=1)
qr.printlog("Saved with Quantarhei version: " + check["qrversion"],
loglevel=1)
qr.printlog("Description: " + check["comment"])
except:
qr.printlog("The file is not a Quantarhei parcel", loglevel=1)
def onOpen(self):
import matplotlib.pyplot as plt
file = askopenfilename()
#print(file, loglevel=qr.LOG_REPORT)
obj = qr.load_parcel(file)
self.figure(obj)
print("Preparing a model system:")
with qr.energy_units("1/cm"):
mol1 = qr.Molecule([0.0, 12010])
mol2 = qr.Molecule([0.0, 12000])
mol3 = qr.Molecule([0.0, 12100])
mol4 = qr.Molecule([0.0, 12110])
agg = qr.Aggregate([mol1, mol2, mol3, mol4])
agg.set_resonance_coupling(2, 3, qr.convert(100.0, "1/cm", "int"))
agg.set_resonance_coupling(1, 3, qr.convert(100.0, "1/cm", "int"))
agg.set_resonance_coupling(1, 2, qr.convert(0.0, "1/cm", "int"))
qr.save_parcel(agg, "agg.qrp")
agg2 = qr.load_parcel("agg.qrp")
agg2.build()
H = agg2.get_Hamiltonian()
print("...done")
print("Setting up Lindblad form relaxation:")
Ndim = 5
with qr.eigenbasis_of(H):
K12 = qr.qm.ProjectionOperator(1, 2, dim=Ndim)
K23 = qr.qm.ProjectionOperator(2, 3, dim=Ndim)
K34 = qr.qm.ProjectionOperator(3, 4, dim=Ndim)
sbi = qr.qm.SystemBathInteraction(sys_operators=[K12, K23, K34],
rates=(1.0 / 200, 1.0 / 100.0,
1.0 / 150))
qr.timeit(show_stamp=True)
Nreal = INP.N_realizations
#
# THIS MAY BE PARALLELIZED
#
data_initialized = False
disM = numpy.zeros((3, Nreal))
sigma = INP.disorder_fwhm / (2.0 *
numpy.sqrt(2.0 * numpy.log(2.0)))
if INP.random_state["reset"]:
try:
random_state = qr.load_parcel(INP.random_state["file"])
numpy.random.set_state(random_state)
except:
raise Exception("Loading random state failed")
if INP.random_state["save"]:
random_state = numpy.random.get_state()
qr.save_parcel(random_state, INP.random_state["file"])
for ri in range(Nreal):
disM[:, ri] = sigma * numpy.random.randn(3)
#
# PARALLEL (if ON) LOOP OVER DISORDER
#
for ds in qr.block_distributed_range(0, Nreal):
# generating random numbers
#
# Unite nodes
#
ii = 0
print("Creating spectral container ...")
for node in nodes:
if do_nodes:
ndp = "_" + str(node)
else:
ndp = ""
file_name = os.path.join(target_dir,
"cont_" + ext[ext_i] + ndp + ".qrp")
conta = qr.load_parcel(file_name)
for tag in conta.spectra:
#print(node, tag, ii)
sp = conta.get_spectrum(tag)
#print("dE = ", sp.params["dE"])
ntag = ii
if normalize:
sp.normalize2(dpart=qr.part_ABS)
cont.set_spectrum(sp, tag=ntag)
ii += 1
mfilename = "movie_" + ext[ext_i] + "_cont=" + str(Ncont) + "." + movie_ext
print("Exporting movie: ", mfilename)
print("Preparing a model system:")
with qr.energy_units("1/cm"):
mol1 = qr.Molecule([0.0, 12000])
mol2 = qr.Molecule([0.0, 12000])
mol3 = qr.Molecule([0.0, 12100])
mol4 = qr.Molecule([0.0, 12100])
agg = qr.Aggregate([mol1, mol2, mol3, mol4])
agg.set_resonance_coupling(2, 3, qr.convert(100.0, "1/cm", "int"))
agg.set_resonance_coupling(1, 3, qr.convert(100.0, "1/cm", "int"))
with tempfile.TemporaryDirectory() as tdir:
path = os.path.join(tdir, "agg.qrp")
qr.save_parcel(agg, path)
agg2 = qr.load_parcel(path)
agg2.build()
H = agg2.get_Hamiltonian()
print("...done")
print("Setting up Lindblad form relaxation:")
Ndim = 5
with qr.eigenbasis_of(H):
K12 = qr.qm.ProjectionOperator(1, 2, dim=Ndim)
K23 = qr.qm.ProjectionOperator(2, 3, dim=Ndim)
K34 = qr.qm.ProjectionOperator(3, 4, dim=Ndim)
sbi = qr.qm.SystemBathInteraction(sys_operators=[K12, K23, K34],
rates=(1.0 / 200, 1.0 / 100.0,
1.0 / 150))
except:
raise Exception("Output directory name '"
+pre_out+"' does not represent a valid directory")
#
# This is needed in version 0.0.36 and later for propagation with Lindblad form
#
qr.Manager().gen_conf.legacy_relaxation = True
#
# Load aggregates constructed in the previous phase of the calculation
#
agg = qr.load_parcel(os.path.join(pre_in,
"fraction_45_2_vibrations_CT_unbuilt.qrp"))
agg2 = qr.load_parcel(os.path.join(pre_in,
"fraction_45_2_vibrations_CT_unbuilt.qrp"))
agg_el = qr.load_parcel(os.path.join(pre_in,
"fraction_eff_40_4_CT_unbuilt.qrp"))
#
# Aggregate with vibrational states, Hamiltonian generated up to single
# exciton states in a Two-particle approximation
# This object is used for calculation of dynamics
#
agg.build(mult=1, vibgen_approx="TPA")
#
# agg2 object will be used for calculation of 2D spectra
# so it needs to know how to represent the spectra (what width it should have).
print("Preparing a model system:")
with qr.energy_units("1/cm"):
mol1 = qr.Molecule([0.0, 12000])
mol2 = qr.Molecule([0.0, 12000])
mol3 = qr.Molecule([0.0, 12100])
mol4 = qr.Molecule([0.0, 12100])
agg = qr.Aggregate([mol1, mol2, mol3, mol4])
agg.set_resonance_coupling(2,3,qr.convert(100.0,"1/cm","int"))
agg.set_resonance_coupling(1,3,qr.convert(100.0,"1/cm","int"))
with tempfile.TemporaryDirectory() as tdir:
path = os.path.join(tdir,"agg.qrp")
qr.save_parcel(agg,path)
agg2 = qr.load_parcel(path)
agg2.build()
H = agg2.get_Hamiltonian()
print("...done")
print("Setting up Lindblad form relaxation:")
Ndim = 5
with qr.eigenbasis_of(H):
K12 = qr.qm.ProjectionOperator(1, 2, dim=Ndim)
K23 = qr.qm.ProjectionOperator(2, 3, dim=Ndim)
K34 = qr.qm.ProjectionOperator(3, 4, dim=Ndim)
sbi = qr.qm.SystemBathInteraction(sys_operators=[K12, K23, K34],
rates=(1.0/200, 1.0/100.0, 1.0/150))
#plt.plot(t2s.data,pp4)
#plt.savefig("points.png")
#
##sp = twods.get_spectrum(t2s.data[-1])
#with energy_units("1/cm"):
# sp.plot(window=window_2D)
#
#sp.save("spectrum.hdf5")
#
#rsp = TwoDSpectrum()
#rsp.load("spectrum.hdf5")
#
#with energy_units("1/cm"):
# rsp.plot(window=window_2D)
with qr.energy_units("1/cm"):
twods.trimall_to(window=window_2D)
twods.save("allspectra.qrp")
#newtw = TwoDSpectrumContainer()
newtw = qr.load_parcel("allspectra.qrp")
#twods = newtw.get_TwoDSpectrumContainer()
#
#sp = twods.get_spectrum(0.0)
#with energy_units("1/cm"):
# sp.plot(window=window_2D)
import sys
import os
import quantarhei as qr
try:
dir = sys.argv[1]
except:
print("Cannot find command line argument: Specify simulation directory.")
qr.stop()
agpath = os.path.join(dir, "aggregate.qrp")
agg = qr.load_parcel(agpath)
agg.exciton_report(start=2)
dname = INP.dname #"sim_up"
#
# Transition energy for which the spectra are calculated
#
Ecalc = INP_pre.E_P #10000.0
calculated_width = INP_pre.max_available_fwhm
#
# load all spectra
#
#for de in des:
# fname = op.path.join(dname,"twod_E0=1000_dE="+str(de)+".qrp")
cont = qr.load_parcel(os.path.join(dname, INP.container_file))
spects = []
for ii in range(cont.length()):
sp = cont.get_spectrum(ii)
prms = sp.get_log_params()
dE = prms["dE"]
spects.append(sp)
#print("dE =", dE)
de_min = cont.get_spectrum(0).get_log_params()["dE"]
de2 = cont.get_spectrum(1).get_log_params()["dE"]
de_step = de2 - de_min
de_N = cont.length()
print("de_min:", de_min)
print("Preparing a model system:")
with qr.energy_units("1/cm"):
mol1 = qr.Molecule([0.0, 12010])
mol2 = qr.Molecule([0.0, 12000])
mol3 = qr.Molecule([0.0, 12100])
mol4 = qr.Molecule([0.0, 12110])
agg = qr.Aggregate([mol1, mol2, mol3, mol4])
agg.set_resonance_coupling(2,3,qr.convert(100.0,"1/cm","int"))
agg.set_resonance_coupling(1,3,qr.convert(100.0,"1/cm","int"))
agg.set_resonance_coupling(1,2,qr.convert(0.0,"1/cm","int"))
qr.save_parcel(agg,"agg.qrp")
agg2 = qr.load_parcel("agg.qrp")
agg2.build()
H = agg2.get_Hamiltonian()
print("...done")
print("Setting up Lindblad form relaxation:")
Ndim = 5
with qr.eigenbasis_of(H):
K12 = qr.qm.ProjectionOperator(1, 2, dim=Ndim)
K23 = qr.qm.ProjectionOperator(2, 3, dim=Ndim)
K34 = qr.qm.ProjectionOperator(3, 4, dim=Ndim)
sbi = qr.qm.SystemBathInteraction(sys_operators=[K12, K23, K34],
rates=(1.0/200, 1.0/100.0, 1.0/150))
agg.build(mult=2)
#agg.save("RC_Model_40_4_adjusted_CT_no_vibrations_built.hdf5")
qr.save_parcel(agg, os.path.join(pre_out,
"RC_Model_40_4_adjusted_CT_no_vibrations_built.qrp"))
# In[5]:
#
# Refitted model of the Reaction Center using effective Gaussian lineshapes
#
#
#
#
# "Environment" modelled by dressing the states
#
molecules_eff = qr.load_parcel(os.path.join(pre_out,"molecules.qrp"))
agg_eff = qr.Aggregate(molecules=molecules_eff)
with qr.energy_units("1/cm"):
agg_eff.set_resonance_coupling_matrix(J_Matrix)
PMe = molecules_eff[0]
PLe = molecules_eff[1]
BMe = molecules_eff[2]
BLe = molecules_eff[3]
HMe = molecules_eff[4]
HLe = molecules_eff[5]
PCT_Me = molecules_eff[6]
PCT_Le = molecules_eff[7]
with qr.energy_units("1/cm"):
#agg.save("RC_Model_40_4_adjusted_CT_no_vibrations_built.hdf5")
qr.save_parcel(
agg,
os.path.join(pre_out, "RC_Model_40_4_adjusted_CT_no_vibrations_built.qrp"))
# In[5]:
#
# Refitted model of the Reaction Center using effective Gaussian lineshapes
#
#
#
#
# "Environment" modelled by dressing the states
#
molecules_eff = qr.load_parcel(os.path.join(pre_out, "molecules.qrp"))
agg_eff = qr.Aggregate(molecules=molecules_eff)
with qr.energy_units("1/cm"):
agg_eff.set_resonance_coupling_matrix(J_Matrix)
PMe = molecules_eff[0]
PLe = molecules_eff[1]
BMe = molecules_eff[2]
BLe = molecules_eff[3]
HMe = molecules_eff[4]
HLe = molecules_eff[5]
PCT_Me = molecules_eff[6]
PCT_Le = molecules_eff[7]
with qr.energy_units("1/cm"):
import time
import quantarhei as qr
import matplotlib.pyplot as plt
plt.switch_backend('agg')
print(qr.Manager().version)
# In[27]:
pre_out = "out"
#frac = qr.load("fraction_40_4_CT_unbuilt.hdf5")
#frac_electronic = qr.load("fraction_40_4_CT_unbuilt.hdf5")
frac = qr.load_parcel(os.path.join(pre_out,
"fraction_eff_40_4_CT_unbuilt.qrp"))
frac_electronic = qr.load_parcel(
os.path.join(pre_out, "fraction_40_4_CT_unbuilt.qrp"))
# In[28]:
#
# Get molecules
#
PM = frac.get_Molecule_by_name("PM")
PL = frac.get_Molecule_by_name("PL")
BL = frac.get_Molecule_by_name("BL")
include_second_B = False
vib_at_second_B = False
import quantarhei as qr
dirn = "c01"
pre_in = os.path.join(dirn,"out")
filename = "pathways_20.0.qrp"
Np = 13
ex2Dfile = "test.png"
plot_window = [11000, 13500, 11000, 13500]
t1axis = qr.TimeAxis(0.0, 1000, 1.0)
t2axis = qr.TimeAxis(0.0, 100, 10.0)
t3axis = qr.TimeAxis(0.0, 1000, 1.0)
pws = qr.load_parcel(os.path.join(pre_in,filename))
print(len(pws))
mscal = qr.MockTwoDSpectrumCalculator(t1axis, t2axis, t3axis)
mscal.bootstrap(rwa=qr.convert(12200,"1/cm","int"))
pw = pws[Np]
mscal.set_pathways([pw])
twod = mscal.calculate()
eUt = qr.load_parcel(os.path.join(pre_in,"eUt.qrp"))
oset = qr.load_parcel(os.path.join(dirn,"A_saved_state.qrp"))
with qr.energy_units("1/cm"):
print("\nSignal component:", ext[ext_i])
cont = qr.TwoDSpectrumContainer()
cont.use_indexing_type("integer")
ii = 0
for node in nodes:
if do_nodes:
ndp = "_"+str(node)
else:
ndp = ""
file_name = os.path.join(target_dir, prefix+ext[ext_i]+ndp+".qrp")
print("Loading file:", file_name)
conta = qr.load_parcel(file_name)
for tag in conta.spectra:
#print("(node, tag, new tag):", node, tag, ii)
sp = conta.get_spectrum(tag)
ntag = ii
cont.set_spectrum(sp, tag=ntag)
ii += 1
#print("Summary ("+ext[ext_i]+"):")
for tag in cont.spectra:
sp = cont.get_spectrum(tag)
#print(tag, sp.params["dE"])
with qr.energy_units("1/cm"):
sing = (INP.disorder and (INP.N_realizations == 1))
if INP.single_realization or sing:
print("Single realization 2D map")
name1 = "cont_p_re"
append_to_dirname = INP.append_to_dirname
file = os.path.join(
"sim_" + INP.location_of_vibrations + append_to_dirname,
name1 + ".qrp")
print("Loading file:", file)
cont = qr.load_parcel(file)
sp = cont.get_spectrum(0)
sp.plot(show=False)
sp.savefig("plot.png")
else:
if INP.disorder:
if INP.N_realizations:
print("Single realization 2D map")
else:
pass
try:
os.makedirs(pre_out, exist_ok=True)
except:
raise Exception("Output directory name '" + pre_out +
"' does not represent a valid directory")
#
# This is needed in version 0.0.36 and later for propagation with Lindblad form
#
qr.Manager().gen_conf.legacy_relaxation = True
#
# Load aggregates constructed in the previous phase of the calculation
#
agg = qr.load_parcel(
os.path.join(pre_in, "fraction_45_2_vibrations_CT_unbuilt.qrp"))
agg2 = qr.load_parcel(
os.path.join(pre_in, "fraction_45_2_vibrations_CT_unbuilt.qrp"))
agg_el = qr.load_parcel(
os.path.join(pre_in, "fraction_eff_40_4_CT_unbuilt.qrp"))
#
# Aggregate with vibrational states, Hamiltonian generated up to single
# exciton states in a Two-particle approximation
# This object is used for calculation of dynamics
#
agg.build(mult=1, vibgen_approx="TPA")
#
# agg2 object will be used for calculation of 2D spectra
# so it needs to know how to represent the spectra (what width it should have).
import quantarhei as qr
ptype = "REPH"
window_L = [11500, 12500, 12000, 13000]
window_U = [11500, 12500, 13000, 13500]
window = window_U
fname = sys.argv[1]
try:
N = int(sys.argv[2])
except:
N = 5
print("Using default value of N =", N)
pws = qr.load_parcel(fname)
Nparcel = len(pws)
print("Number of pathways loaded:", Nparcel)
with qr.energy_units("1/cm"):
pan = qr.LiouvillePathwayAnalyzer(pathways=pws)
pan.select_frequency_window(window=window, replace=True)
pws = pan.select_type(ptype=ptype, replace=False)
Nselect = len(pws)
print("Number of pathways selected:", Nselect)
Nshow = numpy.min([N, Nselect])
print("Showing:", Nshow)