From 913c837f4e30734f47372ab563d6cc3ee89f0f17 Mon Sep 17 00:00:00 2001
From: Blaise Thompson <blaise@untzag.com>
Date: Thu, 10 Aug 2017 18:47:11 -0500
Subject: initial commit
---
.../2016.05.02 17-48-41 old delay space/src/H0.py | 171 +++++++++++++++++++++
.../src/class_maps.p | 17 ++
.../src/inhom.py | 85 ++++++++++
3 files changed, 273 insertions(+)
create mode 100644 figures/instrument/scatter/2016.05.02 17-48-41 old delay space/src/H0.py
create mode 100644 figures/instrument/scatter/2016.05.02 17-48-41 old delay space/src/class_maps.p
create mode 100644 figures/instrument/scatter/2016.05.02 17-48-41 old delay space/src/inhom.py
(limited to 'figures/instrument/scatter/2016.05.02 17-48-41 old delay space/src')
diff --git a/figures/instrument/scatter/2016.05.02 17-48-41 old delay space/src/H0.py b/figures/instrument/scatter/2016.05.02 17-48-41 old delay space/src/H0.py
new file mode 100644
index 0000000..e040203
--- /dev/null
+++ b/figures/instrument/scatter/2016.05.02 17-48-41 old delay space/src/H0.py
@@ -0,0 +1,171 @@
+"""
+@author: Dan
+
+each instance of running this depends on a few initial conditions that have to
+be specified:
+ out_group
+ rho_0
+ wa_central
+ a_coupling
+ gamma
+ dipoles
+
+so create a class where all these can describe the specific instance
+"""
+
+from NISE.lib.misc import *
+
+def gen_w_0(wa_central, a_coupling):
+ # convert nice system parameters into system vector indeces
+ w_ag = wa_central
+ w_2aa = w_ag - a_coupling
+ w_2ag = 2*w_ag - a_coupling
+ w_gg = 0.
+ w_aa = w_gg
+ return np.array( [w_gg, w_ag, -w_ag, w_aa, w_2ag, w_ag, w_2aa] )
+
+def gen_Gamma_0(tau_ag, tau_aa, tau_2ag, tau_2aa):
+ # same as gen_w_0, but for dephasing/relaxation times
+ tau = np.array( [np.inf, tau_ag, tau_ag,
+ tau_aa, tau_2ag,
+ tau_ag, tau_2aa ] )
+ Gamma = 1/tau
+ return Gamma
+
+class Omega:
+ # record the propagator module used to evolve this hamiltonian
+ propagator = 'rk'
+ # phase cycling is not valuable in this hamiltonian
+ pc = False
+ # all attributes should have good initial guesses for parameters
+ dm_vector = ['gg1','ag','ga','aa','2ag','ag2','2aa']
+ #out_group = [[6,7]]#,[7]]
+ out_group = [[5],[6]] # use this to separate alpha/gamma from beta for now
+ #--------------------------Oscillator Properties--------------------------
+ rho_0 = np.zeros((len(dm_vector)), dtype=np.complex64)
+ rho_0[0] = 1.
+ # 1S exciton central position
+ wa_central = 7000.
+ # exciton-exciton coupling
+ a_coupling = 0. # cm-1
+ # dephasing times, fs
+ tau_ag = 50.
+ tau_aa = np.inf #1./2000.
+ tau_2aa = tau_ag
+ tau_2ag = tau_ag
+ # transition dipoles (a.u.)
+ mu_ag = 1.0
+ mu_2aa = 1.0 * mu_ag # HO approx (1.414) vs. uncorr. electron approx. (1.)
+ # TOs sets which time-ordered pathways to include (1-6 for TrEE)
+ # defaults to include all time-orderings included
+ TOs = range(7)[1:]
+ #--------------------------Recorded attributes--------------------------
+ out_vars = ['dm_vector', 'out_group', 'rho_0', 'mu_ag', 'mu_2aa',
+ 'tau_ag', 'tau_aa', 'tau_2aa', 'tau_2ag',
+ 'wa_central', 'a_coupling', 'pc', 'propagator',
+ 'TOs']
+ #--------------------------Methods--------------------------
+ def __init__(self, **kwargs):
+ # inherit all class attributes unless kwargs has them; then use those
+ # values. if kwargs is not an Omega attribute, it gets ignored
+ # careful: don't redefine instance methods as class methods!
+ for key, value in kwargs.items():
+ if key in Omega.__dict__.keys():
+ setattr(self, key, value)
+ else:
+ print 'did not recognize attribute {0}. No assignment made'.format(key)
+ # with this set, initialize parameter vectors
+ self.w_0 = gen_w_0(self.wa_central, self.a_coupling)
+ self.Gamma = gen_Gamma_0(self.tau_ag, self.tau_aa, self.tau_2ag,
+ self.tau_2aa)
+
+ def o(self, efields, t, wl):
+ # combine the two pulse permutations to produce one output array
+ E1, E2, E3 = efields[0:3]
+
+ out1 = self._gen_matrix(E1, E2, E3, t, wl, w1first = True)
+ out2 = self._gen_matrix(E1, E2, E3, t, wl, w1first = False)
+
+ return np.array([out1, out2], dtype=np.complex64)
+
+ def _gen_matrix(self, E1, E2, E3, t, wl, w1first = True):
+ """
+ creates the coupling array given the input e-fields values for a specific time, t
+ w1first selects whether w1 or w2p is the first interacting positive field
+
+ Currently neglecting pathways where w2 and w3 require different frequencies
+ (all TRIVE space, or DOVE on diagonal)
+
+ Matrix formulated such that dephasing/relaxation is accounted for
+ outside of the matrix
+ """
+ wag = wl[1]
+ w2aa = wl[6]
+
+ mu_ag = self.mu_ag
+ mu_2aa = self.mu_2aa
+
+ if w1first==True:
+ first = E1
+ second = E3
+ else:
+ first = E3
+ second = E1
+
+ O = np.zeros((len(t), len(wl), len(wl)), dtype=np.complex64)
+ # from gg1
+ O[:,1,0] = mu_ag * first * rotor(-wag*t)
+ if w1first and 3 in self.TOs:
+ O[:,2,0] = -mu_ag * E2 * rotor(wag*t)
+ if not w1first and 5 in self.TOs:
+ O[:,2,0] = -mu_ag * E2 * rotor(wag*t)
+ # from ag1
+ # to DQC
+ if w1first and 2 in self.TOs:
+ O[:,4,1] = mu_2aa * second * rotor(-w2aa*t)
+ if not w1first and 4 in self.TOs:
+ O[:,4,1] = mu_2aa * second * rotor(-w2aa*t)
+ # to pop
+ if w1first and 1 in self.TOs:
+ O[:,3,1] = -mu_ag * E2 * rotor(wag*t)
+ if not w1first and 6 in self.TOs:
+ O[:,3,1] = -mu_ag * E2 * rotor(wag*t)
+ # from ga
+ O[:,3,2] = mu_ag * first * rotor(-wag*t)
+ # from gg-aa
+ O[:,5,3] = -mu_ag * second * rotor(-wag*t) * mu_ag
+ # because of alpha and gamma pathways, count twice
+ O[:,5,3] -= mu_ag * second * rotor(-wag*t) * mu_ag
+ O[:,6,3] = mu_2aa * second * rotor(-w2aa*t) * mu_2aa
+ # from 2ag
+ O[:,6,4] = mu_ag * E2 * rotor(wag*t) * mu_2aa
+ O[:,5,4] = -mu_2aa * E2 * rotor(w2aa*t) * mu_ag
+
+ # make complex according to Liouville Equation
+ O *= complex(0,0.5)
+
+ # include coherence decay rates:
+ for i in range(O.shape[-1]):
+ O[:,i,i] = -self.Gamma[i]
+
+ return O
+
+ def ws(self, inhom_object):
+ """
+ creates the correspondence of oscillator energies to the state vector
+ contains instructions for how energies change as subsets are changed
+ """
+ z = inhom_object.zeta
+
+ wg = 0.0 + 0*z
+ wa = z + self.wa_central
+ w2a = 2*wa - self.a_coupling
+
+ w_ag = wa - wg
+ w_aa = wa - wa
+ w_gg = wg - wg
+ w_2ag = w2a - wg
+ w_2aa = w2a - wa
+ #array aggregates all frequencies to match state vectors
+ w = np.array( [w_gg, w_ag, -w_ag, w_aa, w_2ag, w_ag, w_2aa] )
+ return w
diff --git a/figures/instrument/scatter/2016.05.02 17-48-41 old delay space/src/class_maps.p b/figures/instrument/scatter/2016.05.02 17-48-41 old delay space/src/class_maps.p
new file mode 100644
index 0000000..44e2a40
--- /dev/null
+++ b/figures/instrument/scatter/2016.05.02 17-48-41 old delay space/src/class_maps.p
@@ -0,0 +1,17 @@
+(dp1
+S'H'
+(lp2
+S'Omega'
+p3
+aS'NISE.hamiltonians.H0'
+p4
+aS'H0.py'
+p5
+asS'Inhom'
+p6
+(lp7
+g6
+ag6
+aS'inhom.py'
+p8
+as.
\ No newline at end of file
diff --git a/figures/instrument/scatter/2016.05.02 17-48-41 old delay space/src/inhom.py b/figures/instrument/scatter/2016.05.02 17-48-41 old delay space/src/inhom.py
new file mode 100644
index 0000000..1438846
--- /dev/null
+++ b/figures/instrument/scatter/2016.05.02 17-48-41 old delay space/src/inhom.py
@@ -0,0 +1,85 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Sat Jun 21 14:07:53 2014
+
+@author: Dan
+"""
+
+from NISE.lib.misc import *
+
+class Inhom():
+ # class contains the list of weights and sampling values to use
+ #--------------------------Recorded attributes--------------------------
+ out_vars = ['inhom_sampling', 'dist_params']
+ #--------------------------Methods--------------------------
+ def __init__(self, inhom_sampling=None, **dist_params):
+ """
+ generates the list of sampling points in the distribution and their weights
+ inhom dists should be normalized (int(f, dzeta) = 1.)
+ """
+ # inherit all class attributes unless kwargs has them; then use those
+ # values. if kwargs is not an Omega attribute, it gets ignored
+ for key, value in dist_params.items():
+ setattr(self, key, value)
+ #print self.__dict__.items()
+ # eliminating other quadrature methods; linear works best anyways
+ if inhom_sampling == 'linear':
+ # currently the only inhomogeneity parameter that can normalize well
+ # in relation to the case of no inhomogeneity
+ if isinstance(dist_params.get('num'), int):
+ num = dist_params.get('num')
+ else:
+ try:
+ num = int(num)
+ except TypeError:
+ print 'no distribution sampling number specified; using 10 points as default'
+ num = 10
+ if 'zeta_bound' in dist_params.keys():
+ zeta_bound = dist_params.get('zeta_bound')
+ else:
+ zeta_bound = 3
+ zeta = np.linspace(-zeta_bound, zeta_bound, num=num)
+ # need parameter 'sigma'
+ sigma = dist_params.get('sigma')
+ # scale our sampling intervals according to sigma
+ zeta = zeta * sigma
+ self.zweight = 1 / (np.sqrt(2*np.pi)*sigma) * np.exp(- 0.5 * ((zeta / sigma)**2))
+ self.dzeta = np.abs(zeta[1] - zeta[0])
+ self.zeta = zeta
+ elif inhom_sampling == 'rect':
+ w = dist_params.get('w')
+ if isinstance(dist_params.get('num'), int):
+ num = dist_params['num']
+ else:
+ try:
+ num = int(num)
+ except TypeError:
+ print 'no distribution sampling number specified; using 10 points as default'
+ num = 10
+ self.zeta = np.linspace(-w,w,num=num)
+ self.dzeta = np.abs(self.zeta[1] - self.zeta[0])
+ self.zweight = np.ones(self.zeta.shape)
+ elif inhom_sampling == 'gh':
+ import NISE.hamiltonians.params.gauss_hermite as gh
+ # gaussian-hermite quadrature
+ # see http://en.wikipedia.org/wiki/Gauss%E2%80%93Hermite_quadrature
+ # for details
+ n = dist_params.get('n')
+ try:
+ gh.quad[n]
+ except KeyError:
+ print 'no table for quadrature of number {0} is available'.format(n)
+ print 'available quadrature numbers: {0}'.format(str(gh.quad.keys()))
+ sigma = dist_params.get('sigma')
+ self.zeta = np.array(gh.quad[n])[0]
+ self.zweight = np.array(gh.quad[n])[1]
+ self.dzeta = 1.
+ # substitution to inhom variables yields the following scaling:
+ self.zeta*= np.sqrt(2) * sigma
+ self.zweight*= np.pi**-0.5
+ else:
+ self.zeta = np.array([0])
+ self.zweight = [1.0]
+ self.dzeta = 1.0
+ self.inhom_sampling = inhom_sampling
+ self.dist_params = dist_params
--
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