initial commit

3 files changed, 273 insertions, 0 deletions

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