Merge pull request #16 from PGelss/PauliMatrices

Pauli matrices

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = wave_train 
-version = 1.0.10
+version = 1.0.11
 author =  Jerome Riedel, Patrick Gelß, Burkhard Schmidt
 author_email = burkhard.schmidt@fu-berlin.de
 description = Numerical quantum mechanics of chain-like systems based on tensor trains

test_scripts/Bath_Map_1/tdse_1.py

@@ -0,0 +1,94 @@
+from wave_train.hamilton.bath_map_1 import Bath_Map_1
+from wave_train.dynamics.tdse import TDSE
+from wave_train.io.load import Load
+from wave_train.io.logging import TeeLogger
+from os.path import basename, splitext
+import numpy as np
+import matplotlib.pyplot as plt
+
+def bath_map_1_tdse(batch_mode):
+    # Detect name of this script file (without extension)
+    base_name   = basename(__file__)
+    my_file     = splitext(base_name)[0]
+
+    # logging instance: will be initialized with 
+    # class for logging to both console and logfile
+    logger = None
+    if not batch_mode:
+        logger = TeeLogger(log_file=my_file + ".log")
+
+    # Set up the excitonic Hamiltonian for a chain
+    hamilton = Bath_Map_1(
+        n_site=50,                       # number of sites
+        eta = 0.5,                       # coupling between TLS and first bath site
+        s = 1,                           # type of spectral density function: s<1 sub-ohmic, s=1 ohmic, s>1 super-ohmic
+        omega_c = 10,                    # cut-off frequency of spectral density function
+        omega_0 = 1                      # eigenfrequency of the TLS
+    )
+
+    # Set up TT representation of the Hamiltonian
+    hamilton.get_TT(
+        n_basis=2,                       # size of electronic basis set
+        qtt=False                        # using quantized TT format
+    )
+
+    # Set up TDSE solver
+    dynamics = TDSE(
+        hamilton=hamilton,               # choice of Hamiltonian, see above
+        num_steps=10,                    # number of main time steps
+        step_size=0.1,                   # size of main time steps
+        sub_steps=1,                     # number of sub steps
+        solver='vp',                     # can be 'se' (symmetrized Euler) or 'sm' (Strang-Marchuk splitting) or ...
+        normalize=0,                     # whether|how to normalize the solution, can be 0|2
+        max_rank=5,                      # max rank of solution
+        repeats=15,                      # number of sweeps (implicit ODE solvers only!)
+        threshold=1e-8,                  # threshold in ALS decomposition
+        save_file=my_file+'.pic',        # if not None, generated data will be saved to this file
+        load_file=None,                  # if not None, reference data will be loaded from this file
+        compare=None                     # How to do the comparison with reference data
+    )
+
+    # Set up initial state
+    dynamics.fundamental(list(np.eye(hamilton.n_site)[0,:]))               # fundamental excitation near center of chain
+    # dynamics.gaussian()
+    # dynamics.sec_hyp(w_0=0.2)
+
+    # Batch mode
+    if batch_mode:
+        dynamics.solve()                 # Solve TDSE *without* visualization
+
+    # Interactive mode: Setup animated visualization
+    else:
+        from wave_train.graphics.factory import VisualTDSE
+        graphics = VisualTDSE(
+            dynamics=dynamics,           # choice of dynamics (EoM), see above
+            plot_type='Populations',     # select your favorite plot type
+            plot_expect=True,            # toggle plotting of expectation values
+            figure_pos=(100, 50),        # specifying position (x,y) of upper left of figure [in pixels]
+            figure_size=(1050, 450),     # specifying size (w,h) of figure [in pixels]
+            image_file=my_file+'.png',   # if not None, image (last frame) will be written to this file
+            movie_file=my_file+'.mp4',   # if not None, animation will be written to this file
+            snapshots=False,             # save each snapshot
+            frame_rate=1,                # frames per second in mp4 animation file
+            plot_style={},               # additional plot style information
+        ).create()
+        graphics.solve()                 # Solve TDSE *with* visualization
+
+
+if __name__ == '__main__':
+    bath_map_1_tdse(batch_mode=False)
+
+
+dynamics = Load(
+    file_name='tdse_1',
+    file_type = 'pic'
+)
+#print(dynamics.qu_numbr)
+plt.figure()
+for i in range(1,100,10):
+    plt.plot(dynamics.qu_numbr[:,i])
+plt.show()
+
+#print(dynamics.qu_sig_1)
+
+

test_scripts/Coupled/qcmd_1.py → test_scripts/Exc_Pho_Coupling/qcmd_1.py

@@ -1,4 +1,4 @@
-from wave_train.hamilton.coupled import Coupled
+from wave_train.hamilton.exc_pho_coupling import Exc_Pho_Coupling
 from wave_train.dynamics.qcmd import QCMD
 from wave_train.io.logging import TeeLogger
 from os.path import basename, splitext
@@ -15,7 +15,7 @@ def coupled_qcmd(batch_mode):
         logger = TeeLogger(log_file=my_file + ".log")
 
     # Set up the coupled exciton-phonon Hamiltonian for a chain
-    hamilton = Coupled(
+    hamilton = Exc_Pho_Coupling(
         n_site=15,                       # number of sites
         periodic=False,                  # periodic boundary conditions
         homogen=True,                    # homogeneous chain/ring

test_scripts/Coupled/qcmd_2.py → test_scripts/Exc_Pho_Coupling/qcmd_2.py

@@ -1,4 +1,4 @@
-from wave_train.hamilton.coupled import Coupled
+from wave_train.hamilton.exc_pho_coupling import Exc_Pho_Coupling
 from wave_train.dynamics.qcmd import QCMD
 from wave_train.io.logging import TeeLogger
 from os.path import basename, splitext
@@ -17,7 +17,7 @@ def coupled_qcmd(batch_mode):
     # Define properties of chain/ring system
 
     # Set up the coupled exciton-phonon Hamiltonian for a chain
-    hamilton = Coupled(
+    hamilton = Exc_Pho_Coupling(
         n_site=15,                       # number of sites
         periodic=False,                  # periodic boundary conditions
         homogen=True,                    # Homogeneous chain/ring

test_scripts/Coupled/qcmd_3.py → test_scripts/Exc_Pho_Coupling/qcmd_3.py

@@ -1,4 +1,4 @@
-from wave_train.hamilton.coupled import Coupled
+from wave_train.hamilton.exc_pho_coupling import Exc_Pho_Coupling
 from wave_train.dynamics.qcmd import QCMD
 from wave_train.io.logging import TeeLogger
 from os.path import basename, splitext
@@ -15,7 +15,7 @@ def coupled_qcmd(batch_mode):
         logger = TeeLogger(log_file=my_file + ".log")
 
     # Set up the coupled exciton-phonon Hamiltonian for a chain
-    hamilton = Coupled(
+    hamilton = Exc_Pho_Coupling(
         n_site=41,                       # number of sites
         periodic=True,                   # periodic boundary conditions
         homogen=True,                    # Homogeneous chain/ring

test_scripts/Coupled/qcmd_4.py → test_scripts/Exc_Pho_Coupling/qcmd_4.py

@@ -1,4 +1,4 @@
-from wave_train.hamilton.coupled import Coupled
+from wave_train.hamilton.exc_pho_coupling import Exc_Pho_Coupling
 from wave_train.dynamics.qcmd import QCMD
 from wave_train.io.logging import TeeLogger
 from os.path import basename, splitext
@@ -15,7 +15,7 @@ def coupled_qcmd(batch_mode):
         logger = TeeLogger(log_file=my_file + ".log")
 
     # Set up the coupled exciton-phonon Hamiltonian for a chain
-    hamilton = Coupled(
+    hamilton = Exc_Pho_Coupling(
         n_site=41,                       # number of sites
         periodic=False,                  # periodic boundary conditions
         homogen=True,                    # Homogeneous chain/ring

test_scripts/Coupled/tdse_1.py → test_scripts/Exc_Pho_Coupling/tdse_1.py

@@ -1,4 +1,4 @@
-from wave_train.hamilton.coupled import Coupled
+from wave_train.hamilton.exc_pho_coupling import Exc_Pho_Coupling
 from wave_train.dynamics.tdse import TDSE
 from wave_train.io.logging import TeeLogger
 from os.path import basename, splitext
@@ -15,7 +15,7 @@ def coupled_tdse(batch_mode):
         logger = TeeLogger(log_file=my_file + ".log")
 
     # Set up the coupled exciton-phonon Hamiltonian for a chain
-    hamilton = Coupled(
+    hamilton = Exc_Pho_Coupling(
         n_site=15,                       # number of sites
         periodic=False,                  # periodic boundary conditions
         homogen=True,                    # homogeneous chain/ring

test_scripts/Coupled/tdse_qe_1.py → test_scripts/Exc_Pho_Coupling/tdse_qe_1.py

@@ -1,4 +1,4 @@
-from wave_train.hamilton.coupled import Coupled
+from wave_train.hamilton.exc_pho_coupling import Exc_Pho_Coupling
 from wave_train.dynamics.tdse import TDSE
 from wave_train.io.logging import TeeLogger
 from os.path import basename, splitext
@@ -15,7 +15,7 @@ def coupled_qe_1(batch_mode):
         logger = TeeLogger(log_file=my_file + ".log")
 
     # Set up the coupled exciton-phonon Hamiltonian for a chain
-    hamilton = Coupled(
+    hamilton = Exc_Pho_Coupling(
         n_site=3,                        # number of sites
         periodic=False,                  # periodic boundary conditions
         homogen=True,                    # homogeneous chain/ring
@@ -39,7 +39,7 @@ def coupled_qe_1(batch_mode):
 
     # Set up TDSE solver
     dynamics = TDSE(
-        hamilton=hamilton,  # choice of Hamiltonian, see above
+        hamilton=hamilton,               # choice of Hamiltonian, see above
         num_steps=50,                    # number of main time steps
         step_size=20,                    # size of main time steps
         sub_steps=None,                  # dummy

test_scripts/Coupled/tdse_qe_2.py → test_scripts/Exc_Pho_Coupling/tdse_qe_2.py

@@ -1,4 +1,4 @@
-from wave_train.hamilton.coupled import Coupled
+from wave_train.hamilton.exc_pho_coupling import Exc_Pho_Coupling
 from wave_train.dynamics.tdse import TDSE
 from wave_train.io.logging import TeeLogger
 from os.path import basename, splitext
@@ -15,7 +15,7 @@ def coupled_qe_2(batch_mode):
         logger = TeeLogger(log_file=my_file + ".log")
 
     # Set up the coupled exciton-phonon Hamiltonian for a chain
-    hamilton = Coupled(
+    hamilton = Exc_Pho_Coupling(
         n_site=3,                        # number of sites
         periodic=False,                  # periodic boundary conditions
         homogen=True,                    # homogeneous chain/ring
@@ -39,7 +39,7 @@ def coupled_qe_2(batch_mode):
 
     # Set up TDSE solver
     dynamics = TDSE(
-        hamilton=hamilton,  # choice of Hamiltonian, see above
+        hamilton=hamilton,               # choice of Hamiltonian, see above
         num_steps=50,                    # number of main time steps
         step_size=20,                    # size of main time steps
         sub_steps=20,                    # number of sub steps

test_scripts/Coupled/tdse_qe_3.py → test_scripts/Exc_Pho_Coupling/tdse_qe_3.py

@@ -1,4 +1,4 @@
-from wave_train.hamilton.coupled import Coupled
+from wave_train.hamilton.exc_pho_coupling import Exc_Pho_Coupling
 from wave_train.dynamics.qcmd import QCMD
 from wave_train.io.logging import TeeLogger
 from os.path import basename, splitext
@@ -15,7 +15,7 @@ def coupled_qe_3(batch_mode):
         logger = TeeLogger(log_file=my_file + ".log")
 
     # Set up the coupled exciton-phonon Hamiltonian for a chain
-    hamilton = Coupled(
+    hamilton = Exc_Pho_Coupling(
         n_site=3,                        # number of sites
         periodic=False,                  # periodic boundary conditions
         homogen=True,                    # homogeneous chain/ring

test_scripts/Coupled/tise_1.py → test_scripts/Exc_Pho_Coupling/tise_1.py

@@ -1,4 +1,4 @@
-from wave_train.hamilton.coupled import Coupled
+from wave_train.hamilton.exc_pho_coupling import Exc_Pho_Coupling
 from wave_train.dynamics.tise import TISE
 from wave_train.io.logging import TeeLogger
 from os.path import basename, splitext
@@ -15,7 +15,7 @@ def coupled_tise(batch_mode):
         logger = TeeLogger(log_file=my_file + ".log")
 
     # Set up the coupled excitonic-phononic Hamiltonian for a chain
-    hamilton = Coupled(
+    hamilton = Exc_Pho_Coupling(
         n_site=5,                        # number of sites
         periodic=True,                   # periodic boundary conditions
         homogen=True,                    # homogeneous chain/ring

wave_train/dynamics/qu_cl_mech.py

@@ -32,7 +32,7 @@ def __init__(self, hamilton):
         # Quantum subsystem
         self.norm = np.zeros(self.num_steps + 1)  # norm of state vector
         self.auto = np.zeros(self.num_steps + 1, dtype=complex) # autocorrelation
-        self.ex_numbr = np.zeros((self.num_steps + 1, self.hamilton.n_site))  # quantum number for excitons
+        self.q1_numbr = np.zeros((self.num_steps + 1, self.hamilton.n_site))  # quantum number for 1st sub-system
 
         # Classical subsystem
         self.position = np.zeros((self.num_steps + 1, self.hamilton.n_site))  # position
@@ -91,16 +91,16 @@ def observe(self, i, iterations=0):
         for j in range(self.hamilton.n_site):
             self.position[i, j] = self.pos[j]
             self.momentum[i, j] = self.mom[j]
-            self.ex_numbr[i, j] = np.abs(self.psi[j]) ** 2
+            self.q1_numbr[i, j] = np.abs(self.psi[j]) ** 2
 
-            print(str("%4d" % j) + ' | ' + str("%10f" % self.ex_numbr[i, j]) + ' | ' + str("%10f" % self.position[i, j]) + ' | ' + str(
+            print(str("%4d" % j) + ' | ' + str("%10f" % self.q1_numbr[i, j]) + ' | ' + str("%10f" % self.position[i, j]) + ' | ' + str(
                 "%10f" % self.momentum[i, j])  )
 
 
         # Footer of table with site-specific information
         print(43 * '-')
         print(' sum' +
-              ' | ' + str("%10f" % np.sum(self.ex_numbr[i, :])) +
+              ' | ' + str("%10f" % np.sum(self.q1_numbr[i, :])) +
               ' | ' + str("%10f" % np.sum(self.position[i, :])) +
               ' | ' + str("%10f" % np.sum(self.momentum[i, :])) )
         print (' ')