fixed shape changes in coordinates and momenta

classical/test_cheb_00_2p_1d_pbc.py

@@ -5,7 +5,7 @@ from systems import MPPS1D
 from mpliouville import MPLPDV
 import matplotlib.pyplot as plt
 
-syspar = {'symbols': ['0', '1'], 'q0': [1, 3], 'p0': [1, -1],
+syspar = {'symbols': ['0', '1'], 'q0': [[1], [3]], 'p0': [[1], [-1]],
           'masses': [1.0, 1.0], 'pbc': True, 'cell': [5.0],
           'numeric': {'tool': 'subs'}}
 ffparams = [{'class': 'FFZero', 'pair': ((0,), (1,))}]

classical/test_cheb_ho_2p_1d.py

@@ -10,7 +10,8 @@ import numpy as np
 M = np.full(2, 2.0)
 r0 = 3.5
 kappa = sp.Rational(1, 2)
-syspar = {'symbols': ['0', '1'], 'q0': [0, 1], 'p0': [1, 0], 'masses': M}
+syspar = {'symbols': ['0', '1'], 'q0': [[0], [1]], 'p0': [[1], [0]],
+          'masses': M}
 ffpar = [{'class': 'FFHarmonic', 'pair': ((0,), (1,)),
           'params': {'distance': r0, 'kappa': kappa}}]
 syst = MPPS1D(ffpar, **syspar)
@@ -29,9 +30,9 @@ prop_ref.analyse()
 
 # analytic solution of equivalent 1p problem
 sys_1p_par = {
-    'q0': np.abs(syspar['q0'][0]-syspar['q0'][1])-r0,
+    'q0': np.abs(syspar['q0'][0][0]-syspar['q0'][1][0])-r0,
     # from the motion of center of mass
-    'p0': (M[0]*syspar['p0'][1]+M[1]*syspar['p0'][0])/np.sum(M),
+    'p0': (M[0]*syspar['p0'][1][0]+M[1]*syspar['p0'][0][0])/np.sum(M),
     # from total kinetic energy = sum of particles's kinetic energies
     # 'p0': np.sqrt((M[0]*syspar['p0'][1]**2+M[1]*syspar['p0'][0]**2)/np.sum(M)),
     'mass': np.prod(M)/np.sum(M)

classical/test_cheb_ho_2p_3d.py

@@ -13,7 +13,8 @@ params = {'tstart': 0.0, 'tend': 1.0, 'tstep': 0.1, 'nterms': 4,
 M = np.full(2, 2.0)
 r0 = 3.5
 kappa = sp.Rational(1, 2)
-syspar_1d = {'symbols': ['0', '1'], 'q0': [-1, 0], 'p0': [1, 0], 'masses': M}
+syspar_1d = {'symbols': ['0', '1'], 'q0': [[-1], [0]], 'p0': [[1], [0]],
+             'masses': M}
 ffpar_1d = [{'class': 'FFHarmonic', 'pair': ((0,), (1,)),
              'params': {'distance': r0, 'kappa': kappa}}]
 syst_1d = MPPS1D(ffpar_1d, **syspar_1d)
@@ -36,9 +37,9 @@ prop_3d.analyse()
 
 # analytic solution of the equivalent 1p problem
 sys_1p_par = {
-    'q0': np.abs(syspar_1d['q0'][0]-syspar_1d['q0'][1])-r0,
+    'q0': np.abs(syspar_1d['q0'][0][0]-syspar_1d['q0'][1][0])-r0,
     # from the motion of center of mass
-    'p0': (M[0]*syspar_1d['p0'][1]+M[1]*syspar_1d['p0'][0])/np.sum(M),
+    'p0': (M[0]*syspar_1d['p0'][1][0]+M[1]*syspar_1d['p0'][0][0])/np.sum(M),
     # from total kinetic energy = sum of particles's kinetic energies
     # 'p0': np.sqrt((M[0]*syspar_1d['p0'][1]**2+M[1]*syspar_1d['p0'][0]**2)/np.sum(M)),
     'mass': np.prod(M)/np.sum(M)

classical/test_cheb_lj_2p_1d.py

@@ -5,7 +5,7 @@ from systems import MPPS1D
 from mpliouville import MPLPQP
 import matplotlib.pyplot as plt
 
-syspar = {'symbols': ['0', '1'], 'q0': [0, 2], 'p0': [0, -1],
+syspar = {'symbols': ['0', '1'], 'q0': [[0], [2]], 'p0': [[0], [-1]],
           'masses': [1.0, 1.0]}
 ffpars = [{'class': 'FFLennardJones', 'pair': ((0,), (1,))}]
 syst = MPPS1D(ffpars, **syspar)

classical/test_cheb_lj_2p_1d_pbc.py

@@ -5,7 +5,7 @@ from systems import MPPS1D
 from mpliouville import MPLPDV
 import matplotlib.pyplot as plt
 
-syspar = {'symbols': ['0', '1'], 'q0': [1, 3], 'p0': [0, -1],
+syspar = {'symbols': ['0', '1'], 'q0': [[1], [3]], 'p0': [[0], [-1]],
           'masses': [1.0, 1.0], 'pbc': True, 'cell': [15.],
           'numeric': {'tool': 'subs'}}
 ffpars = [{'class': 'FFLennardJones', 'pair': ((0,), (1,))}]
@@ -50,7 +50,7 @@ plot = fig.add_subplot(313)
 plt.plot(tir, rtr, label='r(t) verlet')
 plt.plot(ti, rt, label='r(t) chebyshev')
 plot.set_xlabel('time')
-plot.set_ylabel(r'$p_0,\quad p_1$')
+plot.set_ylabel(r'$r = |q_0 - q_1|$')
 plt.legend()
 
 plt.show()