#699 start removing autograd

.gitignore

@@ -3,6 +3,7 @@
 *.tmp
 *.png
 /local/
+*.DS_Store
 
 # don't ignore important .txt files
 !requirements*

input/parameters/lead-acid/anodes/lead_Sulzer2019/lead_ocp_Bode1977.py

@@ -1,7 +1,7 @@
 #
 # Open-circuit voltage in the negative (lead) electrode
 #
-import autograd.numpy as np
+from pybamm import log10
 
 
 def lead_ocp_Bode1977(m):
@@ -16,9 +16,9 @@ def lead_ocp_Bode1977(m):
     """
     U = (
         -0.294
-        - 0.074 * np.log10(m)
-        - 0.030 * np.log10(m) ** 2
-        - 0.031 * np.log10(m) ** 3
-        - 0.012 * np.log10(m) ** 4
+        - 0.074 * log10(m)
+        - 0.030 * log10(m) ** 2
+        - 0.031 * log10(m) ** 3
+        - 0.012 * log10(m) ** 4
     )
     return U

input/parameters/lead-acid/cathodes/lead_dioxide_Sulzer2019/lead_dioxide_ocp_Bode1977.py

@@ -1,7 +1,7 @@
 #
 # Open-circuit voltage in the positive (lead-dioxide) electrode
 #
-import autograd.numpy as np
+from pybamm import log10
 
 
 def lead_dioxide_ocp_Bode1977(m):
@@ -16,9 +16,9 @@ def lead_dioxide_ocp_Bode1977(m):
     """
     U = (
         1.628
-        + 0.074 * np.log10(m)
-        + 0.033 * np.log10(m) ** 2
-        + 0.043 * np.log10(m) ** 3
-        + 0.022 * np.log10(m) ** 4
+        + 0.074 * log10(m)
+        + 0.033 * log10(m) ** 2
+        + 0.043 * log10(m) ** 3
+        + 0.022 * log10(m) ** 4
     )
     return U

input/parameters/lead-acid/electrolytes/sulfuric_acid_Sulzer2019/conductivity_Gu1997.py

@@ -1,7 +1,7 @@
 #
 # Sulfuric acid conductivity
 #
-import autograd.numpy as np
+from pybamm import exp
 
 
 def conductivity_Gu1997(c_e):
@@ -23,4 +23,4 @@ def conductivity_Gu1997(c_e):
            California Univ., Berkeley. Lawrence Radiation Lab., 1968.
 
     """
-    return c_e * np.exp(6.23 - 1.34e-4 * c_e - 1.61e-8 * c_e ** 2) * 1e-4
+    return c_e * exp(6.23 - 1.34e-4 * c_e - 1.61e-8 * c_e ** 2) * 1e-4

input/parameters/lithium-ion/anodes/graphite_mcmb2528_Marquis2019/graphite_electrolyte_reaction_rate_Dualfoil1998.py

@@ -1,4 +1,4 @@
-import autograd.numpy as np
+from pybamm import exp
 
 
 def graphite_electrolyte_reaction_rate_Dualfoil1998(T, T_inf, E_r, R_g):
@@ -26,6 +26,6 @@ def graphite_electrolyte_reaction_rate_Dualfoil1998(T, T_inf, E_r, R_g):
         Reaction rate
     """
     m_ref = 2 * 10 ** (-5)
-    arrhenius = np.exp(E_r / R_g * (1 / T_inf - 1 / T))
+    arrhenius = exp(E_r / R_g * (1 / T_inf - 1 / T))
 
     return m_ref * arrhenius

input/parameters/lithium-ion/anodes/graphite_mcmb2528_Marquis2019/graphite_entropic_change_Moura2016.py

@@ -1,4 +1,4 @@
-import autograd.numpy as np
+from pybamm import exp, cosh
 
 
 def graphite_entropic_change_Moura2016(sto, c_n_max):
@@ -19,15 +19,15 @@ def graphite_entropic_change_Moura2016(sto, c_n_max):
     """
 
     du_dT = (
-        -1.5 * (120.0 / c_n_max) * np.exp(-120 * sto)
-        + (0.0351 / (0.083 * c_n_max)) * ((np.cosh((sto - 0.286) / 0.083)) ** (-2))
-        - (0.0045 / (0.119 * c_n_max)) * ((np.cosh((sto - 0.849) / 0.119)) ** (-2))
-        - (0.035 / (0.05 * c_n_max)) * ((np.cosh((sto - 0.9233) / 0.05)) ** (-2))
-        - (0.0147 / (0.034 * c_n_max)) * ((np.cosh((sto - 0.5) / 0.034)) ** (-2))
-        - (0.102 / (0.142 * c_n_max)) * ((np.cosh((sto - 0.194) / 0.142)) ** (-2))
-        - (0.022 / (0.0164 * c_n_max)) * ((np.cosh((sto - 0.9) / 0.0164)) ** (-2))
-        - (0.011 / (0.0226 * c_n_max)) * ((np.cosh((sto - 0.124) / 0.0226)) ** (-2))
-        + (0.0155 / (0.029 * c_n_max)) * ((np.cosh((sto - 0.105) / 0.029)) ** (-2))
+        -1.5 * (120.0 / c_n_max) * exp(-120 * sto)
+        + (0.0351 / (0.083 * c_n_max)) * ((cosh((sto - 0.286) / 0.083)) ** (-2))
+        - (0.0045 / (0.119 * c_n_max)) * ((cosh((sto - 0.849) / 0.119)) ** (-2))
+        - (0.035 / (0.05 * c_n_max)) * ((cosh((sto - 0.9233) / 0.05)) ** (-2))
+        - (0.0147 / (0.034 * c_n_max)) * ((cosh((sto - 0.5) / 0.034)) ** (-2))
+        - (0.102 / (0.142 * c_n_max)) * ((cosh((sto - 0.194) / 0.142)) ** (-2))
+        - (0.022 / (0.0164 * c_n_max)) * ((cosh((sto - 0.9) / 0.0164)) ** (-2))
+        - (0.011 / (0.0226 * c_n_max)) * ((cosh((sto - 0.124) / 0.0226)) ** (-2))
+        + (0.0155 / (0.029 * c_n_max)) * ((cosh((sto - 0.105) / 0.029)) ** (-2))
     )
 
     return du_dT

input/parameters/lithium-ion/anodes/graphite_mcmb2528_Marquis2019/graphite_mcmb2528_diffusivity_Dualfoil1998.py

@@ -1,4 +1,4 @@
-import autograd.numpy as np
+from pybamm import exp
 
 
 def graphite_mcmb2528_diffusivity_Dualfoil1998(sto, T, T_inf, E_D_s, R_g):
@@ -30,7 +30,7 @@ def graphite_mcmb2528_diffusivity_Dualfoil1998(sto, T, T_inf, E_D_s, R_g):
    """
 
     D_ref = 3.9 * 10 ** (-14)
-    arrhenius = np.exp(E_D_s / R_g * (1 / T_inf - 1 / T))
+    arrhenius = exp(E_D_s / R_g * (1 / T_inf - 1 / T))
 
     # Removing the fudge factor 0 * sto requires different handling of either
     # either simplifications or how sto is passed into this function.

input/parameters/lithium-ion/anodes/graphite_mcmb2528_Marquis2019/graphite_mcmb2528_ocp_Dualfoil1998.py

@@ -1,4 +1,4 @@
-import autograd.numpy as np
+from pybamm import exp, tanh
 
 
 def graphite_mcmb2528_ocp_Dualfoil1998(sto):
@@ -15,15 +15,15 @@ def graphite_mcmb2528_ocp_Dualfoil1998(sto):
 
     u_eq = (
         0.194
-        + 1.5 * np.exp(-120.0 * sto)
-        + 0.0351 * np.tanh((sto - 0.286) / 0.083)
-        - 0.0045 * np.tanh((sto - 0.849) / 0.119)
-        - 0.035 * np.tanh((sto - 0.9233) / 0.05)
-        - 0.0147 * np.tanh((sto - 0.5) / 0.034)
-        - 0.102 * np.tanh((sto - 0.194) / 0.142)
-        - 0.022 * np.tanh((sto - 0.9) / 0.0164)
-        - 0.011 * np.tanh((sto - 0.124) / 0.0226)
-        + 0.0155 * np.tanh((sto - 0.105) / 0.029)
+        + 1.5 * exp(-120.0 * sto)
+        + 0.0351 * tanh((sto - 0.286) / 0.083)
+        - 0.0045 * tanh((sto - 0.849) / 0.119)
+        - 0.035 * tanh((sto - 0.9233) / 0.05)
+        - 0.0147 * tanh((sto - 0.5) / 0.034)
+        - 0.102 * tanh((sto - 0.194) / 0.142)
+        - 0.022 * tanh((sto - 0.9) / 0.0164)
+        - 0.011 * tanh((sto - 0.124) / 0.0226)
+        + 0.0155 * tanh((sto - 0.105) / 0.029)
     )
 
     return u_eq

input/parameters/lithium-ion/cathodes/lico2_Marquis2019/lico2_diffusivity_Dualfoil1998.py

@@ -1,4 +1,4 @@
-import autograd.numpy as np
+from pybamm import exp
 
 
 def lico2_diffusivity_Dualfoil1998(sto, T, T_inf, E_D_s, R_g):
@@ -30,7 +30,7 @@ def lico2_diffusivity_Dualfoil1998(sto, T, T_inf, E_D_s, R_g):
     """
 
     D_ref = 1 * 10 ** (-13)
-    arrhenius = np.exp(E_D_s / R_g * (1 / T_inf - 1 / T))
+    arrhenius = exp(E_D_s / R_g * (1 / T_inf - 1 / T))
 
     # Removing the fudge factor 0 * sto requires different handling of either
     # either simplifications or how sto is passed into this function.

input/parameters/lithium-ion/cathodes/lico2_Marquis2019/lico2_electrolyte_reaction_rate_Dualfoil1998.py

@@ -1,4 +1,4 @@
-import autograd.numpy as np
+from pybamm import exp
 
 
 def lico2_electrolyte_reaction_rate_Dualfoil1998(T, T_inf, E_r, R_g):
@@ -26,6 +26,6 @@ def lico2_electrolyte_reaction_rate_Dualfoil1998(T, T_inf, E_r, R_g):
         Reaction rate
     """
     m_ref = 6 * 10 ** (-7)
-    arrhenius = np.exp(E_r / R_g * (1 / T_inf - 1 / T))
+    arrhenius = exp(E_r / R_g * (1 / T_inf - 1 / T))
 
     return m_ref * arrhenius

input/parameters/lithium-ion/cathodes/lico2_Marquis2019/lico2_entropic_change_Moura2016.py

@@ -1,4 +1,4 @@
-import autograd.numpy as np
+from pybamm import cosh
 
 
 def lico2_entropic_change_Moura2016(sto, c_p_max):
@@ -24,12 +24,12 @@ def lico2_entropic_change_Moura2016(sto, c_p_max):
     sto = stretch * sto
 
     du_dT = (
-        0.07645 * (-54.4806 / c_p_max) * ((1.0 / np.cosh(30.834 - 54.4806 * sto)) ** 2)
-        + 2.1581 * (-50.294 / c_p_max) * ((np.cosh(52.294 - 50.294 * sto)) ** (-2))
-        + 0.14169 * (19.854 / c_p_max) * ((np.cosh(11.0923 - 19.8543 * sto)) ** (-2))
-        - 0.2051 * (5.4888 / c_p_max) * ((np.cosh(1.4684 - 5.4888 * sto)) ** (-2))
-        - (0.2531 / 0.1316 / c_p_max) * ((np.cosh((-sto + 0.56478) / 0.1316)) ** (-2))
-        - (0.02167 / 0.006 / c_p_max) * ((np.cosh((sto - 0.525) / 0.006)) ** (-2))
+        0.07645 * (-54.4806 / c_p_max) * ((1.0 / cosh(30.834 - 54.4806 * sto)) ** 2)
+        + 2.1581 * (-50.294 / c_p_max) * ((cosh(52.294 - 50.294 * sto)) ** (-2))
+        + 0.14169 * (19.854 / c_p_max) * ((cosh(11.0923 - 19.8543 * sto)) ** (-2))
+        - 0.2051 * (5.4888 / c_p_max) * ((cosh(1.4684 - 5.4888 * sto)) ** (-2))
+        - (0.2531 / 0.1316 / c_p_max) * ((cosh((-sto + 0.56478) / 0.1316)) ** (-2))
+        - (0.02167 / 0.006 / c_p_max) * ((cosh((sto - 0.525) / 0.006)) ** (-2))
     )
 
     return du_dT

input/parameters/lithium-ion/cathodes/lico2_Marquis2019/lico2_ocp_Dualfoil1998.py

@@ -1,4 +1,4 @@
-import autograd.numpy as np
+from pybamm import tanh
 
 
 def lico2_ocp_Dualfoil1998(sto):
@@ -28,12 +28,12 @@ def lico2_ocp_Dualfoil1998(sto):
 
     u_eq = (
         2.16216
-        + 0.07645 * np.tanh(30.834 - 54.4806 * sto)
-        + 2.1581 * np.tanh(52.294 - 50.294 * sto)
-        - 0.14169 * np.tanh(11.0923 - 19.8543 * sto)
-        + 0.2051 * np.tanh(1.4684 - 5.4888 * sto)
-        + 0.2531 * np.tanh((-sto + 0.56478) / 0.1316)
-        - 0.02167 * np.tanh((sto - 0.525) / 0.006)
+        + 0.07645 * tanh(30.834 - 54.4806 * sto)
+        + 2.1581 * tanh(52.294 - 50.294 * sto)
+        - 0.14169 * tanh(11.0923 - 19.8543 * sto)
+        + 0.2051 * tanh(1.4684 - 5.4888 * sto)
+        + 0.2531 * tanh((-sto + 0.56478) / 0.1316)
+        - 0.02167 * tanh((sto - 0.525) / 0.006)
     )
 
     return u_eq

input/parameters/lithium-ion/electrolytes/lipf6_Marquis2019/electrolyte_conductivity_Capiglia1999.py

@@ -1,4 +1,4 @@
-import autograd.numpy as np
+from pybamm import exp
 
 
 def electrolyte_conductivity_Capiglia1999(c_e, T, T_inf, E_k_e, R_g):
@@ -38,6 +38,6 @@ def electrolyte_conductivity_Capiglia1999(c_e, T, T_inf, E_k_e, R_g):
         + 0.1554 * (c_e / 1000) ** 3
     )
 
-    arrhenius = np.exp(E_k_e / R_g * (1 / T_inf - 1 / T))
+    arrhenius = exp(E_k_e / R_g * (1 / T_inf - 1 / T))
 
     return sigma_e * arrhenius

input/parameters/lithium-ion/electrolytes/lipf6_Marquis2019/electrolyte_diffusivity_Capiglia1999.py

@@ -1,4 +1,4 @@
-import autograd.numpy as np
+from pybamm import exp
 
 
 def electrolyte_diffusivity_Capiglia1999(c_e, T, T_inf, E_D_e, R_g):
@@ -32,7 +32,7 @@ def electrolyte_diffusivity_Capiglia1999(c_e, T, T_inf, E_D_e, R_g):
         Solid diffusivity
     """
 
-    D_c_e = 5.34e-10 * np.exp(-0.65 * c_e / 1000)
-    arrhenius = np.exp(E_D_e / R_g * (1 / T_inf - 1 / T))
+    D_c_e = 5.34e-10 * exp(-0.65 * c_e / 1000)
+    arrhenius = exp(E_D_e / R_g * (1 / T_inf - 1 / T))
 
     return D_c_e * arrhenius

pybamm/__init__.py

@@ -94,37 +94,7 @@ def version(formatted=False):
 )
 from .expression_tree.array import Array
 from .expression_tree.matrix import Matrix
-from .expression_tree.unary_operators import (
-    UnaryOperator,
-    Negate,
-    AbsoluteValue,
-    Index,
-    SpatialOperator,
-    Gradient,
-    Divergence,
-    Laplacian,
-    Gradient_Squared,
-    Mass,
-    BoundaryMass,
-    BoundaryOperator,
-    BoundaryValue,
-    BoundaryGradient,
-    Integral,
-    IndefiniteIntegral,
-    DefiniteIntegralVector,
-    BoundaryIntegral,
-    DeltaFunction,
-    grad,
-    div,
-    laplacian,
-    grad_squared,
-    surf,
-    x_average,
-    z_average,
-    yz_average,
-    boundary_value,
-    r_average,
-)
+from .expression_tree.unary_operators import *
 from .expression_tree.functions import *
 from .expression_tree.interpolant import Interpolant
 from .expression_tree.parameter import Parameter, FunctionParameter

pybamm/expression_tree/binary_operators.py

@@ -3,7 +3,7 @@
 #
 import pybamm
 
-import autograd.numpy as np
+import numpy as np
 import numbers
 from scipy.sparse import issparse, csr_matrix, kron