Getting there

ipi/engine/motion/al6xxx_kmc.py

@@ -13,7 +13,7 @@
 import collections
 
 from ipi.engine.motion import Motion, GeopMotion
-from ipi.utils.depend import dstrip, depend_value, dd
+from ipi.utils.depend import dstrip, depend_value
 from ipi.engine.cell import Cell
 from ipi.utils.units import Constants
 import ipi.utils.io as io
@@ -164,7 +164,7 @@ def __init__(
         self.idx = idx
 
         # the KMC step is variable and so it cannot be stored as proper timing
-        dd(self).dt = depend_value(name="dt", value=0.0)
+        self._dt = depend_value(name="dt", value=0.0)
         self.fixatoms = np.asarray([])
         self.fixcom = True
         self.optimizer = [None] * self.neval

ipi/engine/motion/alchemy.py

@@ -12,7 +12,7 @@
 import numpy as np
 
 from ipi.engine.motion import Motion
-from ipi.utils.depend import *
+from ipi.utils.depend import inject_depend_properties
 from ipi.utils.units import Constants
 
 
@@ -46,8 +46,7 @@ def __init__(
         self.names = names
         self.nxc = nxc
 
-        dself = dd(self)
-        dself.ealc = depend_value(name="ealc")
+        self._ealc = depend_value(name="ealc")
         if ealc is not None:
             self.ealc = ealc
         else:
@@ -70,7 +69,7 @@ def bind(self, ens, beads, cell, bforce, nm, prng, omaker):
         """
 
         super(AlchemyMC, self).bind(ens, beads, cell, bforce, nm, prng, omaker)
-        self.ensemble.add_econs(dd(self).ealc)
+        self.ensemble.add_econs(self._ealc)
 
     def AXlist(self, atomtype):
         """This compile a list of atoms ready for exchanges."""
@@ -158,3 +157,6 @@ def step(self, step=None):
 
                 # adjusts the conserved quantity counter based on the change in spring energy
                 self.ealc += -difspring
+
+
+inject_depend_properties(AlchemyMC, ["ealc"])

ipi/engine/motion/atomswap.py

@@ -41,8 +41,7 @@ def __init__(
         self.names = names
         self.nxc = nxc
 
-        dself = dd(self)
-        dself.ealc = depend_value(name="ealc")
+        self._ealc = depend_value(name="ealc")
         if ealc is not None:
             self.ealc = ealc
         else:
@@ -65,7 +64,7 @@ def bind(self, ens, beads, cell, bforce, nm, prng, omaker):
         """
 
         super(AtomSwap, self).bind(ens, beads, cell, bforce, nm, prng, omaker)
-        self.ensemble.add_econs(dd(self).ealc)
+        self.ensemble.add_econs(self._ealc)
         self.dbeads = self.beads.copy()
         self.dcell = self.cell.copy()
         self.dforces = self.forces.copy(self.dbeads, self.dcell)
@@ -133,3 +132,6 @@ def step(self, step=None):
                 self.forces.transfer_forces(self.dforces)
 
                 self.ealc += -(new_energy - old_energy)
+
+
+inject_depend_properties(AtomSwap, ["ealc"])

ipi/engine/motion/constrained_dynamics.py

@@ -190,7 +190,10 @@ def bind(self, ens, beads, nm, cell, bforce, prng, omaker):
         self.csolver.bind(beads)
 
 
-class ConstraintSolverBase(dobject):
+inject_depend_properties(ConstrainedDynamics, ["dt", "nmts", "splitting"])
+
+
+class ConstraintSolverBase:
     """Empty base class for the constraint solver. Provides the interface
     that must be used to offer constraint functionalities to an integrator.
     """
@@ -229,7 +232,7 @@ def proj_manifold(self, beads, stepsize=None, proj_p=True):
         raise NotImplementedError()
 
 
-inject_depend_properties(ConstrainedDynamics, ["dt", "nmts", "splitting"])
+inject_depend_properties(ConstraintSolverBase, ["dt"])
 
 
 class ConstraintSolver(ConstraintSolverBase):
@@ -267,7 +270,6 @@ def proj_cotangent(self):
         (sparsely).
         """
 
-        #        m3 = dstrip(self.beads.m3[0])
         p = dstrip(self.beads.p[0]).copy()
         self.beads.p.hold()
 

ipi/engine/thermostats.py

@@ -68,7 +68,7 @@ def __init__(self, temp=1.0, dt=1.0, ethermo=0.0):
               Defaults to 0.0. Will be non-zero if the thermostat is
               initialised from a checkpoint file.
         """
-        
+
         self._temp = depend_value(name="temp", value=temp)
         self._dt = depend_value(name="dt", value=dt)
         self._ethermo = depend_value(name="ethermo", value=ethermo)
@@ -111,8 +111,8 @@ def bind(self, beads=None, atoms=None, pm=None, nm=None, prng=None, fixdof=None)
             self._p = beads.p.flatten()
             self._m = beads.m3.flatten()
         elif atoms is not None:
-            self._p = dd(atoms).p
-            self._m = dd(atoms).m3
+            self._p = atoms._p
+            self._m = atoms._m3
         elif pm is not None:
             self._p = pm[
                 0
@@ -186,7 +186,7 @@ def __init__(self, temp=1.0, dt=1.0, tau=1.0, ethermo=0.0):
         """
 
         super(ThermoLangevin, self).__init__(temp, dt, ethermo)
-        
+
         self._dt = depend_value(value=dt, name="dt")
         self._tau = depend_value(value=tau, name="tau")
         self._T = depend_value(
@@ -215,7 +215,11 @@ def step(self):
         self.p = p
         self.ethermo = et
 
-inject_depend_properties(Thermostat, ["temp", "dt", "ethermo", "p", "m", "sm", "dt", "tau", "T", "S"])
+
+inject_depend_properties(
+    Thermostat, ["temp", "dt", "ethermo", "p", "m", "sm", "dt", "tau", "T", "S"]
+)
+
 
 class ThermoPILE_L(Thermostat):
 
@@ -419,10 +423,12 @@ def step(self):
         for t in self._thermos:
             t.step()
         self.nm.pnm.resume()
-        dd(self).ethermo.resume()
+        self._ethermo.resume()
+
 
 inject_depend_properties(ThermoPILE_L, ["pilescale", "pilect", "npilect", "tauk"])
 
+
 class ThermoSVR(Thermostat):
 
     """Represents a stochastic velocity rescaling thermostat.
@@ -457,7 +463,7 @@ def __init__(self, temp=1.0, dt=1.0, tau=1.0, ethermo=0.0):
         """
 
         super(ThermoSVR, self).__init__(temp, dt, ethermo)
-        
+
         self._tau = depend_value(value=tau, name="tau")
         self._et = depend_value(
             name="et", func=self.get_et, dependencies=[self._tau, self._dt]
@@ -574,8 +580,10 @@ def bind(self, beads=None, atoms=None, pm=None, nm=None, prng=None, fixdof=None)
             t.ethermo = prev_ethermo / nm.nbeads
         self._ethermo._func = self.get_ethermo
 
+
 inject_depend_properties(ThermoSVR, ["et", "K", "pilescale", "pilect", "npilect"])
 
+
 class ThermoGLE(Thermostat):
 
     """Represents a generalized Langevin equation thermostat.
@@ -699,7 +707,7 @@ def bind(self, beads=None, atoms=None, pm=None, nm=None, prng=None, fixdof=None)
 
         super(ThermoGLE, self).bind(
             beads=beads, atoms=atoms, pm=pm, prng=prng, fixdof=fixdof
-        )        
+        )
 
         # allocates, initializes or restarts an array of s's
         if self.s.shape != (self.ns + 1, len(self._m)):
@@ -733,8 +741,10 @@ def step(self):
 
         self.p = self.s[0] * self.sm
 
+
 inject_depend_properties(ThermoGLE, ["A", "C"])
 
+
 class ThermoNMGLE(Thermostat):
 
     """Represents a 'normal-modes' generalized Langevin equation thermostat.
@@ -920,8 +930,10 @@ def get_ethermo(self):
             et += t.ethermo
         return et
 
+
 inject_depend_properties(ThermoNMGLE, ["A", "C"])
 
+
 class ThermoNMGLEG(ThermoNMGLE):
 
     """Represents a 'normal-modes' generalized Langevin equation thermostat + SVR.
@@ -970,7 +982,7 @@ def bind(self, beads=None, atoms=None, pm=None, nm=None, prng=None, fixdof=None)
         dpipe(self._dt, t._dt)
         dpipe(self._tau, t._tau)
 
-        dd(self).ethermo.add_dependency(t._ethermo)
+        self._ethermo.add_dependency(t._ethermo)
         self._thermos.append(t)
 
 
@@ -1108,8 +1120,10 @@ def step(self):
 
         self.idstep = not self.idstep
 
+
 inject_depend_properties(ThermoCL, ["idtau", "intau", "apat", "lgT", "inT", "idT"])
 
+
 class ThermoFFL(Thermostat):
 
     """Represents a fast-forward langevin thermostat.
@@ -1149,7 +1163,7 @@ def __init__(self, temp=1.0, dt=1.0, tau=1.0, ethermo=0.0, flip="rescale"):
         """
 
         super(ThermoFFL, self).__init__(temp, dt, ethermo)
-        
+
         self._dt = depend_value(value=dt, name="dt")
         self._tau = depend_value(value=tau, name="tau")
         self._T = depend_value(
@@ -1218,8 +1232,10 @@ def step(self):
         self.p = p
         self.ethermo = et
 
+
 inject_depend_properties(ThermoFFL, "flip")
 
+
 class MultiThermo(Thermostat):
     def __init__(self, temp=1.0, dt=1.0, ethermo=0.0, thermolist=None):
         """Initialises Thermostat.
@@ -1231,7 +1247,7 @@ def __init__(self, temp=1.0, dt=1.0, ethermo=0.0, thermolist=None):
               Defaults to 0.0. Will be non-zero if the thermostat is
               initialised from a checkpoint file.
         """
-        
+
         self.tlist = thermolist
         self._temp = depend_value(name="temp", value=temp)
         self._dt = depend_value(name="dt", value=dt)
@@ -1252,9 +1268,9 @@ def bind(self, beads=None, atoms=None, pm=None, nm=None, prng=None, fixdof=None)
         # just binds all the sub-thermostats
         for t in self.tlist:
             t.bind(beads=beads, atoms=atoms, pm=pm, nm=nm, prng=prng, fixdof=fixdof)
-            dd(self).ethermo.add_dependency(t._ethermo)
+            self._ethermo.add_dependency(t._ethermo)
 
-        dd(self).ethermo._func = self.get_ethermo
+        self._ethermo._func = self.get_ethermo
 
     def step(self):
         """Steps through all sub-thermostats."""

ipi/inputs/thermostats.py

@@ -207,20 +207,20 @@ def store(self, thermo):
         elif type(thermo) is ethermostats.ThermoGLE:
             self.mode.store("gle")
             self.A.store(thermo.A)
-            if dd(thermo).C._func is None:
+            if thermo._C._func is None:
                 self.C.store(thermo.C)
             self.s.store(thermo.s)
         elif type(thermo) is ethermostats.ThermoNMGLE:
             self.mode.store("nm_gle")
             self.A.store(thermo.A)
-            if dd(thermo).C._func is None:
+            if thermo._C._func is None:
                 self.C.store(thermo.C)
             self.s.store(thermo.s)
         elif type(thermo) is ethermostats.ThermoNMGLEG:
             self.mode.store("nm_gle_g")
             self.A.store(thermo.A)
             self.tau.store(thermo.tau)
-            if dd(thermo).C._func is None:
+            if thermo._C._func is None:
                 self.C.store(thermo.C)
             self.s.store(thermo.s)
         elif type(thermo) is ethermostats.ThermoCL: