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lab-cosmo · Nov 19, 2023 · 07eefc3 · 07eefc3
1 parent 1a18788
commit 07eefc3
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Showing 4 changed files with 96 additions and 20 deletions.
diff --git a/ipi/engine/forces.py b/ipi/engine/forces.py
@@ -72,7 +72,7 @@ class ForceBead:
 
     def __init__(self):
         """Initialises ForceBead."""
-        
+
         # ufvx is a list [ u, f, vir, extra ]  which stores the results of the force calculation
         self._ufvx = depend_value(name="ufvx", func=self.get_all)
         self._threadlock = threading.Lock()
@@ -99,7 +99,7 @@ def bind(self, atoms, cell, ff, output_maker):
         self.atoms = atoms
         self.cell = cell
         self.ff = ff
-        
+
         # ufvx depends on the atomic positions and on the cell
         self._ufvx.add_dependency(dd(self.atoms).q)
         self._ufvx.add_dependency(dd(self.cell).h)
@@ -256,7 +256,11 @@ def get_extra(self):
 
         return self.ufvx[3]
 
-inject_depend_properties(ForceBead, ["ufvx", "pot", "vir", "f", "extra", "fx", "fy", "fz"])
+
+inject_depend_properties(
+    ForceBead, ["ufvx", "pot", "vir", "f", "extra", "fx", "fy", "fz"]
+)
+
 
 class ForceComponent:
     """Computes one component (e.g. bonded interactions) of the force.
@@ -511,7 +515,11 @@ def get_vir(self):
             vir += v
         return vir
 
-inject_depend_properties(ForceComponent, ["weight", "f", "pots", "pot", "virs", "vir", "extras"])
+
+inject_depend_properties(
+    ForceComponent, ["weight", "f", "pots", "pot", "virs", "vir", "extras"]
+)
+
 
 class ScaledForceComponent:
     def __init__(self, baseforce, scaling=1):
@@ -588,7 +596,12 @@ def get_vir(self):
     def queue(self):
         pass  # this should be taken care of when the force/potential/etc is accessed
 
-inject_depend_properties(ScaledForceComponent, ["weight", "scaling", "f", "pots", "pot", "virs", "vir", "extras"])
+
+inject_depend_properties(
+    ScaledForceComponent,
+    ["weight", "scaling", "f", "pots", "pot", "virs", "vir", "extras"],
+)
+
 
 class Forces:
 
@@ -781,8 +794,7 @@ def make_rpc(rpc, beads):
         )
 
         self._potsc = depend_value(
-            name="potsc", dependencies=[self._potssc], 
-            func=(lambda: self.potssc.sum())
+            name="potsc", dependencies=[self._potssc], func=(lambda: self.potssc.sum())
         )
 
         # The coefficients of the physical and the |f|^2 terms
@@ -943,7 +955,9 @@ def transfer_forces(self, refforce):
             # therefore get copied
             dd(mself.beads).q.set(mreff.beads.q, manual=False)
             for b in range(mself.nbeads):
-                mself._forces[b]._ufvx.set(deepcopy(mreff._forces[b]._ufvx._value), manual=False)
+                mself._forces[b]._ufvx.set(
+                    deepcopy(mreff._forces[b]._ufvx._value), manual=False
+                )
                 mself._forces[b]._ufvx.taint(taintme=False)
 
     def transfer_forces_manual(
@@ -1487,4 +1501,32 @@ def get_coeffsc_part_2(self):
         rc[1::2] = (1.0 - self.alpha) / self.omegan2 / 9.0
         return np.asmatrix(rc).T
 
-inject_depend_properties(Forces, [ "f", "pots", "virs", "extras", "pot", "vir", "alpha", "nmtslevels", "omegan2", "potssc", "potsc", "coeffsc_part_1", "coeffsc_part_2", "fvir_4th_order", "f_4th_order", "fsc_part_1", "fsc_part_2", "fsc", "vir_4th_order", "virssc_part_1", "virssc_part_2", "virssc", "potsc"])
+
+inject_depend_properties(
+    Forces,
+    [
+        "f",
+        "pots",
+        "virs",
+        "extras",
+        "pot",
+        "vir",
+        "alpha",
+        "nmtslevels",
+        "omegan2",
+        "potssc",
+        "potsc",
+        "coeffsc_part_1",
+        "coeffsc_part_2",
+        "fvir_4th_order",
+        "f_4th_order",
+        "fsc_part_1",
+        "fsc_part_2",
+        "fsc",
+        "vir_4th_order",
+        "virssc_part_1",
+        "virssc_part_2",
+        "virssc",
+        "potsc",
+    ],
+)
diff --git a/ipi/engine/normalmodes.py b/ipi/engine/normalmodes.py
@@ -901,4 +901,36 @@ def get_kstress(self):
 
         return kmd
 
-inject_depend_properties(NormalModes, ["nmts", "dt", "mode", "transform_method", "propagator", "nm_freqs", "qnm", "pnm", "fnm", "omegan", "omegan2", "omegak", "omegak2", "o_omegak", "nm_factor", "o_nm_factor", "dynm3", "dynomegak", "prop_pq", "o_prop_pq", "kins", "kin", "kstress", "vspring", "vspring_and_fspring_B", "fspring", "fspringnm"])
+
+inject_depend_properties(
+    NormalModes,
+    [
+        "nmts",
+        "dt",
+        "mode",
+        "transform_method",
+        "propagator",
+        "nm_freqs",
+        "qnm",
+        "pnm",
+        "fnm",
+        "omegan",
+        "omegan2",
+        "omegak",
+        "omegak2",
+        "o_omegak",
+        "nm_factor",
+        "o_nm_factor",
+        "dynm3",
+        "dynomegak",
+        "prop_pq",
+        "o_prop_pq",
+        "kins",
+        "kin",
+        "kstress",
+        "vspring",
+        "vspring_and_fspring_B",
+        "fspring",
+        "fspringnm",
+    ],
+)
diff --git a/ipi/engine/simulation.py b/ipi/engine/simulation.py
@@ -144,7 +144,7 @@ def __init__(
         self.prng = prng
         self.mode = mode
         self.threading = threads
-        self.safe_stride = safe_stride        
+        self.safe_stride = safe_stride
 
         self.syslist = syslist
         for s in syslist:
@@ -405,4 +405,5 @@ def run(self):
 
         self.rollback = False
 
-inject_depend_properties(Simulation, ["step"])
+
+inject_depend_properties(Simulation, ["step"])
diff --git a/ipi/utils/depend.py b/ipi/utils/depend.py
@@ -44,7 +44,7 @@
     "dcopy",
     "dstrip",
     "depraise",
-    "inject_depend_properties"
+    "inject_depend_properties",
 ]
 
 
@@ -921,10 +921,10 @@ def __setattr__(self, name, value):
         member objects."""
 
         return object.__setattr__(object.__getattribute__(self, "dobj"), name, value)
-    
+
 
 def inject_depend_property(cls, attr_name):
-    private_name = f'_{attr_name}'
+    private_name = f"_{attr_name}"
 
     def getter(self):
         return getattr(self, private_name).__get__(self, self.__class__)
@@ -934,9 +934,10 @@ def setter(self, value):
 
     setattr(cls, attr_name, property(getter, setter))
 
+
 def inject_depend_properties(cls, attr_names):
-        if not isinstance(attr_names, list):
-            attr_names = [attr_names]
-        
-        for attr_name in attr_names:
-            inject_depend_property(cls, attr_name)
+    if not isinstance(attr_names, list):
+        attr_names = [attr_names]
+
+    for attr_name in attr_names:
+        inject_depend_property(cls, attr_name)