replace calls to equilibrium with Workspace

materialsgenomefoundation · Jul 25, 2024 · b3a992c · b3a992c
1 parent d030474
commit b3a992c
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Showing 16 changed files with 326 additions and 481 deletions.
diff --git a/examples/01_Binary_Precipitation.ipynb b/examples/01_Binary_Precipitation.ipynb
@@ -20,7 +20,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -45,7 +45,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -78,7 +78,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -122,7 +122,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 4,
    "metadata": {
     "tags": []
    },
@@ -146,7 +146,7 @@
       "\tbeta\t0.000e+00\t\t0.0000\t\t0.0000e+00\t5.7737e+03\n",
       "\n",
       "N\tTime (s)\tSim Time (s)\tTemperature (K)\tMatrix Comp\n",
-      "3675\t1.8e+06\t\t36.6\t\t723\t\t0.0126\n",
+      "3675\t1.8e+06\t\t14.3\t\t723\t\t0.0126\n",
       "\n",
       "\tPhase\tPrec Density (#/m3)\tVolume Frac\tAvg Radius (m)\tDriving Force (J/mol)\n",
       "\tbeta\t1.374e+22\t\t1.5504\t\t6.1126e-09\t3.2902e+02\n",
@@ -171,7 +171,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {

diff --git a/examples/02_Multicomponent_Precipitation.ipynb b/examples/02_Multicomponent_Precipitation.ipynb
diff --git a/examples/03_Multiphase_Precipitation.ipynb b/examples/03_Multiphase_Precipitation.ipynb
diff --git a/examples/04_Precipitation_with_Elastic_Energy.ipynb b/examples/04_Precipitation_with_Elastic_Energy.ipynb
@@ -128,7 +128,7 @@
       "\tCU4TI\t0.000e+00\t\t0.0000\t\t0.0000e+00\t1.9660e+03\n",
       "\n",
       "N\tTime (s)\tSim Time (s)\tTemperature (K)\tMatrix Comp\n",
-      "4571\t1.0e+05\t\t78.2\t\t623\t\t0.1757\n",
+      "4571\t1.0e+05\t\t29.3\t\t623\t\t0.1757\n",
       "\n",
       "\tPhase\tPrec Density (#/m3)\tVolume Frac\tAvg Radius (m)\tDriving Force (J/mol)\n",
       "\tCU4TI\t1.455e+23\t\t9.3695\t\t5.1198e-09\t1.2258e+02\n",
@@ -154,7 +154,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {

diff --git a/examples/05_Strength_Modeling.ipynb b/examples/05_Strength_Modeling.ipynb
diff --git a/examples/06_Single_Phase_Diffusion.ipynb b/examples/06_Single_Phase_Diffusion.ipynb
@@ -115,10 +115,10 @@
      "text": [
       "Iteration\tSim Time (h)\tRun time (s)\n",
       "0\t\t0.0e+00\t\t0.0\n",
-      "100\t\t2.9e+01\t\t5.2\n",
-      "200\t\t5.7e+01\t\t9.8\n",
-      "300\t\t8.6e+01\t\t13.1\n",
-      "349\t\t1.0e+02\t\t14.1\n"
+      "100\t\t2.9e+01\t\t2.8\n",
+      "200\t\t5.7e+01\t\t5.3\n",
+      "300\t\t8.6e+01\t\t7.1\n",
+      "349\t\t1.0e+02\t\t7.6\n"
      ]
     }
    ],
@@ -138,7 +138,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {

diff --git a/examples/07_Homogenization_Model.ipynb b/examples/07_Homogenization_Model.ipynb
diff --git a/examples/08_Model_Coupling.ipynb b/examples/08_Model_Coupling.ipynb
diff --git a/examples/09_Thermodynamics.ipynb b/examples/09_Thermodynamics.ipynb
@@ -156,7 +156,7 @@
     {
      "data": {
       "text/plain": [
-       "<matplotlib.legend.Legend at 0x2bf515a4ac0>"
+       "<matplotlib.legend.Legend at 0x1d70c1b50a0>"
       ]
      },
      "execution_count": 5,
@@ -226,7 +226,7 @@
     {
      "data": {
       "text/plain": [
-       "<matplotlib.legend.Legend at 0x2bf55cfadf0>"
+       "<matplotlib.legend.Legend at 0x1d7104ff880>"
       ]
      },
      "execution_count": 6,
@@ -312,7 +312,7 @@
     {
      "data": {
       "text/plain": [
-       "<matplotlib.legend.Legend at 0x2bf581c5c70>"
+       "<matplotlib.legend.Legend at 0x1d712e1dc40>"
       ]
      },
      "execution_count": 7,
@@ -403,7 +403,7 @@
     {
      "data": {
       "text/plain": [
-       "<matplotlib.legend.Legend at 0x2bf58482610>"
+       "<matplotlib.legend.Legend at 0x1d712e1de80>"
       ]
      },
      "execution_count": 8,

diff --git a/examples/10_Surrogates.ipynb b/examples/10_Surrogates.ipynb
diff --git a/examples/12_Custom_Iterators.ipynb b/examples/12_Custom_Iterators.ipynb
@@ -75,7 +75,7 @@
       "\tbeta\t0.000e+00\t\t0.0000\t\t0.0000e+00\t5.7737e+03\n",
       "\n",
       "N\tTime (s)\tSim Time (s)\tTemperature (K)\tMatrix Comp\n",
-      "3831\t1.8e+06\t\t25.9\t\t723\t\t0.0126\n",
+      "3831\t1.8e+06\t\t5.4\t\t723\t\t0.0126\n",
       "\n",
       "\tPhase\tPrec Density (#/m3)\tVolume Frac\tAvg Radius (m)\tDriving Force (J/mol)\n",
       "\tbeta\t1.395e+22\t\t1.5504\t\t6.0887e-09\t3.2954e+02\n",
@@ -140,14 +140,6 @@
    "execution_count": 4,
    "metadata": {},
    "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "C:\\Users\\ury3\\OneDrive - LLNL\\Documents\\Projects\\U-C Modeling\\kawin-development\\kawin\\kawin\\precipitation\\KWNBase.py:1162: RuntimeWarning: divide by zero encountered in scalar divide\n",
-      "  return np.exp(-tau / t)\n"
-     ]
-    },
     {
      "name": "stdout",
      "output_type": "stream",
@@ -159,7 +151,7 @@
       "\tbeta\t0.000e+00\t\t0.0000\t\t0.0000e+00\t5.7737e+03\n",
       "\n",
       "N\tTime (s)\tSim Time (s)\tTemperature (K)\tMatrix Comp\n",
-      "3751\t1.8e+06\t\t39.0\t\t723\t\t0.0126\n",
+      "3751\t1.8e+06\t\t9.1\t\t723\t\t0.0126\n",
       "\n",
       "\tPhase\tPrec Density (#/m3)\tVolume Frac\tAvg Radius (m)\tDriving Force (J/mol)\n",
       "\tbeta\t1.386e+22\t\t1.5505\t\t6.0962e-09\t3.2700e+02\n",
@@ -188,7 +180,7 @@
     {
      "data": {
       "text/plain": [
-       "<matplotlib.legend.Legend at 0x243f92e8400>"
+       "<matplotlib.legend.Legend at 0x12d50fdbc10>"
       ]
      },
      "execution_count": 5,

diff --git a/kawin/diffusion/Homogenization.py b/kawin/diffusion/Homogenization.py
@@ -84,21 +84,10 @@ def _newEqCalc(self, x, T):
         '''
         Calculates equilibrium and returns a CompositionSet
         '''
-        eq = self.therm.getEq(x, T, 0, self.phases)
-        state_variables = np.array([0, 1, 101325, T], dtype=np.float64)
-        stable_phases = eq.Phase.values.ravel()
-        phase_amounts = eq.NP.values.ravel()
-        comp = []
-        for p in stable_phases:
-            if p != '':
-                idx = np.where(stable_phases == p)[0]
-                cs, misc = self.therm._createCompositionSet(eq, state_variables, p, phase_amounts, idx)
-                comp.append(cs)
-
-        if len(comp) == 0:
-            comp = None
-
-        return self.therm.getLocalEq(x, T, 0, self.phases, comp)
+        wks = self.therm.getEq(x, T, 0, self.phases)
+        chemical_potentials = np.squeeze(wks.eq.MU)
+        composition_sets = wks.get_composition_sets()
+        return chemical_potentials, composition_sets
 
     def updateCompSets(self, xarray):
         '''
@@ -127,18 +116,14 @@ def updateCompSets(self, xarray):
             if self.cache:
                 hashValue = self._getHash(xarray[:,i], self.T[i])
                 if hashValue not in self.hashTable:
-                    result, comp = self._newEqCalc(xarray[:,i], self.T[i])
-                    #result, comp = self.therm.getLocalEq(xarray[:,i], self.T, 0, self.phases, self.compSets[i])
-                    self.hashTable[hashValue] = (result, comp, None)
+                    chemical_potentials, comp = self._newEqCalc(xarray[:,i], self.T[i])
+                    self.hashTable[hashValue] = (chemical_potentials, comp, None)
                 else:
-                    result, comp, _ = self.hashTable[hashValue]
-                results, self.compSets[i] = copy.copy(result), copy.copy(comp)
+                    chemical_potentials, comp, _ = self.hashTable[hashValue]
+                chemical_potentials, self.compSets[i] = copy.copy(chemical_potentials), copy.copy(comp)
             else:
-                if self.compSets[i] is None:
-                    results, self.compSets[i] = self._newEqCalc(xarray[:,i], self.T[i])
-                else:
-                    results, self.compSets[i] = self.therm.getLocalEq(xarray[:,i], self.T[i], 0, self.phases, self.compSets[i])
-            self.mu[:,i] = results.chemical_potentials[self.unsortIndices]
+                chemical_potentials, self.compSets[i] = self._newEqCalc(xarray[:,i], self.T[i])
+            self.mu[:,i] = chemical_potentials[self.unsortIndices]
             cs_phases = [cs.phase_record.phase_name for cs in self.compSets[i]]
             for p in range(len(cs_phases)):
                 parray[self._getPhaseIndex(cs_phases[p]), i] = self.compSets[i][p].NP

diff --git a/kawin/tests/test_diffusion.py b/kawin/tests/test_diffusion.py
@@ -309,18 +309,18 @@ def test_homogenization_dxdt():
     dt = m.getDt(dxdt)
 
     #Index 5
-    ind5, vals5 = 5, np.array([-1.592463e-9, 1.211067e-9])
+    ind5, vals5 = 5, np.array([-1.581478e-9, 1.212876e-9])
 
     #Index 10
-    ind10, vals10 = 10, np.array([-9.751858e-10, 1.702190e-9])
+    ind10, vals10 = 10, np.array([-9.722631e-10, 1.703447e-9])
 
     #Index 15
-    ind15, vals15 = 15, np.array([-4.728854e-10, 8.590127e-10])
+    ind15, vals15 = 15, np.array([-4.720562e-10, 8.600518e-10])
 
     assert_allclose(dxdt[0][:,ind5], vals5, atol=0, rtol=1e-3)
     assert_allclose(dxdt[0][:,ind10], vals10, atol=0, rtol=1e-3)
     assert_allclose(dxdt[0][:,ind15], vals15, atol=0, rtol=1e-3)
-    assert_allclose(dt, 61865.352193, rtol=1e-3)
+    assert_allclose(dt, 62271.050081, rtol=1e-3)