Enable reproducibility

bjmorgan · Nov 5, 2023 · 54734c6 · 54734c6
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commit 54734c6
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diff --git a/docs/source/vasp_d.ipynb b/docs/source/vasp_d.ipynb
@@ -21,7 +21,8 @@
     "import numpy as np\n",
     "from kinisi.analyze import DiffusionAnalyzer\n",
     "from pymatgen.io.vasp import Xdatcar\n",
-    "np.random.seed(42)"
+    "np.random.seed(42)\n",
+    "rng = np.random.RandomState(42)"
    ]
   },
   {
@@ -65,7 +66,7 @@
    "outputs": [],
    "source": [
     "xd = Xdatcar('./example_XDATCAR.gz')\n",
-    "diff = DiffusionAnalyzer.from_Xdatcar(xd, parser_params=p_params, uncertainty_params=b_params)"
+    "diff = DiffusionAnalyzer.from_Xdatcar(xd, parser_params=p_params, uncertainty_params=u_params)"
    ]
   },
   {
@@ -126,7 +127,7 @@
    "metadata": {},
    "source": [
     "It appears that the non-Gaussian parameter does okay at predicting the of the diffusive regime for this example (it is slightly underestimated), therefore we will set the start of the diffusive regime as the `ngp_max` object. \n",
-    "If the non-Gaussian parameter gave an incorrect value, the start of the diffusive regim could be set to, say, 4 ps using the keyword argument of `start_dt=4`. \n",
+    "If the non-Gaussian parameter gave an incorrect value, the start of the diffusive regime could be set to, say, 4 ps using the keyword argument of `start_dt=4`. \n",
     "We can then run the diffusion analysis as follows. "
    ]
   },
@@ -136,7 +137,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "diff.diffusion(0.4)"
+    "diff.diffusion(0.4, diffusion_params={'random_state': rng})"
    ]
   },
   {

diff --git a/docs/source/vasp_dj.ipynb b/docs/source/vasp_dj.ipynb
@@ -23,7 +23,8 @@
     "import numpy as np\n",
     "from kinisi.analyze import JumpDiffusionAnalyzer\n",
     "from pymatgen.io.vasp import Xdatcar\n",
-    "np.random.seed(42)"
+    "np.random.seed(42)\n",
+    "rng = np.random.RandomState(42)"
    ]
   },
   {
@@ -150,7 +151,7 @@
    },
    "outputs": [],
    "source": [
-    "diff.jump_diffusion(5)"
+    "diff.jump_diffusion(5, jump_diffusion_params={'random_state': rng})"
    ]
   },
   {
@@ -166,9 +167,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "tags": []
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "diff.D_J.n, diff.D_J.con_int()"