Merge pull request #19 from bjmorgan/test

Revert to sampling all data (using the minimum number of non-overlapping samples)
bjmorgan · Jan 16, 2023 · bdb21aa · bdb21aa
2 parents d741679 + 51f5fcd
commit bdb21aa
Show file tree

Hide file tree

Showing 13 changed files with 559 additions and 116 deletions.
diff --git a/docs/source/arrhenius_t.ipynb b/docs/source/arrhenius_t.ipynb
@@ -112,7 +112,7 @@
    "id": "c204d962-a8f8-4989-9d84-e9a6ae52730f",
    "metadata": {},
    "source": [
-    "The list of diffusion coefficient objects (which are `uravu.distribution.Distribution` type objects) and array of temperatures can then be passed to the `kinisi.arrhenius.StandardArrhenius` class. "
+    "The list of diffusion coefficient objects (which are `uravu.distribution.Distribution` type objects) and array of temperatures can then be passed to the `kinisi.arrhenius.StandardArrhenius` class, where we use the `bounds` keyword argument to give a minimum and maximum value for the activation energy and preexponential factor."
    ]
   },
   {
@@ -122,7 +122,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "s = StandardArrhenius(temperatures, D)"
+    "s = StandardArrhenius(temperatures, D, bounds=((0.01, 0.2), (1e-5, 1e-1)))"
    ]
   },
   {
@@ -140,7 +140,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "s.max_likelihood('diff_evo')"
+    "s.max_likelihood('mini')"
    ]
   },
   {

diff --git a/docs/source/vasp_d.ipynb b/docs/source/vasp_d.ipynb
@@ -125,7 +125,8 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "It appears that the non-Gaussian parameter does not accurately predict the start of the diffusive regime for this example, so we will set the start of the diffusive regime to be 4 ps using the keyword argument of `dt_skip=4`. \n",
+    "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 `use_ngp` keyword argument to `True`. \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 `dt_skip=4`. \n",
     "The `d_params` dictionary defines parameters about the diffusion estimation, documented in the [diffusion module](https://kinisi.readthedocs.io/en/latest/diffusion.html#kinisi.diffusion.MSDBootstrap). "
    ]
   },
@@ -135,7 +136,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "d_params = {'dt_skip': 4}"
+    "d_params = {'use_ngp': True}"
    ]
   },
   {