Actually commit the typo fixes to the notebook
"source": [
"## General Simulation Data:\n",
"\n",
- "Reports the number of iterations, states, and atoms in each phase. If no checkpoint file is found, the number of atoms is reported as `No Cpt.`"
+ "Reports the number of iterations, states, and atoms in each phase. If no checkpoint file is found, the number of atoms is reported as `No Cpt.` as this information is inferred from the checkpoint file. All other information comes from the analysis file."
]
},
{
"See Something Odd?\n",
"-----------------\n",
"\n",
- "* **The scatter plot Y scale looks large and the equalibrum line is at Iteration 0**\n",
+ "* **The scatter plot Y scale looks large and the equilibrium line is at Iteration 0**\n",
"\n",
- "This normally happens when the energy from index 0 comes from the energy minimzied configuraiton. Because this configuration is technically not from the equilibrium distriubtion, it can have large energies far from the true mean equalibrium energy. This can cause the ``detectEquilibration`` algorithm we use to think that the jump in energy from the minimized to the equilibrated is the scale of the energy fluctuations, and therefore all other fluctuations appear as though they are equlibrated. Look close at the first few points: is there are there a few points which are a large shift on the first few steps? If so, consider removing those first few points from the timeseries.\n",
+ "This normally happens when the energy from index 0 comes from the energy minimized configuration. Because this configuration is technically not from the equilibrium distribution, it can have large energies far from the true mean equilibrium energy. This can cause the ``detectEquilibration`` algorithm we use to think that the jump in energy from the minimized to the equilibrated is the scale of the energy fluctuations, and therefore all other fluctuations appear as though they are equilibrated. Look close at the first few points: is there are there a few points which are a large shift on the first few steps? If so, consider removing those first few points from the timeseries.\n",
"\n",
"*Solution:* Increase ``discard_from_start``\n",
"\n",
- "*Warning:* Some simulations (frequently solvent simulations) are often equilbrated *starting* at iteration 0. These simulations are usually scattered over the entire height of the figure. You should only consider discarding samples if the samples are not distributed over the height of the figure. \n",
+ "*Warning:* Some simulations (frequently solvent simulations) are often equilibrated *starting* at iteration 0. These simulations are usually scattered over the entire height of the figure. You should only consider discarding samples if the samples are not distributed over the height of the figure. \n",
"\n",
"Options\n",
"-------\n",
- "* ``discard_from_start``: Integer. Number of samples to discard from the start of the data. This is helpful for simulations where the minimized energy confiugration throws off the equilibration detection."
+ "* ``discard_from_start``: Integer. Number of samples to discard from the start of the data. This is helpful for simulations where the minimized energy configuration throws off the equilibration detection."
]
},
{
