Finished the bibliography and updated all references

alchemistry/Glossary.ipynb

@@ -33,7 +33,7 @@
    "source": [
     "% This syntax reproducex the {glossary} and {term} directives exactly in the tippy\n",
     "(kb)=\n",
-    "##### Boltzmann's Constant\n",
+    "### Boltzmann's Constant\n",
     "\n",
     "Symbol: $ k_B$\n",
     "\n",
@@ -46,7 +46,7 @@
    "metadata": {},
    "source": [
     "(pot)=\n",
-    "##### Potential Energy\n",
+    "### Potential Energy\n",
     "\n",
     "Symbol: $ U $\n",
     "\n",
@@ -59,7 +59,7 @@
    "metadata": {},
    "source": [
     "(temp)=\n",
-    "##### Temperature\n",
+    "### Temperature\n",
     "\n",
     "Symbol: $ T $\n",
     "\n",
@@ -72,7 +72,7 @@
    "metadata": {},
    "source": [
     "(beta)=\n",
-    "##### $\\beta$\n",
+    "### $\\beta$\n",
     "\n",
     "Inverse Boltzmann constant times temperature: $\\beta=(k_BT)^{-1}$\n",
     "\n",
@@ -85,7 +85,7 @@
    "metadata": {},
    "source": [
     "(p)=\n",
-    "##### Pressure\n",
+    "### Pressure\n",
     "\n",
     "Symbol: $P$"
    ]
@@ -96,7 +96,7 @@
    "metadata": {},
    "source": [
     "(rpot)=\n",
-    "##### Reduced Potential\n",
+    "### Reduced Potential\n",
     "\n",
     "Symbol: $u$\n",
     "\n",
@@ -111,7 +111,7 @@
    "metadata": {},
    "source": [
     "(v)=\n",
-    "##### Volume (traditional)\n",
+    "### Volume (traditional)\n",
     "Symbol: $V$\n",
     "\n",
     "**CAUTION:** Volume in this sense is the kind you think of with box size. Not to be confused with the *Phase Space Volume.* This particular volume is not often considered by itself and should only show up on this site within $PV$ terms, or *NVT*."
@@ -123,7 +123,7 @@
    "metadata": {},
    "source": [
     "(gamma)=\n",
-    "##### Phase Space Volume\n",
+    "### Phase Space Volume\n",
     "Symbol: $\\Gamma$\n",
     "\n",
     "Total set of coordinates and momenta where the system has a nonzero probability of being found\n",
@@ -137,7 +137,7 @@
    "metadata": {},
    "source": [
     "(q)=\n",
-    "##### Coordinates and Momentum, collective\n",
+    "### Coordinates and Momentum, collective\n",
     "Symbol: $q$ or $\\vec{q}$\n",
     "\n",
     "Can also be seen as $\\mathbf{x}$, $\\mathbf{\\vec{x}}$, and a number of other terms in literature."
@@ -149,7 +149,7 @@
    "metadata": {},
    "source": [
     "(lj)=\n",
-    "##### Lennard-Jones Parameters\n",
+    "### Lennard-Jones Parameters\n",
     "Symbols: $\\epsilon$ and $\\sigma$\n",
     "\n",
     "Lennard-Jones parameters for the well depth and the radius of the point particle respectively."
@@ -161,7 +161,7 @@
    "metadata": {},
    "source": [
     "(part)=\n",
-    "##### Partition Function\n",
+    "### Partition Function\n",
     "Symbol: $Q$\n",
     "\n",
     "Partition function for the canonical or NVT ensemble, but sometimes also signifies an arbitrary partition function of any ensemble. <br/>$Q=\\int_{\\Gamma}e^{-\\beta U (\\vec{q})}\\,\\mathrm{d}\\vec{q}$\n",
@@ -175,7 +175,7 @@
    "metadata": {},
    "source": [
     "(tau)=\n",
-    "###### Autocorrelation Time\n",
+    "#### Autocorrelation Time\n",
     "Symbol: $\\tau$\n",
     "\n",
     "[Autocorrelation time](correlation)"
@@ -187,7 +187,7 @@
    "metadata": {},
    "source": [
     "(nvt)=\n",
-    "##### NVT\n",
+    "### NVT\n",
     "System held at constant **N**umber of particles, **V**olume, and **T**emperature. Free energy calculations performed in this ensemble yield Helmholtz free energies."
    ]
   },
@@ -197,7 +197,7 @@
    "metadata": {},
    "source": [
     "(npt)=\n",
-    "##### NPT\n",
+    "### NPT\n",
     "System held at constant **N**umber of particles, **P**ressue, and **T**emperature. Free energy calculations performed in this ensemble yield Gibbs free energies."
    ]
   },
@@ -206,19 +206,19 @@
    "id": "da54f896-67a4-428a-ae3d-24aec0dbb2bc",
    "metadata": {},
    "source": [
-    "##### TI\n",
+    "### TI\n",
     "[Thermodynamic Integration](TI)\n",
     "\n",
     "\n",
-    "##### EXP\n",
+    "### EXP\n",
     "[Exponential Averaging](exp_avg)\n",
     "Also called \"free energy perturbation\" and the \"Zwanzig relationship.\"\n",
     "\n",
-    "##### BAR\n",
+    "### BAR\n",
     "[Bennett Acceptance Ratio](BAR)\n",
     "\n",
     "\n",
-    "##### MBAR\n",
+    "### MBAR\n",
     "[Multistate Bennett Acceptance Ratio](fundamentals/MBAR)"
    ]
   },
@@ -228,7 +228,7 @@
    "metadata": {},
    "source": [
     "(boltz_weight)=\n",
-    "##### Boltzmann Weight\n",
+    "### Boltzmann Weight\n",
     "The probability of a microstate $\\vec{q}$, defined $e^{-u(\\vec{q})}/Q$, where $u(\\vec{q})$ is the reduced potential.  It can also refer to simply $e^{-u(\\vec{q})}$, although this is not a full weight because it is not normalized by the partition function."
    ]
   },
@@ -238,7 +238,7 @@
    "metadata": {},
    "source": [
     "(state)=\n",
-    "##### State \n",
+    "### State \n",
     "\n",
     "Variable: $K$ \n",
     "\n",
@@ -251,7 +251,7 @@
    "metadata": {},
    "source": [
     "(lambda)=\n",
-    "##### $\\lambda$\n",
+    "### $\\lambda$\n",
     "Alchemical variable, thermodynamic path coordinate\n",
     "\n",
     "The most common symbol for denoting/tracking the progress along some alchemical pathway. Since most free energy calculations involve an [alchemical thermodynamic path](Intermediate_States), [this site](<welcome>) was named accordingly."
@@ -263,7 +263,7 @@
    "metadata": {},
    "source": [
     "(annihilation)=\n",
-    "##### Annihilating or Annihilated\n",
+    "### Annihilating or Annihilated\n",
     "The act of removing ALL of an atoms interactions with the system, this includes the molecule's interactions with itself.\n",
     "\n",
     "Intermolecular force = OFF, Intramolecular forces = OFF. Also known as disappeared or destroyed. Not to be confused with \"decoupling.\""
@@ -275,7 +275,7 @@
    "metadata": {},
    "source": [
     "(decoupling)=\n",
-    "##### Decoupling\n",
+    "### Decoupling\n",
     "The act of removing an atom or molecules interactions with its surroundings ONLY; the interactions between the molecule itself remain active.\n",
     "\n",
     "Intermolecular force = OFF, Intramolecular forces = ON. Not to be confused with \"annihilation.\""