pseudoatom example

docs/src/molecule.md

@@ -40,6 +40,56 @@ Charges{Cart}(3, [0.7, -0.35, -0.35], Cart([0.0 -1.16 1.16; 0.0 0.0 0.0; 0.0 0.0
 
 To see specific information about the atoms and charges attributes of the molecule see [`Atoms`](@ref) and [`Charges`](@ref).
 
+## Pseudo-Atoms
+
+Sometimes, [e.g. modeling quadrupolar molecules](https://github.com/SimonEnsemble/PorousMaterials.jl/issues/236), it is desirable to add a point charge in a location outside of any atomic nucleus.
+In order to do this, a pseudo-atom label must be chosen (consistent with input data) and added to the global list of atomic masses.
+
+Take the example of using [TraPPE](https://doi.org/10.1002/aic.690470719)-derived charges for the dinitrogen molecule.
+Partial negative charges are assigned to the nitrogen atoms and a corresponding positive charge is placed at a pseudo-atom "dummy site" at the center of mass.
+The atoms and charges input data for this "N2_TraPPE" molecule are like so:
+
+```jldoctest molecule
+dir = joinpath(rc[:paths][:molecules], "N2_TraPPE")
+for file in readdir(dir)
+  @info file data=String(read(joinpath(dir, file)))
+end
+# output
+┌ Info: atoms.csv
+└   data = "atom,x,y,z\r\nN_in_N2,0,0,0.55\r\nPSEUDOATOM_LABEL,0,0,0\r\nN_in_N2,0,0,-0.55"
+┌ Info: charges.csv
+└   data = "q,x,y,z\r\n-0.482,0,0,0.55\r\n0.964,0,0,0\r\n-0.482,0,0,-0.55"
+```
+
+**atoms.csv**
+
+```
+atom,x,y,z
+N_in_N2,0,0,0.55
+PSEUDOATOM_LABEL,0,0,0
+N_in_N2,0,0,-0.55
+```
+
+**charges.csv**
+
+```
+q,x,y,z
+-0.482,0,0,0.55
+0.964,0,0,0
+-0.482,0,0,-0.55
+```
+
+In this example, `PSEUDOATOM_LABEL` is the label for the pseudo-atom; there are several common choices, so make sure you know which one is used in your particular data!
+
+Before loading these data by calling `Molecule`, we need to add our (massless) pseudo-atom to the mass dictionary:
+
+```juliadoctest
+rc[:atomic_masses][:PSEUDOATOM_LABEL] = 0.
+Molecule("N2_TraPPE")
+# ouput
+asdf
+```
+
 ## Moving Molecules
 We can translate and roatate a molecule:
 

test/data/molecules/N2_TraPPE/atoms.csv

@@ -0,0 +1,4 @@
+atom,x,y,z
+N_in_N2,0,0,0.55
+PSEUDOATOM_LABEL,0,0,0
+N_in_N2,0,0,-0.55

test/data/molecules/N2_TraPPE/charges.csv

@@ -0,0 +1,4 @@
+q,x,y,z
+-0.482,0,0,0.55
+0.964,0,0,0
+-0.482,0,0,-0.55