Merge pull request #46 from rsdefever/add/radii

Add Bondi and Alvarez Radii

docs/index.md

@@ -48,7 +48,7 @@ two-character element symbol. If not, it then checks if the string
 matches a full element name. The function returns the matching element.
 If there is no matching element, an `ElementError` is raised.
 
-Each `Element` has four attributes which can be accessed
+Each `Element` has six attributes which can be accessed
 (as demonstrated below for ``na``):
 
 ```python
@@ -58,6 +58,8 @@ na.name
 na.symbol
 na.atomic_number
 na.mass
+na.radius_bondi
+na.radius_alvarez
 ```
 
 The elements can also be accessed by symbol as follows:

docs/sources.md

@@ -1,4 +1,4 @@
-## Atomic weights source
+## Atomic weights
 
 Atomic weights of the elements 2013 (IUPAC Technical Report), Juris Meija, Tyler B. Coplen, Michael Berglund, Willi A. Brand, Paul De Bièvre, Manfred Gröning, Norman E. Holden, Johanna Irrgeher, Robert D. Loss, Thomas Walczyk and Thomas Prohaska
 
@@ -20,7 +20,7 @@ The `bibtex` entry for the reference is:
 	      url = "https://www.degruyter.com/view/journals/pac/88/3/article-p265.xml"
 	}
 
-## Details
+### Details
 
 The values for `Element.mass` were taken from the abridged standard atomic weights (Table 2), with the following exceptions:
 
@@ -30,4 +30,63 @@ The values for `Element.mass` were taken from the abridged standard atomic weigh
 These choices follow the convention used for the [NIST periodic table](
 https://www.nist.gov/pml/periodic-table-elements).
 
+## Atomic radius
+We provide two options for the van der Waals radius, the Bondi radii, and the Alvarez
+radii.
+
+### Bondi radii
+
+The values were taken from Tables I and XIV of 1964 paper by Bondi.
+Values for Hg, Cd, and Zn came from Table I of the 1966 paper. 
+
+J. Phys. Chem. 1964; 68(3): 441-451, doi: 10.1021/j100785a001
+
+J. Phys. Chem. 1966; 70(9): 3006-3007, doi: 10.1021/j100881a503
+
+The `bibtex` entries are:
+
+    @article{Bondi:1964:JPhysChem,
+      title={van der Waals volumes and radii},
+      author={Bondi, A van},
+      journal={The Journal of physical chemistry},
+      volume={68},
+      number={3},
+      pages={441--451},
+      year={1964},
+      publisher={ACS Publications}
+    }
+    @article{Bondi:1966:JPhysChem,
+      title={Van der Waals volumes and radii of metals in covalent compounds},
+      author={Bondi, A},
+      journal={The Journal of Physical Chemistry},
+      volume={70},
+      number={9},
+      pages={3006--3007},
+      year={1966},
+      publisher={ACS Publications}
+    }
+
+### Alvarez radii
+
+Values were taken from Table 1.
+
+Dalton Trans. 2013; 42: 8617-8636, doi: 10.1039/C3DT50599E
+
+The `bibtex` entry for the reference is:
+
+    @article{Alvarez:2013:Dalton,
+    author ="Alvarez, Santiago",
+    title  ="A cartography of the van der Waals territories",
+    journal  ="Dalton Trans.",
+    year  ="2013",
+    volume  ="42",
+    issue  ="24",
+    pages  ="8617-8636",
+    publisher  ="The Royal Society of Chemistry",
+    doi  ="10.1039/C3DT50599E",
+    url  ="http://dx.doi.org/10.1039/C3DT50599E",
+    }
+
+
+
 

ele/element.py

@@ -18,7 +18,7 @@
 )
 
 
-class Element(namedtuple("Element", "atomic_number, name, symbol, mass")):
+class Element(namedtuple("Element", "atomic_number, name, symbol, mass, radius_bondi, radius_alvarez")):
     """Chemical element object
 
     Template to create a chemical element.
@@ -258,6 +258,8 @@ def infer_element_from_string(string):
             name=element_properties["name"],
             symbol=element_properties["symbol"],
             mass=element_properties["mass"],
+            radius_bondi=element_properties["radius_bondi"],
+            radius_alvarez=element_properties["radius_alvarez"],
         )
     )
 

ele/lib/README.md

@@ -1,12 +1,12 @@
+A `.bib` file with all the references is provided in this directory.
+
 ## Atomic weights source
 
 Atomic weights of the elements 2013 (IUPAC Technical Report), Juris Meija, Tyler B. Coplen, Michael Berglund, Willi A. Brand, Paul De Bièvre, Manfred Gröning, Norman E. Holden, Johanna Irrgeher, Robert D. Loss, Thomas Walczyk and Thomas Prohaska
 
 Pure Appl. Chem. 2016; 88(3): 265-291, doi: 10.1515/pac-2015-0305
 
-A `.bib` file with the reference is also present in this directory.
-
-## Details
+### Details
 
 The values for `Element.mass` were taken from the abridged standard atomic weights (Table 2), with the following exceptions:
 
@@ -16,4 +16,22 @@ The values for `Element.mass` were taken from the abridged standard atomic weigh
 These choices follow the convention used for the [NIST periodic table](
 https://www.nist.gov/pml/periodic-table-elements).
 
+## Atomic radius
+We provide two options for the van der Waals radius, the Bondi radii, and the Alvarez
+radii.
+
+### Bondi radii
+
+The values were taken from Tables I and XIV of 1964 paper by Bondi.
+Values for Hg, Cd, and Zn came from Table I of the 1966 paper. 
+
+J. Phys. Chem. 1964; 68(3): 441-451, doi: 10.1021/j100785a001
+
+J. Phys. Chem. 1966; 70(9): 3006-3007, doi: 10.1021/j100881a503
+
+
+### Alvarez radii
+
+Values were taken from Table 1.
 
+Dalton Trans. 2013; 42: 8617-8636, doi: 10.1039/C3DT50599E