[CHNOSZ-commits] r634 - in pkg/CHNOSZ: . inst man vignettes

Sat Feb 20 00:38:57 CET 2021

Author: jedick
Date: 2021-02-20 00:38:57 +0100 (Sat, 20 Feb 2021)
New Revision: 634

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/TODO
   pkg/CHNOSZ/man/diagram.Rd
   pkg/CHNOSZ/vignettes/multi-metal.Rmd
Log:
multi-metal.Rmd: Update DFT energies from Materials Project


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================

--- pkg/CHNOSZ/DESCRIPTION	2021-02-19 07:11:24 UTC (rev 633)
+++ pkg/CHNOSZ/DESCRIPTION	2021-02-19 23:38:57 UTC (rev 634)
@@ -1,6 +1,6 @@
-Date: 2021-02-19
+Date: 2021-02-20
 Package: CHNOSZ
-Version: 1.4.0-4
+Version: 1.4.0-5
 Title: Thermodynamic Calculations and Diagrams for Geochemistry
 Authors at R: c(
     person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),

Modified: pkg/CHNOSZ/inst/TODO
===================================================================
--- pkg/CHNOSZ/inst/TODO	2021-02-19 07:11:24 UTC (rev 633)
+++ pkg/CHNOSZ/inst/TODO	2021-02-19 23:38:57 UTC (rev 634)
@@ -78,3 +78,5 @@
 - Don't use data(thermo) in demo Shiny app (citrate)
 
 - Check all mineral abbreviations in Berman_cr.csv.
+
+- Fix transparency issues in demo/mosaic.R

Modified: pkg/CHNOSZ/man/diagram.Rd
===================================================================
--- pkg/CHNOSZ/man/diagram.Rd	2021-02-19 07:11:24 UTC (rev 633)
+++ pkg/CHNOSZ/man/diagram.Rd	2021-02-19 23:38:57 UTC (rev 634)
@@ -188,7 +188,6 @@
   For 2-D diagrams, \code{plotvals} corresponds to the values of affinity (from \code{eout$values}) divided by the respective balancing coefficients for each species.
   For 2-D diagrams, the output also contains the matrices \code{predominant}, which identifies the predominant species in \code{eout$species} at each grid point, and \code{predominant.values}, which has the affinities of the predominant species divided by the balancing coefficients (if \code{eout} is the output of \code{affinity}) or the activities of the predominant species (if \code{eout} is the output of \code{equilibrate}).
   The rows and columns of these matrices correspond to the \emph{x} and \emph{y} variables, respectively.
-  Finally, the output for 2-D diagrams contains a \code{lines} component, giving the \emph{x} and \emph{y} coordinates of the field boundaries computed using \code{\link{contourLines}}; the values are padded to equal length with NAs to faciliate exporting the results using \code{\link{write.csv}}.
 }
 
 \seealso{ 

Modified: pkg/CHNOSZ/vignettes/multi-metal.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/multi-metal.Rmd	2021-02-19 07:11:24 UTC (rev 633)
+++ pkg/CHNOSZ/vignettes/multi-metal.Rmd	2021-02-19 23:38:57 UTC (rev 634)
@@ -146,9 +146,11 @@
 # m = MPRester("USER_API_KEY")
 # m.query(criteria={"task_id": "mp-1279742"}, properties=["formation_energy_per_atom"])
 # mp-13, mp-1279742, mp-19306, mp-19770
-Fe.cr <- c(Fe = 0, FeO = -1.72803, Fe3O4 = -1.85868, Fe2O3 = -1.90736)  # 20201109
+#Fe.cr <- c(Fe = 0, FeO = -1.72803, Fe3O4 = -1.85868, Fe2O3 = -1.90736)  # 20201109
+Fe.cr <- c(Fe = 0, FeO = -1.72768, Fe3O4 = -1.85838, Fe2O3 = -1.90708)  # 20210219
 # mp-146, mp-18937, mp-1275946, mp-19094, mp-756395, mp-25279
-V.cr <- c(V = 0, V2O3 = -2.52849, V3O5 = -2.52574, VO2 = -2.48496, V3O7 = -2.32836, V2O5 = -2.29524)  # 20201109
+#V.cr <- c(V = 0, V2O3 = -2.52849, V3O5 = -2.52574, VO2 = -2.48496, V3O7 = -2.32836, V2O5 = -2.29524)  # 20201109
+V.cr <- c(V = 0, V2O3 = -2.52787, V3O5 = -2.52516, VO2 = -2.48447, V3O7 = -2.32789, V2O5 = -2.29480)  # 20210219
 
 # Convert formation energies from eV / atom to eV / molecule
 natom.Fe <- sapply(makeup(names(Fe.cr)), sum)
@@ -203,7 +205,8 @@
 
 # Formation energies (eV / atom) for bimetallic solids from Materials API
 # mp-1335, mp-1079399, mp-866134, mp-558525, mp-504509 (triclinic FeVO4)
-FeV.cr <- c(FeV = -0.12928, FeV3 = -0.17128, Fe3V = -0.12854, Fe2V4O13 = -2.23833, FeVO4 = -1.75611)  # 20201109
+#FeV.cr <- c(FeV = -0.12928, FeV3 = -0.17128, Fe3V = -0.12854, Fe2V4O13 = -2.23833, FeVO4 = -1.75611)  # 20201109
+FeV.cr <- c(FeV = -0.12815, FeV3 = -0.17114, Fe3V = -0.12832, Fe2V4O13 = -2.23967, FeVO4 = -1.75573)  # 20210219
 # Convert energies and add to OBIGT
 natom.FeV <- sapply(makeup(names(FeV.cr)), sum)
 FeV.cr <- FeV.cr * natom.FeV
@@ -378,11 +381,10 @@
 eV_mol <- J_mol / 1.602176634e-19
 eV_atom <- eV_mol / 6.02214076e23 / 6
 round(eV_atom, 3)
-stopifnot(round(eV_atom, 3) == 0.413)
+stopifnot(round(eV_atom, 3) == 0.415)
 ```
 
-This is nearly equal to the value for the energy above the hull for [triclinic FeVO~4~ on the MP website](https://materialsproject.org/materials/mp-504509/).
-(As of 2020-11-09, the energy above hull / atom listed on the MP website is 0.415 eV.)
+This is equal to the value for the energy above the hull / atom for [triclinic FeVO~4~ on the MP website](https://materialsproject.org/materials/mp-504509/) (0.415 eV, accessed on 2020-11-09 and 2021-02-19).
 This shows that we successfully made a round trip starting with the input formation energies (eV/atom) from the Materials API, to standard Gibbs energy (J/mol) in the OBIGT database, and back out to energy above the hull (eV/atom).
 
 The concept of using the stable minerals and aqueous species to calculate reaction energetics is formalized in the `mosaic()` function, which is described next.
@@ -878,6 +880,6 @@
 ## Document History
 
 * 2020-07-15 First version.
-* 2021-02-19 Improve mineral abbreviations and placement of labels.
+* 2021-02-20 Improve mineral abbreviations and placement of labels; use updated DFT energies from Materials Project.
 
 ## References

