[CHNOSZ-commits] r162 - in pkg/CHNOSZ: . R inst man src vignettes
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noreply at r-forge.r-project.org
Sat Feb 18 15:18:11 CET 2017
Author: jedick
Date: 2017-02-18 15:18:11 +0100 (Sat, 18 Feb 2017)
New Revision: 162
Added:
pkg/CHNOSZ/src/init.c
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/NAMESPACE
pkg/CHNOSZ/R/water.R
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/man/util.water.Rd
pkg/CHNOSZ/vignettes/anintro.Rmd
pkg/CHNOSZ/vignettes/eos-regress.Rmd
Log:
register native routines
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2017-02-18 10:15:38 UTC (rev 161)
+++ pkg/CHNOSZ/DESCRIPTION 2017-02-18 14:18:11 UTC (rev 162)
@@ -1,6 +1,6 @@
Date: 2017-02-18
Package: CHNOSZ
-Version: 1.0.8-51
+Version: 1.0.8-52
Title: Chemical Thermodynamics and Activity Diagrams
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
Modified: pkg/CHNOSZ/NAMESPACE
===================================================================
--- pkg/CHNOSZ/NAMESPACE 2017-02-18 10:15:38 UTC (rev 161)
+++ pkg/CHNOSZ/NAMESPACE 2017-02-18 14:18:11 UTC (rev 162)
@@ -1,8 +1,9 @@
-# Export all names
-exportPattern(".")
+# Export all names except those beginning with F_
+# (so we don't export F_h2o92 created below)
+exportPattern("^([^F]|F($|[^_])).*")
# Load shared objects
-useDynLib(CHNOSZ)
+useDynLib(CHNOSZ, .registration = TRUE, .fixes = "F_")
# Imports from default packages
importFrom("grDevices", "dev.cur", "dev.off", "extendrange",
@@ -19,4 +20,3 @@
# Imports from colorspace
importFrom("colorspace", "diverge_hcl")
-
Modified: pkg/CHNOSZ/R/water.R
===================================================================
--- pkg/CHNOSZ/R/water.R 2017-02-18 10:15:38 UTC (rev 161)
+++ pkg/CHNOSZ/R/water.R 2017-02-18 14:18:11 UTC (rev 162)
@@ -83,8 +83,8 @@
rho.out[i] <- NA
} else {
# now to the actual calculations
- H2O <- .Fortran("H2O92", as.integer(specs), as.double(states),
- as.double(rep(0, 46)), as.integer(0), PACKAGE="CHNOSZ")
+ H2O <- .Fortran(F_h2o92, as.integer(specs), as.double(states),
+ as.double(rep(0, 46)), as.integer(0))
# errors
err.out[i] <- H2O[[4]]
# density of two states
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2017-02-18 10:15:38 UTC (rev 161)
+++ pkg/CHNOSZ/inst/NEWS 2017-02-18 14:18:11 UTC (rev 162)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.8-51 (2017-02-18)
+CHANGES IN CHNOSZ 1.0.8-52 (2017-02-18)
---------------------------------------
DOCUMENTATION:
Modified: pkg/CHNOSZ/man/util.water.Rd
===================================================================
--- pkg/CHNOSZ/man/util.water.Rd 2017-02-18 10:15:38 UTC (rev 161)
+++ pkg/CHNOSZ/man/util.water.Rd 2017-02-18 14:18:11 UTC (rev 162)
@@ -73,7 +73,7 @@
\references{
- Archer, D. G. and Wang, P. M. (1990) The dielectric constant of water and Debye-Hückel limiting law slopes. \emph{J. Phys. Chem. Ref. Data} \bold{19}, 371--411. \url{https://www.nist.gov/data/PDFfiles/jpcrd383.pdf}
+ Archer, D. G. and Wang, P. M. (1990) The dielectric constant of water and Debye-Hückel limiting law slopes. \emph{J. Phys. Chem. Ref. Data} \bold{19}, 371--411. \url{https://srd.nist.gov/JPCRD/jpcrd383.pdf}
Wagner, W. and Pruß, A. (2002) The IAPWS formulation 1995 for the thermodynamic properties of ordinary water substance for general and scientific use. \emph{J. Phys. Chem. Ref. Data} \bold{31}, 387--535. \url{http://dx.doi.org/10.1063/1.1461829}
Added: pkg/CHNOSZ/src/init.c
===================================================================
--- pkg/CHNOSZ/src/init.c (rev 0)
+++ pkg/CHNOSZ/src/init.c 2017-02-18 14:18:11 UTC (rev 162)
@@ -0,0 +1,17 @@
+#include <R_ext/RS.h>
+#include <stdlib.h> // for NULL
+#include <R_ext/Rdynload.h>
+
+/* .Fortran calls */
+extern void F77_NAME(h2o92)(void *, void *, void *, void *);
+
+static const R_FortranMethodDef FortranEntries[] = {
+ {"h2o92", (DL_FUNC) &F77_NAME(h2o92), 4},
+ {NULL, NULL, 0}
+};
+
+void R_init_CHNOSZ(DllInfo *dll)
+{
+ R_registerRoutines(dll, NULL, NULL, FortranEntries, NULL);
+ R_useDynamicSymbols(dll, FALSE);
+}
Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd 2017-02-18 10:15:38 UTC (rev 161)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd 2017-02-18 14:18:11 UTC (rev 162)
@@ -1795,7 +1795,7 @@
Without additional information, there is often no clear strategy for "fixing" these entries, and they are provided as is.
```{marginfigure}
-See the [Numerical Tools from GEOPIG](http://geopig.asu.edu/tools) for SUPCRT updates (slop files), including corrections that have not yet been ported to CHNOSZ.
+See the [Numerical Tools from GEOPIG](http://geopig.asu.edu/?q=tools) for SUPCRT updates (slop files), including corrections that have not yet been ported to CHNOSZ.
```
## Water: SUPCRT92 or IAPWS-95
Modified: pkg/CHNOSZ/vignettes/eos-regress.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/eos-regress.Rmd 2017-02-18 10:15:38 UTC (rev 161)
+++ pkg/CHNOSZ/vignettes/eos-regress.Rmd 2017-02-18 14:18:11 UTC (rev 162)
@@ -286,8 +286,8 @@
EOScoeffs("Na+", "Cp")
```
-Alrighty! We managed to obtain EOS parameters from synthetic data for Na<sup>+</sup>.
-The regressed values of the EOS parameters (shown in the plot legend) are very close to the database values (printed by the call to <span style="color:green">`EOScoeffs()`</span>) used to generate the synthetic data.
+Alrighty! We managed to obtain HKF coefficients from synthetic data for Na<sup>+</sup>.
+The regressed values of the HKF coefficients (shown in the plot legend) are very close to the database values (printed by the call to <span style="color:green">`EOScoeffs()`</span>) used to generate the synthetic data.
## Doing it for volume
@@ -403,7 +403,6 @@
s1 <- subcrt(c("pseudo-H4SiO4", "SiO2", "H2O"), c(-1, 1, 2))
plot(s1$out$T, s1$out$G, type = "l", ylim = c(-100, 600),
xlab = axis.label("T"), ylab = axis.label("DG0"))
-add.obigt()
s2 <- subcrt(c("H4SiO4_Ste01", "SiO2", "H2O"), c(-1, 1, 2))
lines(s2$out$T, s2$out$G, lty = 2)
abline(h = 0, lty = 3)
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