From noreply at r-forge.r-project.org  Mon May  6 16:36:01 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon,  6 May 2013 16:36:01 +0200 (CEST)
Subject: [CHNOSZ-commits] r52 - in pkg/CHNOSZ: . R inst inst/tests
Message-ID: <20130506143601.85B42185485@r-forge.r-project.org>

Author: jedick
Date: 2013-05-06 16:35:56 +0200 (Mon, 06 May 2013)
New Revision: 52

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/subcrt.R
   pkg/CHNOSZ/R/water.R
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/inst/tests/test-IAPWS95.R
   pkg/CHNOSZ/inst/tests/test-subcrt.R
Log:
IAPWS95: handle lower temperatures, and improve operation with subcrt()


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2013-03-28 15:57:07 UTC (rev 51)
+++ pkg/CHNOSZ/DESCRIPTION	2013-05-06 14:35:56 UTC (rev 52)
@@ -1,6 +1,6 @@
-Date: 2013-03-28
+Date: 2013-05-06
 Package: CHNOSZ
-Version: 1.0.0
+Version: 1.0.0-1
 Title: Chemical Thermodynamics and Activity Diagrams
 Author: Jeffrey M. Dick
 Maintainer: Jeffrey M. Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/R/subcrt.R
===================================================================
--- pkg/CHNOSZ/R/subcrt.R	2013-03-28 15:57:07 UTC (rev 51)
+++ pkg/CHNOSZ/R/subcrt.R	2013-05-06 14:35:56 UTC (rev 52)
@@ -363,6 +363,7 @@
   # logK
   if('logk' %in% prop) {
     for(i in 1:length(out)) {
+      # NOTE: the following depends on the water function renaming g to G
       out[[i]] <- cbind(out[[i]],data.frame(logK=convert(out[[i]]$G,'logK',T=T)))
       colnames(out[[i]][ncol(out[[i]])]) <- 'logK'
     }

Modified: pkg/CHNOSZ/R/water.R
===================================================================
--- pkg/CHNOSZ/R/water.R	2013-03-28 15:57:07 UTC (rev 51)
+++ pkg/CHNOSZ/R/water.R	2013-05-06 14:35:56 UTC (rev 52)
@@ -22,9 +22,9 @@
   rho.0 <- 1000 # kg m-3
   # Equation 1
   epsilon.0 <- 8.8541878E-12 # permittivity of vacuum, C^2 J-1 m-1
-  epsfun.lhs <- function(e) (e-1)*(2*e+1)/(9*e)
+  #epsfun.lhs <- function(e) (e-1)*(2*e+1)/(9*e)
   epsfun.rhs <- function(T,V.m) N.A*(alpha+mufun()/(3*epsilon.0*k*T))/(3*V.m)
-  epsfun <- function(e,T,V.m) epsfun.lhs(e) - epsfun.rhs(T,V.m)
+  #epsfun <- function(e,T,V.m) epsfun.lhs(e) - epsfun.rhs(T,V.m)
   mufun <- function() gfun()*mu^2
   gfun <- function() rhofun()*rho/rho.0 + 1
   # Equation 3
@@ -32,7 +32,9 @@
     b[4]*(T-215)^-0.5 + b[5]*(T-215)^-0.25 +
     exp(b[6]*T^-1 + b[7]*T^-2 + b[8]*P*T^-1 + b[9]*P*T^-2)
   epsilon <- function(T,rho) {
-    tu <- try(uniroot(epsfun,c(1E-1,1E3),T=T,V.m=M/rho)$root,TRUE)
+    #tu <- try(uniroot(epsfun,c(1E-1,1E3),T=T,V.m=M/rho)$root,TRUE)
+    epspoly <- function() epsfun.rhs(T,V.m=M/rho)
+    tu <- (9*epspoly() + 1 + ((9*epspoly()+1)*(9*epspoly()+1) + 8)^0.5) / 4 #Marc Neveu added 4/24/2013
     if(!is.numeric(tu)) {
       warning('water.AW90: no root for density at ',T,' K and ',rho,' kg m-3.',call.=FALSE,immediate.=TRUE)
       tu <- NA
@@ -71,7 +73,9 @@
   } else {
     # here we get properties using IAPWS-95 
     w.out <- water.IAPWS95(property, T, P)
-    colnames(w.out) <- property
+    # normalize the names to use upper case (expected by subcrt())
+    iprop <- match(tolower(property), tolower(water.props("IAPWS95")))
+    colnames(w.out) <- water.props("IAPWS95")[iprop]
     return(w.out)
   }
 }
@@ -87,6 +91,7 @@
     "V", "rho", "Psat", "E", "kT")
   else if(formulation=="IAPWS95")
     props <- c("A", "G", "S", "U", "H", "Cv", "Cp",
+    "Speed", "diel",
     "YBorn", "QBorn", "XBorn", "NBorn", "UBorn",
     "V", "rho", "Psat", "de.dT", "de.dP", "P")
   return(props)
@@ -198,11 +203,17 @@
   rho <- numeric() 
   for(i in 1:length(T)) {
     if(T[i] < 647.096) {
-      rho.lower <- WP02.auxiliary("rho.liquid", T=T[i]) - 2
+      rho.lower <- WP02.auxiliary('rho.liquid',T=T[i])-2
       rho.upper <- rho.lower + 400
       if(P[i] < 5000) rho.upper <- rho.lower + 300
       if(P[i] < 1000) rho.upper <- rho.lower + 200
-      if(P[i] < 300) rho.upper <- rho.lower + 30
+      if(P[i] < 300) {
+        rho.upper <- rho.lower + 30
+        if(T[i] < 250) { #Marc Neveu added 4/23/2013
+          rho.lower <- rho.lower - 10
+          rho.upper <- rho.lower + 40
+        }
+      }
     } else {
       rho.lower <- 0.01
       rho.upper <- 1200
@@ -259,10 +270,10 @@
     return(convert(IAPWS95('cv',T=T,rho=my.rho)$cv*M,'cal')) 
   cp <- function() 
     return(convert(IAPWS95('cp',T=T,rho=my.rho)$cp*M,'cal')) 
-  w <- function()
+  speed <- function()
     return(IAPWS95('w',T=T,rho=my.rho)$w*100) # to cm/s
   ## electrostatic properties
-  epsilon <- function() return(water.AW90(T=T,rho=my.rho,P=convert(P,'MPa')))
+  diel <- function() return(water.AW90(T=T,rho=my.rho,P=convert(P,'MPa')))
   de.dt <- function() {
     p <- numeric()
     for(i in 1:length(T)) {
@@ -378,6 +389,5 @@
     if(i > 1) w.out <- cbind(w.out, wnew) else w.out <- wnew
   }  
   msgout("\n")
-  names(w.out) <- property
   return(w.out)
 }

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2013-03-28 15:57:07 UTC (rev 51)
+++ pkg/CHNOSZ/inst/NEWS	2013-05-06 14:35:56 UTC (rev 52)
@@ -1,3 +1,16 @@
+CHANGES IN CHNOSZ 1.0.0-1 (2013-05-06)
+--------------------------------------
+
+- Fix IAPWS-95 calculations for subcrt(): in water.IAPWS95(), rename
+  internal function from 'epsilon' to 'diel'; in water(), return
+  upper-case versions of names of properties.
+
+- rho.IAPWS95() has modified search interval to give results at
+  T < 250 K and P < 300 bar. Thanks to Marc Neveu.
+
+- In water.AW90(), analytical solution to polynomial equation is
+  now used to calculate dielectric constant. Thanks to Marc Neveu.
+
 CHANGES IN CHNOSZ 1.0.0 (2013-03-28)
 ------------------------------------
 

Modified: pkg/CHNOSZ/inst/tests/test-IAPWS95.R
===================================================================
--- pkg/CHNOSZ/inst/tests/test-IAPWS95.R	2013-03-28 15:57:07 UTC (rev 51)
+++ pkg/CHNOSZ/inst/tests/test-IAPWS95.R	2013-05-06 14:35:56 UTC (rev 52)
@@ -75,6 +75,13 @@
   expect_equal(round(signif(vapor.calc$cp, 5), 4), cp.vapor.ref, tol=1e-1)
 })
 
+test_that("calculations are possible at low temperatures", {
+  # the sequences start at the lowest whole-number temperature (K) 
+  # where the function returns a value of density at the given pressure
+  expect_that(any(is.na(water.IAPWS95("rho", T=seq(234, 274, 3), P=rep(1, 14)))), is_false())
+  expect_that(any(is.na(water.IAPWS95("rho", T=seq(227, 272, 3), P=rep(1000, 16)))), is_false())
+})
+
 # reference
 
 # Wagner, W. and Pruss, A. (2002)

Modified: pkg/CHNOSZ/inst/tests/test-subcrt.R
===================================================================
--- pkg/CHNOSZ/inst/tests/test-subcrt.R	2013-03-28 15:57:07 UTC (rev 51)
+++ pkg/CHNOSZ/inst/tests/test-subcrt.R	2013-05-06 14:35:56 UTC (rev 52)
@@ -87,6 +87,15 @@
   expect_equal(s.H2O$T[22], 0.01)
 })
 
+test_that("calculations using IAPWS-95 are possible", {
+  thermo$opt$water <<- "IAPWS95"
+  sb <- subcrt(c("H2O", "Na+"), T=c(-30, -20, 0, 10), P=1)$out
+  # the test is not a demanding numerical comparison, more that we got numbers and no error
+  expect_that(all(sb$`Na+`$G < sb$water$G), is_true())
+  # clean up
+  suppressMessages(data(thermo))
+})
+
 # references
 
 # Amend, J. P. and Shock, E. L. (2001)