[CHNOSZ-commits] r233 - in pkg/CHNOSZ: . R data demo inst inst/extdata/OBIGT man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Oct 1 10:40:38 CEST 2017
Author: jedick
Date: 2017-10-01 10:40:37 +0200 (Sun, 01 Oct 2017)
New Revision: 233
Added:
pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv.xz
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/info.R
pkg/CHNOSZ/R/subcrt.R
pkg/CHNOSZ/data/thermo.R
pkg/CHNOSZ/demo/activity_ratios.R
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz
pkg/CHNOSZ/man/subcrt.Rd
Log:
add Berman_cr.csv
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2017-10-01 03:39:25 UTC (rev 232)
+++ pkg/CHNOSZ/DESCRIPTION 2017-10-01 08:40:37 UTC (rev 233)
@@ -1,6 +1,6 @@
-Date: 2017-09-30
+Date: 2017-10-01
Package: CHNOSZ
-Version: 1.1.0-31
+Version: 1.1.0-32
Title: Thermodynamic Calculations for Geobiochemistry
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
Modified: pkg/CHNOSZ/R/info.R
===================================================================
--- pkg/CHNOSZ/R/info.R 2017-10-01 03:39:25 UTC (rev 232)
+++ pkg/CHNOSZ/R/info.R 2017-10-01 08:40:37 UTC (rev 233)
@@ -73,7 +73,7 @@
return(out)
}
-info.character <- function(species, state=NULL, check.protein=TRUE) {
+info.character <- function(species, state=NULL, check.protein=TRUE, grep.state=FALSE) {
# returns the rownumbers of thermo$obigt having an exact match of 'species' to
# thermo$obigt$[species|abbrv|formula] or NA otherwise
# a match to thermo$obigt$state is also required if 'state' is not NULL
@@ -113,7 +113,8 @@
# special treatment for H2O: aq retrieves the liq
if(species %in% c("H2O", "water") & state=="aq") state <- "liq"
# the matches for both species and state
- matches.state <- matches.species & grepl(state, get("thermo")$obigt$state)
+ if(grep.state) matches.state <- matches.species & grepl(state, thermo$obigt$state)
+ else matches.state <- matches.species & state == thermo$obigt$state
if(!any(matches.state)) {
# the requested state is not available for this species
available.states <- thermo$obigt$state[matches.species]
@@ -160,19 +161,19 @@
# use new obigt2eos function here
this <- obigt2eos(this, this$state)
# identify any missing GHS values
- naGHS <- which(is.na(this[8:10]))
+ naGHS <- is.na(this[8:10])
# a missing one of G, H or S can cause problems for subcrt calculations at high T
- if(length(naGHS)==1) {
+ if(sum(naGHS)==1) {
# calculate a single missing one of G, H, or S from the others
GHS <- as.numeric(GHS(as.character(this$formula), G=this[,8], H=this[,9], S=this[,10]))
message("info.numeric: ", colnames(this)[8:10][naGHS], " of ",
this$name, "(", this$state, ") is NA; set to ", round(GHS[naGHS],2))
- this[, naGHS+7] <- GHS[naGHS]
+ this[, which(naGHS)+7] <- GHS[naGHS]
}
# now perform consistency checks for GHS and EOS parameters if check.it=TRUE
if(check.it) {
# check GHS if they were all present
- if(length(naGHS)==0) calcG <- checkGHS(this)
+ if(sum(naGHS)==0) calcG <- checkGHS(this)
# check tabulated heat capacities against EOS parameters
calcCp <- checkEOS(this, this$state, "Cp")
# fill in NA heat capacity
Modified: pkg/CHNOSZ/R/subcrt.R
===================================================================
--- pkg/CHNOSZ/R/subcrt.R 2017-10-01 03:39:25 UTC (rev 232)
+++ pkg/CHNOSZ/R/subcrt.R 2017-10-01 08:40:37 UTC (rev 233)
@@ -122,7 +122,7 @@
for(i in 1:length(species)) {
mysearch <- species[i]
if(can.be.numeric(mysearch)) mysearch <- thermo$obigt$name[as.numeric(mysearch)]
- si <- info.character(mysearch, state[i])
+ si <- info.character(mysearch, state[i], grep.state=TRUE)
# that could have the side-effect of adding a protein; re-read thermo
thermo <- get("thermo", "CHNOSZ")
if(is.na(si[1])) stop('no info found for ',species[i],' ',state[i])
Modified: pkg/CHNOSZ/data/thermo.R
===================================================================
--- pkg/CHNOSZ/data/thermo.R 2017-10-01 03:39:25 UTC (rev 232)
+++ pkg/CHNOSZ/data/thermo.R 2017-10-01 08:40:37 UTC (rev 233)
@@ -10,7 +10,7 @@
local({
# create obigt data frame
sources_aq <- paste0(c("H2O", "inorganic", "organic", "biotic"), "_aq")
- sources_cr <- paste0(c("inorganic", "organic"), "_cr")
+ sources_cr <- paste0(c("inorganic", "organic", "Berman"), "_cr")
sources_liq <- paste0(c("organic"), "_liq")
sources_gas <- paste0(c("inorganic", "organic"), "_gas")
OBIGTdir <- system.file("extdata/OBIGT/", package="CHNOSZ")
Modified: pkg/CHNOSZ/demo/activity_ratios.R
===================================================================
--- pkg/CHNOSZ/demo/activity_ratios.R 2017-10-01 03:39:25 UTC (rev 232)
+++ pkg/CHNOSZ/demo/activity_ratios.R 2017-10-01 08:40:37 UTC (rev 233)
@@ -13,7 +13,7 @@
# make the pseudospecies H4SiO4 available for use as a basis species
add.obigt("CHNOSZ_aq", "pseudo-H4SiO4")
basis(c("Al+3", "pseudo-H4SiO4", "K+", "H2O", "H+", "O2"))
-species(c("gibbsite", "muscovite", "kaolinite", "pyrophyllite", "k-feldspar"))
+species(c("gibbsite", "muscovite", "kaolinite", "pyrophyllite", "K-feldspar"))
a <- affinity(H4SiO4 = c(-6, -2, res), `K+` = c(-3, 6, res))
diagram(a, ylab = ratlab("K+"), fill = fill, yline = 1.7)
title(main = syslab(c("K2O", "Al2O3", "SiO2", "H2O")))
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2017-10-01 03:39:25 UTC (rev 232)
+++ pkg/CHNOSZ/inst/NEWS 2017-10-01 08:40:37 UTC (rev 233)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.1.0-30 (2017-09-30)
+CHANGES IN CHNOSZ 1.1.0-32 (2017-10-01)
---------------------------------------
MAJOR CHANGES:
@@ -26,6 +26,12 @@
species) to their defaults. data(thermo) is still used to reset
*everything* (the database and all computational and system settings).
+- In add.obigt(), using 'file' without a file suffix now can be used to
+ locate corresponding files (such as CHNOSZ_aq.csv or DEW_aq.csv) in
+ the extdata/OBIGT package directory.
+
+- add.obigt() gets new argument 'species' for selecting species to add.
+
DATABASE UPDATES:
- Add DEW_aq.csv with aqueous species data from the DEW spreadsheet
@@ -33,12 +39,11 @@
database in CHNOSZ are not included. For the time being, only
selected species are fully referenced.
-- In add.obigt(), using 'file' without a file suffix now can be used to
- locate corresponding files (such as CHNOSZ_aq.csv or DEW_aq.csv) in
- the extdata/OBIGT package directory.
+- Add Berman_cr.csv with names and formulas for minerals whose
+ thermodynamic properties are calculated using the Berman (1988)
+ formulation. The state "cr_Berman" is used to distinguish these
+ minerals from the Helgeson data.
-- add.obigt() gets new argument 'species' for selecting species to add.
-
- Data file CHNOSZ_aq.csv is no longer added to the database by default.
It is now intended to hold provisional updates. Updated heat capacity
and volume HKF parameters for adenine (Lowe et al., 2017) have been
Added: pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv.xz
===================================================================
(Binary files differ)
Property changes on: pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv.xz
___________________________________________________________________
Added: svn:mime-type
+ application/x-xz
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz 2017-10-01 03:39:25 UTC (rev 232)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv.xz 2017-10-01 08:40:37 UTC (rev 233)
@@ -1,66 +1,58 @@
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\ No newline at end of file
Modified: pkg/CHNOSZ/man/subcrt.Rd
===================================================================
--- pkg/CHNOSZ/man/subcrt.Rd 2017-10-01 03:39:25 UTC (rev 232)
+++ pkg/CHNOSZ/man/subcrt.Rd 2017-10-01 08:40:37 UTC (rev 233)
@@ -132,7 +132,7 @@
subcrt(c("glucose", "ethanol", "CO2"))
## properties of reactions
-subcrt(c("H2O", "H+", "k-feldspar", "kaolinite", "K+", "SiO2"),
+subcrt(c("H2O", "H+", "K-feldspar", "kaolinite", "K+", "SiO2"),
c(-1, -2, -2, 1, 2, 4))
subcrt(c("glucose", "ethanol", "CO2"), c(-1, 2, 2))
# to specify the states
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