%% LyX 2.1.3 created this file.  For more info, see http://www.lyx.org/.
%% Do not edit unless you really know what you are doing.
\documentclass[english,noae,round]{article}
\usepackage{mathpazo}
\usepackage[T1]{fontenc}
\usepackage[latin9]{inputenc}
\usepackage[letterpaper]{geometry}
\geometry{verbose,tmargin=2.5cm,bmargin=2.5cm,lmargin=2.5cm,rmargin=2.5cm}
\usepackage{color}
\usepackage{babel}
\usepackage[authoryear]{natbib}
\usepackage[unicode=true,
 bookmarks=true,bookmarksnumbered=false,bookmarksopen=false,
 breaklinks=false,pdfborder={0 0 1},backref=false,colorlinks=true]
 {hyperref}
\hypersetup{pdftitle={Winding journey down (in Gibbs energy)},
 pdfauthor={Jeffrey M. Dick},
 citecolor=blue}
\usepackage{breakurl}

\makeatletter
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Textclass specific LaTeX commands.
<<echo=F>>=
  if(exists(".orig.enc")) options(encoding = .orig.enc)
@

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% User specified LaTeX commands.
%\VignetteIndexEntry{Winding journey down (in Gibbs energy)}

% so DOIs in bibliography show up as hyperlinks
\newcommand*{\doi}[1]{\href{http://dx.doi.org/#1}{doi: #1}}

\makeatother

\begin{document}

\title{Winding journey down (in Gibbs energy)}


\author{Jeffrey M. Dick}

\maketitle

\section{Introduction}

\texttt{wjd()} appeared in CHNOSZ version 0.9-9. It implements the
steepest descent algorithm for Gibbs energy minimization described
by White, Johnson and Dantzig, \citeyear{WJD58}. This vignette shows
some examples of its usage. The help page for \texttt{wjd()} in the
CHNOSZ documentation has details of the implementation that are not
covered in this vignette. The functions demonstrated here are not
intended for aqueous solutions or heterogeneous phase equilibria,
which are covered in some reviews \citep[e.g.][]{NPW+79}.

The arguments of \texttt{wjd()} have default values to simulate the
example problem given by \citealp{WJD58}. In their words, ``The
example taken is the determination of the composition of the gases
arising from the combustion of a stoichiometric mixture of hydrazine
and oxygen at 3500 $^{\circ}$K and a pressure of 750 psi ($\ln P_{\mathrm{atm}}$
=3.932).'' There are ten species included in this example. The value
of temperature does not appear explicitly in the algorithm, or in
the arguments to \texttt{wjd()}. Instead, the standard Gibbs energies
of the species, at the given temperature, are provided in dimensionless
form, i.e. $\Delta G^{\circ}/RT$. Note that White et al., 1958 use
the terminology ``free energy'' and the notation $F^{\circ}$. The
term ``Gibbs energy'' and corresponding notation are used here.

<<libraryCHNOSZ, echo=FALSE>>=
library(CHNOSZ)
data(thermo)
@


\section{Is it winding?}

The ``winding'' in the title refers to the observation that the
abundances of species during a Gibbs energy minimization often do
not all change in a monotonic fashion. This is because at each iteration
a new direction of steepest descent is calculated; this direction
is a vector of changes of mole numbers of all species in the system
and is subject to mass balance constraints as well as the steepest-descent
criterion.

Let's run \texttt{wjd()} with its default settings and save the output.

<<wjd>>=
w <- wjd()
@

What are the most abundant species, and how many iterations were taken?

<<abundant>>=
# the order of species abundance
oX <- order(w$X, decreasing=TRUE)
# the stoichiometries of the two most abundant species
w$A[head(oX,2),]
# the number of iterations
niter <- length(w$lambda)
niter
@

<<abundantnames,echo=FALSE>>=
# the formulas of the two most abundant species
# use CHNOSZ's as.chemical.formula function, after 
# dropping elements with zero stoichiometry
f1 <- as.chemical.formula(w$A[oX[1],w$A[oX[1],]!=0])
f2 <- as.chemical.formula(w$A[oX[2],w$A[oX[2],]!=0])
f4 <- as.chemical.formula(w$A[oX[4],w$A[oX[4],]!=0])
@

We find that \Sexpr{f1} and \Sexpr{f2} are the most abundant species,
after \Sexpr{niter} iterations. The fourth most-abundant species,
\Sexpr{f4}, is discussed below.

Let's track their mole fractions through the iterations. Write a function
that returns the mole fractions of a species, after a specified number
of iterations.

<<iterfun>>=
iterfun <- function(imax, i) {
  w <- wjd(imax=imax)
  x <- w$X[i]/sum(w$X)
  return(x)
}
@

Then apply the function over the different numbers of iterations,
from 0 (initial conditions) to \Sexpr{niter}, and plot the values.

\setkeys{Gin}{width=1.0\textwidth}

<<>>=
<<iterplot, fig=TRUE, height=3>>=
par(mfrow=c(1, 2))
sa <- sapply(0:niter, iterfun, i=oX[1])
plot(0:niter, sa, xlab="iteration", ylab=paste("x", f1))
sa <- sapply(0:niter, iterfun, i=oX[4])
plot(0:niter, sa, xlab="iteration", ylab=paste("x", f4))
@

\setkeys{Gin}{width=1.0\textwidth}

A bit of winding: the mole fraction of \Sexpr{f1} generally increases
(there is a very slight decrease at the fifth iteration), but the
mole fraction of \Sexpr{f4} increases in the first two iterations,
then decreases in following ones. This behavior is consistent with
a decrease in Gibbs energy at \emph{every} iteration; that can be
verified by inspecting the values in the \Sexpr{niter}-iteration
result:

<<Gdown>>=
all(diff(w$F.Y) < 0)
@

The decrease in Gibbs energy becomes smaller with every iteration,
as an equilibrium distribution of species is approached:

<<Gdownslower>>=
identical(diff(w$F.Y), sort(diff(w$F.Y)))
@


\section{Is it near the bottom? Testing for equilibrium}


\subsection{Change in Gibbs energy of the system becomes small}

Equilibrium is synonymous with a global Gibbs energy minimum. Becoming
convinced that the output from \texttt{wjd()} represents a near-equilibrium
condition can be difficult. One type of observation that can be helpful
is the amount of change during the iterations of the algorithm. As
equilibrium is approached, it makes sense that the fractional decreases
in Gibbs energy would become smaller and smaller. This is used as
a stopping condition in the current implementation -- if the fractional
change, relative to the total energy of the system, reaches the value
of \texttt{Gfrac} given in the arguments the iterations stop. Here
are the fractional changes with each iteration:

<<Gfrac>>=
diff(w$F.Y)/w$F.Y[1:7]
@

Only the last value is below the default value of \texttt{Gfrac} in
\texttt{wjd()}.


\subsection{Chemical potentials of the elements (from different species representing
them) become more uniform}

Equilibrium is also synonymous with uniformity of chemical potentials
($\mu$) of the thermodynamic components throughout the system. For
the default system in \texttt{wjd()}, and perhaps other systems of
interest, the elements themselves are a conceivable set of the components.
Often, the number and compositions of the species are such that multiple
combinations of species satisfy the stoichiometric conditions necessary
to be a basis set, and therefore can be used to compute the chemical
potentials of the elements. At equilibrium, these different combinations
of species would all yield the same chemical potentials of the elements. 

There is a supporting function, \texttt{element.potentials()}, that
computes the chemical potentials of the elements using different eligible
combinations of species. It has an option to plot the results. Let's
first look at a plot showing the results after 3 iterations.

\setkeys{Gin}{width=0.6\textwidth}

<<>>=
<<w3_ep_plot, fig=TRUE>>=
w3 <- wjd(imax=3)
ep3 <- element.potentials(w3, plot.it=TRUE)
@

\setkeys{Gin}{width=1.0\textwidth}

Here's the plot for the default settings of \texttt{wjd()} which takes
6 iterations:

\setkeys{Gin}{width=0.6\textwidth}

<<>>=
<<w_ep_plot, fig=TRUE>>=
ep <- element.potentials(w, plot.it=TRUE)
@

\setkeys{Gin}{width=1.0\textwidth}

That one shows considerably less deviation than the first plot. The
differences don't become zero, but perhaps they are small enough to
accept as an operational solution. There is a function, \texttt{is.near.equil()},
that provides a logical type result based on the range of chemical
potentials of the elements calculated from the different eligible
species combinations. It returns TRUE if the maximum difference for
any element is below $\mu/RT=0.01$, but this limit can be changed
through the \texttt{tol} argument to the function. With the default
setting, \texttt{is.near.equil()} does pass the \Sexpr{niter}-iteration
result, but by reducing the tolerance, the tests can be made to fail:

<<w_ep_plot>>=
is.near.equil(w3) # 3 iterations
is.near.equil(w)  # 7 iterations
is.near.equil(w, tol=0.00001)
@


\subsection{Different initial solutions yield similar results}


\paragraph{Different guesses for an underdetermined system}

Although it seems to be the case in the examples shown so far, increasing
the number of iterations does not necessarily bring one closer to
true equilibrium, since being trapped in a local energy minimum is
a possibility. Sometimes local minima can be shown to exist by starting
with different mole numbers of species, that still yield the same
bulk composition (mole numbers of elements). \texttt{guess()} exists
to facilitate this sort of investigation. Its input the stoichiometric
matrix of species in the system (the default refers to the same system
as in \texttt{wjd()}) and the bulk composition; it outputs one set
or a series of sets of mole numbers of species that satisfy the bulk
composition constraints. In general, this in an underdetermined problem,
so there are usually an infinite number of possible solutions. 

Using the default method (``stoich'') a single guess or multiple
guesses are returned based on stoichiometric constraints (see the
help page for details as well as the comments in the function code
itself). If the ``central'' method is chosen instead, the single
guess returned is the central solution from linear optimization using
the package limSolve. Let's compare the guesses made by \texttt{guess()}
with the default (from \citealp{WJD58}) initial composition in \texttt{wjd()}
.

<<guessw12>>=
as.list(args(wjd))$Y
Y1 <- guess(method="stoich")
Y1
#Y2 <- guess(method="central")
#Y2
@

Now let's run the minimization using the different guesses, count
the numbers of iterations, and test them for equilibrium.

\setkeys{Gin}{width=0.6\textwidth}

<<>>=
<<stoich_guess>>=
wY1 <- wjd(Y=Y1)
niterY1 <- length(wY1$lambda)
niterY1
is.near.equil(wY1, tol=0.0001)
@

\setkeys{Gin}{width=0.6\textwidth}

Using the first guess generated using the ``stoich'' method there
were \Sexpr{niterY1-niter} more iterations than using the default
initial solution in \texttt{wjd()}.



Do the different initial guesses actually give similar results?

\setkeys{Gin}{width=0.6\textwidth}

<<>>=
<<compare_guesses, fig=TRUE>>=
plot(1:10, w$X, xlab="species", ylab="mole fraction")
points(1:10, wY1$X, pch=0)
#points(1:10, wY2$X, pch=2)
@

\setkeys{Gin}{width=0.6\textwidth}

At that scale it's fairly difficult to tell them apart.


\paragraph{Comparing many different guesses}

Let's test for closeness to equilibrium of all of the guesses available
from \texttt{guess()} for the default set of species and bulk composition.
First generate all of the guesses. Note that \texttt{guess()} returns
NA for compositionally eligible combinations of species that have
some negative mole numbers, so we filter those out.

<<allguesses>>=
Ys <- guess(iguess=NULL, method="stoich")
# total number of species combinations
length(Ys)
# species combinations that have all-positive mole numbers
iYs <- which(!is.na(Ys))
nguess <- length(iYs)
nguess
@

Now let's run the minimization using each of those guesses, and test
if each one \texttt{is.near.equil()}:

<<allguess.equil>>=
sapply(iYs,function(i) is.near.equil(wjd(Y=Ys[[i]])))
@

Looks like they are. What if we're really picky though and want to
make sure the chemical potentials of the elements are very well-defined?
We can decrease the tolerance of \texttt{is.near.equil()}:

<<allguess.equil.2>>=
sapply(iYs,function(i) is.near.equil(wjd(Y=Ys[[i]]),tol=0.0001))
@

Well some of the tests failed. But maybe this is because we have stopped
iterating too soon. Let's iterate until a we have smaller change in
Gibbs energy of the system:

<<allguess.equil.3>>=
sapply(iYs, function(i) {
  is.near.equil(wjd(Y=Ys[[i]], Gfrac=1e-9), tol=0.0001)
})
@

We're back to passing all but one of the equilibrium tests based on
uniformity of chemical potentials of the elements. What are the standard
deviations of the resulting species abundances?

<<sd.species>>=
Xs <- sapply(iYs, function(i) wjd(Y=Ys[[i]], Gfrac=1e-9)$X)
apply(Xs, 1, sd)
@

Based on this exercise, starting from different initial species abundances
for the same bulk composition, and arriving at a similar near-equilibrium
solution, it seems likely that we are near the global minimum.

(In fact, for ideal reactions in closed chemical systems there is
only a unique solution \citep{Oth76}. Therefore, the algorithm should
converge on the same result for any initial vector of species mole
numbers with the same bulk composition.)


\section{An example from the literature: prebiological atmospheres}

We will try to reproduce a subset of the calculations of equilibrium
between carbon-containing compounds in model prebiological atmospheres
reported by \citet{DLE64}, using standard Gibbs energies from \citet{DLEN67}.
The standard Gibbs energies shown in Figure 2 of \citet{DLEN67} for
the selected compounds listed in Table 1 of \citet{DLE64} are provided
with CHNOSZ. First let's have a look at what species there are:

<<read_dlen>>=
# read formulas and Gibbs energies
file <- system.file("extdata/thermo/DLEN67.csv", package="CHNOSZ")
dlen <- read.csv(file, stringsAsFactors=FALSE, row.names=1)
t(dlen[, 1, drop=FALSE])
@

Now let's write some code to define the system. The bulk composition
in C:H:O space has 40 percent oxygen, a percentage of carbon given
by \texttt{xC}, and hydrogen as the remainder; the C:N ratio is taken
to be 1:1 \citep{DLE64}. The temperature is 500 K and the pressure
is 1 atmosphere.

<<setup_atmos>>=
# turn formulas into a stoichiometric matrix
A <- i2A(dlen$formula)
# assemble Gibbs energies/RT at 500 K
G0.RT <- 1000 * dlen$G500 / thermo$opt$R / thermo$opt$Tr
# a function to minimize Gibbs energy for system with 
# given mole fraction of carbon (xC)
min.atmos <- function(xC) {
  # the bulk composition C:H:N:O
  B <- c(xC, 100-40-xC, xC, 40)
  # guess the initial composition
  Y <- guess(A, B)
  w <- wjd(A=A, G0.RT=G0.RT, Y=Y, P=1, imax=90, Gfrac=1e-14)
  if(!is.near.equil(w)) cat(paste("not near equilibrium for xC=", xC, "\n"))
  return(w)
}
@

Notice the increase in \texttt{imax} and the decrease in \texttt{Gfrac}
from the defaults! These changes are needed to get closer to equilibrium
(and we'll know we're not there if a message is shown). What does
the prebiological atmosphere look like with 15\% (not counting nitrogen)
carbon?

<<atmos_C15>>=
sort(min.atmos(15)$X, decreasing=TRUE)
@

Well that's exciting! The order of abundances of $\mathrm{H_{2}O}$,
$\mathrm{CO_{2}}$, $\mathrm{CH_{4}}$, $\mathrm{NH_{3}}$, $\mathrm{CO}$,
ethane ($\mathrm{C_{2}H_{6}}$), formic acid ($\mathrm{CH_{2}O_{2}}$)
and so on matches the order on the left side of Figure 2 in \citet{DLE64}.
How about changing the carbon content?

<<atmos_figure, fig=TRUE>>=
xCs <- seq(8, 47, 3)
Xs <- sapply(xCs, function(xC) min.atmos(xC)$X)
# normalize the mole numbers to mole fractions
Xs <- t(t(Xs)/colSums(Xs))
plot(-10, 0, xlim=c(0, 55), ylim=c(-25, 1), xlab="mole percent C", ylab="log10 mole fraction")
for(i in 1:nrow(Xs)) lines(xCs, log10(Xs[i, ]))
text(48, log10(Xs[, length(xCs)]), dlen$formula, adj=0)
text(7, log10(Xs[, 1]), dlen$formula, adj=1)
@

We triggered some ``not near equilibrium'' messages, but overall
it seems well behaved (note that using the ``central'' method in
\texttt{guess()} is one way that leads to fewer of these messages).
And, as expected, it is similar to Fig. 2 of \citet{DLE64}, with
a major crossing of curves at about 28\% carbon, together with an
increase in aromatic compounds (e.g. naphthalene, anthracene) going
toward higher carbon content. Unlike the figure in \citet{DLE64},
there appears to be a second major crossing of curves at about 43\%
carbon, corresponding to a rise in CO. (For a higher resolution, try
setting \texttt{xCs <- seq(8, 47, 1)}.)


\section{Running Down: Using a Thermodynamic Database}

So far the examples shown here have been based on the chemical system
defined by the default settings for the arguments to the functions.
What if we're interested in a different system? It can be rather tedious
to manually construct the stoichiometric matrices and vectors of standard
Gibbs energies of the species. The function \texttt{run.wjd()} pulls
the compositional and thermodynamic data for requested species from
the thermodynamic database and then calls \texttt{wjd()}.


\subsection{At a single temperature}

Let's start by finding the indices in the thermodynamic database of
some liquid alkanes and aromatic compounds:

<<alkanes_aromatics>>=
alkanes <- c("n-hexane", "n-heptane", "n-octane", "n-nonane")
ialk <- info(alkanes, "liq")
aromatics <- c("naphthalene", "anthracene", "phenanthrene", "pyrene")
iaro <- info(aromatics, "liq")
@

Let's find the equilibrium distribution of species for a bulk composition
corresponding to a single mole of each species.

<<run_aa>>=
waa <- run.wjd(c(ialk, iaro), Y=rep(1, 8))
waa$elements
is.near.equil(waa)
@

The \texttt{waa\$elements} shows that the bulk chemical composition
in the Gibbs energy minimization was $\mathrm{C_{84}H_{106}}$ (H/C
= 1.261905). That FALSE means the chemical potentials of the elements
calculated from different combinations of species differ by more than
0.01, the default setting of \texttt{tol} in \texttt{is.near.equil()}.
We can make it TRUE by running more iterations and increasing the
number of intervals tested for fractional distance change at each
step (\texttt{nlambda}):

<<run_aa_equil>>=
waa <- run.wjd(c(ialk, iaro), Y=rep(1, 8), imax=20, Gfrac=1e-14, nlambda=501)
is.near.equil(waa)
@

Let's plot the abundances of the species:

<<barplot_aa, fig=TRUE>>=
bp <- barplot(waa$X, ylab="moles")
text(bp, rep(0.2,8), c(alkanes, aromatics), srt=90, adj=0)
@

Now let's calculate the chemical potentials of the elements (dimensionless
values, $\mu/RT$) ...

<<element_potentials_C84H106>>=
ep <- equil.potentials(waa)
print(ep)
@

... and the corresponding logarithms of chemical activities of a set
of basis species:

<<basis_potentials_C84H106>>=
basis(c("graphite", "H2"), c("cr", "gas"))
basis.logact(ep)
@


\subsection{Bulk composition instead of moles of species}

\texttt{run.wjd()} can be given B (bulk chemical composition), instead
of Y (initial numbers of moles of species). When this happens, the
function tests the different initial compositions generated by \texttt{guess()}
until one is found that is within the specified tolerance of chemical
potentials of elements. Here's an example:

<<run_aa_C100H70, fig=TRUE>>=
waa <- run.wjd(c(ialk, iaro), B="C100H70")
bp <- barplot(waa$X, ylab="moles")
text(bp, rep(0.2,8), c(alkanes, aromatics), srt=90, adj=0)
@

Compared with the previous example, here the lower H/C = 0.7 defines
a more oxidized system, so the increase in aromatic content is expected.
As before, we can calculate the chemical potentials of the elements
and of a corresponding set of basis species:

<<basis_potentials_C84H106>>=
print(ep <- equil.potentials(waa))
basis.logact(ep)
@


\section{Document Information}

Revision history
\begin{itemize}
\item 2012-01-01 Initial version
\item 2012-06-16 Running Down using alkanes and aromatics
\item 2012-09-20 Add example from Dayhoff et al.
\end{itemize}
R session information

<<sessionInfo>>=
sessionInfo()
@

\bibliographystyle{plainnat}
\bibliography{vig}

\end{document}
