Add species to or alter properties of species in the thermodynamic database or in the buffer definition table. Show references for sources of thermodynamic data in a web browser. Check internal consistency of individual entries in database.
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add.obigt(file = system.file("extdata/thermo/OBIGT-2.csv", package = "CHNOSZ"), force = FALSE, E.units = "cal") mod.obigt(...) today() browse.refs(key=NULL) checkEOS(eos, state, prop, ret.diff = FALSE) checkGHS(ghs, ret.diff = FALSE) check.obigt() obigt2eos(obigt, state, fixGHS = FALSE) RH2obigt(compound = NULL, state = "cr", file = system.file("extdata/thermo/RH98_Table15.csv", package = "CHNOSZ"))
character, path to a file
logical, force replacement of already existing species?
character, units of energy, cal or J
character or numeric, properties of species to modify in the thermodynamic database
character, numeric, or list, containing reference key(s) for which to show URL(s) in browser
dataframe, containing equations-of-state parameters in the format of
character, physical state of species
character, property of interest (Cp or V)
logical, return the difference between calculated and tabulated values?
dataframe, containing G, H and S, in the format of
dataframe, in the format of
logical, calculate one of missing G, H, or S?
character, name of compound(s) in group additivity calculation
add.obigt reads data from the specified
file and adds it to
force to TRUE to replace species that exist in the thermodynamic database (each unique combination of a name and a state in the database is considered to be a unique species).
force, if not specified, reverts to TRUE if the
file is left at its default. Given the default setting of
E.units, the function does not perform any unit conversions. If
E.units is set to J, then the thermodynamic parameters are converted from units of Joules to calories, as used in the CHNOSZ database.
mod.obigt changes one or more of the properties of species or adds species to the thermodynamic database.
These changes are lost if you reload the database by calling
data(thermo) or if you quit the R session without saving it.
The name of the species to add or change must be supplied as the first argument of
... or as a named argument (named name).
When adding new species, a chemical formula should be included along with the values of any of the thermodynamic properties.
The formula is taken from the formula argument, or if that is missing, is taken to be the same as the name of the species.
An error results if the formula is not valid (i.e. can not be parsed by
Additional arguments refer to the name of the property(s) to be updated and are matched to any part of compound column names in
thermo$obigt, such as z or T in z.T.
Unless state is specified as one of the properties, its value is taken from
When adding species, properties that are not specified become NA (except for state).
The values provided should be in the units specifed in the documentation for the
thermo data object, including any order-of-magnitude scaling factors.
today returns the current date in the format adopted for
thermo$obigt (inherited from SUPCRT-format data files) e.g. 13.May.12 for May 13, 2012.
change is a wrapper function to
name provided in the argument refers to the name or numeric index of the species to update or add using
mod.obigt, unless the
name begins with an underscore character, in which case the remaining part of the name (after the underscore) is passed to
mod.buffer. The arguments in
... are sent without change to the subordinate function.
browse.refs with default arguments uses
browseURL to display the sources of thermodynamic data in
thermo$refs, with the URLs in that table showing as hyperlinks in the browser. Otherwise, if
key is character, the URLs of those reference
keys are opened in the browser. If
key is numeric, the values refer to the species in those rows of
thermo$obigt, and the URLs for each listed reference (
thermo$obigt$ref2) are opened. If
key is a list, it is interpreted as the result of a call to
subcrt, and the reference URLs for each species involved in the calculation are opened.
checkEOS compares heat capacity and volume calculated from equation-of-state parameters with reference (tabulated) values at 25 °C and 1 bar and prints a message and returns the calculated value if tolerance is exceeded. The Helgeson-Kirkham-Flowers equations of state parameters are in
eos, which is a data frame with columns (and column names) in the same format as
property can be one of Cp or
V. The code only distinguishes between
states of aq and all others. The default tolerances, given in
thermo$opt$V.tol, are 1 cal/K.mol for Cp and 1 cm3/mol for V. If
ret.diff is TRUE, the differences are returned irrespective of their values, and no messages are printed.
checkGHS compares G (standard molal Gibbs energy of formation from the elements) calculated from H (standard molal enthalpy of formation) and S (standard molal entropy) with reference (tabulated) values of G at 25 °C and 1 bar. A message is printed and the calculated difference is returned if it exceeds the value given in
thermo$opt$G.tol, which has a default value of 100 cal/mol. The calculation requires that G, H and S, and the chemical formula of the species all be present.
checkGHS are used by
info when retrieving species parameters from the database.
check.obigt is a function to check self-consistency of each entry (with itself) in the thermodynamic database, using
checkGHS. The function checks data in both
extdata/thermo/OBIGT-2.csv. The output is a table listing only species that exceed at least one of the tolerance limits, giving the name of the database (OBIGT or OBIGT-2), the species index (rownumber in the database), species name and state, and DCp, DV and DG, for the calculated differences (only those above the tolerances are given). This function is used to generate the file found at
obigt2eos takes a data frame in the format of
thermo$obigt of one or more rows, removes scaling factors from equations-of-state parameters, and applies new column names depending on the
state. This function is used by both
subcrt when retrieving entries from the thermodynamic database. If
fixGHS is TRUE a missing one of G, H or S for any species is calculated from the other two and the chemical formula of the species (used by
subcrt when retrieving database entries).
RH2obigt implements a group additivity algorithm for standard molal thermodynamic properties and equations of state parameters of crystalline and liquid organic molecules from Richard and Helgeson, 1998. The names of the
compounds and their physical
state are searched for in the indicated
file, that also contains chemical formulas and group stoichiometries; the names of the groups are stored in the column names of this file, and must be present in
thermo$obigt. The default
extdata/thermo/RH98_Table15.csv) includes data taken from Table 15 of Richard and Helgeson, 1998 for high molecular weight compounds in crystalline and liquid states. An error is produced if any of the
state combinations is not found in the
file, if any of the group names for a given
state combination is not found in
thermo$obigt, or if the chemical formula calculated from group additivity (with the aid of
as.chemical.formula) is not identical to that listed in the
The values returned (
mod.obigt are the rownumbers of the affected species.
add.obigt affects the order of entries in
thermo$obigt; therefore, it should be called before any
species definition. Also, there is no attempt made to keep the order of physical states in the database (aq-cr-liq-gas); the function simply adds new rows to the end of
thermo$obigt. As a result, retrieving the properties of an added aqueous species using
info requires an explicit
state="aq" argument to that function if a species with the same name is in one of the cr, liq or gas states.
Richard, L. and Helgeson, H. C. (1998) Calculation of the thermodynamic properties at elevated temperatures and pressures of saturated and aromatic high molecular weight solid and liquid hydrocarbons in kerogen, bitumen, petroleum, and other organic matter of biogeochemical interest. Geochim. Cosmochim. Acta 62, 3591–3636. http://dx.doi.org/10.1016/S0016-7037(97)00345-1
The default supplementary thermodynamic database for
extdata/thermo/OBIGT-2.csv) is used in some of the example calculations in the help page for
diagram and also in
mod.buffer for updating the list of available buffers.
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## modify an existing species with fake properties ialanine <- mod.obigt("alanine", state="cr", G=0, H=0, S=0) # we have made the values of G, H, and S inconsistent # with the elemental composition of alanine so the following # produces a message about that info(ialanine) ## add a species iCl2O <- mod.obigt("Cl2O", G=20970) info(iCl2O) # add a species with a name that is distinct from the formula mod.obigt("buckminsterfullerene", formula="C60", state="cr") ## Not run: ## marked dontrun because they open pages in a browser # show the contents of thermo$refs browse.refs() # Internet needed for the following examples: # open URL for Helgeson et al., 1998 browse.refs("HOK+98") # open two URLs for alanine browse.refs(info("alanine")) # open three URLs for species in the reaction s <- subcrt(c("O2","O2"),c("gas","aq"),c(-1,1)) browse.refs(s) ## End(Not run) ## calculate thermodynamic properties of organic compounds ## using group additivity, after Richard and Helgeson, 1998 RH2obigt()