CHNOSZ (version 1.1.0)

thermo: Thermodynamic Database and System Definition

Description

Data files provided with CHNOSZ are in the data and extdata directories of the package. The *.csv files under data and extdata/OBIGT are used to build the thermo data object on loading the package. Other data files, supporting the examples and vignettes, are documented separately at extdata.

The thermo object holds the thermodynamic database of properties of species, some thermodynamic constants and operational parameters for functions in CHNOSZ, the properties of elements, references to literature sources of thermodynamic data, compositions of chemical activity buffers, and amino acid compositions of proteins. The thermo object also holds intermediate data used in calculations, in particular the definitions of basis species and species of interest input by the user, and the calculated properties of water so that subsequent calculations at the same temperature-pressure conditions can be accelerated.

The thermo object is a list composed of data.frames or lists each representing a class of data. The object is created in an environment named thermo. At any time, the user can restore the data object to its initial state by calling data(thermo). This is sometimes a useful command to use during an interactive session, when previous definitions of basis species and species of interest are longer desired.

Usage

data(thermo)

Format

The items in the thermo object are documented below.

• thermo$opt List of operational parameters. Square brackets indicate default values.

  Tr	numeric	Reference temperature (K) [298.15]
  Pr	numeric	Reference pressure (bar) [1]
  Theta	numeric	\(\Theta\) in the revised HKF equations of state (K) [228]
  Psi	numeric	\(\Psi\) in the revised HKF equations of state (bar) [2600]
  R	numeric	Value of the gas constant (cal K mol) [1.9872]
  cutoff	numeric	Cutoff below which values are taken to be zero [1e-10] (see makeup)
  E.units	character	The user's units of energy ([cal] or J)
  T.units	character	The user's units of temperature ([C] or K)
  P.units	character	The user's units of pressure ([bar] or MPa)
  state	character	The default physical state for searching species [aq]
  water	character	Computational option for properties of water ([SUPCRT] or IAPWS)
  online	logical	Allow online searches of protein composition? Default [NA] is to ask the user.
  G.tol	numeric	Difference in G above which checkGHS produces a message (cal mol) [100]
  Cp.tol	numeric	Difference in Cp above which checkEOS produces a message (cal K mol) [1]
  V.tol	numeric	Difference in V above which checkEOS produces a message (cm mol) [1]
  varP	logical	Use variable-pressure standard state for gases? [FALSE] (see subcrt)
  IAPWS.sat	character	State of water for saturation properties [liquid] (see util.water)
  paramin	integer	Minimum number of calculations to launch parallel processes [1000] (see palply)
  ideal.H	logical	Should nonideal ignore the proton? [TRUE]

• thermo$element Dataframe containing the thermodynamic properties of elements taken from Cox et al., 1989 and Wagman et al., 1982. The standard molal entropy (\(S\)(Z)) at 25 \(^{\circ}\)C and 1 bar for the “element” of charge (Z) was calculated from \(S\)(H2,g) + 2\(S\)(Z) = 2\(S\)(H+), where the standard molal entropies of H2,g and H+ were taken from Cox et al., 1989. The mass of Z is taken to be zero. Accessing this data frame using mass or entropy will select the first entry found for a given element; i.e., values from Wagman et al., 1982 will only be retrieved if the properties of the element are not found from Cox et al., 1989.

  element	character	Symbol of element
  state	character	Stable state of element at 25 \(^{\circ}\)C and 1 bar
  source	character	Source of data
  mass	numeric	Mass of element (in natural isotopic distribution;
  		referenced to a mass of 12 for \(^{12}\)C)
  s	numeric	Entropy of the compound of the element in its stable
  		state at 25 \(^{\circ}\)C and 1 bar (cal K\(^{-1}\) mol\(^{-1}\))
  n	numeric	Number of atoms of the element in its stable

• thermo$obigt

  This dataframe is a thermodynamic database of standard molal thermodynamic properties and equations of state parameters of species. Note the following database conventions:

  • The combination of name and state defines a species in thermo$obigt. A species can not be duplicated (this is checked when running data(thermo)).

  • English names of gases are used only for the gas state. The dissolved species is named with the chemical formula. Therefore, info("oxygen") refers to the gas, and info("O2") refers to the aqueous species.

  OrganoBioGeoTherm is the name of a GUI program to use SUPCRT in Windows, produced in Harold C. Helgeson's Laboratory of Theoretical Geochemistry and Biogeochemistry at the University of California, Berkeley. The OBIGT database was originally developed for that program, and has been ported to CHNOSZ, with additional modifications. There may be an additional meaning for the acronym: “One BIG Table” of thermodynamic data.

  Each entry is referenced to one or two literature sources listed in thermo$refs. Use thermo.refs to look up the citation information for the references. OBIGT was initially built from the SUPCRT92 (Johnson et al., 1992) and slop98.dat data files (Shock et al., 1998), and the references in those files are included here. Some data in slop98.dat were corrected or modified as noted in that file; these modifications are indicated in OBIGT by having SLOP98 as one of the sources of data. Other additions or modifications used in CHNOSZ are indicated by having CHNOSZ as one of the sources of data. See the vignette Thermodynamic data in CHNOSZ for a complete description of the sources of data.

  In order to represent thermodynamic data for minerals with phase transitions, the different phases of these minerals are represented as phase species that have states denoted by cr1, cr2, etc. The standard molar thermodynamic properties at 25 \(^{\circ}\)C and 1 bar (\(T_r\) and \(P_r\)) of the cr2 phase species of minerals were generated by first calculating those of the cr1 phase species at the transition temperature (\(T_{tr}\)) and 1 bar then taking account of the volume and entropy of transition (the latter can be retrieved by combining the former with the Clausius-Clapeyron equation and values of \((dP/dT)\) of transitions taken from the SUPCRT92 data file) to calculate the standard molar entropy of the cr2 phase species at \(T_{tr}\), and taking account of the enthalpy of transition (\({\Delta}H^{\circ}\), taken from the SUPCRT92 data file) to calculate the standard molar enthalpy of the cr2 phase species at \(T_{tr}\). The standard molar properties of the cr2 phase species at \(T_{tr}\) and 1 bar calculated in this manner were combined with the equations-of-state parameters of the species to generate values of the standard molar properties at 25 \(^{\circ}\)C and 1 bar. This process was repeated as necessary to generate the standard molar properties of phase species represented by cr3 and cr4, referencing at each iteration the previously calculated values of the standard molar properties of the lower-temperature phase species (i.e., cr2 and cr3). A consequence of tabulating the standard molar thermodynamic properties of the phase species is that the values of \((dP/dT)\) and \({\Delta}H^{\circ}\) of phase transitions can be calculated using the equations of state and therefore do not need to be stored in the thermodynamic database. However, the transition temperatures (\(T_{tr}\)) generally can not be assessed by comparing the Gibbs energies of phase species and are tabulated in the database.

  The identification of species and their standard molal thermodynamic properties at 25 \({^\circ}\)C and 1 bar are located in the first 12 columns of thermo$obigt:

  name	character	Species name
  abbrv	character	Species abbreviation
  formula	character	Species formula
  state	character	Physical state
  ref1	character	Primary source
  ref2	character	Secondary source
  date	character	Date of data entry (formatted as in SUPCRT92)
  G	numeric	Standard molal Gibbs energy of formation
  		from the elements (cal mol\(^{-1}\))
  H	numeric	Standard molal enthalpy of formation
  		from the elements (cal mol\(^{-1}\))
  S	numeric	Standard molal entropy (cal mol\(^{-1}\) K\(^{-1}\))
  Cp	numeric	Standard molal isobaric heat capacity (cal mol\(^{-1}\) K\(^{-1}\))

  The meanings of the remaining columns depend on the physical state of a particular species. If it is aqueous, the values in these columns represent parameters in the revised HKF equations of state (see hkf), otherwise they denote parameters in a general equations for crystalline, gas and liquid species (see cgl). The names of these columns are compounded from those of the parameters in each of the equations of state (for example, column 13 is named a1.a). Scaling of the values by orders of magnitude is adopted for some of the parameters, following common usage in the literature.

  Columns 13-20 for aqueous species (parameters in the revised HKF equations of state):

  a1	numeric	\(a_1\times10\) (cal mol\(^{-1}\) bar\(^{-1}\))
  a2	numeric	\(a_2\times10^{-2}\) (cal mol\(^{-1}\))
  a3	numeric	\(a_3\) (cal K mol\(^{-1}\) bar\(^{-1}\))
  a4	numeric	\(a_4\times10^{-4}\) (cal mol\(^{-1}\) K)
  c1	numeric	\(c_1\) (cal mol\(^{-1}\) K\(^{-1}\))
  c2	numeric	\(c_2\times10^{-4}\) (cal mol\(^{-1}\) K)
  omega	numeric	\(\omega\times10^{-5}\) (cal mol\(^{-1}\))

  Columns 13-20 for crystalline, gas and liquid species (\(Cp=a+bT+cT^{-2}+dT^{-0.5}+eT^2+fT^{\lambda}\)).

  a	numeric	\(a\) (cal K\(^{-1}\) mol\(^{-1}\))
  b	numeric	\(b\times10^3\) (cal K\(^{-2}\) mol\(^{-1}\))
  c	numeric	\(c\times10^{-5}\) (cal K mol\(^{-1}\))
  d	numeric	\(d\) (cal K\(^{-0.5}\) mol\(^{-1}\))
  e	numeric	\(e\times10^5\) (cal K\(^{-3}\) mol\(^{-1}\))
  f	numeric	\(f\) (cal K\(^{-\lambda-1}\) mol\(^{-1}\))
  lambda	numeric	\(\lambda\) (exponent on the \(f\) term)
  T	numeric	Temperature of phase transition or upper

• thermo$refs Dataframe of references to sources of thermodynamic data.

  key	character	Source key
  author	character	Author(s)
  year	character	Year
  citation	character	Citation (journal title, volume, and article number or pages; or book or report title)
  note	character	Short description of the compounds or species in this data source
  URL	character	URL

• thermo$buffers

  Dataframe which contains definitions of buffers of chemical activity. Each named buffer can be composed of one or more species, which may include any species in the thermodynamic database and/or any protein. The calculations provided by buffer do not take into account phase transitions of minerals, so individual phase species of such minerals must be specified in the buffers.

  name	character	Name of buffer
  species	character	Name of species
  state	character	Physical state of species

• thermo$protein Data frame of amino acid compositions of selected proteins. Most of the compositions were taken from the SWISS-PROT/UniProt online database (Boeckmann et al., 2003) and the protein and organism names usually follow the conventions adopted there. In some cases different isoforms of proteins are identified using modifications of the protein names; for example, MOD5.M and MOD5.N proteins of YEAST denote the mitochondrial and nuclear isoforms of this protein. See pinfo to search this data frame by protein name, and other functions to work with the amino acid compositions.

  protein	character	Identification of protein
  organism	character	Identification of organism
  ref	character	Reference key for source of compositional data
  abbrv	character	Abbreviation or other ID for protein
  chains	numeric	Number of polypeptide chains in the protein

• thermo$groups This is a dataframe with 22 columns for the amino acid sidechain, backbone and protein backbone groups ([Ala]..[Tyr],[AABB],[UPBB]) whose rows correspond to the elements C, H, N, O, S. It is used to quickly calculate the chemical formulas of proteins that are selected using the iprotein argument in affinity.

• thermo$basis Initially NULL, reserved for a dataframe written by basis upon definition of the basis species. The number of rows of this dataframe is equal to the number of columns in “...” (one for each element).

  ...	numeric	One or more columns of stoichiometric
  		coefficients of elements in the basis species
  ispecies	numeric	Rownumber of basis species in thermo$obigt
  logact	numeric	Logarithm of activity or fugacity of basis species
  state	character	Physical state of basis species

• thermo$species Initially NULL, reserved for a dataframe generated by species to define the species of interest. The number of columns in “...” is equal to the number of basis species (i.e., rows of thermo$basis).

  ...	numeric	One or more columns of stoichiometric
  		coefficients of basis species in the species of interest
  ispecies	numeric	Rownumber of species in thermo$obigt
  logact	numeric	Logarithm of activity or fugacity of species
  state	character	Physical state of species
  name	character	Name of species

References

Cox, J. D., Wagman, D. D. and Medvedev, V. A., eds. (1989) CODATA Key Values for Thermodynamics. Hemisphere Publishing Corporation, New York, 271 p. http://www.worldcat.org/oclc/18559968

Johnson, J. W., Oelkers, E. H. and Helgeson, H. C. (1992) SUPCRT92: A software package for calculating the standard molal thermodynamic properties of minerals, gases, aqueous species, and reactions from 1 to 5000 bar and 0 to 1000\(^{\circ}\)C. Comp. Geosci. 18, 899--947. https://doi.org/10.1016/0098-3004(92)90029-Q

Shock, E. L. et al. 1998 SLOP98.dat (computer data file). http://geopig.asu.edu/supcrt92_data/slop98.dat, accessed on 2005-11-05. Current location: http://geopig.asu.edu/?q=tools.

Wagman, D. D., Evans, W. H., Parker, V. B., Schumm, R. H., Halow, I., Bailey, S. M., Churney, K. L. and Nuttall, R. L. (1982) The NBS tables of chemical thermodynamic properties. Selected values for inorganic and C\(_1\) and C\(_2\) organic substances in SI units. J. Phys. Chem. Ref. Data 11 (supp. 2), 1--392. https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf

See Also

add.obigt

Examples

# NOT RUN {
## where are the data files in CHNOSZ?
system.file("data", package="CHNOSZ")
system.file("extdata", package="CHNOSZ")

## exploring thermo$obigt
# what physical states there are
unique(thermo$obigt$state)
# formulas of ten random species
n <- nrow(thermo$obigt)
thermo$obigt$formula[runif(10)*n]
# }