man Chemeq (1): Chemical Equation Parser and Renderer

SYNOPSIS

chemeq [-M] [-m] [-l] [-c] [-w] [-C] [-e] [-s] [-n] [-W]
chemeq [-h] [-v]

DESCRIPTION

chemeq

is a chemical equation analyzer. It is a fast lexical and syntaxic analyser which helps to find out chemical informations embedded in source chemical equations. Data can be output in various sophisticated formats, depending on options. 'chemeq' defaults to 'chemeq -mlcwCn'.

OPTIONS

-M

: Outputs al list of space separated molecular weights.

-m

: Outputs a minimal output. It allows chemeq to be idempotent, i.e. the command 'chemeq | chemeq' is equivalent to 'chemeq'.

-l

: Outputs a LaTeX string representing the chemical equation.

-c

: Outputs a message giving informations about the Conservation of elements and charges in the equation. 'OK' means that both elements and electric charges are balanced.

-w

: Outputs the LaTeX string representing the Gulder-Waage equation related to the input chemical equation, or the Nernst equation, if the input equation is a redox semi-equation.

-C

: Outputs a detailed Count of the molecules and atoms contained in each member of the chemical equation. For example for the equation "H2_g + 1/2 O2_g --> H2O" it outputs: "H2_g|H:1*2, 1/2 O2_g|O:1/2*2; H2O|H:1*2 O:1*1"

-e

: Outputs a detailed count of the Electrical charges.

-s

: Outputs a list of the chemical Species.

-n

: Outputs a Normalized string accounting for the input equation. Two chemical equations having the same normalized string are chemically equivalent, even if the molecules are scrambled around and the coefficient are not equal but proportionnal.

-W

: Changes the behavior of the renderer for some versions of Wims : works around a bug whith the macro \rightarrow.

-h

: Displays Help.

-v

: Displays the Version number

ENVIRONMENT

chemeq_input, w_chemeq_input

: if set, this variables's value overrides the standard input. If this variable is not set, the variable w_chemeq_input is taken in account (useful for the WIMS server). See above (useful for the WIMS server).

chemeq_option

: if set, this variable's value overrides the options.If this variable is not set, the variable w_chemeq_option is taken in account (useful for the WIMS server).

w_chemeq_option

: See above (useful for the WIMS server).

EXAMPLES

echo "1/2 Cu^2+ + OH- -> 1/2Cu(OH)2s" | chemeq

: will display informations about the reaction of hydroxyde and Cu II ions.

echo "MnO4^- + 8H3O^+ + 5e- --> Mn^2+ + 12 H2O" | chemeq

: will display informations about the reaction of reduction of permanganate ions in an acid environment.

echo "MnO4^- + 8H3O^+ + 5e- --> Mn^2+ + 12 H2O" | chemeq -w

: will display the LaTeX format for the Nernst law related to the reduction of permanganate ions in an acid environment.

echo "MnO4^- + 8H3O^+ + 5e- --> Mn^2+ + 8 H2O" | chemeq -c

: will highlight the lack of conservation of elements H and O (water molecules are not well balanced).

NOTES

syntax of ions

: allthough in some cases, shorter expressions are sucessfully parsed, it is safer to consider that an "up arrow" (^) must be put before the charge symbols of an ion. Examples : H3O^+, Fe(CN)6^4-, OH^-

Composing chemical equations

Two operators are defined, # as an additive oprator and ~ (tilde) as a substractive operator: they allow to compose several chemical equations

echo "MnO4^- + 8H3O^+ + 5e- --> Mn^2+ + 8 H2O ~ 5Fe^3+ + 5e- -> 5Fe^2+" | chemeq

will display the pure redox equation from the first equation, minus the second one. Electrons are simplified. So it will be equivalent to:

echo "MnO4^- + 8H3O^+ + 5Fe^2+--> Mn^2+ + 8 H2O + 5Fe^3+" | chemeq which is their combination.

Mutiplying a chemical equation by one coefficient

The operator * permits to multiply a whole equation by one coefficient which may be a fraction. Here is an example:

echo "5 * Fe^3+ + e- -> Fe^2+" | chemeq

will be equivalent to

echo "5Fe^3+ + 5e- -> 5Fe^2+" | chemeq

Combining chemical equations, with coefficients

The two previous techniques can be used at the same time, which enables you to make more comlicated combinations, like this one:

echo "Fe^3+ + e^- -> Fe^2+ (0.77 V) # Fe^2+ + 6CN^- -> Fe(CN)6^4- (Kfa=1e24) ~ Fe^3+ + 6CN^- -> Fe(CN)6^3- (Kfb=1e31)" | chemeq

which will work as expected, and yeld a good value for the stan- dard potential of the redox couple of hexacyanoferrate II and III ions.

KNOWN BUGS

When not specified, chemical entities coming from the standard input are believed to be in aqueous solutions. Water is considered by default as the main solvent. Only one liquid (aqueous) phase is currently taken in account. All solid chemical entities are considered as parts of separated phases. Suffixes _s, _g and _aq can be used to enforce the type of some chemical entities. There may be problemes when you write a standard potential with no decimal dot. For example, the entry Mn^2+ + 2e^- -> Mn_s (-1 V) would trigger an error. Then write Mn^2+ + 2e^- -> Mn_s (-1.0 V) or the more accurate value Mn^2+ + 2e^- -> Mn_s (-1.18 V) and there will be no error.

AUTHOR

Georges Khaznadar <[email protected]>

: Wrote this manpage.

COPYRIGHT

Redistribution and use of this manpage in source and binary forms, with or without modification, are permitted under the terms of the GNU General Public Licenses, version 2

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