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basis> ## Don't show:
basis> data(thermo)
thermo$obigt has 1800 aqueous, 2925 total species
basis> ## End Don't show
basis> ## define basis species
basis> basis("O2") # one element
O ispecies logact state
O2 2 2691 0 gas
basis> basis(c("H2O","O2")) # two elements
basis: changed basis to H2O O2.
H O ispecies logact state
H2O 2 1 1 0 liq
O2 0 2 2691 0 gas
basis> basis(c("H2O","O2","H+"))
basis: changed basis to H2O O2 H+.
H O Z ispecies logact state
H2O 2 1 0 1 0 liq
O2 0 2 0 2691 0 gas
H+ 1 0 1 3 0 aq
basis> ## Not run:
basis> ##D # marked dontrun because they produce intentional errors
basis> ##D # fewer basis species than elements
basis> ##D basis(c("H2O","H+"))
basis> ##D # more basis species than elements
basis> ##D basis(c("H2O","O2","H2","H+"))
basis> ##D # non-independent basis species
basis> ##D basis(c("CO2","H2O","HCl","Cl-","H+"))
basis> ##D
basis> ## End(Not run)
basis>
basis> ## specify activities and states
basis> basis(c("H2O","O2","CO2"),c(-2,-78,-3),c("liq","gas","aq"))
C H O ispecies logact state
H2O 0 2 1 1 -2 liq
O2 0 0 2 2691 -78 gas
CO2 1 0 2 69 -3 aq
basis> # change logarithms of activities/fugacities
basis> basis(c("H2O","O2"),c(0,-80))
C H O ispecies logact state
H2O 0 2 1 1 0 liq
O2 0 0 2 2691 -80 gas
CO2 1 0 2 69 -3 aq
basis> # change state of CO2
basis> basis("CO2","gas")
C H O ispecies logact state
H2O 0 2 1 1 0 liq
O2 0 0 2 2691 -80 gas
CO2 1 0 2 2683 -3 gas
basis> ## get the basis stoichiometry of species
basis> basis("CHNOS")
C H N O S ispecies logact state
CO2 1 0 0 2 0 69 -3 aq
H2O 0 2 0 1 0 1 0 liq
NH3 0 3 1 0 0 68 -4 aq
H2S 0 2 0 0 1 70 -7 aq
O2 0 0 0 2 0 2691 -80 gas
basis> ispecies <- info(c("glutamic acid","phenylalanine"))
info: glutamic acid (C5H9NO4) available in aq, cr.
info: phenylalanine (C9H11NO2) available in aq, cr.
info: 1514 refers to glutamic acid, C5H9NO4 aq (AH97b, DLH06, 25.Aug.06)
info: 1526 refers to phenylalanine, C9H11NO2 aq (AH97b, DLH06, 25.Aug.06)
basis> basis(ispecies)
CO2 H2O NH3 H2S O2
1 5 3 1 0 -4.5
2 9 4 1 0 -10.0
basis> ## changing basis species
basis> b1 <- basis("CHNOS+")
basis> # different basis species, same elements
basis> b2 <- basis(c("HCO3-","H2O","NH4+","HS-","H2","H+"))
basis: changed basis to HCO3- H2O NH4+ HS- H2 H+.
basis: elements unchanged. maintaining elemental chemical potentials.
basis> # back to starting basis species
basis> b3 <- basis(c("CO2","H2O","NH3","H2S","O2","H+"))
basis: changed basis to CO2 H2O NH3 H2S O2 H+.
basis: elements unchanged. maintaining elemental chemical potentials.
basis> stopifnot(all.equal(b1$logact,b3$logact))
basis> ## changing the basis species
basis> basis("MgCHNOPS+")
C H Mg N O P S Z ispecies logact state
Mg+2 0 0 1 0 0 0 0 2 9 -3 aq
CO2 1 0 0 0 2 0 0 0 69 -3 aq
H2O 0 2 0 0 1 0 0 0 1 0 liq
NH3 0 3 0 1 0 0 0 0 68 -4 aq
H3PO4 0 3 0 0 4 1 0 0 73 -3 aq
H2S 0 2 0 0 0 0 1 0 70 -7 aq
e- 0 0 0 0 0 0 0 -1 2 -7 aq
H+ 0 1 0 0 0 0 0 1 3 -7 aq
basis> # load species whose names are like "ATP"
basis> species(info("ATP ")[[1]])
info: no match for ATP .
info: approximately matching species are:
name abbrv formula state
1678 ATP-4 <NA> C10H12N5O13P3-4 aq
1679 HATP-3 <NA> C10H13N5O13P3-3 aq
1680 H2ATP-2 <NA> C10H14N5O13P3-2 aq
1681 H3ATP- <NA> C10H15N5O13P3- aq
1682 H4ATP <NA> C10H16N5O13P3 aq
1703 dATP-4 <NA> C10H12N5O12P3-4 aq
1704 dHATP-3 <NA> C10H13N5O12P3-3 aq
1705 dH2ATP-2 <NA> C10H14N5O12P3-2 aq
1706 dH3ATP- <NA> C10H15N5O12P3- aq
1707 dH4ATP <NA> C10H16N5O12P3 aq
1736 MgATP-2 MgATP-2 MgC10H12N5O13P3-2 aq
1737 MgHATP- MgHATP- MgC10H13N5O13P3- aq
1738 MgH2ATP MgH2ATP MgC10H14N5O13P3 aq
1739 Mg2ATP Mg2ATP Mg2C10H12N5O13P3 aq
Mg+2 CO2 H2O NH3 H3PO4 H2S e- H+ ispecies logact state name
1 0 10 -19 5 3 0 30 26 1678 -3 aq ATP-4
2 0 10 -19 5 3 0 30 27 1679 -3 aq HATP-3
3 0 10 -19 5 3 0 30 28 1680 -3 aq H2ATP-2
4 0 10 -19 5 3 0 30 29 1681 -3 aq H3ATP-
5 0 10 -19 5 3 0 30 30 1682 -3 aq H4ATP
6 0 10 -20 5 3 0 32 28 1703 -3 aq dATP-4
7 0 10 -20 5 3 0 32 29 1704 -3 aq dHATP-3
8 0 10 -20 5 3 0 32 30 1705 -3 aq dH2ATP-2
9 0 10 -20 5 3 0 32 31 1706 -3 aq dH3ATP-
10 0 10 -20 5 3 0 32 32 1707 -3 aq dH4ATP
11 1 10 -19 5 3 0 30 26 1736 -3 aq MgATP-2
12 1 10 -19 5 3 0 30 27 1737 -3 aq MgHATP-
13 1 10 -19 5 3 0 30 28 1738 -3 aq MgH2ATP
14 2 10 -19 5 3 0 30 26 1739 -3 aq Mg2ATP
basis> # different basis species, but same elements
basis> basis(c("MgSO4","HCHO","CH4","NO","CO","H3PO4","CS2","OH-"))
basis: changed basis to MgSO4 HCHO CH4 NO CO H3PO4 CS2 OH-.
basis: elements unchanged. maintaining elemental chemical potentials.
basis: restoring species using new basis definition.
C H Mg N O P S Z ispecies logact state
MgSO4 0 0 1 0 4 0 1 0 881 77.551602 aq
HCHO 1 2 0 0 1 0 0 0 255 -65.913719 aq
CH4 1 4 0 0 0 0 0 0 80 -93.478925 aq
NO 0 0 0 1 1 0 0 0 1486 1.890505 aq
CO 1 0 0 0 1 0 0 0 252 -36.043086 aq
H3PO4 0 3 0 0 4 1 0 0 73 -3.000000 aq
CS2 1 0 0 0 0 0 2 0 2597 -22.719651 liq
OH- 0 1 0 0 1 0 0 -1 21 -6.995296 aq
basis> species() # formation reactions were updated
MgSO4 HCHO CH4 NO CO H3PO4 CS2 OH- ispecies logact state name
1 0 -36.5 18.0 5 28.5 3 0.0 4 1678 -3 aq ATP-4
2 0 -33.5 17.0 5 26.5 3 0.0 3 1679 -3 aq HATP-3
3 0 -30.5 16.0 5 24.5 3 0.0 2 1680 -3 aq H2ATP-2
4 0 -27.5 15.0 5 22.5 3 0.0 1 1681 -3 aq H3ATP-
5 0 -24.5 14.0 5 20.5 3 0.0 0 1682 -3 aq H4ATP
6 0 -38.5 19.0 5 29.5 3 0.0 4 1703 -3 aq dATP-4
7 0 -35.5 18.0 5 27.5 3 0.0 3 1704 -3 aq dHATP-3
8 0 -32.5 17.0 5 25.5 3 0.0 2 1705 -3 aq dH2ATP-2
9 0 -29.5 16.0 5 23.5 3 0.0 1 1706 -3 aq dH3ATP-
10 0 -26.5 15.0 5 21.5 3 0.0 0 1707 -3 aq dH4ATP
11 1 -40.5 20.5 5 30.5 3 -0.5 2 1736 -3 aq MgATP-2
12 1 -37.5 19.5 5 28.5 3 -0.5 1 1737 -3 aq MgHATP-
13 1 -34.5 18.5 5 26.5 3 -0.5 0 1738 -3 aq MgH2ATP
14 2 -44.5 23.0 5 32.5 3 -1.0 0 1739 -3 aq Mg2ATP
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Previous: makeup