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chnosz

R version 2.10.0 (2009-10-26)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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CHNOSZ version 0.9 (2009-11-30)
thermo: loaded 1997 aqueous, 3089 total species to thermo$obigt
thermo: loaded 5264 proteins to thermo$ECO
thermo: loaded 6717 proteins to thermo$SGD
thermo: loaded 4155 localizations and 3570 abundances to thermo$yeastgfp
> examples(do.png=TRUE)

CHNOSZ>   ## Don't show:
CHNOSZ> data(thermo)
thermo: loaded 1997 aqueous, 3089 total species to thermo$obigt
thermo: loaded 5264 proteins to thermo$ECO
thermo: loaded 6717 proteins to thermo$SGD
thermo: loaded 4155 localizations and 3570 abundances to thermo$yeastgfp

CHNOSZ> ## End Don't show
CHNOSZ>
CHNOSZ>   ### Getting Started
CHNOSZ>
CHNOSZ>   ## standard thermodynamic properties of species
CHNOSZ>   subcrt("H2O")
subcrt: 1 species at 15 values of T and P (wet)
$species
   name formula state ispecies
1 water     H2O   liq        1

$out
$out$water
        T          P       rho     logK         G         H        S        V       Cp
1    0.01   1.000000 0.9998289 45.03529 -56289.50 -68767.75 15.13238 18.01828 18.20559
2   25.00   1.000000 0.9970614 41.55247 -56687.71 -68316.76 16.71228 18.06830 18.01160
3   50.00   1.000000 0.9880295 38.63281 -57123.89 -67866.54 18.16234 18.23346 18.00464
4   75.00   1.000000 0.9748643 36.15435 -57594.93 -67416.13 19.50485 18.47970 18.04163
5  100.00   1.013220 0.9583926 34.02698 -58098.40 -66963.78 20.75956 18.79731 18.15793
6  125.00   2.320144 0.9390726 32.18315 -58631.71 -66507.34 21.94192 19.18403 18.33334
7  150.00   4.757169 0.9170577 30.57178 -59193.26 -66045.55 23.06398 19.64456 18.56643
8  175.00   8.918049 0.8923427 29.15313 -59781.38 -65576.63 24.13602 20.18866 18.88296
9  200.00  15.536499 0.8647434 27.89596 -60394.50 -65097.99 25.16818 20.83300 19.32884
10 225.00  25.478603 0.8338733 26.77533 -61031.25 -64605.89 26.17117 21.60424 19.97039
11 250.00  39.736493 0.7990719 25.77115 -61690.35 -64095.00 27.15694 22.54515 20.91232
12 275.00  59.431251 0.7592362 24.86701 -62370.65 -63557.52 28.14000 23.72806 22.35126
13 300.00  85.837843 0.7124075 24.04945 -63071.13 -62980.94 29.14072 25.28777 24.73943
14 325.00 120.457572 0.6545772 23.30725 -63790.84 -62341.39 30.19520 27.52189 29.44748
15 350.00 165.211289 0.5746875 22.63103 -64528.89 -61575.58 31.39713 31.34782 43.59852



CHNOSZ>   subcrt("alanine")
subcrt: 1 species at 15 values of T and P (wet)
$species
        name formula state ispecies
1618 alanine C3H7NO2    aq     1618

$out
$out$alanine
        T          P       rho     logK          G         H        S         V          Cp
1    0.01   1.000000 0.9998289 70.30240  -87870.78 -133143.0 36.59025  58.15163    13.35591
2   25.00   1.000000 0.9970614 65.09832  -88810.00 -132500.0 38.83000  60.44989    33.63547
3   50.00   1.000000 0.9880295 60.74360  -89817.71 -131567.5 41.83000  61.47819    39.95193
4   75.00   1.000000 0.9748643 57.06243  -90902.11 -130532.1 44.91490  62.00512    42.52415
5  100.00   1.013220 0.9583926 53.91911  -92062.64 -129453.2 47.90722  62.25878    43.62247
6  125.00   2.320144 0.9390726 51.20954  -93294.24 -128355.5 50.74951  62.31853    43.93543
7  150.00   4.757169 0.9170577 48.85487  -94593.11 -127255.5 53.42020  62.19875    43.66337
8  175.00   8.918049 0.8923427 46.79312  -95953.92 -126166.7 55.90616  61.87009    42.77390
9  200.00  15.536499 0.8647434 44.97516  -97370.83 -125105.3 58.19021  61.25002    41.02070
10 225.00  25.478603 0.8338733 43.36142  -98837.31 -124096.1 60.23970  60.16335    37.79811
11 250.00  39.736493 0.7990719 41.91942 -100345.70 -123184.4 61.98685  58.23514    31.65498
12 275.00  59.431251 0.7592362 40.62173 -101886.14 -122466.1 63.28058  54.58032    18.65083
13 300.00  85.837843 0.7124075 39.44393 -103444.11 -122181.7 63.73470  46.71705   -14.64596
14 325.00 120.457572 0.6545772 38.36121 -104992.85 -123133.0 62.06967  25.31938  -136.10771
15 350.00 165.211289 0.5746875 37.33653 -106459.36 -130048.2 50.83581 -73.97749 -1156.84047



CHNOSZ>   # names of proteins have an underscore
CHNOSZ>   subcrt("LYSC_CHICK")
protein: found LYSC_CHICK (C613H959N193O185S10, 129 residues)
subcrt: 1 species at 15 values of T and P (wet)
$species
           name             formula state ispecies
3090 LYSC_CHICK C613H959N193O185S10    aq     3090

$out
$out$LYSC_CHICK
        T          P       rho     logK        G         H         S        V        Cp
1    0.01   1.000000 0.9998289 3286.749 -4108100 -10510350  3684.406 10049.21  4409.319
2   25.00   1.000000 0.9970614 3083.063 -4206050 -10369700  4175.860 10420.95  6415.518
3   50.00   1.000000 0.9880295 2919.759 -4317263 -10199867  4722.506 10600.23  7073.981
4   75.00   1.000000 0.9748643 2788.465 -4442106 -10018826  5261.992 10708.15  7376.581
5  100.00   1.013220 0.9583926 2682.511 -4580176  -9832092  5779.892 10782.93  7548.444
6  125.00   2.320144 0.9390726 2596.618 -4730554  -9641537  6273.262 10840.94  7665.198
7  150.00   4.757169 0.9170577 2526.937 -4892670  -9448098  6742.892 10891.15  7760.881
8  175.00   8.918049 0.8923427 2470.400 -5065799  -9251881  7190.897 10940.05  7856.945
9  200.00  15.536499 0.8647434 2424.600 -5249238  -9052464  7620.111 10994.29  7974.628
10 225.00  25.478603 0.8338733 2387.629 -5442322  -8848798  8034.140 11063.40  8146.453
11 250.00  39.736493 0.7990719 2357.970 -5644451  -8638774  8438.039 11165.02  8439.891
12 275.00  59.431251 0.7592362 2334.423 -5855127  -8417956  8840.380 11338.89  9030.924
13 300.00  85.837843 0.7124075 2316.077 -6074053  -8175407  9259.928 11694.88 10513.444
14 325.00 120.457572 0.6545772 2302.355 -6301438  -7875355  9754.686 12644.61 15882.325
15 350.00 165.211289 0.5746875 2293.455 -6539432  -7308661 10654.664 17027.35 60917.017



CHNOSZ>   # custom temperature range
CHNOSZ>   T <- seq(0,500,100)

CHNOSZ>   subcrt("H2O",T=T,P=1000)
subcrt: 1 species at 6 values of T and P (wet)
$species
   name formula state ispecies
1 water     H2O   liq        1

$out
$out$water
      T    P       rho     logK         G         H        S        V       Cp
1 1e-02 1000 1.0453039 44.69896 -55869.12 -68357.26 15.09618 17.23441 16.83217
2 1e+02 1000 0.9997047 33.76984 -57659.35 -66636.81 20.45920 18.02052 17.39197
3 2e+02 1000 0.9237063 27.67746 -59921.46 -64877.46 24.63450 19.50317 17.82843
4 3e+02 1000 0.8232085 23.85604 -62563.91 -63049.14 28.13676 21.88413 18.90798
5 4e+02 1000 0.6925791 21.27795 -65538.85 -61056.82 31.33601 26.01176 21.14435
6 5e+02 1000 0.5282114 19.45590 -68829.13 -58794.93 34.46421 34.10604 23.92897



CHNOSZ>   # temperature - pressure grid
CHNOSZ>   P <- seq(1000,4000,1000)

CHNOSZ>   subcrt("H2O",T=T,P=P,grid="P")
subcrt: 1 species at 24 values of T and P (wet)
$species
   name formula state ispecies
1 water     H2O   liq        1

$out
$out$water
     T    P       rho     logK         G         H        S        V       Cp
1    0 1000 1.0453039 44.70060 -55869.12 -68357.26 15.09618 17.23441 16.83217
2  100 1000 0.9997047 33.76984 -57659.35 -66636.81 20.45920 18.02052 17.39197
3  200 1000 0.9237063 27.67746 -59921.46 -64877.46 24.63450 19.50317 17.82843
4  300 1000 0.8232085 23.85604 -62563.91 -63049.14 28.13676 21.88413 18.90798
5  400 1000 0.6925791 21.27795 -65538.85 -61056.82 31.33601 26.01176 21.14435
6  500 1000 0.5282114 19.45590 -68829.13 -58794.93 34.46421 34.10604 23.92897
7    0 2000 1.0811283 44.37678 -55464.39 -67982.69 14.98576 16.66333 16.30348
8  100 2000 1.0334820 33.52187 -57235.96 -66308.09 20.20549 17.43156 16.91712
9  200 2000 0.9664077 27.46718 -59466.20 -64605.61 24.24685 18.64141 17.10929
10 300 2000 0.8856264 23.66428 -62061.00 -62879.52 27.55524 20.34176 17.48122
11 400 2000 0.7926555 21.09085 -64962.58 -61098.54 30.41795 22.72766 18.15935
12 500 2000 0.6911768 19.25955 -68134.50 -59252.24 32.97429 26.06453 18.69974
13   0 3000 1.1091248 44.06233 -55071.38 -67618.58 14.87997 16.24272 15.55743
14 100 3000 1.0624799 33.28130 -56825.20 -65981.48 19.97998 16.95580 16.59773
15 200 3000 1.0009181 27.26508 -59028.65 -64315.32 23.93563 17.99867 16.67637
16 300 3000 0.9308254 23.48365 -61587.30 -62644.80 27.13829 19.35400 16.77910
17 400 3000 0.8538773 20.92133 -64440.43 -60952.19 29.85969 21.09811 17.08586
18 500 3000 0.7728854 19.09379 -67548.09 -59230.72 32.24365 23.30902 17.30423
19   0 4000 1.1322377 43.75500 -54687.25 -67251.91 14.81606 15.91115 14.29720
20 100 4000 1.0879893 33.04680 -56424.82 -65657.47 19.77532 16.55825 16.36203
21 200 4000 1.0304204 27.06931 -58604.82 -64016.37 23.67170 17.48335 16.38994
22 300 4000 0.9673852 23.31074 -61133.84 -62381.24 26.80696 18.62257 16.34873
23 400 4000 0.9001040 20.76205 -63949.83 -60739.96 29.44616 20.01458 16.49248
24 500 4000 0.8304559 18.94215 -67011.63 -59083.92 31.73966 21.69315 16.60454



CHNOSZ>   ## information about species
CHNOSZ>   # query the database using formulas
CHNOSZ>   info("C6H12O6")
info: C6H12O6 matches these species:
          name     abbrv formula state source1
1885   glucose   glucose C6H12O6    aq    AP01
1886   mannose   mannose C6H12O6    aq    AP01
1887 galactose galactose C6H12O6    aq    AP01
1888  fructose  fructose C6H12O6    aq    AP01
1889   sorbose   sorbose C6H12O6    aq    AP01
info: 1885 refers to glucose aq (AP01, 24.Aug.06).

CHNOSZ>   info("SiO2")
info: SiO2 matches these species:
                   name   abbrv formula state source1
72                 SiO2    SiO2    SiO2    aq   SHS89
2018   amorphous silica Amor-Sl    SiO2    cr  HDN+78
2053         chalcedony     Cha    SiO2    cr  HDN+78
2067            coesite     Cos    SiO2   cr1  HDN+78
2068            coesite     Cos    SiO2   cr2  HDN+78
2074       cristobalite     Crs    SiO2   cr1  HDN+78
2075       cristobalite     Crs    SiO2   cr2  HDN+78
2076 cristobalite,alpha   A-Crs    SiO2    cr  HDN+78
2077  cristobalite,beta   B-Crs    SiO2    cr  HDN+78
2202             quartz     Qtz    SiO2   cr1  HDN+78
2203             quartz     Qtz    SiO2   cr2  HDN+78
info: 72 refers to SiO2 aq (SHS89, 13.Jan.89).

CHNOSZ>   # query using names
CHNOSZ>   info("quartz")
info: quartz (SiO2) available in cr1, cr2.
info: 2202 refers to quartz, SiO2 cr1 (HDN+78, 5.May.78).

CHNOSZ>   t <- info(c("glucose","mannose"))
info: 1885 refers to glucose, C6H12O6 aq (AP01, 24.Aug.06).
info: 1886 refers to mannose, C6H12O6 aq (AP01, 24.Aug.06).

CHNOSZ>   # show the equations of state parameters
CHNOSZ>   info(t)
info: Cp (from EOS) of glucose aq differs by 1.31 from tabulated value.
info: Cp (from EOS) of mannose aq differs by 1.46 from tabulated value.
        name   abbrv formula state source1 source2      date         G         H        S       Cp
1885 glucose glucose C6H12O6    aq    AP01    <NA> 24.Aug.06 -218905.4 -301670.7 64.89006 86.75908
1886 mannose mannose C6H12O6    aq    AP01    <NA> 24.Aug.06 -217731.8 -300827.0 63.79063 81.26195
         V       a1        a2        a3        a4       c1        c2     omega Z
1885 112.2 2.552581 310.70746 12.380497 -48757.17 89.72275  -78871.9 -157743.8 0
1886 111.9 2.684034  47.80115  1.720841 -27485.66 91.32409 -113049.7 -157743.8 0

CHNOSZ>   # approximate matches for names or formulas
CHNOSZ>   info("acid ")
info: no match for acid .
info: similar species names, abbreviations, or formulas are:
 [1] "a-aminobutyric acid"     "formic acid"             "acetic acid"
 [4] "propanoic acid"          "n-butanoic acid"         "n-pentanoic acid"
 [7] "n-hexanoic acid"         "n-heptanoic acid"        "n-octanoic acid"
[10] "n-nonanoic acid"         "n-decanoic acid"         "n-undecanoic acid"
[13] "n-dodecanoic acid"       "n-benzoic acid"          "o-toluic acid"
[16] "m-toluic acid"           "p-toluic acid"           "oxalic acid"
[19] "malonic acid"            "succinic acid"           "glutaric acid"
[22] "adipic acid"             "pimelic acid"            "suberic acid"
[25] "azelaic acid"            "sebacic acid"            "glycolic acid"
[28] "lactic acid"             "2-hydroxybutanoic acid"  "2-hydroxypentanoic acid"
[31] "2-hydroxyhexanoic acid"  "2-hydroxyheptanoic acid" "2-hydroxyoctanoic acid"
[34] "2-hydroxynonanoic acid"  "2-hydroxydecanoic acid"  "aspartic acid"
[37] "glutamic acid"           "citric acid"             "phosphoric acid"
[40] "acide fulvique"          "acide humique"           "n-tridecanoic acid"
[43] "n-tetradecanoic acid"    "n-pentadecanoic acid"    "n-hexadecanoic acid"
[46] "n-heptadecanoic acid"    "n-octadecanoic acid"     "n-nonadecanoic acid"
[49] "n-eicosanoic acid"       "hydrofluoric acid"

CHNOSZ>   info("SiO2 ")
info: no match for SiO2 .
info: approximately matching species are:
                   name   abbrv formula state
72                 SiO2    SiO2    SiO2    aq
2018   amorphous silica Amor-Sl    SiO2    cr
2053         chalcedony     Cha    SiO2    cr
2067            coesite     Cos    SiO2   cr1
2068            coesite     Cos    SiO2   cr2
2074       cristobalite     Crs    SiO2   cr1
2075       cristobalite     Crs    SiO2   cr2
2076 cristobalite,alpha   A-Crs    SiO2    cr
2077  cristobalite,beta   B-Crs    SiO2    cr
2202             quartz     Qtz    SiO2   cr1
2203             quartz     Qtz    SiO2   cr2

CHNOSZ>   ## standard thermodynamic properties of reactions
CHNOSZ>   # fermentation example
CHNOSZ>   info(c("fructose","ethanol"))
info: ethanol (C2H5OH) available in aq, liq, gas.
info: 1888 refers to fructose, C6H12O6 aq (AP01, 24.Aug.06).
info: 1344 refers to ethanol, C2H5OH aq (AH97b, CHNOSZ, 1.Sep.06).

CHNOSZ>   subcrt(c("fructose","C2H5OH","CO2"),c(-1,2,2))
subcrt: 3 species at 15 values of T and P (wet)
$reaction
     coeff     name formula state ispecies
1888    -1 fructose C6H12O6    aq     1888
1344     2  ethanol  C2H5OH    aq     1344
69       2      CO2     CO2    aq       69

$out
        T          P       rho     logK         G         H         S          V           Cp
1    0.01   1.000000 0.9998289 41.45637 -51816.20 -39889.98  43.92883   57.04921   242.587540
2   25.00   1.000000 0.9970614 38.94880 -53135.66 -35300.96  60.06399   62.83007   145.362462
3   50.00   1.000000 0.9880295 37.04231 -54772.12 -32133.61  70.28277   65.22858   112.661349
4   75.00   1.000000 0.9748643 35.54849 -56629.78 -29533.73  78.03941   66.22470    96.863927
5  100.00   1.013220 0.9583926 34.35741 -58662.58 -27242.08  84.40003   66.37254    87.047672
6  125.00   2.320144 0.9390726 33.39513 -60839.70 -25161.51  89.79420   65.80328    79.370703
7  150.00   4.757169 0.9170577 32.61014 -63139.96 -23264.68  94.40778   64.45952    71.848904
8  175.00   8.918049 0.8923427 31.96335 -65544.00 -21565.20  98.29783   62.09697    62.862352
9  200.00  15.536499 0.8647434 31.42400 -68032.68 -20118.75 101.42091   58.20895    50.308864
10 225.00  25.478603 0.8338733 30.96659 -70584.72 -19044.10 103.61135   51.79505    30.436868
11 250.00  39.736493 0.7990719 30.56824 -73173.52 -18581.82 104.49216   40.76468    -4.988893
12 275.00  59.431251 0.7592362 30.20578 -75761.19 -19255.00 103.21913   20.22536   -77.810835
13 300.00  85.837843 0.7124075 29.85052 -78284.81 -22389.91  97.65030  -23.49959  -262.051963
14 325.00 120.457572 0.6545772 29.45436 -80615.20 -32402.65  80.72544 -141.75144  -931.318847
15 350.00 165.211289 0.5746875 28.88855 -82371.25 -75324.04  11.42675 -688.77988 -6549.616632


CHNOSZ>   # weathering example -- also see transfer()
CHNOSZ>   subcrt(c("k-feldspar","H2O","H+","kaolinite","K+","SiO2"),
CHNOSZ+     c(-2,-1,-2,1,2,4))
subcrt: 6 species at 15 values of T and P (wet)
$reaction
     coeff       name       formula state ispecies
2141    -2 k-feldspar    K(AlSi3)O8    cr     2141
1       -1      water           H2O   liq        1
3       -2         H+            H+    aq        3
2146     1  kaolinite Al2Si2O5(OH)4    cr     2146
6        2         K+            K+    aq        6
72       4       SiO2          SiO2    aq       72

$out
        T          P       rho      logK         G           H          S          V           Cp
1    0.01   1.000000 0.9998289 -9.451752 11813.720  39338.2001 101.037908  -44.45760  -941.315278
2   25.00   1.000000 0.9970614 -7.360641 10041.711  24831.7553  49.857720  -54.01690  -349.644469
3   50.00   1.000000 0.9880295 -6.136706  9073.958  18785.9482  30.286323  -59.01240  -163.141374
4   75.00   1.000000 0.9748643 -5.298797  8441.137  15826.5800  21.428921  -62.44680   -83.488468
5  100.00   1.013220 0.9583926 -4.665077  7965.252  14287.7248  17.144501  -65.31326   -43.880256
6  125.00   2.320144 0.9390726 -4.151839  7563.877  13483.8390  15.047763  -68.08975   -22.842309
7  150.00   4.757169 0.9170577 -3.717503  7197.853  13070.3223  14.030222  -71.12250   -11.993008
8  175.00   8.918049 0.8923427 -3.339037  6847.025  12844.9084  13.501163  -74.74984    -7.903078
9  200.00  15.536499 0.8647434 -3.003487  6502.522  12651.2416  13.067065  -79.46467   -10.251158
10 225.00  25.478603 0.8338733 -2.704162  6163.823  12316.6809  12.363201  -86.27006   -20.738785
11 250.00  39.736493 0.7990719 -2.439021  5838.469  11610.2462  10.966953  -97.24159   -43.800069
12 275.00  59.431251 0.7592362 -2.210199  5543.551  10165.2552   8.267154 -116.71119   -91.071487
13 300.00  85.837843 0.7124075 -2.025097  5310.940   7209.9258   3.025926 -155.04184  -202.796812
14 325.00 120.457572 0.6545772 -1.903001  5208.424    247.5404  -8.732556 -246.90325  -584.941499
15 350.00 165.211289 0.5746875 -1.911364  5449.958 -24848.5653 -49.245722 -616.91895 -3449.033414


CHNOSZ>   # partial reaction auto-completion is possible
CHNOSZ>   basis(c("SiO2","H2O","K+","H+","O2"))
     H K O Si Z ispecies logact state
SiO2 0 0 2  1 0       72      0    aq
H2O  2 0 1  0 0        1      0   liq
K+   0 1 0  0 1        6      0    aq
H+   1 0 0  0 1        3      0    aq
O2   0 0 2  0 0     2852      0   gas

CHNOSZ>   subcrt(c("k-feldspar","kaolinite"),c(-2,1))
subcrt: 2 species at 15 values of T and P
subcrt: reaction is not balanced; it is missing this composition:
 K O Si  H
 2 7  4 -4
subcrt: adding missing composition from basis definition and restarting...
subcrt: 6 species at 15 values of T and P (wet)
$reaction
     coeff       name       formula state ispecies
2141    -2 k-feldspar    K(AlSi3)O8    cr     2141
2146     1  kaolinite Al2Si2O5(OH)4    cr     2146
72       4       SiO2          SiO2    aq       72
1       -1      water           H2O   liq        1
6        2         K+            K+    aq        6
3       -2         H+            H+    aq        3

$out
        T          P      logK         G           H          S          V           Cp
1    0.01   1.000000 -9.451752 11813.720  39338.2001 101.037908  -44.45760  -941.315278
2   25.00   1.000000 -7.360641 10041.711  24831.7553  49.857720  -54.01690  -349.644469
3   50.00   1.000000 -6.136706  9073.958  18785.9482  30.286323  -59.01240  -163.141374
4   75.00   1.000000 -5.298797  8441.137  15826.5800  21.428921  -62.44680   -83.488468
5  100.00   1.013220 -4.665077  7965.252  14287.7248  17.144501  -65.31326   -43.880256
6  125.00   2.320144 -4.151839  7563.877  13483.8390  15.047763  -68.08975   -22.842309
7  150.00   4.757169 -3.717503  7197.853  13070.3223  14.030222  -71.12250   -11.993008
8  175.00   8.918049 -3.339037  6847.025  12844.9084  13.501163  -74.74984    -7.903078
9  200.00  15.536499 -3.003487  6502.522  12651.2416  13.067065  -79.46467   -10.251158
10 225.00  25.478603 -2.704162  6163.823  12316.6809  12.363201  -86.27006   -20.738785
11 250.00  39.736493 -2.439021  5838.469  11610.2462  10.966953  -97.24159   -43.800069
12 275.00  59.431251 -2.210199  5543.551  10165.2552   8.267154 -116.71119   -91.071487
13 300.00  85.837843 -2.025097  5310.940   7209.9258   3.025926 -155.04184  -202.796812
14 325.00 120.457572 -1.903001  5208.424    247.5404  -8.732556 -246.90325  -584.941499
15 350.00 165.211289 -1.911364  5449.958 -24848.5653 -49.245722 -616.91895 -3449.033414


CHNOSZ>   ## chemical affinities
CHNOSZ>   # basis species
CHNOSZ>   basis(c("CO2","H2O","O2"))
basis: changed basis to CO2 H2O O2.
    C H O ispecies logact state
CO2 1 0 2       69      0    aq
H2O 0 2 1        1      0   liq
O2  0 0 2     2852      0   gas

CHNOSZ>   # species of interest
CHNOSZ>   species(c("CH4","C2H4O2","CO2"))

CHNOSZ>   # chemical affinities of formation reactions
CHNOSZ>   # take off $values for complete output
CHNOSZ>   affinity()$values
affinity: temperature is 25 C
energy.args: pressure is Psat
subcrt: 6 species at 298.15 K and 1 bar (wet)
$`1291`
[1] -141.7361

$`486`
[1] -145.8850

$`69`
[1] 3


CHNOSZ>   affinity(O2=c(-90,-60,5))$values
affinity: temperature is 25 C
energy.args: pressure is Psat
energy.args: variable 1 is O2 at 5 increments from -90 to -60
subcrt: 6 species at 298.15 K and 1 bar (wet)
$`1291`
         [,1]     [,2]    [,3]     [,4]      [,5]
[1,] 38.26386 23.26386 8.26386 -6.73614 -21.73614

$`486`
         [,1]     [,2]     [,3]      [,4]      [,5]
[1,] 34.11504 19.11504 4.115043 -10.88496 -25.88496

$`69`
     [,1] [,2] [,3] [,4] [,5]
[1,]    3    3    3    3    3


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