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[4] subcrt

## Don't show: data(thermo)
thermo$obigt: 1809 aqueous, 3368 total species
## End(Don't show) ## properties of species subcrt("water")
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 -62301.65 -62867.52 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
# calculating at different temperatures subcrt("water", T=seq(0, 100, 10))
subcrt: 1 species at 11 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 1.00000 0.9998289 45.03529 -56289.50 -68767.75 15.13238 18.01828 18.20559 2 1e+01 1.00000 0.9996022 43.56558 -56443.94 -68586.98 15.78234 18.01988 18.03185 3 2e+01 1.00000 0.9982319 42.19946 -56604.91 -68406.81 16.40767 18.04711 18.01124 4 3e+01 1.00000 0.9956535 40.92791 -56772.02 -68226.70 17.01183 18.09384 18.01160 5 4e+01 1.00000 0.9922098 39.74171 -56945.08 -68046.60 17.59634 18.15664 18.00788 6 5e+01 1.00000 0.9880295 38.63281 -57123.89 -67866.54 18.16234 18.23346 18.00464 7 6e+01 1.00000 0.9831991 37.59415 -57308.27 -67686.48 18.71111 18.32304 18.00972 8 7e+01 1.00000 0.9777800 36.61946 -57498.06 -67506.30 19.24397 18.42460 18.02755 9 8e+01 1.00000 0.9718175 35.70322 -57693.10 -67325.88 19.76223 18.53764 18.05904 10 9e+01 1.00000 0.9653461 34.84052 -57893.26 -67145.08 20.26708 18.66191 18.10308 11 1e+02 1.01322 0.9583926 34.02698 -58098.40 -66963.78 20.75956 18.79731 18.15793
# calculating at even increments subcrt("water", T=seq(500, 1000, length.out=10), P=seq(5000, 10000, length.out=10))
subcrt: 1 species at 10 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 1 500.0000 5000.000 0.8760285 18.79959 -66507.32 -58880.39 31.35063 20.56463 16.16781 2 555.5556 5555.556 0.8654972 17.93302 -68000.34 -57864.89 32.27595 20.81486 15.96931 3 611.1111 6111.111 0.8568124 17.18675 -69539.51 -56860.87 33.12421 21.02584 15.76695 4 666.6667 6666.667 0.8497821 16.53864 -71121.37 -55867.36 33.90642 21.19979 15.56827 5 722.2222 7222.222 0.8442069 15.97160 -72742.99 -54883.29 34.63177 21.33979 15.37902 6 777.7778 7777.778 0.8398955 15.47225 -74401.85 -53907.60 35.30791 21.44934 15.20286 7 833.3333 8333.333 0.8366718 15.02998 -76095.79 -52939.27 35.94119 21.53198 15.04167 8 888.8889 8888.889 0.8343802 14.63624 -77822.91 -51977.35 36.53696 21.59112 14.89599 9 944.4444 9444.444 0.8328838 14.28409 -79581.54 -51021.02 37.09966 21.62991 14.76549 10 1000.0000 10000.000 0.8320646 13.96782 -81301.21 -50069.54 37.63302 21.65120 14.64932
# calculating on a temperature-pressure grid subcrt("water", T=c(500, 1000), P=c(5000, 10000), grid="P")
subcrt: 1 species at 4 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 1 500 5000 0.8760285 18.79959 -66507.32 -58880.39 31.35063 20.56463 16.16781 2 1000 5000 0.6092264 14.47661 -84334.20 -51042.45 39.19692 29.57062 14.91983 3 500 10000 1.0289410 18.16400 -64258.78 -57563.56 30.14555 17.50849 15.21216 4 1000 10000 0.8320646 13.96782 -81301.21 -50069.54 37.63302 21.65120 14.64932
# to calculate only selected properties subcrt("water", property=c("G", "E"))
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 G E 1 0.01 1.000000 -56289.50 -0.001441834 2 25.00 1.000000 -56687.71 0.004687396 3 50.00 1.000000 -57123.89 0.008336313 4 75.00 1.000000 -57594.93 0.011305255 5 100.00 1.013220 -58098.40 0.014099350 6 125.00 2.320144 -58631.71 0.016974282 7 150.00 4.757169 -59193.26 0.020162709 8 175.00 8.918049 -59781.38 0.023939775 9 200.00 15.536499 -60394.50 0.028691290 10 225.00 25.478603 -61031.25 0.035033012 11 250.00 39.736493 -61690.35 0.044074816 12 275.00 59.431251 -62301.65 0.058105094 13 300.00 85.837843 -63071.13 0.082759476 14 325.00 120.457572 -63790.84 0.136405967 15 350.00 165.211289 -64528.89 0.324943485
# the properties of multiple species subcrt(c("glucose", "ethanol", "CO2"))
info.character: found ethanol(aq), also available in liq, gas info.character: found CO2(aq), also available in gas subcrt: 3 species at 15 values of T and P (wet) $species name formula state ispecies 1757 glucose C6H12O6 aq 1757 112 ethanol C2H5OH aq 112 69 CO2 CO2 aq 69 $out $out$glucose T P rho logK G H S V Cp 1 0.01 1.000000 0.9998289 173.91268 -217373.0 -303657.6 57.94307 110.0960 67.00495 2 25.00 1.000000 0.9970614 160.45908 -218905.4 -301670.7 64.89006 112.3803 88.06603 3 50.00 1.000000 0.9880295 149.20560 -220620.9 -299347.6 72.36728 114.0163 96.92799 4 75.00 1.000000 0.9748643 139.68572 -222523.4 -296847.1 79.81780 115.6152 102.89809 5 100.00 1.013220 0.9583926 131.54961 -224610.6 -294206.6 87.13992 117.4675 108.30133 6 125.00 2.320144 0.9390726 124.53290 -226875.8 -291419.9 94.35666 119.8244 114.57459 7 150.00 4.757169 0.9170577 118.43651 -229317.5 -288455.5 101.55804 123.0132 122.69331 8 175.00 8.918049 0.8923427 113.10609 -231935.2 -285247.3 108.89241 127.5389 134.38261 9 200.00 15.536499 0.8647434 108.42168 -234732.0 -281678.4 116.59260 134.2686 152.51168 10 225.00 25.478603 0.8338733 104.29011 -237717.2 -277539.6 125.04220 144.8245 182.78652 11 250.00 39.736493 0.7990719 100.64038 -240910.5 -272432.4 134.93342 162.5468 238.16104 12 275.00 59.431251 0.7592362 97.42215 -244351.2 -265510.6 147.68301 195.2258 353.31619 13 300.00 85.837843 0.7124075 94.60943 -248119.0 -254650.7 166.76286 264.6322 646.05718 14 325.00 120.457572 0.6545772 92.21918 -252399.6 -232809.2 203.46509 452.5063 1711.25099 15 350.00 165.211289 0.5746875 90.40601 -257778.8 -158523.2 323.14500 1322.9173 8587.10627 $out$ethanol T P rho logK G H S V Cp 1 0.01 1.000000 0.9998289 34.00279 -42500.00 -70209.10 30.43813 55.07924 62.81686 2 25.00 1.000000 0.9970614 31.76118 -43330.00 -68650.00 35.90000 55.14331 62.17949 3 50.00 1.000000 0.9880295 29.95389 -44290.91 -67095.45 40.90686 55.24494 62.23937 4 75.00 1.000000 0.9748643 28.48182 -45372.36 -65536.19 45.55435 55.38602 62.52880 5 100.00 1.013220 0.9583926 27.27279 -46566.14 -63967.66 49.90504 55.58456 62.98048 6 125.00 2.320144 0.9390726 26.27260 -47863.79 -62383.92 54.00844 55.85278 63.63056 7 150.00 4.757169 0.9170577 25.44144 -49259.87 -60779.16 57.90925 56.22997 64.58211 8 175.00 8.918049 0.8923427 24.74841 -50749.05 -59143.26 61.65207 56.77551 66.02582 9 200.00 15.536499 0.8647434 24.16957 -52326.91 -57459.80 65.28732 57.59584 68.32020 10 225.00 25.478603 0.8338733 23.68631 -53990.18 -55700.55 68.88128 58.89490 72.19535 11 250.00 39.736493 0.7990719 23.28422 -55737.20 -53812.85 72.53739 61.09827 79.32006 12 275.00 59.431251 0.7592362 22.95262 -57569.03 -51686.23 76.45058 65.20609 94.17030 13 300.00 85.837843 0.7124075 22.68475 -59492.14 -49045.15 81.07926 74.02376 131.95703 14 325.00 120.457572 0.6545772 22.48000 -61526.71 -44978.60 87.89049 98.10058 269.49638 15 350.00 165.211289 0.5746875 22.28692 -63744.45 -34130.56 105.33174 210.26990 1424.69512 $out$CO2 T P rho logK G H S V Cp 1 0.01 1.000000 0.9998289 73.29142 -91606.76 -100328.21 23.08743 30.27577 66.65869 2 25.00 1.000000 0.9970614 67.61986 -92250.00 -98900.00 28.10000 33.28796 51.09345 3 50.00 1.000000 0.9880295 62.89754 -93002.60 -97692.15 31.99278 34.78578 46.31744 4 75.00 1.000000 0.9748643 58.91003 -93845.38 -96561.05 35.36508 35.73921 44.44646 5 100.00 1.013220 0.9583926 55.50301 -94768.21 -95460.39 38.41842 36.46276 43.73909 6 125.00 2.320144 0.9390726 52.56481 -95763.30 -94367.89 41.24934 37.09777 43.68297 7 150.00 4.757169 0.9170577 50.00811 -96826.01 -93269.40 43.91970 37.60261 44.15483 8 175.00 8.918049 0.8923427 47.76770 -97952.38 -92150.95 46.47874 38.48142 45.23246 9 200.00 15.536499 0.8647434 45.79209 -99139.47 -90994.47 48.97605 39.44172 47.20274 10 225.00 25.478603 0.8338733 44.04063 -100385.48 -89771.76 51.47392 40.82846 50.72891 11 250.00 39.736493 0.7990719 42.48106 -101690.14 -88432.04 54.06884 43.05494 57.37755 12 275.00 59.431251 0.7592362 41.08805 -103055.76 -86870.02 56.94382 47.07750 71.38713 13 300.00 85.837843 0.7124075 39.84265 -104489.77 -84823.97 60.53182 55.56485 107.19221 14 325.00 120.457572 0.6545772 38.73382 -106012.64 -81429.06 66.22352 78.53012 237.71986 15 350.00 165.211289 0.5746875 37.76948 -107693.85 -71600.43 82.03713 185.14818 1334.45989
## properties of reactions subcrt(c("H2O", "H+", "k-feldspar", "kaolinite", "K+", "SiO2"), c(-1, -2, -2, 1, 2, 4))
info.character: found H2O(liq), also available in gas info.character: found SiO2(aq), also available in cr, cr, cr1, cr2, cr1, cr2, cr, cr, cr1, cr2 subcrt: 6 species at 15 values of T and P (wet) $reaction coeff name formula state ispecies 1 -1 water H2O liq 1 3 -2 H+ H+ aq 3 1953 -2 k-feldspar K(AlSi3)O8 cr 1953 1958 1 kaolinite Al2Si2O5(OH)4 cr 1958 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
subcrt(c("glucose", "ethanol", "CO2"), c(-1, 2, 2))
info.character: found ethanol(aq), also available in liq, gas info.character: found CO2(aq), also available in gas subcrt: 3 species at 15 values of T and P (wet) $reaction coeff name formula state ispecies 1757 -1 glucose C6H12O6 aq 1757 112 2 ethanol C2H5OH aq 112 69 2 CO2 CO2 aq 69 $out T P rho logK G H S V Cp 1 0.01 1.000000 0.9998289 40.67574 -50840.51 -37417.08 49.10806 60.614025 191.94614 2 25.00 1.000000 0.9970614 38.30300 -52254.65 -33429.35 63.10994 64.482264 138.47985 3 50.00 1.000000 0.9880295 36.49726 -53966.18 -30227.56 73.43200 66.045138 120.18563 4 75.00 1.000000 0.9748643 35.09797 -55912.08 -27347.38 82.02106 66.638013 111.05242 5 100.00 1.013220 0.9583926 34.00338 -58058.10 -24649.49 89.50701 66.627164 105.06881 6 125.00 2.320144 0.9390726 33.14193 -60378.42 -22083.69 96.15890 66.076737 100.05246 7 150.00 4.757169 0.9170577 32.46258 -62854.25 -19641.63 102.09987 64.927923 94.78058 8 175.00 8.918049 0.8923427 31.92612 -65467.66 -17341.08 107.36922 62.974911 88.13396 9 200.00 15.536499 0.8647434 31.50165 -68200.80 -15230.09 111.93414 59.806569 78.53419 10 225.00 25.478603 0.8338733 31.16376 -57234.17 -13404.99 115.66820 54.622231 63.06201 11 250.00 39.736493 0.7990719 30.89018 -73944.17 -12057.43 118.27903 45.759630 35.23418 12 275.00 59.431251 0.7592362 30.65919 -76898.42 -11601.90 119.10509 29.341359 -22.20133 13 300.00 85.837843 0.7124075 30.44537 -79844.84 -13087.52 116.45860 -5.455002 -167.75869 14 325.00 120.457572 0.6545772 30.20845 -82679.12 -20006.12 104.76292 -99.231110 -696.81852 15 350.00 165.211289 0.5746875 29.84479 -85097.81 -52938.72 51.59275 -532.081102 -5138.79625
# to specify the states subcrt(c("glucose", "ethanol", "CO2"), c(-1, 2, 2), c("aq", "aq", "gas"))
subcrt: 3 species at 15 values of T and P (wet) $reaction coeff name formula state ispecies 1757 -1 glucose C6H12O6 aq 1757 112 2 ethanol C2H5OH aq 112 3087 2 carbon dioxide CO2 gas 3087 $out T P rho logK G H S V Cp 1 0.01 1.000000 0.9998289 42.88396 -53600.56 -25294.51 103.591072 0.06248682 75.394461 2 25.00 1.000000 0.9970614 41.24089 -56262.65 -23731.35 109.079943 -2.09365746 54.050416 3 50.00 1.000000 0.9880295 39.92977 -59041.62 -22491.05 113.078944 -3.52643038 46.102599 4 75.00 1.000000 0.9748643 38.86337 -61910.47 -21400.88 116.330543 -4.84041492 41.362626 5 100.00 1.013220 0.9583926 37.98350 -64853.84 -20417.22 119.060706 -6.29836213 37.338953 6 125.00 2.320144 0.9390726 37.24863 -67860.06 -19536.76 121.346693 -8.11881147 32.899768 7 150.00 4.757169 0.9170577 36.62744 -70918.28 -18781.19 123.190309 -10.55330285 27.087185 8 175.00 8.918049 0.8923427 36.09541 -60217.21 -18197.62 124.535260 -13.98793739 18.639863 9 200.00 15.536499 0.8647434 35.63233 -77143.68 -17871.30 125.252611 -19.07688015 5.415598 10 225.00 25.478603 0.8338733 35.22035 -80280.68 -17955.81 125.094372 -27.03468816 -16.823847 11 250.00 39.736493 0.7990719 34.84206 -83404.08 -18745.10 123.578072 -40.35024694 -57.689057 12 275.00 59.431251 0.7592362 34.47771 -86475.90 -20864.79 119.678920 -64.81364569 -142.904543 13 300.00 85.837843 0.7124075 34.09960 -89428.26 -25887.92 110.845738 -116.58457208 -359.850067 14 325.00 120.457572 0.6545772 33.65607 -92115.09 -39036.39 88.722884 -256.30515718 -1149.757537 15 350.00 165.211289 0.5746875 32.99957 -94093.17 -91061.28 4.850808 -902.37745473 -7785.019792
## auto balancing reactions # the basis species must first be defined basis(c("CO2", "H2O", "NH3", "H2S", "O2"))
C H N O S ispecies logact state CO2 1 0 0 2 0 69 0 aq H2O 0 2 0 1 0 1 0 liq NH3 0 3 1 0 0 68 0 aq H2S 0 2 0 0 1 70 0 aq O2 0 0 0 2 0 67 0 aq
subcrt(c("glucose", "ethanol"), c(-1, 3))
info.character: found ethanol(aq), also available in liq, gas subcrt: 2 species at 15 values of T and P (wet) subcrt: reaction is not balanced; it is missing this composition: H O -6 3 subcrt: adding missing composition from basis definition and restarting... subcrt: 4 species at 15 values of T and P (wet) $reaction coeff name formula state ispecies 1757 -1 glucose C6H12O6 aq 1757 112 3 ethanol C2H5OH aq 112 1 -3 water H2O liq 1 67 3 O2 O2 aq 67 $out T P logK G H S V Cp 1 0.01 1.000000 -217.90302 272356.4 285726.6 48.86029 84.09351 308.0140 2 25.00 1.000000 -198.52788 270840.5 291970.9 70.79310 90.34734 212.3150 3 50.00 1.000000 -181.83436 268866.9 296834.6 86.47450 92.96816 181.5148 4 75.00 1.000000 -167.31577 266538.9 301183.8 99.44410 94.13730 167.9989 5 100.00 1.013220 -154.56515 263907.8 305286.2 110.82641 94.54523 160.8691 6 125.00 2.320144 -143.26908 261009.6 309254.8 121.11444 94.45970 156.7310 7 150.00 4.757169 -133.18178 257867.4 313145.7 130.57982 94.03822 154.2854 8 175.00 8.918049 -124.11048 254500.8 316995.2 139.39735 93.37375 152.9977 9 200.00 15.536499 -115.90157 250925.9 320831.9 147.69654 92.55679 152.7696 10 225.00 25.478603 -108.43104 247155.9 324687.7 155.59225 91.73374 153.9868 11 250.00 39.736493 -101.59746 243201.6 328611.8 163.21661 91.22750 157.9954 12 275.00 59.431251 -95.31650 239069.8 332705.8 170.77904 91.87656 168.8929 13 300.00 85.837843 -89.51617 234761.6 337231.5 178.74271 96.24685 201.4475 14 325.00 120.457572 -84.13113 230263.0 343091.3 188.58960 114.64562 333.1825 15 350.00 165.211289 -79.08602 225505.5 286795.6 209.04531 221.73300 1518.5725
# a bug in CHNOSZ <0.9 caused the following # to initiate an infinite loop basis(c("H2O", "H2S", "O2", "H+"))
H O S Z ispecies logact state H2O 2 1 0 0 1 0 liq H2S 2 0 1 0 70 0 aq O2 0 2 0 0 67 0 aq H+ 1 0 0 1 3 0 aq
subcrt(c("HS-", "SO4-2"), c(-1, 1))
subcrt: 2 species at 15 values of T and P (wet) subcrt: reaction is not balanced; it is missing this composition: H O Z 1 -4 1 subcrt: adding missing composition from basis definition and restarting... subcrt: 4 species at 15 values of T and P (wet) $reaction coeff name formula state ispecies 22 -1 HS- HS- aq 22 24 1 SO4-2 SO4-2 aq 24 67 -2 O2 O2 aq 67 3 1 H+ H+ aq 3 $out T P logK G H S V Cp 1 0.01 1.000000 152.09929 -190108.5 -203112.5 -47.58301 -65.26364 -237.3256 2 25.00 1.000000 138.31689 -188698.0 -207750.0 -63.88000 -68.29359 -153.0663 3 50.00 1.000000 126.43759 -186955.2 -211222.0 -75.07540 -70.60404 -129.1002 4 75.00 1.000000 116.10567 -184959.7 -214336.5 -84.36212 -72.97053 -121.6743 5 100.00 1.013220 107.02950 -182744.4 -217363.5 -92.75848 -75.79064 -121.3545 6 125.00 2.320144 98.98249 -180327.7 -220442.4 -100.73722 -79.41030 -125.5894 7 150.00 4.757169 91.78553 -177715.7 -223677.2 -108.60281 -84.27817 -133.8745 8 175.00 8.918049 85.29700 -174909.9 -227171.8 -116.60314 -91.00760 -147.0027 9 200.00 15.536499 79.40248 -171905.7 -231091.0 -125.07483 -100.71187 -169.3016 10 225.00 25.478603 74.00643 -168689.0 -235743.7 -134.59501 -115.98979 -208.2014 11 250.00 39.736493 69.02565 -165232.0 -241638.0 -146.03817 -142.43837 -275.9048 12 275.00 59.431251 64.38407 -161486.1 -249626.6 -160.78513 -191.66455 -400.8890 13 300.00 85.837843 60.00618 -157369.8 -261518.9 -181.70257 -290.70754 -679.1648 14 325.00 120.457572 55.79820 -152717.1 -283287.1 -218.27939 -527.91937 -1603.7790 15 350.00 165.211289 51.55551 -147002.6 -348574.1 -323.46203 -1468.38436 -8259.5136
# note the next one is a non-reaction # (products same as reactants) subcrt("H2O", 1)
info.character: found H2O(liq), also available in gas subcrt: 1 species at 15 values of T and P (wet) subcrt: reaction is not balanced; it is missing this composition: H O -2 -1 subcrt: balanced reaction, but it is a non-reaction; restarting... subcrt: 2 species at 15 values of T and P (wet) $reaction coeff name formula state ispecies 1 1 water H2O liq 1 2 -1 water H2O liq 1 $out T P logK G H S V Cp 1 0.01 1.000000 0 0 0 0 0 0 2 25.00 1.000000 0 0 0 0 0 0 3 50.00 1.000000 0 0 0 0 0 0 4 75.00 1.000000 0 0 0 0 0 0 5 100.00 1.013220 0 0 0 0 0 0 6 125.00 2.320144 0 0 0 0 0 0 7 150.00 4.757169 0 0 0 0 0 0 8 175.00 8.918049 0 0 0 0 0 0 9 200.00 15.536499 0 0 0 0 0 0 10 225.00 25.478603 0 0 0 0 0 0 11 250.00 39.736493 0 0 0 0 0 0 12 275.00 59.431251 0 0 0 0 0 0 13 300.00 85.837843 0 0 0 0 0 0 14 325.00 120.457572 0 0 0 0 0 0 15 350.00 165.211289 0 0 0 0 0 0
# but this one auto-balances into a reaction # (water to steam) subcrt("H2O", 1, "gas")
subcrt: 1 species at 15 values of T and P subcrt: reaction is not balanced; it is missing this composition: H O -2 -1 subcrt: adding missing composition from basis definition and restarting... subcrt: 2 species at 15 values of T and P (wet) $reaction coeff name formula state ispecies 3100 1 steam H2O gas 3100 1 -1 water H2O liq 1 $out T P logK G H S V Cp 1 0.01 1.000000 -2.29851343 2872.9060 10590.025 28.78056 -18.01828 -8.365347 2 25.00 1.000000 -1.58542852 2162.9115 10381.655 28.05072 -18.06830 -8.434168 3 50.00 1.000000 -0.99438432 1470.3330 10167.594 27.36141 -18.23346 -8.689500 4 75.00 1.000000 -0.49878485 794.5787 9946.790 26.70340 -18.47970 -8.988325 5 100.00 1.013220 -0.07905088 134.9732 9717.501 26.06755 -18.79731 -9.366129 6 125.00 2.320144 0.27968054 -509.5259 9477.595 25.44694 -19.18403 -9.802786 7 150.00 4.757169 0.58835881 -1139.1840 9225.803 24.83650 -19.64456 -10.296919 8 175.00 8.918049 0.85560981 -1754.5123 8960.358 24.23173 -20.18866 -10.874349 9 200.00 15.536499 1.08822734 -2356.0025 8678.676 23.62730 -20.83300 -11.580994 10 225.00 25.478603 1.29162861 -2944.1170 8377.014 23.01658 -21.60424 -12.483222 11 250.00 39.736493 1.47017929 -3519.2798 8050.046 22.39110 -22.54515 -13.685746 12 275.00 59.431251 1.62743189 -4081.8732 7689.976 21.73935 -23.72806 -15.385218 13 300.00 85.837843 1.76630441 -4632.2407 7284.288 21.04354 -25.28777 -18.033855 14 325.00 120.457572 1.88921708 -5170.6988 6809.122 20.26983 -27.52189 -23.002334 15 350.00 165.211289 1.99819572 -5697.5506 6201.186 19.32651 -31.34782 -37.413768
# properties of a species and a formation # reaction for that species subcrt("C2H5OH") # species
info.character: found C2H5OH(aq), also available in liq, gas subcrt: 1 species at 15 values of T and P (wet) $species name formula state ispecies 112 ethanol C2H5OH aq 112 $out $out$ethanol T P rho logK G H S V Cp 1 0.01 1.000000 0.9998289 34.00279 -42500.00 -70209.10 30.43813 55.07924 62.81686 2 25.00 1.000000 0.9970614 31.76118 -43330.00 -68650.00 35.90000 55.14331 62.17949 3 50.00 1.000000 0.9880295 29.95389 -44290.91 -67095.45 40.90686 55.24494 62.23937 4 75.00 1.000000 0.9748643 28.48182 -45372.36 -65536.19 45.55435 55.38602 62.52880 5 100.00 1.013220 0.9583926 27.27279 -46566.14 -63967.66 49.90504 55.58456 62.98048 6 125.00 2.320144 0.9390726 26.27260 -47863.79 -62383.92 54.00844 55.85278 63.63056 7 150.00 4.757169 0.9170577 25.44144 -49259.87 -60779.16 57.90925 56.22997 64.58211 8 175.00 8.918049 0.8923427 24.74841 -50749.05 -59143.26 61.65207 56.77551 66.02582 9 200.00 15.536499 0.8647434 24.16957 -52326.91 -57459.80 65.28732 57.59584 68.32020 10 225.00 25.478603 0.8338733 23.68631 -53990.18 -55700.55 68.88128 58.89490 72.19535 11 250.00 39.736493 0.7990719 23.28422 -55737.20 -53812.85 72.53739 61.09827 79.32006 12 275.00 59.431251 0.7592362 22.95262 -57569.03 -51686.23 76.45058 65.20609 94.17030 13 300.00 85.837843 0.7124075 22.68475 -59492.14 -49045.15 81.07926 74.02376 131.95703 14 325.00 120.457572 0.6545772 22.48000 -61526.71 -44978.60 87.89049 98.10058 269.49638 15 350.00 165.211289 0.5746875 22.28692 -63744.45 -34130.56 105.33174 210.26990 1424.69512
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 3095 -80 gas
subcrt("C2H5OH",1) # reaction
info.character: found C2H5OH(aq), also available in liq, gas subcrt: 1 species at 15 values of T and P (wet) subcrt: reaction is not balanced; it is missing this composition: C H O -2 -6 -1 subcrt: adding missing composition from basis definition and restarting... subcrt: 4 species at 15 values of T and P (wet) $reaction coeff name formula state ispecies 112 1 ethanol C2H5OH aq 112 69 -2 CO2 CO2 aq 69 1 -3 water H2O liq 1 3095 3 oxygen O2 gas 3095 $out T P logK G H S V Cp 1 0.01 1.000000 -250.6087 313235.2 336229.2 84.12698 -59.52715 -104.42604 2 25.00 1.000000 -228.1360 311233.1 334100.3 76.65016 -65.63750 -73.01769 3 50.00 1.000000 -209.2382 309387.2 332417.6 71.22545 -69.02702 -63.10912 4 75.00 1.000000 -193.1318 307664.5 330899.0 66.69688 -71.53014 -58.95459 5 100.00 1.013220 -179.2458 306048.2 329450.1 62.67723 -73.73289 -57.23386 6 125.00 2.320144 -167.1552 304525.6 328025.2 58.98723 -75.89487 -56.81794 7 150.00 4.757169 -156.5381 303090.1 326597.6 55.52082 -78.18495 -57.34757 8 175.00 8.918049 -147.1453 301735.9 325143.7 52.20107 -80.75331 -58.86103 9 200.00 15.536499 -138.7805 300458.5 323635.7 48.95553 -83.78661 -61.70836 10 225.00 25.478603 -131.2876 299254.8 322033.9 45.69954 -87.57474 -66.68276 11 250.00 39.736493 -124.5411 298123.5 320273.3 42.31272 -92.64707 -75.56100 12 275.00 59.431251 -118.4394 297065.9 318230.2 38.58497 -100.13308 -92.93267 13 300.00 85.837843 -112.9005 296088.5 315618.9 34.05142 -112.96927 -133.81151 14 325.00 120.457572 -107.8608 295210.0 311549.2 27.29292 -141.53914 -271.34671 15 350.00 165.211289 -103.2832 294496.1 301017.3 10.44249 -254.06991 -1351.97980
## properties of mineral phases # properties of phase species subcrt(c("pyrrhotite", "pyrrhotite"), state=c("cr1", "cr2"))
subcrt: 2 species at 15 values of T and P subcrt: some points above transition temperature for pyrrhotite cr1 (using NA for G) subcrt: some points below transition temperature for pyrrhotite cr2 (using NA for G) subcrt: some points above transition temperature for pyrrhotite cr2 (using NA for G) $species name formula state ispecies 2011 pyrrhotite FeS cr1 2011 2012 pyrrhotite FeS cr2 2012 $out $out$pyrrhotite T P logK G H S V Cp 1 0.01 1.000000 18.99174 -23737.73 -24318.15 13.29594 18.2 12.40142 2 25.00 1.000000 17.65373 -24084.00 -24000.00 14.41000 18.2 13.06116 3 50.00 1.000000 16.54077 -24457.79 -23665.22 15.48790 18.2 13.72116 4 75.00 1.000000 15.60432 -24858.14 -23313.94 16.53464 18.2 14.38116 5 100.00 1.013220 14.80847 -25284.30 -22946.16 17.55455 18.2 15.04116 6 125.00 2.320144 14.12608 -25735.09 -22561.88 18.55111 18.2 15.70116 7 150.00 4.757169 NA NA -22161.10 19.52717 18.2 16.36116 8 175.00 8.918049 NA NA -21743.83 20.48509 18.2 17.02116 9 200.00 15.536499 NA NA -21310.05 21.42682 18.2 17.68116 10 225.00 25.478603 NA NA -20859.77 22.35405 18.2 18.34116 11 250.00 39.736493 NA NA -20392.99 23.26819 18.2 19.00116 12 275.00 59.431251 NA NA -19909.71 24.17046 18.2 19.66116 13 300.00 85.837843 NA NA -19409.93 25.06193 18.2 20.32116 14 325.00 120.457572 NA NA -18893.65 25.94351 18.2 20.98116 15 350.00 165.211289 NA NA -18360.87 26.81602 18.2 21.64116 $out$pyrrhotite T P logK G H S V Cp 1 0.01 1.000000 NA NA -24186.36 13.33352 18.2 17.4 2 25.00 1.000000 NA NA -23751.53 14.85670 18.2 17.4 3 50.00 1.000000 NA NA -23316.53 16.25775 18.2 17.4 4 75.00 1.000000 NA NA -22881.53 17.55434 18.2 17.4 5 100.00 1.013220 NA NA -22446.53 18.76098 18.2 17.4 6 125.00 2.320144 NA NA -22011.53 19.88934 18.2 17.4 7 150.00 4.757169 13.54563 -26227.13 -21576.53 20.94896 18.2 17.4 8 175.00 8.918049 13.05065 -26761.64 -21141.53 21.94774 18.2 17.4 9 200.00 15.536499 12.61870 -27319.37 -20706.53 22.89229 18.2 17.4 10 225.00 25.478603 12.23956 -27898.65 -20271.53 23.78820 18.2 17.4 11 250.00 39.736493 11.90499 -28497.89 -19836.53 24.64022 18.2 17.4 12 275.00 59.431251 11.60830 -29115.56 -19401.53 25.45247 18.2 17.4 13 300.00 85.837843 11.34393 -29750.16 -18966.53 26.22848 18.2 17.4 14 325.00 120.457572 NA NA -18531.53 26.97136 18.2 17.4 15 350.00 165.211289 NA NA -18096.53 27.68382 18.2 17.4
# properties of the stable phases subcrt("pyrrhotite")
info.character: found pyrrhotite(cr1), also available in cr2, cr3 subcrt: 1 species at 15 values of T and P subcrt: some points above transition temperature for pyrrhotite cr1 (using NA for G) subcrt: some points below transition temperature for pyrrhotite cr2 (using NA for G) subcrt: some points above transition temperature for pyrrhotite cr2 (using NA for G) subcrt: some points below transition temperature for pyrrhotite cr3 (using NA for G) subcrt: 3 phases for pyrrhotite ... phases 1 2 3 are stable $species name formula state ispecies 2011 pyrrhotite FeS cr* 2011 $out $out$pyrrhotite T P logK G H S V Cp state 1 0.01 1.000000 18.99174 -23737.73 -24318.15 13.29594 18.2 12.40142 1 2 25.00 1.000000 17.65373 -24084.00 -24000.00 14.41000 18.2 13.06116 1 3 50.00 1.000000 16.54077 -24457.79 -23665.22 15.48790 18.2 13.72116 1 4 75.00 1.000000 15.60432 -24858.14 -23313.94 16.53464 18.2 14.38116 1 5 100.00 1.013220 14.80847 -25284.30 -22946.16 17.55455 18.2 15.04116 1 6 125.00 2.320144 14.12608 -25735.09 -22561.88 18.55111 18.2 15.70116 1 7 150.00 4.757169 13.54563 -26227.13 -21576.53 20.94896 18.2 17.40000 2 8 175.00 8.918049 13.05065 -26761.64 -21141.53 21.94774 18.2 17.40000 2 9 200.00 15.536499 12.61870 -27319.37 -20706.53 22.89229 18.2 17.40000 2 10 225.00 25.478603 12.23956 -27898.65 -20271.53 23.78820 18.2 17.40000 2 11 250.00 39.736493 11.90499 -28497.89 -19836.53 24.64022 18.2 17.40000 2 12 275.00 59.431251 11.60830 -29115.56 -19401.53 25.45247 18.2 17.40000 2 13 300.00 85.837843 11.34393 -29750.16 -18966.53 26.22848 18.2 17.40000 2 14 325.00 120.457572 11.10731 -30400.19 -18412.10 27.15729 18.2 13.62360 3 15 350.00 165.211289 10.89557 -31067.03 -18070.77 27.73012 18.2 13.68310 3
# phase transitions in a reaction subcrt(c("pyrite", "pyrrhotite", "H2O", "H2S", "O2"), c(-1, 1, -1, 1, 0.5))
info.character: found pyrrhotite(cr1), also available in cr2, cr3 info.character: found H2O(liq), also available in gas info.character: found H2S(aq), also available in gas info.character: found O2(aq), also available in gas subcrt: 5 species at 15 values of T and P (wet) subcrt: some points above transition temperature for pyrrhotite cr1 (using NA for G) subcrt: some points below transition temperature for pyrrhotite cr2 (using NA for G) subcrt: some points above transition temperature for pyrrhotite cr2 (using NA for G) subcrt: some points below transition temperature for pyrrhotite cr3 (using NA for G) subcrt: 3 phases for pyrrhotite ... phases 1 2 3 are stable $reaction coeff name formula state ispecies 2007 -1 pyrite FeS2 cr 2007 2011 1 pyrrhotite FeS cr* 2011 2012 1 water H2O liq 1 2013 1 H2S H2S aq 70 1 -1 O2 O2 aq 67 $out T P rho logK G H S V Cp 1 0.01 1.000000 0.9998289 -53.47570 66839.14 73282.31 22.50153 23.22796 82.55619 2 25.00 1.000000 0.9970614 -48.52556 66200.71 74865.76 28.06772 26.52409 51.07023 3 50.00 1.000000 0.9880295 -44.26444 65451.01 76001.77 31.73170 28.06805 41.41841 4 75.00 1.000000 0.9748643 -40.56429 64620.08 76983.87 34.66074 28.96016 37.70796 5 100.00 1.013220 0.9583926 -37.32003 63721.03 77906.08 37.21936 29.56422 36.33410 6 125.00 2.320144 0.9390726 -34.45018 62761.81 78811.99 39.56636 30.05144 36.24182 7 150.00 4.757169 0.9170577 -31.88158 61729.32 80313.51 43.21638 30.54717 38.18008 8 175.00 8.918049 0.8923427 -29.56410 60624.10 81284.44 45.43699 31.18067 39.48670 9 200.00 15.536499 0.8647434 -27.46694 59465.68 82306.00 47.64168 32.13957 42.30380 10 225.00 25.478603 0.8338733 -25.55699 58254.19 83425.50 49.92730 33.75880 47.73213 11 250.00 39.736493 0.7990719 -23.80640 56987.19 84728.55 52.45031 36.72747 58.44650 12 275.00 59.431251 0.7592362 -22.19062 55657.81 86395.07 55.51870 42.67361 81.78847 13 300.00 85.837843 0.7124075 -20.68596 54250.18 88878.56 59.87974 56.21192 142.99465 14 325.00 120.457572 0.6545772 -19.26424 52725.31 93814.01 68.16960 94.88043 366.72402 15 350.00 165.211289 0.5746875 -17.87014 50953.95 109856.40 94.01149 280.85628 2304.70608 $state T P pyrrhotite 1 0.01 1.000000 1 2 25.00 1.000000 1 3 50.00 1.000000 1 4 75.00 1.000000 1 5 100.00 1.013220 1 6 125.00 2.320144 1 7 150.00 4.757169 2 8 175.00 8.918049 2 9 200.00 15.536499 2 10 225.00 25.478603 2 11 250.00 39.736493 2 12 275.00 59.431251 2 13 300.00 85.837843 2 14 325.00 120.457572 3 15 350.00 165.211289 3
## these produce messages about problems with the calculation # Psat is not defined above the critical point subcrt("alanine", T=seq(0, 5000, by=1000))
water.SUPCRT92: errors calculating 5 of 6 points; for Psat we need 273.16 < T < 647.067 K info.character: found alanine(aq), also available in cr subcrt: 1 species at 6 values of T and P (wet) $species name formula state ispecies 1504 alanine C3H7NO2 aq 1504 $out $out$alanine T P rho logK G H S V Cp 1 1e-02 1 0.9998289 70.3024 -87870.78 -133143 36.59025 58.15163 13.28691 2 1e+03 NA NA NA NA NA NA NA NA 3 2e+03 NA NA NA NA NA NA NA NA 4 3e+03 NA NA NA NA NA NA NA NA 5 4e+03 NA NA NA NA NA NA NA NA 6 5e+03 NA NA NA NA NA NA NA NA
# above the T, P limits for the H2O equations of state subcrt("alanine", T=c(2250, 2251), P=c(30000, 30001), grid="T")
info.character: found alanine(aq), also available in cr subcrt: 1 species at 4 values of T and P (wet) water.SUPCRT92: errors calculating 3 of 4 points; T < Tfusion@P, T > 2250 degC, or P > 30kb. $species name formula state ispecies 1504 alanine C3H7NO2 aq 1504 $out $out$alanine T P rho logK G H S V Cp 1 2250 30000 1.026316 -Inf Inf NaN NaN NaN NaN 2 2250 30001 0.000000 NA NA NA NA NA NA 3 2251 30000 0.000000 NA NA NA NA NA NA 4 2251 30001 0.000000 NA NA NA NA NA NA
## heat capacity of Fe(cr) # compare calculated values of heat capacity with # values from Robie and Hemingway, 1995, (from which # the parameters in the database were derived) # set the units T.units("K")
[1] "K"
E.units("J")
[1] "J"
# we set pressure here otherwise subcrt goes for Psat (saturation # vapor pressure of H2O above 100 degrees C) which can not be # calculated above the critical point of H2O (~647 K) s <- subcrt("Fe", T=seq(300, 1800, 20), P=1)
info.character: found Fe(cr1), also available in cr2, cr3, cr4 subcrt: 1 species at 76 values of T and P subcrt: some points above transition temperature for Fe cr1 (using NA for G) subcrt: some points below transition temperature for Fe cr2 (using NA for G) subcrt: some points above transition temperature for Fe cr2 (using NA for G) subcrt: some points below transition temperature for Fe cr3 (using NA for G) subcrt: some points above transition temperature for Fe cr3 (using NA for G) subcrt: some points below transition temperature for Fe cr4 (using NA for G) subcrt: 4 phases for Fe ... phases 1 2 3 4 are stable
plot(s$out[[1]]$T, s$out[[1]]$Cp, type="l", xlab=axis.label("T"), ylab=axis.label("Cp")) # add points from RH95 RH95 <- read.csv(system.file("extdata/cpetc/RH95.csv", package="CHNOSZ")) points(RH95[,1], RH95[,2]) title(main=paste("Heat capacity of Fe(cr)\n", "(points - Robie and Hemingway, 1995)"))

Image subcrt1

 

# reset the units to default values T.units("C")
[1] "C"
E.units("cal")
[1] "cal"
## Skarn example after Johnson et al., 1992 P <- seq(500, 5000, 500) # this is like the temperature specification used # in the example by Johnson et al., 1992 # T <- seq(0, 1000, 100) # we use this one to avoid warnings at 0 deg C, 5000 bar T <- c(2, seq(100, 1000, 100)) s <- subcrt(c("andradite", "carbon dioxide", "H2S", "Cu+", "quartz", "calcite", "chalcopyrite", "H+", "H2O"), coeff=c(-1, -3, -4, -2, 3, 3, 2, 2, 3), state=c("cr", "g", "aq", "aq", "cr", "cr", "cr", "aq", "liq"), P=P, T=T, grid="P")
subcrt: 9 species at 110 values of T and P (wet) subcrt: some points above transition temperature for andradite cr (using NA for G) subcrt: some points above transition temperature for quartz cr1 (using NA for G) subcrt: some points below transition temperature for quartz cr2 (using NA for G) subcrt: some points above transition temperature for calcite cr (using NA for G) subcrt: some points above transition temperature for chalcopyrite cr1 (using NA for G) subcrt: some points below transition temperature for chalcopyrite cr2 (using NA for G) subcrt: some points above transition temperature for chalcopyrite cr2 (using NA for G) subcrt: some points below transition temperature for chalcopyrite cr3 (using NA for G) subcrt: some points above transition temperature for chalcopyrite cr3 (using NA for G) subcrt: 2 phases for quartz ... phases 1 2 are stable subcrt: 3 phases for chalcopyrite ... phases 1 2 3 are stable
# the results are not identical to SUPCRT92, at least because CHNOSZ # doesn't have volume changes for quartz, and has updated # parameters for species e.g. Cu+ from Shock et al., 1997 # the following is to help detect unintended changes to the code # across revisions; the code *should* be fixed sometime so that # the last 1 becomes a 3 stopifnot(all.equal(s$state$chalcopyrite[1:11], c(1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 1))) ## Standard Gibbs energy of reactions with HCN and ## formaldehyde, after Schulte and Shock, 1995 Fig. 1 rxn1 <- subcrt(c("formaldehyde","HCN","H2O","glycolic acid","NH3"), c(-1,-1,-2,1,1),P=300)
info.character: found H2O(liq), also available in gas info.character: found NH3(aq), also available in gas subcrt: 5 species at 15 values of T and P (wet)
rxn2 <- subcrt(c("formaldehyde","HCN","H2O","glycine"), c(-1,-1,-1,1),P=300)
info.character: found H2O(liq), also available in gas info.character: found glycine(aq), also available in cr subcrt: 4 species at 15 values of T and P (wet)
plot(x=rxn1$out$T,rxn1$out$G/1000,type="l",ylim=c(-40,-10), xlab=axis.label("T"),ylab=axis.label("DG0r","k")) lines(rxn1$out$T,rxn2$out$G/1000) # write the reactions on the plot text(150, -14, describe.reaction(rxn1$reaction, iname=c(1,2,4))) text(200, -35, describe.reaction(rxn2$reaction, iname=c(1,2))) title(main=paste("Standard Gibbs energy of reactions", "after Schulte and Shock, 1995",sep="\n"))

Image subcrt2

 

## Calculation of chemical affinities # after LaRowe and Helgeson, 2007, Fig. 3 (a): reduction of nicotinamide # adenine dinucleotide (NAD) coupled to oxidation of glucose # list the available NAD species info("NAD ")
info.approx: 'NAD ' is ambiguous; has approximate matches to 16 species: [1] "H2NAD(red)" "HNAD(red)-" "NAD(red)-2" "H2NAD(ox)+" "HNAD(ox)" "NAD(ox)-" [7] "H4NADP(red)" "H3NADP(red)-" "H2NADP(red)-2" "HNADP(red)-3" "NADP(red)-4" "H4NADP(ox)+" [13] "H3NADP(ox)" "H2NADP(ox)-" "HNADP(ox)-2" "NADP(ox)-3" [1] NA
T <- seq(0, 120, 10) # oxidation of glucose (C6H12O6) basis(c("glucose", "H2O", "NH3", "CO2", "H+"), c(-3, 0, 999, -3, -7))
C H N O Z ispecies logact state C6H12O6 6 12 0 6 0 1757 -3 aq H2O 0 2 0 1 0 1 0 liq NH3 0 3 1 0 0 68 999 aq CO2 1 0 0 2 0 69 -3 aq H+ 0 1 0 0 1 3 -7 aq
s <- subcrt(c("NAD(ox)-", "NAD(red)-2"), c(-12, 12), logact=c(0, 0), T=T)
subcrt: 2 species at 13 values of T and P (wet) subcrt: reaction is not balanced; it is missing this composition: H Z -12 12 subcrt: adding missing composition from basis definition and restarting... subcrt: 6 species at 13 values of T and P (wet)
# LH07's diagrams are shown per mole of electron (24 e- per 12 NAD) A <- s$out$A/24/1000 plot(x=T, y=A, xlim=range(T), ylim=c(1.4, 5.4), xlab=axis.label("T"), ylab=axis.label("A", prefix="k"), type="l") text("NAD(ox)-/NAD(red)-2 = 1", x=53, y=median(A), srt=21) # different activity ratio s <- subcrt(c("NAD(ox)-","NAD(red)-2"), c(-12, 12), logact=c(1, 0), T=T)
subcrt: 2 species at 13 values of T and P (wet) subcrt: reaction is not balanced; it is missing this composition: H Z -12 12 subcrt: adding missing composition from basis definition and restarting... subcrt: 6 species at 13 values of T and P (wet)
A <- s$out$A/24/1000 lines(x=T, y=A) text("NAD(ox)-/NAD(red)-2 = 10", x=55, y=median(A), srt=24) # different activity ratio s <- subcrt(c("NAD(ox)-","NAD(red)-2"), c(-12, 12), logact=c(0, 1), T=T)
subcrt: 2 species at 13 values of T and P (wet) subcrt: reaction is not balanced; it is missing this composition: H Z -12 12 subcrt: adding missing composition from basis definition and restarting... subcrt: 6 species at 13 values of T and P (wet)
A <- s$out$A/24/1000 lines(x=T, y=A) text("NAD(ox)-/NAD(red)-2 = 0.1", x=52, y=median(A), srt=18) # print the reaction and chemical conditions on the plot text(0, 5.3, describe.reaction(s$reaction, iname=c(1, 2)), adj=0) text(0, 5.1, describe.basis(oneline=TRUE, ibasis=c(1, 2, 4, 5)), adj=0) # label the plot title(main=paste("Reduction of NAD coupled to oxidation of glucose", "after LaRowe and Helgeson, 2007", sep="\n"))

Image subcrt3

 

## Subzero (degrees C) calculations # uncomment the following to try IAPWS95 instead of SUPCRT92 #thermo$opt$water <<- "IAPWS95" # the limit for H2O92D.f (from SUPCRT92) is currently -20 deg C # but we go to -30 knowing properties will become NA sb <- subcrt(c("H2O", "Na+"), T=seq(-30, 10), P=1)$out
info.character: found H2O(liq), also available in gas subcrt: 2 species at 41 values of T and P (wet) water.SUPCRT92: errors calculating 10 of 41 points; T < Tfusion@P, T > 2250 degC, or P > 30kb. water.SUPCRT92: errors calculating 10 of 41 points; T < Tfusion@P, T > 2250 degC, or P > 30kb.
# start plot with extra room on right par(mar=c(5, 4, 4, 4)) # plot G plot(sb$water$T, sb$water$G, ylim=c(-63000, -56000), xlab=axis.label("T"), ylab=axis.label("DG0")) points(sb$`Na+`$T, sb$`Na+`$G, pch=2) # add Cp # change y-axis par("usr"=c(par("usr")[1:2], -100, 25)) axis(4) mtext(axis.label("Cp0"), side=4, line=3) points(sb$water$T, sb$water$Cp, pch=16) points(sb$`Na+`$T, sb$`Na+`$Cp, pch=17) legend("topleft", pch=c(16, 1, 17, 2), legend=c("H2O Cp", "H2O G", "Na+ Cp", "Na+ G")) H2O <- expr.species("H2O") Na <- expr.species("Na+") degC <- expr.units("T") title(main=substitute(H2O~and~Na~to~-20~degC, list(H2O=H2O, Na=Na, degC=degC)))

Image subcrt4

 


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