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info> ## Don't show:
info> data(thermo)
thermo$obigt has 1800 aqueous, 2925 total species
info> ## End Don't show
info> ## basic operation
info> ## Not run:
info> ##D # run a consistency check on each species in the database
info> ##D # (marked dontrun because it takes a while)
info> ##D info(check=TRUE)
info> ##D
info> ## End(Not run)
info>
info> ## species information
info> # search for something named (or whose formula is) "Fe"
info> si <- info("Fe")
info: Fe available in cr1, cr2, cr3, cr4.
info: 2315 refers to Fe cr1 (RH95, CHNOSZ, 05.Aug.07)
info> # use the number to get the full record
info> info(si)
name abbrv formula state ref1 ref2 date G H S Cp V a b c d e f
2315 Fe iron Fe cr1 RH95 CHNOSZ 05.Aug.07 0 0 6.475 5.994 7.092 7.162 -0.0069682 0 0 1.2294e-05 0
lambda T
2315 0 1043
info> # it is possible to get a range of records
info> info(si:(si+3))
info: Cp of Fe cr2 is NA; set by EOS parameters to 293.01
info: Cp of Fe cr3 is NA; set by EOS parameters to 7.58
info: Cp of Fe cr4 is NA; set by EOS parameters to 9.11
name abbrv formula state ref1 ref2 date G H S Cp V a
2315 Fe iron Fe cr1 RH95 CHNOSZ 05.Aug.07 0.0 0.0 6.4750 5.994000 7.092 7.1620
2316 Fe iron Fe cr2 RH95 CHNOSZ 05.Aug.07 -32284.5 -87223.4 -177.7910 293.013353 7.092 504.5770
2317 Fe iron Fe cr3 RH95 CHNOSZ 05.Aug.07 1348.8 1843.8 8.1352 7.580456 7.092 5.1938
2318 Fe iron Fe cr4 RH95 CHNOSZ 05.Aug.07 3190.2 4835.6 11.9940 9.106491 7.092 -4.0330
b c d e f lambda T
2315 -0.0069682 0 0 1.2294e-05 0 0 1043
2316 -0.8072440 0 0 3.2754e-04 0 0 1185
2317 0.0023381 150190 0 0.0000e+00 0 0 1667
2318 0.0080055 955840 0 0.0000e+00 0 0 1809
info> ## dealing with states
info> # default order of preference for names: aq > gas > cr,liq
info> info(c("methane","ethanol","glycinate")) # aq, aq, aq
info: methane (CH4) available in aq, liq, gas.
info: ethanol (C2H5OH) available in aq, liq, gas.
info: 80 refers to methane, CH4 aq (SH90, 31.Aug.87)
info: 112 refers to ethanol, C2H5OH aq (SH90, 2.Sep.87)
info: 592 refers to glycinate, C2H4NO2- aq (SK95, CHNOSZ, 3.Sep.06)
info> info(c("adenosine","alanine","hydroxyapatite")) # aq, aq, cr
info: adenosine (C10H13N5O4) available in aq, cr.
info: alanine (C3H7NO2) available in aq, cr.
info: no match for hydroxyapatite.
info: approximately matching species are:
name abbrv formula state
576 2-hydroxypentanoic acid <NA> C5H10O3 aq
585 2-hydroxypentanoate <NA> C5H9O3- aq
info: 1598 refers to adenosine, C10H13N5O4 aq (LH06a, 3.Feb.03)
info: 1504 refers to alanine, C3H7NO2 aq (AH97b, DLH06, 25.Aug.06)
info> # state argument overrides the default
info> info(c("ethanol","adenosine"),state=c("gas","cr"))
info: 2815 refers to ethanol, C2H5OH gas (HOK+98, 30.Aug.06)
info: 2268 refers to adenosine, C10H13N5O4 cr (LH06a, 14.Aug.06)
info> # formulas default to aqueous species, if available
info> info(c("CH4","CO2","CS2","MgO")) # aq, aq, gas, cr
info: CH4 (methane) available in aq, liq, gas.
info: CO2 matches these species:
name abbrv formula state ref1
69 CO2 carbon dioxide CO2 aq SSW01
2683 carbon dioxide CO2 CO2 gas WEP+82
info: CS2 (carbon disulfide) available in liq, gas.
info: 80 refers to methane aq (SH90, 31.Aug.87)
info: 69 refers to CO2 aq (SSW01, SHS89, 11.Oct.07)
info: 2597 refers to carbon disulfide liq (Ric01, 1.Sep.06)
info: 1993 refers to periclase cr (HDN+78, 5.May.78)
info> # state argument overrides the default
info> info(c("CH4","CO2","MgO"),"gas") # gas, gas, NA
info: no match for MgO gas, and no approximate matches.
info: 2682 refers to methane gas (WEP+82, Kel60, 15.Dec.87)
info: 2683 refers to carbon dioxide gas (WEP+82, Kel60, 27.Dec.89)
info> # exceptions to the aqueous default is O2
info> info("O2") # gas
info: O2 matches these species:
name abbrv formula state ref1
2691 oxygen O2 O2 gas WEP+82
67 O2 oxygen O2 aq SHS89
info: 2691 refers to oxygen gas (WEP+82, Kel60, 27.Dec.89)
info> ## partial name or formula searches
info> info("ATP")
info: no match for ATP.
info: similar species names, abbreviations, or formulas are:
[1] "AMYA-PYRFU" "RNT1-ASPOR" "AMP-2" "HAMP-" "H2AMP" "dAMP-2"
[7] "dHAMP-" "dH2AMP" "ADP-3" "HADP-2" "H2ADP-" "H3ADP"
[13] "dADP-3" "dHADP-2" "dH2ADP-" "dH3ADP" "ATP-4" "HATP-3"
[19] "H2ATP-2" "H3ATP-" "H4ATP" "CTP-4" "HCTP-3" "H2CTP-2"
[25] "H3CTP-" "H4CTP" "GTP-4" "HGTP-3" "H2GTP-2" "H3GTP-"
[31] "H4GTP" "TTP-4" "HTTP-3" "H2TTP-2" "H3TTP-" "H4TTP"
[37] "UTP-4" "HUTP-3" "H2UTP-2" "H3UTP-" "H4UTP" "dATP-4"
[43] "dHATP-3" "dH2ATP-2" "dH3ATP-" "dH4ATP" "dCTP-4" "dHCTP-3"
[49] "dH2CTP-2" "dH3CTP-" "dH4CTP" "dGTP-4" "dHGTP-3" "dH2GTP-2"
[55] "dH3GTP-" "dH4GTP" "dTTP-4" "dHTTP-3" "dH2TTP-2" "dH3TTP-"
[61] "dH4TTP" "dUTP-4" "dHUTP-3" "dH2UTP-2" "dH3UTP-" "dH4UTP"
[67] "MgAMP" "MgADP-" "MgHADP" "Mg2ADP+" "MgATP-2" "MgHATP-"
[73] "MgH2ATP" "Mg2ATP" "H4NADP(red)" "H3NADP(red)-" "H2NADP(red)-2" "HNADP(red)-3"
[79] "NADP(red)-4" "H4NADP(ox)+" "H3NADP(ox)" "H2NADP(ox)-" "HNADP(ox)-2" "NADP(ox)-3"
info> info("thiol")
info: no match for thiol.
info: similar species names, abbreviations, or formulas are:
[1] "methanethiol" "ethanethiol" "n-propanethiol"
[4] "n-butanethiol" "n-pentanethiol" "n-hexanethiol"
[7] "n-heptanethiol" "n-octanethiol" "n-nonanethiol"
[10] "n-decanethiol" "n-undecanethiol" "n-dodecanethiol"
[13] "methionine" "glutathione" "glutathione,ox"
[16] "benzenethiol" "poly(thio-1,4-phenylene)" "thiophene"
[19] "benzo[b]thiophene" "dibenzo[b,d]thiophene" "n-tridecanethiol"
[22] "n-tetradecanethiol" "n-pentadecanethiol" "n-hexadecanethiol"
[25] "n-heptadecanethiol" "n-octadecanethiol" "n-nonadecanethiol"
[28] "n-eicosanethiol" "thiophenol" "2-propanethiol"
[31] "2-butanethiol" "2-methyl-1-propanethiol" "2-methyl-2-propanethiol"
[34] "2-methyl-1-butanethiol" "2-methyl-2-butanethiol" "3-methyl-1-butanethiol"
[37] "3-methyl-2-butanethiol" "2,2-dimethyl-1-propanethiol" "2-methyl-2-pentanethiol"
[40] "2,3-dimethyl-2-butanethiol" "cyclopentanethiol" "cyclohexanethiol"
[43] "phenylmethanethiol" "2-methylthiophene" "3-methylthiophene"
[46] "2,5-dimethylthiophene" "2-isopropylthiophene"
info> info("MgC")
info: no match for MgC.
info: similar species names, abbreviations, or formulas are:
[1] "Mg+2" "Mg(Ac)+" "Mg(Ac)2"
[4] "Mg(For)+" "Mg(For)2" "Mg(Prop)+"
[7] "Mg(Prop)2" "Mg(But)+" "Mg(But)2"
[10] "Mg(Pent)+" "Mg(Pent)2" "Mg(Glyc)+"
[13] "Mg(Glyc)2" "Mg(Lac)+" "Mg(Lac)2"
[16] "Mg(Gly)+" "Mg(Gly)2" "Mg(Alan)+"
[19] "Mg(Alan)2" "Mg(HCO3)+" "MgSO4"
[22] "AgCl" "AgCl2-" "MgCl+"
[25] "MgF+" "MgCO3" "MnCl+"
[28] "AgCl3-2" "AgCl4-3" "HgCl+"
[31] "HgCl2" "HgCl3-" "HgCl4-2"
[34] "Mg(HSiO3)+" "MgOH+" "Mg(Mal)"
[37] "Mg(Oxal)" "Mg(Succ)" "Mg(Glut)"
[40] "Mg(Adip)" "MgAMP" "MgADP-"
[43] "MgHADP" "Mg2ADP+" "MgATP-2"
[46] "MgHATP-" "MgH2ATP" "Mg2ATP"
[49] "Hydro-Mgs" "Mg-Hs" "Mg-Rbk"
[52] "Mgs" "MgCH3COO+" "MnCH3COO+"
[55] "HgCH3COO+" "AgCH3COO" "Mg(CH3COO)2"
[58] "MgCHO2+" "Mg(CHO2)2" "MnCHO2+"
[61] "MgCH3CH2CO2+" "Mg(CH3CH2CO2)2" "MnCH3CH2CO2+"
[64] "MgCH3(CH2)2CO2+" "Mg(CH3CH2CH2CO2)2" "MnCH3(CH2)2CO2+"
[67] "MgCH3(CH2)3CO2+1" "Mg(CH3CH2CH2CH2CO2)2" "MnCH3(CH2)3CO2+"
[70] "MgCH3OCO2+" "Mg(CH3OCO2)2" "MnCH3OCO2+"
[73] "MgCH3CH2OCO2+" "Mg(CH3CH2OCO2)2" "MnCH3CH2OCO2+"
[76] "Mg(C2H4NO2)+" "Mg(C2H4NO2)2" "Mg(C3H6NO2)+"
[79] "Mg(C3H6NO2)2" "MnC2O4" "MgC3H2O4"
[82] "MnC4H4O4" "MgC2O4" "HgC2O4"
[85] "MnC3H2O4" "MgC4H4O4" "MnC5H6O4"
[88] "MgC5H6O4" "MgC6H8O4" "MnC6H8O4"
[91] "MgC10H12N5O7P" "MgC10H12N5O10P2-" "MgC10H13N5O10P2"
[94] "Mg2C10H12N5O10P2+" "MgC10H12N5O13P3-2" "MgC10H13N5O13P3-"
[97] "MgC10H14N5O13P3" "Mg2C10H12N5O13P3" "Ca2MgSi2O7"
[100] "Mg4Al2(Al2Si2)O10(OH)8" "Mg2Al(AlSi)O5(OH)4" "Mg7Si8O22(OH)2"
[103] "Mg48Si34O85(OH)62" "Mg2(OH)2(CO3)*3H2O" "Mg(OH)2"
[106] "K(MgAl)Si4O10(OH)2" "Mg3Si2O5(OH)4" "Mg5Al(AlSi3)O10(OH)8"
[109] "Mg2Al3(AlSi5)O18" "Mg2Al3(AlSi5)O18*H2O" "CaMg(SiO3)2"
[112] "CaMg(CO3)2" "Na(Ca2Mg5)(AlSi7)O22(OH2)" "MgSiO3"
[115] "Na(Ca2Mg5)(AlSi7)O22(F)2" "KMg3(AlSi3)O10(F)2" "(Ca2Mg5)Si8O22(F)2"
[118] "Mg2SiO4" "Na2(Mg3Al2)Si8O22(OH)2" "CaMg3(CO3)4"
[121] "Mg5(OH)2(CO3)4*4H2O" "Na(Ca2Mg4Fe)(Al2Si6)O22(OH)2" "Na2(Mg3Fe2)Si8O22(OH)2"
[124] "Ca3Mg(SiO4)2" "CaMgSiO4" "MgCO3*3H2O"
[127] "Na(Ca2Mg4Al)(Al2Si6)O22(OH)2" "MgO" "KMg3(AlSi3)O10(OH)2"
[130] "Mg3Al2Si3O12" "MnCO3" "Na2(CaMg5)Si8O22(OH)2"
[133] "Mg4Si6O15(OH)2(H2O)2*4H2O" "MgAl2O4" "Mg3Si4O10(OH)2"
[136] "(Ca2Mg5)Si8O22(OH)2"
info> # add an extra character to refine a search
info> # or to search using terms that have exact matches
info> info("MgC ")
info: no match for MgC .
info: similar species names, abbreviations, or formulas are:
[1] "MgCl+" "MgCO3" "MgCH3COO+" "MgCHO2+" "MgCH3CH2CO2+"
[6] "MgCH3(CH2)2CO2+" "MgCH3(CH2)3CO2+1" "MgCH3OCO2+" "MgCH3CH2OCO2+" "MgC3H2O4"
[11] "MgC2O4" "MgC4H4O4" "MgC5H6O4" "MgC6H8O4" "MgC10H12N5O7P"
[16] "MgC10H12N5O10P2-" "MgC10H13N5O10P2" "MgC10H12N5O13P3-2" "MgC10H13N5O13P3-" "MgC10H14N5O13P3"
[21] "MgCO3*3H2O"
info> info("acetate ")
info: no match for acetate .
info: approximately matching species are:
name abbrv formula state
138 ethylacetate <NA> CH3COOCH2CH3 aq
540 acetate <NA> C2H3O2- aq
2505 ethyl acetate <NA> C4H8O2 liq
2857 ethyl acetate <NA> C4H8O2 gas
info> info(" H2O")
info: no match for H2O.
info: similar species names, abbreviations, or formulas are:
[1] "H2O2" "[-CH2OH]" "H2O"
[4] "C2H2O4" "C3H2O4-2" "NaCH3CH2OCO2"
[7] "Na(CH3CH2OCO2)2-" "KCH3CH2OCO2" "K(CH3CH2OCO2)2-"
[10] "CaCH3CH2OCO2+" "Ca(CH3CH2OCO2)2" "MgCH3CH2OCO2+"
[13] "Mg(CH3CH2OCO2)2" "SrCH3CH2OCO2+" "Sr(CH3CH2OCO2)2"
[16] "BaCH3CH2OCO2+" "Ba(CH3CH2OCO2)2" "MnCH3CH2OCO2+"
[19] "Mn(CH3CH2OCO2)2" "FeCH3CH2OCO2+" "Fe(CH3CH2OCO2)2"
[22] "NiCH3CH2OCO2+" "Ni(CH3CH2OCO2)2" "CuCH3CH2OCO2+"
[25] "Cu(CH3CH2OCO2)2" "ZnCH3CH2OCO2+" "Zn(CH3CH2OCO2)2"
[28] "PbCH3CH2OCO2+" "Pb(CH3CH2OCO2)2" "CoCH3CH2OCO2+"
[31] "Co(CH3CH2OCO2)2" "CdCH3CH2OCO2+" "Cd(CH3CH2OCO2)2"
[34] "Eu(CH3CH2OCO2)+" "Eu(CH3CH2OCO2)2" "LuCH3CH2OCO2+2"
[37] "LaCH3CH2OCO2+2" "LiCH3CH2OCO2" "LiC3H2O4-"
[40] "MgC3H2O4" "ZnC3H2O4" "CdC3H2O4"
[43] "AlC3H2O4+" "PbC3H2O4" "CuC3H2O4"
[46] "LaC3H2O4+" "GdC3H2O4+" "LuC3H2O4+"
[49] "YbC3H2O4+" "ThC3H2O4+2" "UO2C3H2O4"
[52] "CeC3H2O4+" "NdC3H2O4+" "SmC3H2O4+"
[55] "PrC3H2O4+" "EuC3H2O4+" "TbC3H2O4+"
[58] "DyCC3H2O4+" "TmC3H2O4+" "HoC3H2O4+"
[61] "ErC3H2O4+" "ScC3H2O4+" "FeC3H2O4+"
[64] "CsC3H2O4-" "NH4C3H2O4-" "SrC3H2O4"
[67] "CrC3H2O4" "BeC3H2O4" "FeC3H2O4"
[70] "InC3H2O4+" "YC3H2O4+" "CaC3H2O4"
[73] "BaC3H2O4" "MnC3H2O4" "CoC3H2O4"
[76] "NiC3H2O4" "C2H2O2-" "NaAlSi2O6*H2O"
[79] "Mg2(OH)2(CO3)*3H2O" "Ca(Al2Si5)O14*5H2O" "Ca(Al2Si4)O12*6H2O"
[82] "Mg2Al3(AlSi5)O18*H2O" "Ca(Al2Si6)O16*5H2O" "Ca(Al2Si7)O18*6H2O"
[85] "Mg5(OH)2(CO3)4*4H2O" "K2(Al2Si5)O14*5H2O" "Ca(Al2Si4)O12*4H2O"
[88] "CaAl2Si2O7(OH)2*H2O" "Ca2(Al4Si8)O24*7H2O" "Na2(Al2Si5)O14*5H2O"
[91] "Na2(Al2Si3)O10*2H2O" "MgCO3*3H2O" "Mg4Si6O15(OH)2(H2O)2*4H2O"
[94] "NaCa2(Al5Si13)O36*14H2O" "Ca(Al2Si4)O12*2H2O"
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