Error(s) in re-building vignettes:
  ...
--- re-building ‘OBIGT.Rmd’ using rmarkdown
--- finished re-building ‘OBIGT.Rmd’

--- re-building ‘anintro.Rmd’ using rmarkdown
info.character: found CH4(aq); also available in gas, liq
checkEOS: Cp of CH4(aq) differs by -2.61 cal K-1 mol-1 from tabulated value
checkEOS: Cp of CH4(aq) differs by -2.61 cal K-1 mol-1 from tabulated value
checkEOS: Cp of CH4(aq) differs by -2.61 cal K-1 mol-1 from tabulated value
subcrt: 1 species at 5511 values of T (ºC) and P (bar) (wet) [energy units: cal]
changed temperature units to K
changed pressure units to MPa
changed energy units to J
info.character: found CH4(aq); also available in gas, liq
subcrt: 1 species at 298.15 K and 0.1 MPa (wet) [energy units: J]
info.character: found CH4(aq); also available in gas, liq
checkEOS: Cp of CH4(aq) differs by -2.61 cal K-1 mol-1 from tabulated value
subcrt: 2 species at 36 values of T (ºC) and P (bar) (wet) [energy units: cal]
subcrt: 2 species at 36 values of T (ºC) and P (bar) (wet) [energy units: cal]
subcrt: 2 species at 36 values of T (ºC) and P (bar) (wet) [energy units: cal]
info.character: found CH4(aq); also available in gas, liq
subcrt: 2 species at 15 values of T (ºC) and P (bar) (wet) [energy units: cal]
subcrt: reaction is not balanced; it is missing this composition:
 C  H  O  Z 
 1 -1  2 -1 
subcrt: adding missing composition from basis definition and restarting...
subcrt: 4 species at 15 values of T (ºC) and P (bar) (wet) [energy units: cal]
subcrt: 1 species at 15 values of T (ºC) and P (bar) (wet) [energy units: cal]
subcrt: reaction is not balanced; it is missing this composition:
 C  H  O  Z 
 2  3  2 -1 
subcrt: adding missing composition from basis definition and restarting...
subcrt: 5 species at 15 values of T (ºC) and P (bar) (wet) [energy units: cal]
info.character: found CH4(aq); also available in gas, liq
subcrt: 1 species at 15 values of T (ºC) and P (bar) (wet) [energy units: cal]
subcrt: reaction is not balanced; it is missing this composition:
 C  H 
-1 -4 
subcrt: adding missing composition from basis definition and restarting...
subcrt: 4 species at 15 values of T (ºC) and P (bar) (wet) [energy units: cal]
info.character: found CH4(aq); also available in gas, liq
subcrt: 2 species at 15 values of T (ºC) and P (bar) (wet) [energy units: cal]
subcrt: reaction is not balanced; it is missing this composition:
 C  H  O  Z 
 1 -1  2 -1 
subcrt: adding missing composition from basis definition and restarting...
subcrt: 4 species at 15 values of T (ºC) and P (bar) (wet) [energy units: cal]
Quitting from lines 445-452 (anintro.Rmd) 
Error: processing vignette ‘anintro.Rmd’ failed with diagnostics:
figure margins too large
--- failed re-building ‘anintro.Rmd’

--- re-building ‘eos-regress.Rmd’ using rmarkdown
EOSplot: plotting line for P=279.96 bar
EOSplot: plotting line for P=279.96 bar
checkEOS: Cp of CH4(aq) differs by -2.61 cal K-1 mol-1 from tabulated value
EOSplot: plotting line for P=279.96 bar
checkEOS: Cp of CH4(aq) differs by -2.61 cal K-1 mol-1 from tabulated value
checkEOS: Cp of CH4(aq) differs by -2.61 cal K-1 mol-1 from tabulated value
EOSplot: plotting line for P=280.010526315789 bar
EOSplot: plotting line for P=280.010526315789 bar
EOSplot: plotting line for P=280.010526315789 bar
EOSplot: plotting line for P=280.010526315789 bar
EOSplot: plotting line for P=1000 bar
EOSplot: plotting line for P=1000 bar
add.OBIGT: read 3 rows; made 2 replacements, 1 additions [energy units: cal]
info.character: found SiO2(aq); also available in cr
info.character: found H2O(liq) [water]; also available in cr
subcrt: 2 species at 25 ºC and 1 bar (wet) [energy units: cal]
subcrt: reaction is not balanced; it is missing this composition:
 H  O Si 
-4 -4 -1 
info.character: found SiO2(aq); also available in cr
info.character: found H2O(liq) [water]; also available in cr
subcrt: 2 species at 50 values of T (ºC) and P (bar) (wet) [energy units: cal]
subcrt: reaction is not balanced; it is missing this composition:
 H  O Si 
-4 -4 -1 
info.character: found SiO2(aq); also available in cr
info.character: found H2O(liq) [water]; also available in cr
subcrt: 2 species at 11 values of T (ºC) and P (bar) (wet) [energy units: cal]
subcrt: reaction is not balanced; it is missing this composition:
 H  O Si 
-4 -4 -1 
info.character: found SiO2(aq); also available in cr
info.character: found H2O(liq) [water]; also available in cr
subcrt: 2 species at 15 values of T (ºC) and P (bar) (wet) [energy units: cal]
subcrt: reaction is not balanced; it is missing this composition:
 H  O Si 
-4 -4 -1 
info.character: found SiO2(aq); also available in cr
info.character: found H2O(liq) [water]; also available in cr
subcrt: 2 species at 11 values of T (ºC) and P (bar) (wet) [energy units: cal]
subcrt: reaction is not balanced; it is missing this composition:
 H  O Si 
-4 -4 -1 
info.character: found SiO2(aq); also available in cr
info.character: found H2O(liq) [water]; also available in cr
subcrt: 2 species at 11 values of T (ºC) and P (bar) (wet) [energy units: cal]
subcrt: reaction is not balanced; it is missing this composition:
 H  O Si 
-4 -4 -1 
info.character: found H4SiO4(aq); also available in aq
info.character: found SiO2(aq); also available in cr
info.character: found H2O(liq) [water]; also available in cr
subcrt: 3 species at 15 values of T (ºC) and P (bar) (wet) [energy units: cal]
info.character: found H4SiO4(aq); also available in aq
info.character: found SiO2(aq); also available in cr
info.character: found H2O(liq) [water]; also available in cr
subcrt: 3 species at 15 values of T (ºC) and P (bar) (wet) [energy units: cal]
affinity: temperature is 25 ºC
affinity: pressure is Psat
affinity: variable 1 is log10(a_H4SiO4) at 300 values from -8 to 0
affinity: variable 2 is log10(a_K+) at 300 values from -1 to 8
subcrt: 11 species at 25 ºC and 1 bar (wet) [energy units: cal]
balance: on moles of Al+3 in formation reactions
diagram: using maximum affinity method for 2-D diagram
[WARNING] Could not convert TeX math 'coefficients[["TXBorn"]], "cm3bar")V_sol <- Vomega * QBornV_non <- Vdat', rendering as TeX:
  coefficients[["TXBorn"]], "cm3bar")V_sol
                ^
  unexpected '"'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'outs_near25 <- subcrt(c("SiO2", "H2O"), c(1, 2), T = seq(20, 30, length.out=50))', rendering as TeX:
  near25 <- subcrt(c("SiO2", "H2O"), c(1, 
                     ^
  unexpected '"'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'outs_Psat <- subcrt(c("SiO2", "H2O"), c(1, 2))', rendering as TeX:
  s_Psat <- subcrt(c("SiO2", "H2O"), c(1, 
                     ^
  unexpected '"'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'outs_P1000 <- subcrt(c("SiO2", "H2O"), c(1, 2), T = seq(0, 1000, 100), P = 1000)', rendering as TeX:
  _P1000 <- subcrt(c("SiO2", "H2O"), c(1, 
                     ^
  unexpected '"'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'coefficients[["TXBorn"]], "cm3bar")V_sol <- Vomega * QBornV_non <- Vdat', rendering as TeX:
  coefficients[["TXBorn"]], "cm3bar")V_sol
                ^
  unexpected '"'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
--- finished re-building ‘eos-regress.Rmd’

--- re-building ‘equilibrium.Rmd’ using rmarkdown
reset: resetting "thermo" object
OBIGT: loading default database with 1903 aqueous, 3443 total species
affinity: temperature is 25 ºC
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 256 values from -90 to -70
affinity: variable 2 is log10(a_H2O) at 256 values from -20 to 10
subcrt: 25 species at 25 ºC and 1 bar (wet) [energy units: cal]
balance: on supplied numeric argument (1) [1 means balance on formula units]
diagram: using maximum affinity method for 2-D diagram
affinity: temperature is 25 ºC
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 256 values from -90 to -70
affinity: variable 2 is log10(a_H2O) at 256 values from -20 to 10
subcrt: 25 species at 25 ºC and 1 bar (wet) [energy units: cal]
balance: on supplied numeric argument (1) [1 means balance on formula units]
equilibrate: n.balance is 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
equilibrate: loga.balance is -1.69897000433602
equilibrate: using boltzmann method
affinity: temperature is 25 ºC
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 256 values from -71 to -66
affinity: variable 2 is log10(a_H2O) at 256 values from -8 to 4
subcrt: 25 species at 25 ºC and 1 bar (wet) [energy units: cal]
balance: on moles of CO2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
affinity: temperature is 25 ºC
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 256 values from -71 to -66
affinity: variable 2 is log10(a_H2O) at 256 values from -8 to 4
subcrt: 25 species at 25 ºC and 1 bar (wet) [energy units: cal]
balance: on moles of CO2 in formation reactions
equilibrate: n.balance is 3 3 4 5 9 2 6 6 6 6 5 4 5 5 6 3 4 5 11 9
equilibrate: loga.balance is -0.97061622231479
equilibrate: using reaction method
palply: equil.reaction running 65536 calculations on 2 cores
affinity: temperature is 25 ºC
affinity: pressure is Psat
affinity: variable 1 is log10(a_H2O) at 256 values from -8 to 4
subcrt: 25 species at 25 ºC and 1 bar (wet) [energy units: cal]
balance: on moles of CO2 in formation reactions
equilibrate: n.balance is 3 3 4 5 9 2 6 6 6 6 5 4 5 5 6 3 4 5 11 9
equilibrate: loga.balance is -0.97061622231479
equilibrate: using reaction method
affinity: temperature is 25 ºC
affinity: pressure is Psat
affinity: variable 1 is log10(a_H2O) at 256 values from -8 to 4
subcrt: 25 species at 25 ºC and 1 bar (wet) [energy units: cal]
balance: on moles of CO2 in formation reactions
equilibrate: n.balance is 3 3 4 5 9 2 6 6 6 6 5 4 5 5 6 3 4 5 11 9
equilibrate: loga.balance is -4.97061622231479
equilibrate: using reaction method
affinity: temperature is 25 ºC
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 256 values from -90 to -70
affinity: variable 2 is log10(a_H2O) at 256 values from -20 to 0
subcrt: 12 species at 25 ºC and 1 bar (wet) [energy units: cal]
subcrt: 18 species at 25 ºC and 1 bar (wet) [energy units: cal]
balance: on protein length
diagram: using maximum affinity method for 2-D diagram
affinity: temperature is 25 ºC
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 256 values from -90 to -70
affinity: variable 2 is log10(a_H2O) at 256 values from -20 to 0
subcrt: 12 species at 25 ºC and 1 bar (wet) [energy units: cal]
subcrt: 18 species at 25 ºC and 1 bar (wet) [energy units: cal]
balance: on protein length
diagram: using maximum affinity method for 2-D diagram
diagram: using 'normalize' in calculation of predominant species
affinity: temperature is 25 ºC
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 256 values from -90 to -70
affinity: variable 2 is log10(a_H2O) at 256 values from -20 to 0
subcrt: 12 species at 25 ºC and 1 bar (wet) [energy units: cal]
subcrt: 18 species at 25 ºC and 1 bar (wet) [energy units: cal]
balance: on protein length
diagram: using maximum affinity method for 2-D diagram
diagram: using 'as.residue' in calculation of predominant species
affinity: temperature is 25 ºC
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 256 values from -90 to -70
subcrt: 12 species at 25 ºC and 1 bar (wet) [energy units: cal]
subcrt: 18 species at 25 ºC and 1 bar (wet) [energy units: cal]
balance: on protein length
equilibrate: n.balance is 530 828 553 736 1198 844
equilibrate: loga.balance is 0.671080232738849
equilibrate: using reaction method
affinity: temperature is 25 ºC
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 256 values from -90 to -70
subcrt: 12 species at 25 ºC and 1 bar (wet) [energy units: cal]
subcrt: 18 species at 25 ºC and 1 bar (wet) [energy units: cal]
balance: on protein length
equilibrate: n.balance is 530 828 553 736 1198 844
equilibrate: loga.balance is 0.671080232738849
equilibrate: using 'normalize' for molar formulas
equilibrate: using boltzmann method
affinity: temperature is 25 ºC
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 256 values from -90 to -70
subcrt: 12 species at 25 ºC and 1 bar (wet) [energy units: cal]
subcrt: 18 species at 25 ºC and 1 bar (wet) [energy units: cal]
balance: on protein length
equilibrate: n.balance is 530 828 553 736 1198 844
equilibrate: loga.balance is 0
equilibrate: using 'as.residue' for molar formulas
equilibrate: using boltzmann method
affinity: temperature is 25 ºC
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 256 values from -100 to -65
subcrt: 16 species at 25 ºC and 1 bar (wet) [energy units: cal]
subcrt: 18 species at 25 ºC and 1 bar (wet) [energy units: cal]
balance: on protein length
equilibrate: n.balance is 571 530 571 553 278 828 736 1198 844 481
equilibrate: loga.balance is 0.81888541459401
equilibrate: using reaction method
balance: on protein length
equilibrate: n.balance is 571 530 571 553 278 828 736 1198 844 481
equilibrate: loga.balance is 0.81888541459401
equilibrate: using 'normalize' for molar formulas
equilibrate: using boltzmann method
[WARNING] Could not convert TeX math 'loga.balance[1], 2)), cex.main=1)label.figure("C", yfrac=0.92, xfrac=0.1, font = 2)## row 2 (balance = nCO2)opar <- par(mar=c(0, 0, 0, 0))plot.new()text(0.5, 0.5, 'balance = "CO2"', srt=90, cex=1.4)par(opar)# figure Cst <- system.time(dC <- aaC())showtime(st)title(main="loga(species) = -3", cex.main=1)label.figure("B", yfrac=0.92, xfrac=0.1, font = 2)# figure Dst <- system.time(dD <- aaD())showtime(st)title(main=paste("loga(total CO2) =", round(dD', rendering as TeX:
  ain=1)label.figure("C", yfrac=0.92, xfra
                     ^
  unexpected '"'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'loga.balance[1], 2)), cex.main=1)label.figure("E", yfrac=0.92, xfrac=0.1, font = 2)# figure Fst <- system.time(dF <- aaF())showtime(st)title(main=paste("loga(total CO2) =", round(dF', rendering as TeX:
  ain=1)label.figure("E", yfrac=0.92, xfra
                     ^
  unexpected '"'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
--- finished re-building ‘equilibrium.Rmd’

--- re-building ‘multi-metal.Rmd’ using rmarkdown
affinity: temperature is 25 ºC
affinity: pressure is Psat
affinity: variable 1 is pH at 256 values from 0 to 14
affinity: variable 2 is log10(f_O2) at 256 values from -75 to -60
subcrt: 10 species at 25 ºC and 1 bar (wet) [energy units: cal]
balance: on moles of CO2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
affinity: temperature is 25 ºC
affinity: pressure is Psat
affinity: variable 1 is pH at 256 values from 0 to 14
affinity: variable 2 is log10(f_O2) at 256 values from -75 to -60
subcrt: 10 species at 25 ºC and 1 bar (wet) [energy units: cal]
balance: on moles of H2S in formation reactions
diagram: using maximum affinity method for 2-D diagram
balance: on moles of CO2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
mod.OBIGT: updated Fe(cr)
mod.OBIGT: updated FeO(cr)
mod.OBIGT: updated Fe3O4(cr)
mod.OBIGT: updated Fe2O3(cr)
mod.OBIGT: updated Fe+2(aq)
mod.OBIGT: updated Fe+3(aq)
mod.OBIGT: added FeO2-2(aq) with energy units of J
mod.OBIGT: updated FeOH+(aq)
mod.OBIGT: updated FeOH+2(aq)
mod.OBIGT: updated HFeO2-(aq)
mod.OBIGT: added Fe(OH)2+(aq) with energy units of J
mod.OBIGT: added Fe(OH)3(aq) with energy units of J
mod.OBIGT: updated FeO2-(aq)
mod.OBIGT: added FeO4-2(aq) with energy units of J
mod.OBIGT: added V(cr) with energy units of J
mod.OBIGT: added V2O3(cr) with energy units of J
mod.OBIGT: added V3O5(cr) with energy units of J
mod.OBIGT: added VO2(cr) with energy units of J
mod.OBIGT: added V3O7(cr) with energy units of J
mod.OBIGT: added V2O5(cr) with energy units of J
mod.OBIGT: updated VO+2(aq)
mod.OBIGT: updated VO2+(aq)
mod.OBIGT: added VO3-(aq) with energy units of J
mod.OBIGT: updated VO4-3(aq)
mod.OBIGT: added V2O7-4(aq) with energy units of J
mod.OBIGT: added HVO4(aq) with energy units of J
mod.OBIGT: updated HVO4-2(aq)
mod.OBIGT: added VOH2O2+3(aq) with energy units of J
mod.OBIGT: added VO2H2O2+(aq) with energy units of J
mod.OBIGT: added V2HO7-3(aq) with energy units of J
mod.OBIGT: added V2H3O7-(aq) with energy units of J
mod.OBIGT: added HV10O28-5(aq) with energy units of J
mod.OBIGT: added H2V10O28-4(aq) with energy units of J
mod.OBIGT: added FeV(cr) with energy units of J
mod.OBIGT: added FeV3(cr) with energy units of J
mod.OBIGT: added Fe3V(cr) with energy units of J
mod.OBIGT: added Fe2V4O13(cr) with energy units of J
mod.OBIGT: added FeVO4(cr) with energy units of J
affinity: temperature is 25 ºC
affinity: pressure is Psat
affinity: variable 1 is pH at 150 values from 4 to 10
affinity: variable 2 is Eh at 150 values from -1.5 to 0 V
subcrt: 19 species at 25 ºC and 1 bar (wet) [energy units: cal]
balance: on moles of Fe+2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
affinity: temperature is 25 ºC
affinity: pressure is Psat
affinity: variable 1 is pH at 150 values from 4 to 10
affinity: variable 2 is Eh at 150 values from -1.5 to 0 V
subcrt: 24 species at 25 ºC and 1 bar (wet) [energy units: cal]
balance: on moles of VO+2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
affinity: temperature is 25 ºC
affinity: pressure is Psat
affinity: variable 1 is pH at 150 values from 4 to 10
affinity: variable 2 is Eh at 150 values from -1.5 to 0 V
subcrt: 10 species at 25 ºC and 1 bar (wet) [energy units: cal]
balance: on moles of VO+2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
mix: removing 1 combination with a singular stoichiometric matrix
balance: on moles of VO+2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
mix: removing 1 combination with a singular stoichiometric matrix
balance: on moles of VO+2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
mix: removing 1 combination with a singular stoichiometric matrix
balance: on moles of VO+2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
affinity: temperature is 25 ºC
affinity: pressure is Psat
affinity: variable 1 is pH at 200 values from 0 to 14
affinity: variable 2 is Eh at 200 values from -1.5 to 2 V
subcrt: 19 species at 25 ºC and 1 bar (wet) [energy units: cal]
balance: on moles of Fe+2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
affinity: temperature is 25 ºC
affinity: pressure is Psat
affinity: variable 1 is pH at 200 values from 0 to 14
affinity: variable 2 is Eh at 200 values from -1.5 to 2 V
subcrt: 24 species at 25 ºC and 1 bar (wet) [energy units: cal]
balance: on moles of VO+2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
affinity: temperature is 25 ºC
affinity: pressure is Psat
affinity: variable 1 is pH at 200 values from 0 to 14
affinity: variable 2 is Eh at 200 values from -1.5 to 2 V
subcrt: 10 species at 25 ºC and 1 bar (wet) [energy units: cal]
balance: on moles of VO+2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
mix: removing 1 combination with a singular stoichiometric matrix
info.character: found Fe2O3(cr); also available in hematite
balance: on moles of VO+2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
affinity: temperature is 25 ºC
affinity: pressure is Psat
affinity: variable 1 is pH at 200 values from 0 to 14
affinity: variable 2 is Eh at 200 values from -1.5 to 2 V
subcrt: 6 species at 25 ºC and 1 bar (wet) [energy units: cal]
balance: on moles of VO+2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
balance: on moles of VO+2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
subcrt: 1 species at 25 ºC and 1 bar [energy units: cal]
subcrt: reaction is not balanced; it is missing this composition:
Fe  V  O 
-1 -1 -4 
subcrt: adding missing composition from basis definition and restarting...
subcrt: 3 species at 25 ºC and 1 bar [energy units: cal]
reset: resetting "thermo" object
OBIGT: loading default database with 1903 aqueous, 3443 total species
info.character: found H2S(aq); also available in gas
affinity: temperature is 200 ºC
affinity: pressure is Psat
affinity: variable 1 is pH at 200 values from 0 to 14
affinity: variable 2 is log10(f_O2) at 200 values from -48 to -33
subcrt: 14 species at 200 ºC and 15.54 bar (wet) [energy units: cal]
subcrt: 3 phases for pyrrhotite ... phase 2 is stable
mosaic: calculating affinities of basis species group 1: H2S HS- HSO4- SO4-2
mosaic: calculating affinities of species for all 4 combinations of the basis species
balance: on moles of H2S in formation reactions
equilibrate: n.balance is 1 1 1 1
equilibrate: loga.balance is -2
equilibrate: using boltzmann method
balance: on moles of H2S in formation reactions
diagram: using maximum affinity method for 2-D diagram
balance: on moles of FeS2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
info.character: found H2S(aq); also available in gas
info.character: found pyrrhotite(cr) with 2 phase transitions
affinity: temperature is 200 ºC
affinity: pressure is Psat
affinity: variable 1 is pH at 200 values from 0 to 14
affinity: variable 2 is log10(f_O2) at 200 values from -48 to -33
subcrt: 21 species at 200 ºC and 15.54 bar (wet) [energy units: cal]
subcrt: 3 phases for chalcopyrite ... phase 1 is stable
subcrt: 3 phases for bornite ... phase 1 is stable
subcrt: 3 phases for chalcocite ... phase 2 is stable
subcrt: 3 phases for pyrrhotite ... phase 2 is stable
mosaic: calculating affinities of basis species group 1: H2S HS- HSO4- SO4-2
mosaic: calculating affinities of basis species group 2: pyrite pyrrhotite magnetite hematite
mosaic: calculating affinities of species for all 16 combinations of the basis species
balance: on moles of H2S in formation reactions
equilibrate: n.balance is 1 1 1 1
equilibrate: loga.balance is -2
equilibrate: using boltzmann method
balance: on moles of Cu+ in formation reactions
diagram: using maximum affinity method for 2-D diagram
balance: on moles of Cu+ in formation reactions
diagram: using maximum affinity method for 2-D diagram
checkGHS: G of HFeO2(aq) differs by -4600 cal mol-1 from tabulated value
checkGHS: G of FeO2-(aq) differs by -4641 cal mol-1 from tabulated value
checkEOS: Cp of Cu+2(aq) differs by 3.62 cal K-1 mol-1 from tabulated value
checkEOS: V of CuCl4-2(aq) differs by -1.07 cm3 mol-1 from tabulated value
checkEOS: V of CuO2-2(aq) differs by -1.09 cm3 mol-1 from tabulated value
checkEOS: Cp of CuHS(aq) differs by 7.35 cal K-1 mol-1 from tabulated value
checkEOS: V of CuHS(aq) differs by -16.2 cm3 mol-1 from tabulated value
info.character: found NaCl(aq); also available in cr
subcrt: 3 species at 200 ºC and 15.54 bar (wet) [energy units: cal]
info.character: found NaCl(aq); also available in cr
info.character: found H2S(aq); also available in gas
affinity: temperature is 200 ºC
affinity: pressure is Psat
affinity: ionic strength is 0.0950342045548425
affinity: variable 1 is pH at 200 values from 0 to 14
affinity: variable 2 is log10(f_O2) at 200 values from -48 to -33
subcrt: 28 species at 200 ºC and 15.54 bar (wet) [energy units: cal]
nonideal: calculations for Cu+, Cl-, FeCl+, FeCl+2, Fe+2, Fe+3, FeOH+, HFeO2-, FeOH+2, FeO+, FeO2-, HS-, HSO4-, SO4-2 (Bdot equation)
nonideal: calculations for H2S, FeCl2, FeO, HFeO2, FeSO4, H2S (Setchenow equation)
subcrt: 3 phases for pyrrhotite ... phase 2 is stable
mosaic: calculating affinities of basis species group 1: H2S HS- HSO4- SO4-2
mosaic: calculating affinities of species for all 4 combinations of the basis species
balance: on moles of H2S in formation reactions
equilibrate: n.balance is 1 1 1 1
equilibrate: loga.balance is -2
equilibrate: using boltzmann method
balance: on moles of FeS2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
checkGHS: G of HFeO2(aq) differs by -4600 cal mol-1 from tabulated value
checkGHS: G of FeO2-(aq) differs by -4641 cal mol-1 from tabulated value
mod.OBIGT: updated FeCl+(aq)
mod.OBIGT: updated FeCl2(aq)
mod.OBIGT: updated FeCl+2(aq)
mod.OBIGT: updated Fe+2(aq)
mod.OBIGT: updated Fe+3(aq)
mod.OBIGT: updated FeOH+(aq)
mod.OBIGT: updated FeO(aq)
mod.OBIGT: updated HFeO2-(aq)
mod.OBIGT: updated FeOH+2(aq)
mod.OBIGT: updated FeO+(aq)
mod.OBIGT: updated HFeO2(aq)
mod.OBIGT: updated FeO2-(aq)
mod.OBIGT: updated FeSO4(aq)
info.character: found H2S(aq); also available in gas
info.character: found pyrrhotite(cr) with 2 phase transitions
affinity: temperature is 200 ºC
affinity: pressure is Psat
affinity: ionic strength is 0.0950342045548425
affinity: variable 1 is pH at 200 values from 0 to 14
affinity: variable 2 is log10(f_O2) at 200 values from -48 to -33
subcrt: 43 species at 200 ºC and 15.54 bar (wet) [energy units: cal]
nonideal: calculations for Cu+, Cl-, Cu+2, CuCl3-2, CuCl+, CuCl3-, CuCl4-2, CuOH+, HCuO2-, CuO2-2, Cu+, Cu(OH)2-, Cu(HS)2-, CuCl2-, HS-, HSO4-, SO4-2, Fe+2, HFeO2-, FeO2- (Bdot equation)
nonideal: calculations for H2S, CuCl2, CuO, CuOH, CuHS, CuCl, H2S, FeSO4 (Setchenow equation)
subcrt: 3 phases for chalcopyrite ... phase 1 is stable
subcrt: 3 phases for bornite ... phase 1 is stable
subcrt: 3 phases for chalcocite ... phase 2 is stable
subcrt: 3 phases for pyrrhotite ... phase 2 is stable
mosaic: calculating affinities of basis species group 1: H2S HS- HSO4- SO4-2
mosaic: calculating affinities of basis species group 2: pyrite pyrrhotite magnetite hematite Fe+2 HFeO2- FeO2- FeSO4
mosaic: calculating affinities of species for all 32 combinations of the basis species
balance: on moles of H2S in formation reactions
equilibrate: n.balance is 1 1 1 1
equilibrate: loga.balance is -2
equilibrate: using boltzmann method
balance: on moles of Cu+ in formation reactions
diagram: using maximum affinity method for 2-D diagram
balance: on moles of Cu+ in formation reactions
diagram: using maximum affinity method for 2-D diagram
balance: on moles of H2S in formation reactions
diagram: using maximum affinity method for 2-D diagram
balance: on moles of FeS2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
OBIGT: loading default database with 1903 aqueous, 3443 total species
info.character: found pyrrhotite(cr) with 2 phase transitions
info.character: found chalcocite(cr) with 2 phase transitions
info.character: found chalcopyrite(cr) with 2 phase transitions
info.character: found bornite(cr) with 2 phase transitions
info.character: found H2S(aq); also available in gas
info.character: found FeO(aq); also available in cr
info.character: found CuO(aq); also available in cr
info.character: found H2S(aq); also available in gas
affinity: temperature is 200 ºC
affinity: pressure is Psat
affinity: variable 1 is pH at 256 values from 0 to 14
affinity: variable 2 is log10(f_O2) at 256 values from -60 to -25
subcrt: 14 species at 200 ºC and 15.54 bar (wet) [energy units: cal]
subcrt: 3 phases for pyrrhotite ... phase 2 is stable
mosaic: calculating affinities of basis species group 1: H2S HS- HSO4- SO4-2
mosaic: calculating affinities of species for all 4 combinations of the basis species
balance: on moles of H2S in formation reactions
equilibrate: n.balance is 1 1 1 1
equilibrate: loga.balance is -2
equilibrate: using boltzmann method
balance: on moles of H2S in formation reactions
diagram: using maximum affinity method for 2-D diagram
info.character: found pyrrhotite(cr) with 2 phase transitions
info.numeric: Cp of pyrite(cr) is NA; set by EOS parameters to 14.84 cal K-1 mol-1
info.numeric: Cp of pyrrhotite(cr) is NA; set by EOS parameters to 13.06 cal K-1 mol-1
balance: on moles of Fe+2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
info.character: found H2S(aq); also available in gas
affinity: temperature is 200 ºC
affinity: pressure is Psat
affinity: variable 1 is pH at 256 values from 0 to 14
affinity: variable 2 is log10(f_O2) at 256 values from -60 to -25
subcrt: 15 species at 200 ºC and 15.54 bar (wet) [energy units: cal]
subcrt: 3 phases for chalcocite ... phase 2 is stable
mosaic: calculating affinities of basis species group 1: H2S HS- HSO4- SO4-2
mosaic: calculating affinities of species for all 4 combinations of the basis species
balance: on moles of H2S in formation reactions
equilibrate: n.balance is 1 1 1 1
equilibrate: loga.balance is -2
equilibrate: using boltzmann method
info.character: found chalcocite(cr) with 2 phase transitions
info.numeric: Cp of copper(cr) is NA; set by EOS parameters to 5.86 cal K-1 mol-1
info.numeric: Cp of cuprite(cr) is NA; set by EOS parameters to 14.98 cal K-1 mol-1
info.numeric: Cp of tenorite(cr) is NA; set by EOS parameters to 10.11 cal K-1 mol-1
info.numeric: Cp of chalcocite(cr) is NA; set by EOS parameters to 18.24 cal K-1 mol-1
info.numeric: Cp of covellite(cr) is NA; set by EOS parameters to 11.39 cal K-1 mol-1
balance: on moles of Cu+ in formation reactions
diagram: using maximum affinity method for 2-D diagram
info.character: found H2S(aq); also available in gas
affinity: temperature is 200 ºC
affinity: pressure is Psat
affinity: variable 1 is pH at 256 values from 0 to 14
affinity: variable 2 is log10(f_O2) at 256 values from -60 to -25
subcrt: 12 species at 200 ºC and 15.54 bar (wet) [energy units: cal]
subcrt: 3 phases for chalcopyrite ... phase 1 is stable
subcrt: 3 phases for bornite ... phase 1 is stable
mosaic: calculating affinities of basis species group 1: H2S HS- HSO4- SO4-2
mosaic: calculating affinities of species for all 4 combinations of the basis species
balance: on moles of H2S in formation reactions
equilibrate: n.balance is 1 1 1 1
equilibrate: loga.balance is -2
equilibrate: using boltzmann method
info.character: found chalcopyrite(cr) with 2 phase transitions
info.character: found bornite(cr) with 2 phase transitions
info.numeric: Cp of chalcopyrite(cr) is NA; set by EOS parameters to 23.1 cal K-1 mol-1
info.numeric: Cp of bornite(cr) is NA; set by EOS parameters to 58.7 cal K-1 mol-1
balance: on moles of Cu+ in formation reactions
diagram: using maximum affinity method for 2-D diagram
balance: on moles of Cu+ in formation reactions
diagram: using maximum affinity method for 2-D diagram
balance: on moles of Cu+ in formation reactions
diagram: using maximum affinity method for 2-D diagram
balance: on moles of Cu+ in formation reactions
diagram: using maximum affinity method for 2-D diagram
affinity: temperature is 125 ºC
affinity: pressure is Psat
affinity: variable 1 is log10(f_S2) at 150 values from -34 to -10
affinity: variable 2 is log10(f_O2) at 150 values from -55 to -40
subcrt: 10 species at 125 ºC and 2.32 bar (wet) [energy units: cal]
info.numeric: Cp of pyrite(cr) is NA; set by EOS parameters to 14.84 cal K-1 mol-1
balance: on moles of Fe2O3 in formation reactions
diagram: using maximum affinity method for 2-D diagram
affinity: temperature is 125 ºC
affinity: pressure is Psat
affinity: variable 1 is log10(f_S2) at 150 values from -34 to -10
affinity: variable 2 is log10(f_O2) at 150 values from -55 to -40
subcrt: 15 species at 125 ºC and 2.32 bar (wet) [energy units: cal]
subcrt: 3 phases for chalcocite ... phase 2 is stable
subcrt: 3 phases for chalcopyrite ... phase 1 is stable
subcrt: 3 phases for bornite ... phase 1 is stable
mosaic: calculating affinities of basis species group 1: hematite magnetite pyrite
mosaic: calculating affinities of species for all 3 combinations of the basis species
info.numeric: Cp of copper(cr) is NA; set by EOS parameters to 5.86 cal K-1 mol-1
info.numeric: Cp of chalcocite(cr) is NA; set by EOS parameters to 18.24 cal K-1 mol-1
info.numeric: Cp of covellite(cr) is NA; set by EOS parameters to 11.39 cal K-1 mol-1
info.numeric: Cp of chalcopyrite(cr) is NA; set by EOS parameters to 23.1 cal K-1 mol-1
info.numeric: Cp of bornite(cr) is NA; set by EOS parameters to 58.7 cal K-1 mol-1
balance: on moles of Cu in formation reactions
diagram: using maximum affinity method for 2-D diagram
balance: on moles of Cu in formation reactions
diagram: using maximum affinity method for 2-D diagram
info.character: found NaCl(aq); also available in cr
subcrt: 3 species at 125 ºC and 1000 bar (wet) [energy units: cal]
info.character: found NaCl(aq); also available in cr
solubility: calculating for copper
balance: on moles of Cu in formation reactions
solubility: converting to ppm by weight using the mass of Cu
balance: on moles of Cu in formation reactions
diagram: using maximum affinity method for 2-D diagram
subcrt: 3 species at 125 ºC and 2.32 bar (wet) [energy units: cal]
mod.OBIGT: updated CuCl2-(aq)
subcrt: 3 species at 125 ºC and 2.32 bar (wet) [energy units: cal]
mod.OBIGT: updated CuCl3-2(aq)
solubility: calculating for copper
balance: on moles of Cu in formation reactions
solubility: converting to ppm by weight using the mass of Cu
balance: on moles of Cu in formation reactions
diagram: using maximum affinity method for 2-D diagram
solubility: calculating for sulfur
balance: on moles of S2 in formation reactions
solubility: converting to ppm by weight using the mass of SO4-2
balance: on moles of Cu in formation reactions
diagram: using maximum affinity method for 2-D diagram
subcrt: 3 species at 125 ºC and 2.32 bar (wet) [energy units: cal]
subcrt: 3 species at 125 ºC and 2.32 bar (wet) [energy units: cal]
reset: resetting "thermo" object
OBIGT: loading default database with 1903 aqueous, 3443 total species
subcrt: 3 species at 125 ºC and 2.32 bar (wet) [energy units: cal]
subcrt: 3 species at 125 ºC and 2.32 bar (wet) [energy units: cal]
affinity: temperature is 400 ºC
affinity: pressure is 2000 bar
affinity: variable 1 is log10(a_Fe+2) at 256 values from 0 to 12
affinity: variable 2 is log10(f_O2) at 256 values from -40 to -16
subcrt: 10 species at 400 ºC and 2000 bar (wet) [energy units: cal]
subcrt: 3 phases for pyrrhotite ... phase 3 is stable
info.numeric: Cp of pyrite(cr) is NA; set by EOS parameters to 14.84 cal K-1 mol-1
info.numeric: Cp of pyrrhotite(cr) is NA; set by EOS parameters to 13.06 cal K-1 mol-1
balance: on moles of Fe+2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
affinity: temperature is 400 ºC
affinity: pressure is 2000 bar
affinity: variable 1 is log10(a_Fe+2) at 256 values from 0 to 12
affinity: variable 2 is log10(f_O2) at 256 values from -40 to -16
subcrt: 10 species at 400 ºC and 2000 bar (wet) [energy units: cal]
subcrt: 3 phases for chalcocite ... phase 2 is stable
info.numeric: Cp of covellite(cr) is NA; set by EOS parameters to 11.39 cal K-1 mol-1
info.numeric: Cp of chalcocite(cr) is NA; set by EOS parameters to 18.24 cal K-1 mol-1
info.numeric: Cp of tenorite(cr) is NA; set by EOS parameters to 10.11 cal K-1 mol-1
info.numeric: Cp of cuprite(cr) is NA; set by EOS parameters to 14.98 cal K-1 mol-1
balance: on moles of Cu+ in formation reactions
diagram: using maximum affinity method for 2-D diagram
affinity: temperature is 400 ºC
affinity: pressure is 2000 bar
affinity: variable 1 is log10(a_Fe+2) at 256 values from 0 to 12
affinity: variable 2 is log10(f_O2) at 256 values from -40 to -16
subcrt: 8 species at 400 ºC and 2000 bar (wet) [energy units: cal]
subcrt: 3 phases for chalcopyrite ... phase 1 is stable
subcrt: 3 phases for bornite ... phase 3 is stable
info.numeric: Cp of chalcopyrite(cr) is NA; set by EOS parameters to 23.1 cal K-1 mol-1
info.numeric: Cp of bornite(cr) is NA; set by EOS parameters to 58.7 cal K-1 mol-1
balance: on moles of H+ in formation reactions
diagram: using maximum affinity method for 2-D diagram
balance: on moles of H+ in formation reactions
info.numeric: Cp of pyrite(cr) is NA; set by EOS parameters to 14.84 cal K-1 mol-1
info.numeric: Cp of pyrrhotite(cr) is NA; set by EOS parameters to 13.06 cal K-1 mol-1
info.numeric: Cp of covellite(cr) is NA; set by EOS parameters to 11.39 cal K-1 mol-1
info.numeric: Cp of chalcocite(cr) is NA; set by EOS parameters to 18.24 cal K-1 mol-1
info.numeric: Cp of tenorite(cr) is NA; set by EOS parameters to 10.11 cal K-1 mol-1
info.numeric: Cp of cuprite(cr) is NA; set by EOS parameters to 14.98 cal K-1 mol-1
balance: on supplied numeric argument (1) [1 means balance on formula units]
diagram: using maximum affinity method for 2-D diagram
balance: on moles of H+ in formation reactions
info.numeric: Cp of pyrite(cr) is NA; set by EOS parameters to 14.84 cal K-1 mol-1
info.numeric: Cp of pyrrhotite(cr) is NA; set by EOS parameters to 13.06 cal K-1 mol-1
info.numeric: Cp of covellite(cr) is NA; set by EOS parameters to 11.39 cal K-1 mol-1
info.numeric: Cp of chalcocite(cr) is NA; set by EOS parameters to 18.24 cal K-1 mol-1
info.numeric: Cp of tenorite(cr) is NA; set by EOS parameters to 10.11 cal K-1 mol-1
info.numeric: Cp of cuprite(cr) is NA; set by EOS parameters to 14.98 cal K-1 mol-1
info.numeric: Cp of chalcopyrite(cr) is NA; set by EOS parameters to 23.1 cal K-1 mol-1
info.numeric: Cp of bornite(cr) is NA; set by EOS parameters to 58.7 cal K-1 mol-1
balance: on supplied numeric argument (1) [1 means balance on formula units]
diagram: using maximum affinity method for 2-D diagram
affinity: temperature is 400 ºC
affinity: pressure is 2000 bar
affinity: variable 1 is log10(a_Cu+) at 500 values from -8 to 2
affinity: variable 2 is log10(a_Fe+2) at 500 values from -4 to 12
subcrt: 13 species at 400 ºC and 2000 bar (wet) [energy units: cal]
subcrt: 3 phases for chalcopyrite ... phase 1 is stable
subcrt: 3 phases for bornite ... phase 3 is stable
info.numeric: Cp of pyrite(cr) is NA; set by EOS parameters to 14.84 cal K-1 mol-1
info.numeric: Cp of covellite(cr) is NA; set by EOS parameters to 11.39 cal K-1 mol-1
info.numeric: Cp of tenorite(cr) is NA; set by EOS parameters to 10.11 cal K-1 mol-1
info.numeric: Cp of chalcopyrite(cr) is NA; set by EOS parameters to 23.1 cal K-1 mol-1
info.numeric: Cp of bornite(cr) is NA; set by EOS parameters to 58.7 cal K-1 mol-1
balance: on moles of O2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
affinity: temperature is 400 ºC
affinity: pressure is 2000 bar
affinity: variable 1 is log10(a_Cu+) at 500 values from -8 to 2
affinity: variable 2 is log10(a_Fe+2) at 500 values from -4 to 12
subcrt: 10 species at 400 ºC and 2000 bar (wet) [energy units: cal]
subcrt: 3 phases for pyrrhotite ... phase 3 is stable
subcrt: 3 phases for chalcocite ... phase 2 is stable
diagram: plotting saturation lines for 2-D diagram
info.character: found acetic acid(aq); also available in liq
info.character: found NH3(aq); also available in gas
info.character: found acetamide(aq); also available in cr
info.character: found H2O(liq) [water]; also available in cr
subcrt: 4 species at 128 values of T (ºC) and P (bar) (wet) [energy units: cal]
info.character: found acetic acid(aq); also available in liq
subcrt: 3 species at 128 values of T (ºC) and P (bar) (wet) [energy units: cal]
info.character: found NH3(aq); also available in gas
subcrt: 3 species at 128 values of T (ºC) and P (bar) (wet) [energy units: cal]
info.character: found NH3(aq); also available in gas
affinity: temperature is 100 ºC
affinity: pressure is Psat
affinity: variable 1 is pH at 128 values from 0 to 14
subcrt: 10 species at 100 ºC and 1.01 bar (wet) [energy units: cal]
mosaic: calculating affinities of basis species group 1: NH3 NH4+
mosaic: calculating affinities of species for all 2 combinations of the basis species
balance: on moles of NH3 in formation reactions
equilibrate: n.balance is 1 1
equilibrate: loga.balance is -3
equilibrate: using boltzmann method
balance: on moles of CO2 in formation reactions
equilibrate: n.balance is 2 2 2
equilibrate: loga.balance is -1.69897000433602
equilibrate: using reaction method
[WARNING] Could not convert TeX math 'ispecies == paste(iFeO, iV2O3, sep = ",")] <- 90srt[a11', rendering as TeX:
  iFeO, iV2O3, sep = ",")] <- 90srt[a11
                     ^
  unexpected '"'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'ispecies == paste(iV2O3, iFe3V, sep = ",")] <- -13diagram(a11, min.area = 0.01, srt = srt)title("Fe:V = 1:1")label.figure(lTP(25, 1), xfrac = 0.12)# 1:3 mixturea13 <- mix(dFe, dV, dFeV, c(1, 3))srt <- rep(0, nrow(a13', rendering as TeX:
  V2O3, iFe3V, sep = ",")] <- -13diagram(a
                     ^
  unexpected '"'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'ispecies == paste(iFeO, iV2O3, sep = ",")] <- 90srt[a15', rendering as TeX:
  iFeO, iV2O3, sep = ",")] <- 90srt[a15
                     ^
  unexpected '"'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'ispecies == paste(iV2O3, iFe3V, sep = ",")] <- -13srt[a15', rendering as TeX:
  V2O3, iFe3V, sep = ",")] <- -13srt[a15
                     ^
  unexpected '"'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'namespecies(1:length(iFe.aq), loga.Fe)aFe <- affinity(pH = c(0, 14, res2), Eh = c(-1.5, 2, res2))dFe <- diagram(aFe, plot.it = FALSE)# V-bearing speciesspecies(c(iV.aq, iV.cr))', rendering as TeX:
  e, plot.it = FALSE)# V-bearing speciessp
                     ^
  unexpected '#'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'ispecies == paste(iV2O3, iFe3V, sep = ",")] <- -13srt[a11', rendering as TeX:
  V2O3, iFe3V, sep = ",")] <- -13srt[a11
                     ^
  unexpected '"'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'nameiCu.aq <- retrieve("Cu", c("S", "O", "H", "Cl"), "aq")Cu.aq <- info(iCu.aq)', rendering as TeX:
  iCu.aq <- retrieve("Cu", c("S", "O", "H"
                     ^
  unexpected '"'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'm_Cl))# Fe-bearing mineralsspecies(Fe.cr)# Add aqueous species 20210220species(iFe.aq, logm_aq, add = TRUE)mFe <- mosaic(S.aq, pH = pH, O2 = O2, T = T, IS = nacl', rendering as TeX:
  m_Cl))# Fe-bearing mineralsspecies(Fe.cr
        ^
  unexpected '#'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'A.species, lwd = 0, names = FALSE)# Cu-bearing mineralsspecies(c(FeCu.cr, Cu.cr))# Add aqueous species 20210220species(iCu.aq, logm_aq, add = TRUE)# TODO: limitation in mosaic() when using both solid and aqueous basis species (i.e. c(Fe.cr, Fe.aq)):# Only the activity of the first-defined basis species is used for all basis species.# The first-defined basis species is pyrite (logact = 0), but logact < 0 for the aq Fe species.# Workaround: Adjust standard Gibbs energies of aq Fe species to virtually change their activitiesDG <- convert(-logm_aq, "G", T = convert(T, "K"))G.orig <- info(iFe.aq)', rendering as TeX:
  = 0, names = FALSE)# Cu-bearing minerals
                     ^
  unexpected '#'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'predominant))# Use only predominant species as basis species (to speed up calculation) 20210224predom <- dFe', rendering as TeX:
  predominant))# Use only predominant spec
               ^
  unexpected '#'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'IS)# Adjust labelsbold <- c(rep(TRUE, length(FeCu.abbrv)), rep(FALSE, length(Cu.aq)))names <- c(FeCu.abbrv, Cu.aq)srt <- dx <- dy <- rep(0, length(names))cex <- rep(1, length(names))dx[names == "Cu"] <- -1.5dx[names == "Bn"] <- 1.4dx[names == "CuHS"] <- 1dx[names == "Cu+"] <- -0.5dy[names == "Cu"] <- 3dx[names == "Cct"] <- -2dy[names == "Cct"] <- 4dy[names == "CuHS"] <- 1dy[names == "Bn"] <- -0.9dx[names == "CuCl2-"] <- -1dy[names == "CuCl2-"] <- 2cex[names == "Bn"] <- 0.8srt[names == "Bn"] <- 85diagram(mFeCu', rendering as TeX:
  IS)# Adjust labelsbold <- c(rep(TRUE, le
     ^
  unexpected '#'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'A.species, add = TRUE, col = col, lwd = 2, col.names = col.names, bold = TRUE, names = names, fill = NA)# Plot the Fe-system lines and names "on top" so they are not covered by fill colorsdiagram(mFe', rendering as TeX:
  = names, fill = NA)# Plot the Fe-system 
                     ^
  unexpected '#'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'A.species, add = TRUE, col = 2, col.names = col.names, names = names)text(12, -55, "Cu", col = 2)legend("topright", legend = lTP(T, "Psat"), bty = "n")title(paste("Fe-S-O-H and Cu-S-O-H; Total S =", 10^logaH2S, "m"))species(FeCu.cr)mFeCu <- mosaic(S.aq, pH = pH, O2 = O2, T = T)names <- info(info(FeCu.cr))', rendering as TeX:
  ames)text(12, -55, "Cu", col = 2)legend(
                     ^
  unexpected '"'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'A.species, plot.it = FALSE, names = names)fill <- function(a) { ifelse(grepl("Ccp", a', rendering as TeX:
  (a) { ifelse(grepl("Ccp", a
                     ^
  unexpected "\""
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname", white space or "}"
[WARNING] Could not convert TeX math 'name), "#FF8C0088", ifelse(grepl("Bn", a', rendering as TeX:
  name), "#FF8C0088", ifelse(grepl("Bn", a
         ^
  unexpected '"'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'name), "#DC143C88", NA))}srt <- function(a) ifelse(a', rendering as TeX:
  name), "#DC143C88", NA))}srt <- function
         ^
  unexpected '"'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'name, switch, "Mag+Bn" = 0.15, "Mag+Cct" = 0.5, 0)dy <- function(a) sapply(a', rendering as TeX:
  name, switch, "Mag+Bn" = 0.15, "Mag+Cct"
                ^
  unexpected '"'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'nameaFe <- affinity(S2 = c(-34, -10, res1), O2 = c(-55, -40, res1), T = T)# Order species by a function of composition to make colorsoFe <- order(aFe', rendering as TeX:
   -40, res1), T = T)# Order species by a 
                     ^
  unexpected '#'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'A.species, names = abbrv, fill = fill, dx = c(0, 0, 0, 0, 1.8))title("Cu-Fe-S-O-H")# Mash the diagrams and adjust labelsaFeCu <- mash(dFe, dCu)names <- aFeCu', rendering as TeX:
  , 0, 0, 1.8))title("Cu-Fe-S-O-H")# Mash 
                     ^
  unexpected '"'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'm_Cl))# Initial setup: dissolve a single mineral to form aqueous Cu complexesspecies("copper")iaq <- retrieve("Cu", c("O", "H", "Cl", "S"), "aq")# Function to calculate solubility of Cu for stable assemblages of Fe and Cu minerals# (i.e. equilibrium is imposed with all of these minerals, not only Cu(s))mfun <- function() { s <- solubility(iaq, bases = list(bFe, bCu), S2 = c(-34, -10, res1), O2 = c(-55, -40, res1), T = T, IS = calc', rendering as TeX:
  m_Cl))# Initial setup: dissolve a single
        ^
  unexpected '#'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'G + dGmod.OBIGT("CuCl2-", G = newG)# Do the same thing for CuCl3-2logK <- subcrt(c("CuCl3-2", "Cu+", "Cl-"), c(-1, 1, 3), T = T)', rendering as TeX:
  G + dGmod.OBIGT("CuCl2-", G = newG)# Do 
                  ^
  unexpected '"'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'logKdlogK <- logK - -5.6dG <- convert(dlogK, "G", T = convert(T, "K"))newG <- info(info("CuCl3-2"))', rendering as TeX:
   <- convert(dlogK, "G", T = convert(T, "
                     ^
  unexpected '"'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'IS## [1] 1.86169 # Logarithm of activity of Cl-log10(calc', rendering as TeX:
  IS## [1] 1.86169 # Logarithm of activity
    ^
  unexpected '#'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'abbrvdFe <- diagram(aFe, xlab = xlab, names = names)title(bquote("Only Fe; 1° balance:" ~ .(expr.species(dFe', rendering as TeX:
  names)title(bquote("Only Fe; 1° balance:
                     ^
  unexpected '"'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'abbrvdCu <- diagram(aCu, xlab = xlab, names = names)title(bquote("Only Cu; 1° balance:" ~ .(expr.species(dCu', rendering as TeX:
  names)title(bquote("Only Cu; 1° balance:
                     ^
  unexpected '"'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'abbrvdFeCu <- diagram(aFeCu, xlab = xlab, balance = "H+", names = names)title(bquote("Only Fe+Cu; 1° balance:" ~ .(expr.species(dFeCu', rendering as TeX:
   = xlab, balance = "H+", names = names)t
                     ^
  unexpected '"'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'abbrvd1 <- diagram(ad1, xlab = xlab, balance = 1, names = names)title(bquote("Only Fe or Cu; 2° balance:" ~ .(expr.species("H+"))))label.plot("D")# All mineralsd1', rendering as TeX:
  names)title(bquote("Only Fe or Cu; 2° ba
                     ^
  unexpected '"'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'abbrvdFe <- diagram(aFe, xlab = xlab, names = names)title(bquote("Only Fe; 1° balance:" ~ .(expr.species(dFe', rendering as TeX:
  names)title(bquote("Only Fe; 1° balance:
                     ^
  unexpected '"'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'abbrvdCu <- diagram(aCu, xlab = xlab, names = names)title(bquote("Only Cu; 1° balance:" ~ .(expr.species(dCu', rendering as TeX:
  names)title(bquote("Only Cu; 1° balance:
                     ^
  unexpected '"'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'abbrvdFeCu <- diagram(aFeCu, xlab = xlab, balance = "H+", names = names)title(bquote("Only Fe+Cu; 1° balance:" ~ .(expr.species(dFeCu', rendering as TeX:
   = xlab, balance = "H+", names = names)t
                     ^
  unexpected '"'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'abbrvd1 <- diagram(ad1, xlab = xlab, balance = 1, names = names)title(bquote("Only Fe or Cu; 2° balance:" ~ .(expr.species("H+"))))label.plot("D")# All mineralsd1', rendering as TeX:
  names)title(bquote("Only Fe or Cu; 2° ba
                     ^
  unexpected '"'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
[WARNING] Could not convert TeX math 'abbrvd <- diagram(a, xlab = ratlab("Cu+"), ylab = ratlab("Fe+2"), balance = "O2", names = names)title(bquote("Cu-Fe-S-O-H; 1° balance:" ~ .(expr.species(d', rendering as TeX:
  m(a, xlab = ratlab("Cu+"), ylab = ratlab
                     ^
  unexpected '"'
  expecting "\\bangle", "\\brace", "\\brack", "\\choose", "\\displaystyle", "{", letter, digit, ".", "\\mbox", "\\text", "\\textbf", "\\textit", "\\textrm", "\\textsf", "\\texttt", "\\bm", "\\boldsymbol", "\\mathbb", "\\mathbf", "\\mathbfcal", "\\mathbffrak", "\\mathbfit", "\\mathbfscr", "\\mathbfsfit", "\\mathbfsfup", "\\mathbfup", "\\mathbold", "\\mathcal", "\\mathds", "\\mathfrak", "\\mathit", "\\mathrm", "\\mathscr", "\\mathsf", "\\mathsfit", "\\mathsfup", "\\mathtt", "\\mathup", "\\pmb", "\\symbf", "\\texttt", "\\sqrt", "\\surd", "\\mspace", "\\hspace", "\\mathop", "\\mathrel", "\\mathbin", "\\mathord", "\\mathopen", "\\mathclose", "\\mathpunct", "\\phantom", "\\boxed", "\\overset", "\\stackrel", "\\underset", "\\frac", "\\tfrac", "\\dfrac", "\\binom", "\\genfrac", "\\substack", "_", "^", "\\begin", "\\ensuremath", "\\bigg", "\\Bigg", "\\big", "\\Big", "\\biggr", "\\Biggr", "\\bigr", "\\Bigr", "\\biggl", "\\Biggl", "\\bigl", "\\", "\\left", "\\not", "!", "'", "''", "'''", "''''", "*", "+", ",", "-", ".", "/", ":", ":=", ";", "<", "=", ">", "?", "@", "~", "\\operatorname" or end of input
--- finished re-building ‘multi-metal.Rmd’

SUMMARY: processing the following file failed:
  ‘anintro.Rmd’

Error: Vignette re-building failed.
Execution halted