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]
changed energy units to J
subcrt: 2 species at 55 ºC and 50 bar (wet) [energy units: J]
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 55 ºC and 50 bar (wet) [energy units: J]
subcrt: 1 species at 55 ºC and 50 bar [energy units: J]
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 55 ºC and 50 bar (wet) [energy units: J]
subcrt: 2 species at 55 ºC and 50 bar (wet) [energy units: J]
subcrt: 2 species at 55 ºC and 50 bar (wet) [energy units: J]
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: 6 species at 55 ºC and 50 bar (wet) [energy units: J]
subcrt: 2 species at 55 ºC and 50 bar (wet) [energy units: J]
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 55 ºC and 50 bar (wet) [energy units: J]
subcrt: 2 species at 55 ºC and 50 bar (wet) [energy units: J]
subcrt: reaction is not balanced; it is missing this composition:
 C  H 
-1 -4 
subcrt: adding missing composition from basis definition and restarting...
subcrt: 5 species at 55 ºC and 50 bar (wet) [energy units: J]
subcrt: 2 species at 55 ºC and 50 bar (wet) [energy units: J]
subcrt: 2 species at 55 ºC and 50 bar (wet) [energy units: J]
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: 6 species at 55 ºC and 50 bar (wet) [energy units: J]
subcrt: 2 species at 55 ºC and 50 bar (wet) [energy units: J]
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 55 ºC and 50 bar (wet) [energy units: J]
subcrt: 2 species at 55 ºC and 50 bar (wet) [energy units: J]
subcrt: reaction is not balanced; it is missing this composition:
 C  H 
-1 -4 
subcrt: adding missing composition from basis definition and restarting...
subcrt: 5 species at 55 ºC and 50 bar (wet) [energy units: J]
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 pH at 256 values from 0 to 12
affinity: variable 2 is Eh at 256 values from -0.5 to 1 V
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 H2S in formation reactions
diagram: using maximum affinity method for 2-D diagram
affinity: temperature is 100 ºC
affinity: pressure is Psat
affinity: variable 1 is pH at 400 values from 4 to 16
affinity: variable 2 is Eh at 400 values from -1.5 to 1.5 V
subcrt: 12 species at 100 ºC and 1.01 bar (wet) [energy units: cal]
balance: on moles of Mn+2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
affinity: temperature is 100 ºC
affinity: pressure is Psat
affinity: variable 1 is pH at 400 values from 4 to 16
affinity: variable 2 is Eh at 400 values from -1.5 to 1.5 V
subcrt: 18 species at 100 ºC and 1.01 bar (wet) [energy units: cal]
balance: on moles of Mn+2 in formation reactions
diagram: using maximum affinity method for 2-D diagram
info.numeric: Cp of chalcocite(cr) is NA; set by EOS parameters to 18.24 cal K-1 mol-1
info.numeric: Cp of chalcocite(cr2) is NA; set by EOS parameters to 24.59 cal K-1 mol-1
info.numeric: Cp of chalcocite(cr3) is NA; set by EOS parameters to 20.32 cal K-1 mol-1
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 12
affinity: variable 2 is Eh at 200 values from -1.2 to 0.75 V
subcrt: 21 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 -6
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 H2S in formation reactions
diagram: using maximum affinity method for 2-D diagram
affinity: pressure is Psat
affinity: variable 1 is T at 18 values from 278.596 to 622.8 K
affinity: variable 2 is log10(a_CO2) at 18 values from -3.6506 to -1.8288
affinity: variable 3 is log10(a_H2) at 18 values from -47.4549 to -1.8288
affinity: variable 4 is log10(a_NH4+) at 18 values from -6.2165 to -4.5641
affinity: variable 5 is log10(a_H2S) at 18 values from -5.2891 to -2.9213
affinity: variable 6 is pH at 18 values from 3.0312 to 7.1784
subcrt: 14 species at 18 values of T (ºC) and P (bar) (wet) [energy units: cal]
balance: on supplied numeric argument (1) [1 means balance on formula units]
diagram: plotting A/(2.303RT) / n.balance
affinity: temperature is 300 ºC
affinity: pressure is 100 bar
subcrt: 5 species at 300 ºC and 100 bar (wet) [energy units: cal]
affinity: temperature is 300 ºC
affinity: pressure is 100 bar
affinity: loading buffer species
subcrt: 7 species at 300 ºC and 100 bar (wet) [energy units: cal]
buffer: 'PPM' for activity of H2S O2 (active), FeS2 (conserved)
add.OBIGT: read 177 rows; made 65 replacements, 112 additions [energy units: cal]
affinity: pressure is 300 bar
affinity: variable 1 is T at 256 values from 273.15 to 623.15 K
affinity: loading buffer species
subcrt: 9 species at 256 values of T (ºC) and P (bar) (wet) [energy units: cal]
subcrt: 4 phases for iron ... phases 2,1 are stable
subcrt: 4 phases for iron ... phases 2,1 are stable
buffer: 'FeFeO' for activity of H2 (active), Fe (conserved)
affinity: pressure is 300 bar
affinity: variable 1 is T at 256 values from 273.15 to 623.15 K
affinity: loading buffer species
subcrt: 10 species at 256 values of T (ºC) and P (bar) (wet) [energy units: cal]
info.numeric: H of magnetite(cr2) is NA; set to -265601.09 cal mol-1
info.numeric: H of magnetite(cr2) is NA; set to -265601.09 cal mol-1
subcrt: 4 phases for iron ... phases 2,1 are stable
subcrt: 2 phases for quartz ... phase 1 is stable
subcrt: 2 phases for magnetite ... phase 1 is stable
buffer: 'QFM' for activity of H2 (active), SiO2, Fe (conserved)
affinity: pressure is 300 bar
affinity: variable 1 is T at 256 values from 273.15 to 623.15 K
affinity: loading buffer species
subcrt: 10 species at 256 values of T (ºC) and P (bar) (wet) [energy units: cal]
subcrt: temperature(s) of 598.444117647059 K and above exceed limit for pyrrhotite cr2 (extrapolating G)
info.numeric: H of magnetite(cr2) is NA; set to -265601.09 cal mol-1
info.numeric: H of magnetite(cr2) is NA; set to -265601.09 cal mol-1
subcrt: 4 phases for iron ... phases 2,1 are stable
subcrt: 2 phases for magnetite ... phase 1 is stable
buffer: 'PPM' for activity of H2 (active), H2S, Fe (conserved)
affinity: pressure is 300 bar
affinity: variable 1 is T at 256 values from 273.15 to 623.15 K
affinity: loading buffer species
subcrt: 9 species at 256 values of T (ºC) and P (bar) (wet) [energy units: cal]
info.numeric: H of magnetite(cr2) is NA; set to -265601.09 cal mol-1
info.numeric: H of magnetite(cr2) is NA; set to -265601.09 cal mol-1
subcrt: 4 phases for iron ... phases 2,1 are stable
subcrt: 3 phases for hematite ... phases 2,1 are stable
subcrt: 2 phases for magnetite ... phase 1 is stable
buffer: 'HM' for activity of H2 (active), Fe (conserved)
affinity: pressure is 300 bar
affinity: variable 1 is T at 256 values from 273.15 to 623.15 K
subcrt: 9 species at 256 values of T (ºC) and P (bar) (wet) [energy units: cal]
subcrt: 4 phases for iron ... phase 1 is stable
affinity: pressure is 300 bar
affinity: variable 1 is T at 256 values from 273.15 to 623.15 K
subcrt: 9 species at 256 values of T (ºC) and P (bar) (wet) [energy units: cal]
subcrt: 4 phases for iron ... phase 1 is stable
affinity: pressure is 300 bar
affinity: variable 1 is T at 256 values from 273.15 to 623.15 K
subcrt: 9 species at 256 values of T (ºC) and P (bar) (wet) [energy units: cal]
subcrt: 4 phases for iron ... phase 1 is stable
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 pH at 256 values from 4 to 13
subcrt: 9 species at 25 ºC and 1 bar (wet) [energy units: cal]
affinity: temperature is 150 ºC
affinity: pressure is Psat
affinity: variable 1 is pH at 256 values from 4 to 13
subcrt: 9 species at 150 ºC and 4.76 bar (wet) [energy units: cal]
balance: on moles of CO2 in formation reactions
diagram: plotting A/(2.303RT) / n.balance
balance: on moles of CO2 in formation reactions
diagram: plotting A/(2.303RT) / n.balance
balance: on moles of CO2 in formation reactions
equilibrate: n.balance is 1 1 1
equilibrate: loga.balance is -3
equilibrate: using boltzmann method
balance: on moles of CO2 in formation reactions
equilibrate: n.balance is 1 1 1
equilibrate: loga.balance is -3
equilibrate: using boltzmann method
add.OBIGT: read 172 rows; made 43 replacements, 129 additions [energy units: cal]
solubility: calculating for corundum
balance: on moles of Al2O3 in formation reactions
reset: resetting "thermo" object
OBIGT: loading default database with 1903 aqueous, 3443 total species
affinity: temperature is 100 ºC
affinity: pressure is Psat
affinity: variable 1 is pH at 256 values from 3 to 9
subcrt: 13 species at 100 ºC and 1.01 bar (wet) [energy units: cal]
balance: on moles of CO2 in formation reactions
equilibrate: n.balance is 10 10 10 10 10
equilibrate: loga.balance is -1.30102999566398
equilibrate: using reaction method
affinity: temperature is 100 ºC
affinity: pressure is Psat
affinity: ionic strength is 0.25
affinity: variable 1 is pH at 256 values from 3 to 9
subcrt: 13 species at 100 ºC and 1.01 bar (wet) [energy units: cal]
nonideal: calculations for Mg+2, C10H12N5O13P3-4, C10H13N5O13P3-3, C10H14N5O13P3-2, C10H15N5O13P3- (Alberty equation)
nonideal: calculations for CO2, NH3, H3PO4, H2S, C10H16N5O13P3 (Setchenow equation)
balance: on moles of CO2 in formation reactions
equilibrate: n.balance is 10 10 10 10 10
equilibrate: loga.balance is -1.30102999566398
equilibrate: using reaction method
affinity: temperature is 100 ºC
affinity: pressure is Psat
affinity: ionic strength is 0.25
affinity: variable 1 is pH at 256 values from 3 to 9
subcrt: 17 species at 100 ºC and 1.01 bar (wet) [energy units: cal]
nonideal: calculations for Mg+2, C10H12N5O13P3-4, C10H13N5O13P3-3, C10H14N5O13P3-2, C10H15N5O13P3-, MgC10H12N5O13P3-2, MgC10H13N5O13P3- (Alberty equation)
nonideal: calculations for CO2, NH3, H3PO4, H2S, C10H16N5O13P3, MgC10H14N5O13P3, Mg2C10H12N5O13P3 (Setchenow equation)
balance: on moles of CO2 in formation reactions
equilibrate: n.balance is 10 10 10 10 10 10 10 10 10
equilibrate: loga.balance is -1.04575749056068
equilibrate: using reaction method
affinity: temperature is 100 ºC
affinity: pressure is Psat
affinity: ionic strength is 0.25
affinity: variable 1 is pH at 256 values from 3 to 9
subcrt: 17 species at 100 ºC and 1.01 bar (wet) [energy units: cal]
nonideal: calculations for Mg+2, C10H12N5O13P3-4, C10H13N5O13P3-3, C10H14N5O13P3-2, C10H15N5O13P3-, MgC10H12N5O13P3-2, MgC10H13N5O13P3- (Alberty equation)
nonideal: calculations for CO2, NH3, H3PO4, H2S, C10H16N5O13P3, MgC10H14N5O13P3, Mg2C10H12N5O13P3 (Setchenow equation)
balance: on moles of CO2 in formation reactions
equilibrate: n.balance is 10 10 10 10 10 10 10 10 10
equilibrate: loga.balance is -1.04575749056068
equilibrate: using reaction method
affinity: temperature is 100 ºC
affinity: pressure is Psat
affinity: ionic strength is 0.25
affinity: variable 1 is pH at 256 values from 3 to 9
subcrt: 17 species at 100 ºC and 1.01 bar (wet) [energy units: cal]
nonideal: calculations for Mg+2, C10H12N5O13P3-4, C10H13N5O13P3-3, C10H14N5O13P3-2, C10H15N5O13P3-, MgC10H12N5O13P3-2, MgC10H13N5O13P3- (Alberty equation)
nonideal: calculations for CO2, NH3, H3PO4, H2S, C10H16N5O13P3, MgC10H14N5O13P3, Mg2C10H12N5O13P3 (Setchenow equation)
balance: on moles of CO2 in formation reactions
equilibrate: n.balance is 10 10 10 10 10 10 10 10 10
equilibrate: loga.balance is -1.04575749056068
equilibrate: using reaction method
affinity: temperature is 100 ºC
affinity: pressure is Psat
affinity: ionic strength is 0.25
affinity: variable 1 is pH at 256 values from 3 to 9
subcrt: 17 species at 100 ºC and 1.01 bar (wet) [energy units: cal]
nonideal: calculations for Mg+2, C10H12N5O13P3-4, C10H13N5O13P3-3, C10H14N5O13P3-2, C10H15N5O13P3-, MgC10H12N5O13P3-2, MgC10H13N5O13P3- (Alberty equation)
nonideal: calculations for CO2, NH3, H3PO4, H2S, C10H16N5O13P3, MgC10H14N5O13P3, Mg2C10H12N5O13P3 (Setchenow equation)
balance: on moles of CO2 in formation reactions
equilibrate: n.balance is 10 10 10 10 10 10 10 10 10
equilibrate: loga.balance is -1.04575749056068
equilibrate: using reaction method
affinity: temperature is 100 ºC
affinity: pressure is Psat
affinity: ionic strength is 0.25
affinity: variable 1 is pH at 256 values from 3 to 9
subcrt: 17 species at 100 ºC and 1.01 bar (wet) [energy units: cal]
nonideal: calculations for Mg+2, C10H12N5O13P3-4, C10H13N5O13P3-3, C10H14N5O13P3-2, C10H15N5O13P3-, MgC10H12N5O13P3-2, MgC10H13N5O13P3- (Alberty equation)
nonideal: calculations for CO2, NH3, H3PO4, H2S, C10H16N5O13P3, MgC10H14N5O13P3, Mg2C10H12N5O13P3 (Setchenow equation)
balance: on moles of CO2 in formation reactions
equilibrate: n.balance is 10 10 10 10 10 10 10 10 10
equilibrate: loga.balance is -1.04575749056068
equilibrate: using reaction method
affinity: temperature is 100 ºC
affinity: pressure is Psat
affinity: ionic strength is 0.25
affinity: variable 1 is log10(a_Mg+2) at 256 values from -2 to -7
subcrt: 17 species at 100 ºC and 1.01 bar (wet) [energy units: cal]
nonideal: calculations for Mg+2, C10H12N5O13P3-4, C10H13N5O13P3-3, C10H14N5O13P3-2, C10H15N5O13P3-, MgC10H12N5O13P3-2, MgC10H13N5O13P3- (Alberty equation)
nonideal: calculations for CO2, NH3, H3PO4, H2S, C10H16N5O13P3, MgC10H14N5O13P3, Mg2C10H12N5O13P3 (Setchenow equation)
balance: on moles of CO2 in formation reactions
equilibrate: n.balance is 10 10 10 10 10 10 10 10 10
equilibrate: loga.balance is -1.04575749056068
equilibrate: using reaction method
affinity: temperature is 100 ºC
affinity: pressure is Psat
affinity: ionic strength is 0.25
affinity: variable 1 is log10(a_Mg+2) at 256 values from -2 to -7
subcrt: 17 species at 100 ºC and 1.01 bar (wet) [energy units: cal]
nonideal: calculations for Mg+2, C10H12N5O13P3-4, C10H13N5O13P3-3, C10H14N5O13P3-2, C10H15N5O13P3-, MgC10H12N5O13P3-2, MgC10H13N5O13P3- (Alberty equation)
nonideal: calculations for CO2, NH3, H3PO4, H2S, C10H16N5O13P3, MgC10H14N5O13P3, Mg2C10H12N5O13P3 (Setchenow equation)
balance: on moles of CO2 in formation reactions
equilibrate: n.balance is 10 10 10 10 10 10 10 10 10
equilibrate: loga.balance is -1.04575749056068
equilibrate: using reaction method
affinity: temperature is 100 ºC
affinity: pressure is Psat
affinity: ionic strength is 0.25
affinity: variable 1 is log10(a_Mg+2) at 256 values from -2 to -7
subcrt: 17 species at 100 ºC and 1.01 bar (wet) [energy units: cal]
nonideal: calculations for Mg+2, C10H12N5O13P3-4, C10H13N5O13P3-3, C10H14N5O13P3-2, C10H15N5O13P3-, MgC10H12N5O13P3-2, MgC10H13N5O13P3- (Alberty equation)
nonideal: calculations for CO2, NH3, H3PO4, H2S, C10H16N5O13P3, MgC10H14N5O13P3, Mg2C10H12N5O13P3 (Setchenow equation)
balance: on moles of CO2 in formation reactions
equilibrate: n.balance is 10 10 10 10 10 10 10 10 10
equilibrate: loga.balance is -1.04575749056068
equilibrate: using reaction method
affinity: temperature is 100 ºC
affinity: pressure is Psat
affinity: ionic strength is 0.25
affinity: variable 1 is log10(a_Mg+2) at 256 values from -2 to -7
subcrt: 17 species at 100 ºC and 1.01 bar (wet) [energy units: cal]
nonideal: calculations for Mg+2, C10H12N5O13P3-4, C10H13N5O13P3-3, C10H14N5O13P3-2, C10H15N5O13P3-, MgC10H12N5O13P3-2, MgC10H13N5O13P3- (Alberty equation)
nonideal: calculations for CO2, NH3, H3PO4, H2S, C10H16N5O13P3, MgC10H14N5O13P3, Mg2C10H12N5O13P3 (Setchenow equation)
balance: on moles of CO2 in formation reactions
equilibrate: n.balance is 10 10 10 10 10 10 10 10 10
equilibrate: loga.balance is -1.04575749056068
equilibrate: using reaction method
affinity: temperature is 100 ºC
affinity: pressure is Psat
affinity: ionic strength is 0.25
affinity: variable 1 is log10(a_Mg+2) at 256 values from -2 to -7
subcrt: 17 species at 100 ºC and 1.01 bar (wet) [energy units: cal]
nonideal: calculations for Mg+2, C10H12N5O13P3-4, C10H13N5O13P3-3, C10H14N5O13P3-2, C10H15N5O13P3-, MgC10H12N5O13P3-2, MgC10H13N5O13P3- (Alberty equation)
nonideal: calculations for CO2, NH3, H3PO4, H2S, C10H16N5O13P3, MgC10H14N5O13P3, Mg2C10H12N5O13P3 (Setchenow equation)
balance: on moles of CO2 in formation reactions
equilibrate: n.balance is 10 10 10 10 10 10 10 10 10
equilibrate: loga.balance is -1.04575749056068
equilibrate: using reaction method
affinity: temperature is 100 ºC
affinity: pressure is Psat
affinity: ionic strength is 0.25
affinity: variable 1 is log10(a_Mg+2) at 256 values from -2 to -7
subcrt: 17 species at 100 ºC and 1.01 bar (wet) [energy units: cal]
nonideal: calculations for Mg+2, C10H12N5O13P3-4, C10H13N5O13P3-3, C10H14N5O13P3-2, C10H15N5O13P3-, MgC10H12N5O13P3-2, MgC10H13N5O13P3- (Alberty equation)
nonideal: calculations for CO2, NH3, H3PO4, H2S, C10H16N5O13P3, MgC10H14N5O13P3, Mg2C10H12N5O13P3 (Setchenow equation)
balance: on moles of CO2 in formation reactions
equilibrate: n.balance is 10 10 10 10 10 10 10 10 10
equilibrate: loga.balance is -1.04575749056068
equilibrate: using reaction method
affinity: temperature is 100 ºC
affinity: pressure is Psat
affinity: ionic strength is 0.25
affinity: variable 1 is log10(a_Mg+2) at 256 values from -2 to -7
subcrt: 17 species at 100 ºC and 1.01 bar (wet) [energy units: cal]
nonideal: calculations for Mg+2, C10H12N5O13P3-4, C10H13N5O13P3-3, C10H14N5O13P3-2, C10H15N5O13P3-, MgC10H12N5O13P3-2, MgC10H13N5O13P3- (Alberty equation)
nonideal: calculations for CO2, NH3, H3PO4, H2S, C10H16N5O13P3, MgC10H14N5O13P3, Mg2C10H12N5O13P3 (Setchenow equation)
balance: on moles of CO2 in formation reactions
equilibrate: n.balance is 10 10 10 10 10 10 10 10 10
equilibrate: loga.balance is -1.04575749056068
equilibrate: using reaction method
protein.OBIGT: found LYSC_CHICK (C613H959N193O185S10, 129 residues)
subcrt: 1 species at 15 values of T (ºC) and P (bar) (wet) [energy units: cal]
protein.OBIGT: found CYC_BOVIN (C517H825N143O150S4, 104 residues)
subcrt: 1 species at 151 values of T (ºC) and P (bar) (wet) [energy units: cal]
protein.OBIGT: found CYC_BOVIN (C517H825N143O150S4, 104 residues)
subcrt: 1 species at 151 values of T (ºC) and P (bar) [energy units: cal]
subcrt: 1 species at 151 values of T (ºC) and P (bar) (wet) [energy units: cal]
protein.OBIGT: found LYSC_CHICK (C613H959N193O185S10, 129 residues)
subcrt: 1 species at 151 values of T (ºC) and P (bar) [energy units: cal]
protein.OBIGT: found MYG_PHYCA (C783H1240N216O216S2, 153 residues)
subcrt: 1 species at 151 values of T (ºC) and P (bar) (wet) [energy units: cal]
protein.OBIGT: found MYG_PHYCA (C783H1240N216O216S2, 153 residues)
subcrt: 1 species at 151 values of T (ºC) and P (bar) [energy units: cal]
protein.OBIGT: found RNAS1_BOVIN (C575H909N171O193S12, 124 residues)
subcrt: 1 species at 151 values of T (ºC) and P (bar) (wet) [energy units: cal]
protein.OBIGT: found RNAS1_BOVIN (C575H909N171O193S12, 124 residues)
subcrt: 1 species at 151 values of T (ºC) and P (bar) [energy units: cal]
affinity: temperature is 25 ºC
affinity: pressure is Psat
affinity: variable 1 is pH at 256 values from 0 to 14
subcrt: 27 species at 25 ºC and 1 bar (wet) [energy units: cal]
subcrt: 18 species at 25 ºC and 1 bar (wet) [energy units: cal]
affinity: temperature is 25 ºC
affinity: pressure is Psat
subcrt: 26 species at 25 ºC and 1 bar (wet) [energy units: cal]
affinity: temperature is 25 ºC
affinity: pressure is Psat
subcrt: 9 species at 25 ºC and 1 bar (wet) [energy units: cal]
read.fasta: reading rubisco.fasta ... 239 lines ... 27 sequences
affinity: temperature is 25 ºC
affinity: pressure is Psat
affinity: variable 1 is log10(f_O2) at 256 values from -80 to -73
subcrt: 27 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 1273 929 297 876 2195
equilibrate: loga.balance is 0
equilibrate: using reaction method
balance: on protein length
equilibrate: n.balance is 1273 929 297 876 2195
equilibrate: loga.balance is 0
equilibrate: using 'normalize' for molar formulas
equilibrate: using boltzmann method
revisit: calculating DGinf in 1 dimensions
read.fasta: reading EF-Tu.aln ... 64 lines ... 8 sequences
info.character: found C2H5OH(aq); also available in gas, liq
info.character: found O2(aq); also available in gas
info.character: found CO2(aq); also available in gas
info.character: found H2O(liq) [water]; also available in cr, aq
subcrt: 4 species at 15 values of T (ºC) and P (bar) (wet) [energy units: cal]
subcrt: 3 species at 8 values of T (ºC) and P (bar) (wet) [energy units: cal]
--- finished 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
--- 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
--- 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
Warning in hook_png(before, options, envir, "pngquant", function(x) { :
  cannot find pngquant; please install and put it in PATH
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
Quitting from lines 726-726 (multi-metal.Rmd) 
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non-numeric argument to binary operator
--- failed re-building 'multi-metal.Rmd'

SUMMARY: processing the following file failed:
  'multi-metal.Rmd'

Error: Vignette re-building failed.
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