R Under development (unstable) (2024-02-10 r85885 ucrt) -- "Unsuffered Consequences"
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> # Test variations on stacked mosaic diagrams culminating with stack_mosaic() wrapper function
> # 20220722 v1 adapted from Mosaic Stacking 2 from multi-metal.Rmd
> 
> library(CHNOSZ)
CHNOSZ version 2.1.0 (2024-02-11)
reset: creating "thermo" object
OBIGT: loading default database with 1940 aqueous, 3486 total species
> 
> # Use low resolution for routine package checking
> res <- 20
> ## Increase resolution for nicer-looking PDF (the one kept in the test directory)
> #res <- 200
> # Define system
> pH <- c(0, 14, res)
> O2 <- c(-48, -33, res)
> T <- 200
> logmS <- -2
> m_NaCl <- 0.1
> logm_aq <- -6 # for both Fe- and Cu-bearing aq species
> # Define basis species
> S.aq <- c("H2S", "HS-", "HSO4-", "SO4-2")
> # Define minerals
> Fe.cr <- c("pyrite", "pyrrhotite", "magnetite", "hematite")
> Fe.abbrv <- c("Py", "Po", "Mag", "Hem")
> FeCu.cr <- c("chalcopyrite", "bornite")
> Cu.cr <- c("copper", "cuprite", "tenorite", "chalcocite", "covellite")
> FeCu.abbrv <- c("Ccp", "Bn", "Cu", "Cpr", "Tnr", "Cct", "Cv")
> # Define aqueous species
> iFe.aq <- retrieve("Fe", c("S", "O", "H", "Cl"), "aq")
> Fe.aq <- info(iFe.aq)$name
check.GHS: calculated ΔG°f of HFeO2(aq) differs by -4600 cal mol-1 from database value
check.GHS: calculated ΔG°f of FeO2-(aq) differs by -4641 cal mol-1 from database value
> iCu.aq <- retrieve("Cu", c("S", "O", "H", "Cl"), "aq")
> Cu.aq <- info(iCu.aq)$name
check.EOS: calculated Cp° of Cu+2(aq) differs by 3.62 cal K-1 mol-1 from database value
check.EOS: calculated V° of CuCl4-2(aq) differs by -1.07 cm3 mol-1 from database value
check.EOS: calculated V° of CuO2-2(aq) differs by -1.09 cm3 mol-1 from database value
check.EOS: calculated Cp° of CuHS(aq) differs by 7.35 cal K-1 mol-1 from database value
check.EOS: calculated V° of CuHS(aq) differs by -16.2 cm3 mol-1 from database value
> nacl <- NaCl(T = T, P = "Psat", m_tot = m_NaCl)
> 
> setup <- function() {
+   reset()
+   # Setup basis species
+   basis(c("Cu+", "pyrite", "H2S", "oxygen", "H2O", "H+", "Cl-"))
+   basis("H2S", logmS)
+   basis("Cl-", log10(nacl$m_Cl))
+ }
> 
> ref_Cu_craq <- function() {
+   # Load Cu-bearing minerals
+   species(Cu.cr)
+   # Add aqueous species 20210220
+   species(iCu.aq, logm_aq, add = TRUE)
+ 
+   mCu <- mosaic(list(S.aq), pH = pH, O2 = O2, T = T, IS = nacl$IS)
+   diagram(mCu$A.species)
+ }
> 
> ref_FeCu_cr <- function() {
+   # Load Fe-bearing minerals
+   species(Fe.cr)
+   mFe <- mosaic(S.aq, pH = pH, O2 = O2, T = T, IS = nacl$IS)
+   dFe <- diagram(mFe$A.species, lwd = 0, names = FALSE, plot.it = FALSE)
+ 
+   # Load Cu-bearing minerals
+   species(c(FeCu.cr, Cu.cr))
+   # Mosaic with all Fe species as basis species
+   mFeCu <- mosaic(list(S.aq, Fe.cr), pH = pH, O2 = O2, T = T, IS = nacl$IS, stable = list(NULL, dFe$predominant))
+ 
+   diagram(mFeCu$A.species)
+ }
> 
> setup_FeCu <- function() {
+   # Load Fe-bearing minerals
+   species(Fe.cr)
+   # Add aqueous species 20210220
+   species(iFe.aq, logm_aq, add = TRUE)
+   mFe <- mosaic(S.aq, pH = pH, O2 = O2, T = T, IS = nacl$IS)
+   dFe <- diagram(mFe$A.species, lwd = 0, names = FALSE, plot.it = FALSE)
+ 
+   # Load Cu-bearing minerals
+   species(c(FeCu.cr, Cu.cr))
+   # Add aqueous species 20210220
+   species(iCu.aq, logm_aq, add = TRUE)
+   
+   # Return Fe diagram for stacked mosaic calculations
+   dFe
+ }
> 
> 
> test_FeCu_old <- function() {
+   dFe <- setup_FeCu()
+ 
+   # NOTE: 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 activities
+   DG_J <- convert(-logm_aq, "G", T = convert(T, "K"))
+   # We should use calories here because the database values are in calories 20220604
+   stopifnot(all(info(iFe.aq)$E_units == "cal"))
+   DG_cal <- convert(DG_J, "cal")
+   G.orig <- info(iFe.aq)$G
+   G.new <- G.orig + DG_cal
+   mod.OBIGT(iFe.aq, G = G.new)
+ 
+   # Mosaic with all Fe species as basis species
+   mFeCu <- mosaic(list(S.aq, c(Fe.cr, Fe.aq)), pH = pH, O2 = O2, T = T, IS = nacl$IS, stable = list(NULL, dFe$predominant))
+ 
+   diagram(mFeCu$A.species)
+ }
> 
> test_FeCu_new <- function() {
+   dFe <- setup_FeCu()
+ 
+   # Mosaic with all Fe species as basis species
+   # Use loga_aq argument to control the activity of aqueous species in mosaic calculation 20220722
+   # c(NA, logm_aq) means to use:
+   #   basis()'s value for logact of aqueous S species
+   #   logm_aq for logact of aqueous Fe species
+   mFeCu <- mosaic(list(S.aq, c(Fe.cr, Fe.aq)), pH = pH, O2 = O2, T = T, IS = nacl$IS, stable = list(NULL, dFe$predominant), loga_aq = c(NA, logm_aq))
+ 
+   diagram(mFeCu$A.species)
+ }
> 
> test_FeCu_stack <- function() {
+   # Aqueous S species
+   bases <- S.aq
+   # Fe-bearing minerals
+   species1 <- Fe.cr
+   # Cu-bearing and FeCu-bearing minerals
+   species2 <- Cu.cr
+   species12 <- FeCu.cr
+ 
+   # Fe-bearing aqueous species
+   species1 <- c(species1, Fe.aq)
+   # Cu-bearing aqueous species
+   species2 <- c(species2, Cu.aq)
+ 
+   sm <- stack_mosaic(bases, species1, species2, species12, pH = pH, O2 = O2, T = T, IS = nacl$IS, loga_aq = logm_aq, plot.it = FALSE)
+   diagram(sm[[2]])
+ }
> 
> ## Setup plot
> pdf("stack_mosaic.pdf", width = 8, height = 9)
> mat <- matrix(c(1,6,2, 6,3,6, 4,6,5), nrow = 3, byrow = TRUE)
> layout(mat, widths = c(2, 3, 2), heights = c(2, 3, 2, 3))
> par(mar = c(4, 4, 3, 1))
> 
> ## Run tests
> # This first one is a simple mosaic diagram (no stacking)
> setup()
reset: resetting "thermo" object
OBIGT: loading default database with 1940 aqueous, 3486 total species
     Cl Cu Fe H O S  Z ispecies    logact state
Cu+   0  1  0 0 0 0  1      801  0.000000    aq
FeS2  0  0  1 0 0 2  0     2082  0.000000    cr
H2S   0  0  0 2 0 1  0       65 -2.000000    aq
O2    0  0  0 0 2 0  0     2679  0.000000   gas
H2O   0  0  0 2 1 0  0        1  0.000000   liq
H+    0  0  0 1 0 0  1        3  0.000000    aq
Cl-   1  0  0 0 0 0 -1       29 -1.022401    aq
> ref_Cu_craq()
info.character: found H2S(aq); also available in gas
affinity: temperature is 200 ºC
affinity: pressure is Psat
affinity: ionic strength is 0.0949726913845165
affinity: variable 1 is pH at 20 values from 0 to 14
affinity: variable 2 is log10(f_O2) at 20 values from -48 to -33
subcrt: 33 species at 200 ºC and 15.54 bar (wet) [energy units: J]
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 (Bdot equation)
nonideal: calculations for H2S, CuCl2, CuO, CuOH, CuHS, CuCl, H2S (Setchenow equation)
subcrt: 3 polymorphs for chalcocite ... polymorph 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 Cu+ in formation reactions
diagram: using maximum affinity method for 2-D diagram
> title("Cu\ncr+aq", font.main = 1)
> 
> setup()
reset: resetting "thermo" object
OBIGT: loading default database with 1940 aqueous, 3486 total species
     Cl Cu Fe H O S  Z ispecies    logact state
Cu+   0  1  0 0 0 0  1      801  0.000000    aq
FeS2  0  0  1 0 0 2  0     2082  0.000000    cr
H2S   0  0  0 2 0 1  0       65 -2.000000    aq
O2    0  0  0 0 2 0  0     2679  0.000000   gas
H2O   0  0  0 2 1 0  0        1  0.000000   liq
H+    0  0  0 1 0 0  1        3  0.000000    aq
Cl-   1  0  0 0 0 0 -1       29 -1.022401    aq
> ref_FeCu_cr()
info.character: found H2S(aq); also available in gas
affinity: temperature is 200 ºC
affinity: pressure is Psat
affinity: ionic strength is 0.0949726913845165
affinity: variable 1 is pH at 20 values from 0 to 14
affinity: variable 2 is log10(f_O2) at 20 values from -48 to -33
subcrt: 15 species at 200 ºC and 15.54 bar (wet) [energy units: J]
nonideal: calculations for Cu+, Cl-, HS-, HSO4-, SO4-2 (Bdot equation)
nonideal: calculations for H2S, H2S (Setchenow equation)
subcrt: 3 polymorphs for pyrrhotite ... polymorph 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
info.character: found H2S(aq); also available in gas
info.character: found pyrrhotite(cr) with 2 polymorphic transitions
affinity: temperature is 200 ºC
affinity: pressure is Psat
affinity: ionic strength is 0.0949726913845165
affinity: variable 1 is pH at 20 values from 0 to 14
affinity: variable 2 is log10(f_O2) at 20 values from -48 to -33
subcrt: 22 species at 200 ºC and 15.54 bar (wet) [energy units: J]
nonideal: calculations for Cu+, Cl-, HS-, HSO4-, SO4-2 (Bdot equation)
nonideal: calculations for H2S, H2S (Setchenow equation)
subcrt: 3 polymorphs for chalcopyrite ... polymorph 1 is stable
subcrt: 3 polymorphs for bornite ... polymorph 1 is stable
subcrt: 3 polymorphs for chalcocite ... polymorph 2 is stable
subcrt: 3 polymorphs for pyrrhotite ... polymorph 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
> title("Fe-Cu\ncr", font.main = 1)
> 
> T1result <- "(TODO: looks ok)"
> 
> setup()
reset: resetting "thermo" object
OBIGT: loading default database with 1940 aqueous, 3486 total species
     Cl Cu Fe H O S  Z ispecies    logact state
Cu+   0  1  0 0 0 0  1      801  0.000000    aq
FeS2  0  0  1 0 0 2  0     2082  0.000000    cr
H2S   0  0  0 2 0 1  0       65 -2.000000    aq
O2    0  0  0 0 2 0  0     2679  0.000000   gas
H2O   0  0  0 2 1 0  0        1  0.000000   liq
H+    0  0  0 1 0 0  1        3  0.000000    aq
Cl-   1  0  0 0 0 0 -1       29 -1.022401    aq
> d_FeCu_old <- test_FeCu_old()
info.character: found H2S(aq); also available in gas
affinity: temperature is 200 ºC
affinity: pressure is Psat
affinity: ionic strength is 0.0949726913845165
affinity: variable 1 is pH at 20 values from 0 to 14
affinity: variable 2 is log10(f_O2) at 20 values from -48 to -33
subcrt: 28 species at 200 ºC and 15.54 bar (wet) [energy units: J]
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 polymorphs for pyrrhotite ... polymorph 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
check.GHS: calculated ΔG°f of HFeO2(aq) differs by -4600 cal mol-1 from database value
check.GHS: calculated ΔG°f of FeO2-(aq) differs by -4641 cal mol-1 from database value
check.GHS: calculated ΔG°f of HFeO2(aq) differs by -4600 cal mol-1 from database value
check.GHS: calculated ΔG°f of FeO2-(aq) differs by -4641 cal mol-1 from database 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 polymorphic transitions
affinity: temperature is 200 ºC
affinity: pressure is Psat
affinity: ionic strength is 0.0949726913845165
affinity: variable 1 is pH at 20 values from 0 to 14
affinity: variable 2 is log10(f_O2) at 20 values from -48 to -33
subcrt: 43 species at 200 ºC and 15.54 bar (wet) [energy units: J]
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 polymorphs for chalcopyrite ... polymorph 1 is stable
subcrt: 3 polymorphs for bornite ... polymorph 1 is stable
subcrt: 3 polymorphs for chalcocite ... polymorph 2 is stable
subcrt: 3 polymorphs for pyrrhotite ... polymorph 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
> title("Fe-Cu\ncr+aq", font.main = 1)
> 
> T2result <- "(TODO: looks ok)"
> T3result <- "(TODO: looks different)"
> 
> setup()
reset: resetting "thermo" object
OBIGT: loading default database with 1940 aqueous, 3486 total species
     Cl Cu Fe H O S  Z ispecies    logact state
Cu+   0  1  0 0 0 0  1      801  0.000000    aq
FeS2  0  0  1 0 0 2  0     2082  0.000000    cr
H2S   0  0  0 2 0 1  0       65 -2.000000    aq
O2    0  0  0 0 2 0  0     2679  0.000000   gas
H2O   0  0  0 2 1 0  0        1  0.000000   liq
H+    0  0  0 1 0 0  1        3  0.000000    aq
Cl-   1  0  0 0 0 0 -1       29 -1.022401    aq
> d_FeCu_new <- test_FeCu_new()
info.character: found H2S(aq); also available in gas
affinity: temperature is 200 ºC
affinity: pressure is Psat
affinity: ionic strength is 0.0949726913845165
affinity: variable 1 is pH at 20 values from 0 to 14
affinity: variable 2 is log10(f_O2) at 20 values from -48 to -33
subcrt: 28 species at 200 ºC and 15.54 bar (wet) [energy units: J]
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 polymorphs for pyrrhotite ... polymorph 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
info.character: found H2S(aq); also available in gas
info.character: found pyrrhotite(cr) with 2 polymorphic transitions
affinity: temperature is 200 ºC
affinity: pressure is Psat
affinity: ionic strength is 0.0949726913845165
affinity: variable 1 is pH at 20 values from 0 to 14
affinity: variable 2 is log10(f_O2) at 20 values from -48 to -33
subcrt: 43 species at 200 ºC and 15.54 bar (wet) [energy units: J]
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 polymorphs for chalcopyrite ... polymorph 1 is stable
subcrt: 3 polymorphs for bornite ... polymorph 1 is stable
subcrt: 3 polymorphs for chalcocite ... polymorph 2 is stable
subcrt: 3 polymorphs for pyrrhotite ... polymorph 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
> title("Fe-Cu\ncr+aq", font.main = 1, xpd = NA)
> 
> if(identical(d_FeCu_old$predominant, d_FeCu_new$predominant)) T4result <- "(OK)" else T4result <- "(FAILED)"
> 
> setup()
reset: resetting "thermo" object
OBIGT: loading default database with 1940 aqueous, 3486 total species
     Cl Cu Fe H O S  Z ispecies    logact state
Cu+   0  1  0 0 0 0  1      801  0.000000    aq
FeS2  0  0  1 0 0 2  0     2082  0.000000    cr
H2S   0  0  0 2 0 1  0       65 -2.000000    aq
O2    0  0  0 0 2 0  0     2679  0.000000   gas
H2O   0  0  0 2 1 0  0        1  0.000000   liq
H+    0  0  0 1 0 0  1        3  0.000000    aq
Cl-   1  0  0 0 0 0 -1       29 -1.022401    aq
> d_FeCu_stack <- test_FeCu_stack()
info.character: found H2S(aq); also available in gas
affinity: temperature is 200 ºC
affinity: pressure is Psat
affinity: ionic strength is 0.0949726913845165
affinity: variable 1 is pH at 20 values from 0 to 14
affinity: variable 2 is log10(f_O2) at 20 values from -48 to -33
subcrt: 28 species at 200 ºC and 15.54 bar (wet) [energy units: J]
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 polymorphs for pyrrhotite ... polymorph 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
info.character: found H2S(aq); also available in gas
info.character: found pyrrhotite(cr) with 2 polymorphic transitions
affinity: temperature is 200 ºC
affinity: pressure is Psat
affinity: ionic strength is 0.0949726913845165
affinity: variable 1 is pH at 20 values from 0 to 14
affinity: variable 2 is log10(f_O2) at 20 values from -48 to -33
subcrt: 43 species at 200 ºC and 15.54 bar (wet) [energy units: J]
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 polymorphs for chalcopyrite ... polymorph 1 is stable
subcrt: 3 polymorphs for bornite ... polymorph 1 is stable
subcrt: 3 polymorphs for chalcocite ... polymorph 2 is stable
subcrt: 3 polymorphs for pyrrhotite ... polymorph 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
> title("Fe-Cu\ncr+aq", font.main = 1, xpd = NA)
> 
> if(identical(d_FeCu_new$predominant, d_FeCu_stack$predominant)) T5result <- "(OK)" else T5result <- "(FAILED)"
> 
> ## Add arrows and text
> plot.new()
> text(0.5, 0.99, "mosaic()\nWITHOUT 'loga_aq'", font = 2, xpd = NA)
> 
> arrows(0.35, 0.9, 0.65, 0.9)
> text(0.5, 0.93, paste0("Test 1: Cu mineral reactions unaffected\n", T1result))
> 
> arrows(0.1, 0.72, 0.25, 0.65)
> text(0.05, 0.62, paste0("Test 2: aq reactions unaffected\n", T2result), xpd = NA)
> 
> arrows(0.9, 0.72, 0.75, 0.65)
> text(0.9, 0.62, paste0("Test 3: cr reactions unaffected\n", T3result), xpd = NA)
> 
> abline(h = 0.25, lty = 2, col = 8)
> text(0.4, 0.23, "mosaic()\nWITH 'loga_aq'", font = 2)
> lines(c(0.5, 0.5), c(0.15, 0.25), lty = 2, col = 8)
> text(0.6, 0.23, "stack_mosaic()", font = 2)
> 
> arrows(0.25, 0.4, 0.1, 0.3)
> text(0.05, 0.35, paste0("Test 4: identical diagram\n", T4result), xpd = NA)
> 
> arrows(0.35, 0.1, 0.65, 0.1)
> text(0.5, 0.05, paste0("Test 5: identical diagram\n", T5result))
> 
> dev.off()
null device 
          1 
> 
> proc.time()
   user  system elapsed 
   8.98    0.34    9.32