* using log directory 'd:/Rcompile/CRANpkg/local/3.6/CHNOSZ.Rcheck' * using R version 3.6.3 (2020-02-29) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'CHNOSZ/DESCRIPTION' ... OK * this is package 'CHNOSZ' version '1.4.1' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'CHNOSZ' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK ** checking loading without being on the library search path ... OK ** checking use of S3 registration ... OK * loading checks for arch 'x64' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK ** checking loading without being on the library search path ... OK ** checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [38s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking pragmas in C/C++ headers and code ... OK * checking compiled code ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... [63s] OK ** running examples for arch 'x64' ... [64s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... [34s] OK Running 'testthat.R' [34s] ** running tests for arch 'x64' ... [38s] OK Running 'testthat.R' [37s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking re-building of vignette outputs ... [153s] WARNING 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) Error: processing vignette 'multi-metal.Rmd' failed with diagnostics: 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. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 WARNING