Mashing | Mixing 1 | Convert formation energies from eV / atom to eV / molecule | Convert formation energies from eV / molecule to J / mol | Gibbs energies of formation (J / mol) for aqueous species | Most are from Wagman et al., 1982 | Gibbs energies of formation (J / mol) for solids from Wagman et al., 1982 | Calculate correction for difference between reference and DFT energies (Persson et al., 2012) | Apply correction to standard Gibbs energies of aqueous species (Persson et al., 2012) | Add energies to OBIGT | This function modifies OBIGT and returns the species indices of the affected species | We explicitly set the units to Joules (this is the default as of CHNOSZ 2.0.0) | We need model = "CGL" to override the Berman model for some minerals 20220919 | Formation energies (eV / atom) for bimetallic solids from Materials API | mp-1335, mp-1079399, mp-866134, mp-558525, mp-504509 (triclinic FeVO4) | Convert energies and add to OBIGT | Mosaic Stacking 1 | Mosaic Stacking 2 | Setup basis species | Fe-bearing minerals | Add aqueous species 20210220 | Start plot with just the fields for transparency effect | Cu-bearing minerals | Mosaic with all Fe species as basis species | Use only predominant Fe species as basis species (to speed up calculation) 20210224 | 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 | Adjust labels | Highlight Ccp and Bn in orange | Thick line around Ccp field | Add second Cu label | Plot the Fe-system lines and names "on top" so they are not covered by fill colors | Restore default OBIGT database | Mixing 2 | Mosaic Stacking 3 | Fe-S-O-H diagram | Order species by a function of composition to make colors | Cu-Fe-S-O-H diagram based on reactions with the | stable Fe-bearing minerals (mosaic stack) | Mash the diagrams and adjust labels | Function to calculate solubility of Cu for stable assemblages of Fe and Cu minerals | (i.e. equilibrium is imposed with all of these minerals, not only Cu(s)) | DIAGRAM 1 | Load SLOP98 data to use legacy parameters for CuCl2- and CuCl3-2 | Calculate logK for CuCl2- dissociation at 125 °C | Sverjensky (1987) used Helgeson (1969) value, which is ca. -5.2 | Calculate the difference in ΔG° corresponding to this logK difference | We should use calories here because the database values are in calories 20220604 | Apply this difference to the CuCl2- entry in OBIGT | Do the same thing for CuCl3-2 | DIAGRAM 2 | Set up system to dissolve S2(gas) | Calculate concentration of SO4-2 | DIAGRAM 3 | Secondary Balancing | PRIMARY balancing | Only Fe-bearing minerals | Only Cu-bearing minerals | Only Fe- AND Cu-bearing minerals | SECONDARY balancing | Fe- or Cu-bearing minerals | All minerals | Other Possibilities | Balancing on a Non-Metal | Mosaic Combo | A function to calculate Keff for any combination of T and pH | Make T and pH the same length | Calculate activity of H+ | Calculate logKs | Calculate Ks | Calculate Keff (Eq. 7) | Calculate logKeff as a function of pH at 100 °C | Calculate activity of acetamide for | acetic acid + acetate = 0.01 m | ammonia + ammonium = 0.001 m | METHOD 2: Mosaic combo | Define total activities | This is 2 * 0.01 because acetic acid has 2 carbons | Load all C-bearing species (including acetamide) | Calculate distribution of C-bearing species accounting for ammonia/ammonium speciation | Plot and label diagram | Start with empty diagram | Add pH = 6 line | Add line for acetamide activity calculated with Keff | Add lines from CHNOSZ calculations | Check that we got equal values | Document History | References

Aqueous Species H2O Inorganic Organic | Solids Inorganic Organic Berman | Gases Inorganic Organic    Liquids Inorganic Organic | Optional Data SUPCRT92 SLOP98 AD DEW Testing | References

Getting Started | Basic Functionality | Organization of CHNOSZ | Functions without side effects (return values) | Functions with side effects (modify system state) | Querying the thermodynamic database | Calculating thermodynamic properties | Working with reactions | Chemical affinity and stability diagrams | Equilibrium calculations | Activity coefficients | References | Interlude: Affinity, Formation Reactions, and Balancing | Caution: Quasisolubility contours on predominance diagrams underestimate total solubility | Advanced Uses | 1. Use helper functions to create formatted labels for diagrams | 2. Use retrieve() to search species by elements | 3. Load optional data with add.OBIGT() | 4. Use OBIGT() and reset() to restore the default database and settings | 5. Use basis() species to define the compositional space | 6. Set activities of formed species() to define a quasisolubility contour | 7. When to use add = TRUE | 8. Set grid resolution and constant T, P, or ionic strength in affinity() | 9. Use NaCl() to estimate ionic strength from NaCl concentration | 10. Use solubility() to draw total solubility contours | 11. Use convert() for common unit conversions | 12. Use the transect mode of affinity() for synchronized variables | 13. Choose non-default balancing constraints in diagram() | 14. Calculate adjusted and non-standard Gibbs energy with subcrt() | 15. Calculate non-standard Gibbs energy with affinity() | And swap basis species, remove formed species, and label reactions | 16. Extract results from the output of diagram() | 17. Writing chemical formulas and counting and summing elements with makeup() | 18: Accessing and changing settings with thermo() | Interlude: From Activity to Molality | Buffers | 1. Defining buffers with mod.buffer() | 2. Retrieving buffered activities with affinity(return.buffer = TRUE) | 3. Working with multiple buffered species (e.g., r h2s and r o2 in PPM) | 4. Using diagram(type = ) to display buffered activities | 5. Using fr o2 Buffers in downstream calculations | 6. Using buffer calculations in transects with affinity() | 7. Calculating the neutral pH of water | 8. Working with mineral pH buffers | Comprehensive example: Ore formation environments | Proteins | 1. Identifying proteins | 2. Adding proteins from FASTA or CSV files | 3. Calculating protein properties | Protein length and formula | Carbon oxidation state | 4. Thermodynamic calculations for proteins | Standard thermodynamic properties | Ionization effects | 5. Setting up a chemical system with proteins | 6. Calculating affinities and equilibrium distributions | Affinities of formation reactions | Equilibrium distributions | Scaling protein abundances | 7. Additional protein analysis | End-to-end example: Parameter optimization to fit experimental protein abundances | Environmental controls on protein evolution: A case study with CRISPR-Cas systems | Further Resources - Demos | More use cases for mosaic() | Solubility contours with solubility() | Other contour plots | Calculations using the output of diagram() | Activity buffers | Other thermodynamic models | Calculations with proteins | Further Resources - Vignettes | Frequently asked questions | OBIGT thermodynamic database | Customizing the thermodynamic database | Fitting thermodynamic data | Creating multi-metal diagrams | Getting Help | Document History

Where do the names CHNOSZ, OBIGT, and subcrt come from? | How should CHNOSZ be cited? | What thermodynamic models are used in CHNOSZ? | What are the main limitations of CHNOSZ? | When and why do equal-activity boundaries depend on total activity? | Set up subplots | Activate DEW model | logfO2-pH diagram for aqueous inorganic and organic carbon species at high pressure | After Figure 1b of Sverjensky et al., 2014b [SSH14] | (Nature Geoscience, https://doi.org/10.1038/NGEO2291) | Define system | A function to make the diagrams | Set total C concentration to 0.03 molal | (from EQ3NR model for eclogite [Supporting Information of SSH14]) | Restore default settings for the questions below | How can minerals with polymorphic transitions be added to the database? | How can I make a diagram with the trisulfur radical ion (r S3minus)? | Why does the published diagram have a much larger stability field for r S3minus? | Can I make the diagram using the Deep Earth Water (DEW) model? | In OBIGT, what is the meaning of T for solids, liquids, and gases? | How can mineral pH buffers be plotted? | Why are mineral stability boundaries curved on mosaic diagrams? | Get the pKa of H2S (note the minus sign!) | Reaction 1 between pyrite and pyrrhotite with H2S | Reaction 1 law of mass action (LMA) | logf_O2 = 2 logK_1 - 2 loga_H2S | Reaction 2 between pyrite and pyrrhotite with HS- | Reaction 2 LMA | logf_O2 = 2 pH + 2 logK_2 - 2 loga_HS- | The logf_O2 for each reaction is the same at the pKa of H2S | How is the sum of activities of basis species defined for mosaic diagrams? | The basis species we are speciating | The basis species defining the system | Note 1: for mosaic(), the first species in 'bases' must be in this list | Note 2: for solubility(), the first species in this list must contain S | Define a low fO2 so reduced sulfur dominates over most of the pH range | The pH range we'll look at | The logarithm of activity used for aH2S or sum(S) | Left-hand plot: Constant log aH2S, variable sum(S) | Set it up as a solubility calculation | Define a single log aH2S | Specify the aqueous species in equilibrium with H2S | Run the calculation to calculate all species' activities | Diagram individual activities then total activity | Right-hand plot: Constant sum(S), variable log aH2S | Start by loading all the candidate species with preset activities | Calculate affinities of formation reactions | Equilibrate the species for a total activity of S | Look at the stabilities of calcite and anhydrite | For afffinity(), these are single activities | For mosaic(), these are total activities for groups of species in the 'bases' list | affinity() calculation | mosaic() calculation | References

Mashing | Mixing 1 | Convert formation energies from eV / atom to eV / molecule | Convert formation energies from eV / molecule to J / mol | Gibbs energies of formation (J / mol) for aqueous species | Most are from Wagman et al., 1982 | Gibbs energies of formation (J / mol) for solids from Wagman et al., 1982 | Calculate correction for difference between reference and DFT energies (Persson et al., 2012) | Apply correction to standard Gibbs energies of aqueous species (Persson et al., 2012) | Add energies to OBIGT | This function modifies OBIGT and returns the species indices of the affected species | We explicitly set the units to Joules (this is the default as of CHNOSZ 2.0.0) | We need model = "CGL" to override the Berman model for some minerals 20220919 | Formation energies (eV / atom) for bimetallic solids from Materials API | mp-1335, mp-1079399, mp-866134, mp-558525, mp-504509 (triclinic FeVO4) | Convert energies and add to OBIGT | Mosaic Stacking 1 | Mosaic Stacking 2 | Setup basis species | Fe-bearing minerals | Add aqueous species 20210220 | Start plot with just the fields for transparency effect | Cu-bearing minerals | Mosaic with all Fe species as basis species | Use only predominant Fe species as basis species (to speed up calculation) 20210224 | 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 | Adjust labels | Highlight Ccp and Bn in orange | Thick line around Ccp field | Add second Cu label | Plot the Fe-system lines and names "on top" so they are not covered by fill colors | Restore default OBIGT database | Mixing 2 | Mosaic Stacking 3 | Fe-S-O-H diagram | Order species by a function of composition to make colors | Cu-Fe-S-O-H diagram based on reactions with the | stable Fe-bearing minerals (mosaic stack) | Mash the diagrams and adjust labels | Function to calculate solubility of Cu for stable assemblages of Fe and Cu minerals | (i.e. equilibrium is imposed with all of these minerals, not only Cu(s)) | DIAGRAM 1 | Load SLOP98 data to use legacy parameters for CuCl2- and CuCl3-2 | Calculate logK for CuCl2- dissociation at 125 °C | Sverjensky (1987) used Helgeson (1969) value, which is ca. -5.2 | Calculate the difference in ΔG° corresponding to this logK difference | We should use calories here because the database values are in calories 20220604 | Apply this difference to the CuCl2- entry in OBIGT | Do the same thing for CuCl3-2 | DIAGRAM 2 | Set up system to dissolve S2(gas) | Calculate concentration of SO4-2 | DIAGRAM 3 | Secondary Balancing | PRIMARY balancing | Only Fe-bearing minerals | Only Cu-bearing minerals | Only Fe- AND Cu-bearing minerals | SECONDARY balancing | Fe- or Cu-bearing minerals | All minerals | Other Possibilities | Balancing on a Non-Metal | Mosaic Combo | A function to calculate Keff for any combination of T and pH | Make T and pH the same length | Calculate activity of H+ | Calculate logKs | Calculate Ks | Calculate Keff (Eq. 7) | Calculate logKeff as a function of pH at 100 °C | Calculate activity of acetamide for | acetic acid + acetate = 0.01 m | ammonia + ammonium = 0.001 m | METHOD 2: Mosaic combo | Define total activities | This is 2 * 0.01 because acetic acid has 2 carbons | Load all C-bearing species (including acetamide) | Calculate distribution of C-bearing species accounting for ammonia/ammonium speciation | Plot and label diagram | Start with empty diagram | Add pH = 6 line | Add line for acetamide activity calculated with Keff | Add lines from CHNOSZ calculations | Check that we got equal values | Document History | References

Aqueous Species H2O Inorganic Organic | Solids Inorganic Organic Berman | Gases Inorganic Organic    Liquids Inorganic Organic | Optional Data SUPCRT92 SLOP98 AD DEW Testing | References

Getting Started | Basic Functionality | Organization of CHNOSZ | Functions without side effects (return values) | Functions with side effects (modify system state) | Querying the thermodynamic database | Calculating thermodynamic properties | Working with reactions | Chemical affinity and stability diagrams | Equilibrium calculations | Activity coefficients | References | Interlude: Affinity, Formation Reactions, and Balancing | Caution: Quasisolubility contours on predominance diagrams underestimate total solubility | Advanced Uses | 1. Use helper functions to create formatted labels for diagrams | 2. Use retrieve() to search species by elements | 3. Load optional data with add.OBIGT() | 4. Use OBIGT() and reset() to restore the default database and settings | 5. Use basis() species to define the compositional space | 6. Set activities of formed species() to define a quasisolubility contour | 7. When to use add = TRUE | 8. Set grid resolution and constant T, P, or ionic strength in affinity() | 9. Use NaCl() to estimate ionic strength from NaCl concentration | 10. Use solubility() to draw total solubility contours | 11. Use convert() for common unit conversions | 12. Use the transect mode of affinity() for synchronized variables | 13. Choose non-default balancing constraints in diagram() | 14. Calculate adjusted and non-standard Gibbs energy with subcrt() | 15. Calculate non-standard Gibbs energy with affinity() | And swap basis species, remove formed species, and label reactions | 16. Extract results from the output of diagram() | 17. Writing chemical formulas and counting and summing elements with makeup() | 18: Accessing and changing settings with thermo() | Interlude: From Activity to Molality | Buffers | 1. Defining buffers with mod.buffer() | 2. Retrieving buffered activities with affinity(return.buffer = TRUE) | 3. Working with multiple buffered species (e.g., r h2s and r o2 in PPM) | 4. Using diagram(type = ) to display buffered activities | 5. Using fr o2 Buffers in downstream calculations | 6. Using buffer calculations in transects with affinity() | 7. Calculating the neutral pH of water | 8. Working with mineral pH buffers | Comprehensive example: Ore formation environments | Proteins | 1. Identifying proteins | 2. Adding proteins from FASTA or CSV files | 3. Calculating protein properties | Protein length and formula | Carbon oxidation state | 4. Thermodynamic calculations for proteins | Standard thermodynamic properties | Ionization effects | 5. Setting up a chemical system with proteins | 6. Calculating affinities and equilibrium distributions | Affinities of formation reactions | Equilibrium distributions | Scaling protein abundances | 7. Additional protein analysis | End-to-end example: Parameter optimization to fit experimental protein abundances | Environmental controls on protein evolution: A case study with CRISPR-Cas systems | Further Resources - Demos | More use cases for mosaic() | Solubility contours with solubility() | Other contour plots | Calculations using the output of diagram() | Activity buffers | Other thermodynamic models | Calculations with proteins | Further Resources - Vignettes | Frequently asked questions | OBIGT thermodynamic database | Customizing the thermodynamic database | Fitting thermodynamic data | Creating multi-metal diagrams | Getting Help | Document History

Where do the names CHNOSZ, OBIGT, and subcrt come from? | How should CHNOSZ be cited? | What thermodynamic models are used in CHNOSZ? | What are the main limitations of CHNOSZ? | When and why do equal-activity boundaries depend on total activity? | Set up subplots | Activate DEW model | logfO2-pH diagram for aqueous inorganic and organic carbon species at high pressure | After Figure 1b of Sverjensky et al., 2014b [SSH14] | (Nature Geoscience, https://doi.org/10.1038/NGEO2291) | Define system | A function to make the diagrams | Set total C concentration to 0.03 molal | (from EQ3NR model for eclogite [Supporting Information of SSH14]) | Restore default settings for the questions below | How can minerals with polymorphic transitions be added to the database? | How can I make a diagram with the trisulfur radical ion (r S3minus)? | Why does the published diagram have a much larger stability field for r S3minus? | Can I make the diagram using the Deep Earth Water (DEW) model? | In OBIGT, what is the meaning of T for solids, liquids, and gases? | How can mineral pH buffers be plotted? | Why are mineral stability boundaries curved on mosaic diagrams? | Get the pKa of H2S (note the minus sign!) | Reaction 1 between pyrite and pyrrhotite with H2S | Reaction 1 law of mass action (LMA) | logf_O2 = 2 logK_1 - 2 loga_H2S | Reaction 2 between pyrite and pyrrhotite with HS- | Reaction 2 LMA | logf_O2 = 2 pH + 2 logK_2 - 2 loga_HS- | The logf_O2 for each reaction is the same at the pKa of H2S | How is the sum of activities of basis species defined for mosaic diagrams? | The basis species we are speciating | The basis species defining the system | Note 1: for mosaic(), the first species in 'bases' must be in this list | Note 2: for solubility(), the first species in this list must contain S | Define a low fO2 so reduced sulfur dominates over most of the pH range | The pH range we'll look at | The logarithm of activity used for aH2S or sum(S) | Left-hand plot: Constant log aH2S, variable sum(S) | Set it up as a solubility calculation | Define a single log aH2S | Specify the aqueous species in equilibrium with H2S | Run the calculation to calculate all species' activities | Diagram individual activities then total activity | Right-hand plot: Constant sum(S), variable log aH2S | Start by loading all the candidate species with preset activities | Calculate affinities of formation reactions | Equilibrate the species for a total activity of S | Look at the stabilities of calcite and anhydrite | For afffinity(), these are single activities | For mosaic(), these are total activities for groups of species in the 'bases' list | affinity() calculation | mosaic() calculation | References

Basic structure of OBIGT | Conventions for data entry in OBIGT | Types of data | Ranges of HKF and CGL models | Required and optional data | NA or 0? | OOM scaling and r info_ | Case study: NA and 0 in the default database | Examples of adding data from a file | r add.OBIGT_ with optional data files | r add.OBIGT_ with other CSV files | Examples of adding and modifying data with a function | r mod.OBIGT_ for aqueous species | r mod.OBIGT_ for minerals | Case study: Formation constants for aqueous tungsten species | Fitting formation constants | Diagram 1: Constant molality of r F_ | Diagram 2: Variable molality of r F_ | References

A note on the equations | A note on the algorithms | An example for neutral species | Setting the value of omega | An example for charged species | Doing it for volume | Making a pseudospecies: r h4sio4 | References

Basic structure of OBIGT | Conventions for data entry in OBIGT | Types of data | Ranges of HKF and CGL models | Required and optional data | NA or 0? | OOM scaling and r info_ | Case study: NA and 0 in the default database | Examples of adding data from a file | r add.OBIGT_ with optional data files | r add.OBIGT_ with other CSV files | Examples of adding and modifying data with a function | r mod.OBIGT_ for aqueous species | r mod.OBIGT_ for minerals | Case study: Formation constants for aqueous tungsten species | Fitting formation constants | Diagram 1: Constant molality of r F_ | Diagram 2: Variable molality of r F_ | References

A note on the equations | A note on the algorithms | An example for neutral species | Setting the value of omega | An example for charged species | Doing it for volume | Making a pseudospecies: r h4sio4 | References

Reading FASTA files | Human proteins in canprot | References

More details on chemical metrics | Implementation details | GRAVY, pI, and molecular weight | References

Required packages | Reference proteomes for taxa | r Zc for genera in selected phyla and classes | Prokaryotic genera, aggregated to phylum | Prokaryotic genera, aggregated to class | Stoichiometric hydration state (r nH2O) | Viruses and prokaryotes | Other metrics | Take-home messages | References

Load required packages | Mouse microbiome data | Lowest-level taxa | Taxonomic mapping | From taxonomy to amino acid composition | From taxonomy to chemical metrics | Using GTDB for reference proteomes | Take-home messages | References

Load required packages | GlobalPatterns | Humboldt Sulfuretum (Marine Sediment) | Qinghai-Tibet Plateau (Hot Springs) | Comparing more datasets | Take-home messages | References

canprot demo #1: Thermophiles | canprot demo #2: Subcellular locations | canprot demo #3: Redoxins | References