phreeqc-geochem

PHREEQC Aqueous Geochemistry Skill

Runs the USGS PHREEQC (pH-REdox-EQuilibrium in C) geochemical code to compute speciation, activity coefficients, and mineral saturation indices for produced waters and high-TDS oilfield brines. This skill is the chemistry complement to the usgs-produced-waters skill: once you know the brine composition, use this to decide whether it will scale, whether DLE is viable, and which minerals control Li/Mg recovery.

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Credential

None required. PHREEQC is free, open-source USGS software. No API key, no login, no rate limits. The only prerequisite is a local phreeqc binary.

# Template for consistency with other skills; not used here:
# KEY=$(grep '^api_key=' ~/.config/usgs/credentials 2>/dev/null | cut -d= -f2)

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Install

PHREEQC must be installed locally. This skill does not install it for you — ask the user to pick one of the methods below.

Platform	Method	Command
macOS (Homebrew tap)	brew via geo-smart or third-party tap	No official homebrew-core formula. Build from source or use conda.
macOS / Linux (conda)	conda-forge	conda install -c conda-forge phreeqc (verify with conda search phreeqc -c conda-forge)
Linux (apt)	Debian/Ubuntu	sudo apt install phreeqc (may lag USGS release)
All platforms	Official USGS build	Download from https://www.usgs.gov/software/phreeqc-version-3
Source	Autotools / CMake	./configure && make && sudo make install

Current version (as of Jan 2025): PHREEQC 3.8.6 (build 17100), released January 7, 2025. USGS releases 1-2 builds per year; check the official page for the latest.

Verify install:

phreeqc --version
# or
phreeqc -v

Find the database directory:

# Standard install locations:
ls /usr/local/share/doc/phreeqc/database/   # Linux source build
ls /opt/homebrew/share/phreeqc/database/    # Homebrew ARM
ls $CONDA_PREFIX/share/doc/phreeqc/database/ # conda
ls "C:\Program Files\USGS\phreeqc-3.8.6\database\"  # Windows

# Or search:
find / -name "pitzer.dat" 2>/dev/null | head

Set PHREEQC_DATABASE_DIR env var (or pass the full path as the second CLI argument) so input decks don't need to hardcode paths.

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Command-Line Interface

PHREEQC is a single binary invoked with up to four positional arguments:

phreeqc [input_file] [output_file] [database_file] [screen_output_file]

Position	Meaning	Example
1	Input deck	marcellus_brine.pqi
2	Main output (long)	marcellus_brine.pqo
3	Thermodynamic database	/opt/homebrew/share/phreeqc/database/pitzer.dat
4	Screen log (short)	marcellus_brine.log

Minimal run:

phreeqc input.pqi output.pqo $DB/pitzer.dat

Exit code: 0 on success, non-zero on parse or convergence errors. Stderr captures most diagnostics; parse errors also appear at the top of the output file.

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Workflow

Step 1 — Resolve Intent

Map the user's question to a PHREEQC simulation type:

User asks about...	PHREEQC block
"Will this brine scale?"	SOLUTION + EQUILIBRIUM_PHASES or SELECTED_OUTPUT with -saturation_indices
"What's the SI of barite in sample X?"	SOLUTION + SELECTED_OUTPUT
"Speciation of this produced water"	SOLUTION (then read output)
"Will calcite precipitate if I raise pH?"	SOLUTION + REACTION (add NaOH) + EQUILIBRIUM_PHASES
"What if I dilute this 10:1?"	SOLUTION + MIX
"What happens as I heat this to 90 C?"	SOLUTION + REACTION_TEMPERATURE
"DLE feedstock check"	Compute SI for barite, celestite, calcite, gypsum, halite; report Ca/Li, Mg/Li, SO4/Li ratios

Step 2 — Select Database

Critical decision. The wrong database produces nonsense at oilfield ionic strengths. See references/thermo_databases.md for the full matrix.

Database	TDS range	Best for	Key limitation
phreeqc.dat	< 30,000 mg/L	Fresh / brackish water	Davies / extended Debye-Huckel; unreliable above seawater ionic strength
wateq4f.dat	< 30,000 mg/L	Natural waters with many trace metals	Same activity model limits as phreeqc.dat; more elements
pitzer.dat	> 30,000 mg/L, up to halite saturation	Produced waters, Smackover, Marcellus, Bakken, seawater evaporites	Limited element set; Li, Sr, Ba parameters incomplete at high T
sit.dat	Intermediate ionic strength	Mid-salinity, nuclear waste studies	Less mature than Pitzer for Cl brines
llnl.dat	< 30,000 mg/L but wider T/P	High-temperature geothermal	B-dot activity model; not for hypersaline
minteq.v4.dat	Dilute	EPA MINTEQA2 port; contamination / sorption	Not for brines
frezchem.dat	Sub-zero to moderate T	Cryogenic / sea-ice chemistry	Niche

Default for produced-water work: pitzer.dat. Produced waters from Marcellus, Utica, Bakken, and Smackover routinely exceed 100,000 mg/L TDS — well outside the Debye-Huckel range of phreeqc.dat.

Step 3 — Build the Input Deck

PHREEQC input is block-structured. Each block starts with a keyword. Minimum useful deck has SOLUTION, SELECTED_OUTPUT, and END.

TITLE Marcellus produced water - scaling check
SOLUTION 1
    temp      60         # deg C
    pH        5.8
    pe        4.0
    redox     pe
    units     mg/l
    density   1.12        # optional; Pitzer calculates if omitted
    Na        45000
    K         600
    Ca        12000
    Mg        1200
    Sr        2500
    Ba        2000
    Li        80
    Cl        95000  charge   # balance charge on Cl
    Alkalinity 120 as HCO3
    S(6)      50           # SO4 as sulfate-S(6)
    Br        800
    Fe(2)     30
    B         20
    Si        15
SELECTED_OUTPUT
    -file           marcellus.sel
    -reset          false
    -saturation_indices Barite Calcite Celestite Gypsum Anhydrite Halite \
                        Strontianite Witherite Siderite Dolomite
    -molalities     Li+ Mg+2 Ca+2 Ba+2 Sr+2 SO4-2
    -totals         Li Mg Ca Ba Sr S(6)
    -ionic_strength true
    -temperature    true
    -pH             true
END

Key gotchas in the deck:

• Units: mg/L is per liter of solution; mg/kgs is per kg of solution (better for hypersaline). ppm is ambiguous — avoid.
• Charge balance: append charge to one major ion (usually Cl or Na). PHREEQC will adjust that concentration to balance.
• Alkalinity: report as HCO3 or as CaCO3; PHREEQC computes the carbonate speciation at the input pH.
• Redox: for produced water, pe 4 or lower is realistic; highly reducing formations may need pe -2 to 0. The skill should ask if the user cares about Fe/sulfide redox.
• Barium + sulfate: report both even if SO4 is low; barite supersaturation is a common surprise.
• Element lists in -molalities and -saturation_indices are whitespace-separated; use \ for line continuation.

Step 4 — Run PHREEQC

DB=/opt/homebrew/share/phreeqc/database   # adjust for your install
phreeqc marcellus.pqi marcellus.pqo $DB/pitzer.dat marcellus.log

# Check exit code
if [ $? -ne 0 ]; then
  grep -i 'error\|warning' marcellus.pqo | head -20
fi

Step 5 — Parse Output

Two output streams:

1. Main output (marcellus.pqo): human-readable, contains every block executed. Big but browsable. Look for the Saturation indices table and the Distribution of species table.
2. Selected output (marcellus.sel): tab-delimited; one row per simulation. Easy to pipe into awk, pandas, or Go.

Extracting SI values from marcellus.sel:

# Header row has si_<mineral> columns
head -1 marcellus.sel | tr '\t' '\n' | grep -n '^si_'
awk -F'\t' 'NR==1 || NR==2' marcellus.sel | cut -f $(header_cols)

Go wrapper — see references/golang_wrapper.go — shells out, captures both output files, parses the SELECTED_OUTPUT TSV, and returns a SIReport struct with SI values keyed by mineral name.

Step 6 — Interpret Saturation Indices

The saturation index is:

SI = log10(IAP / Ksp)

where IAP is the ion activity product and Ksp is the solubility product at the given T and P.

SI range	Interpretation	Action in produced-water context
SI > 1	Strongly supersaturated	Likely already precipitating; scale forming downhole or at surface
0 < SI < 1	Supersaturated	Will precipitate given nucleation sites / time; add scale inhibitor
-0.3 < SI < 0	Near equilibrium	Watch on T/P/pH change; borderline
SI < -0.3	Undersaturated	Dissolution if mineral present; safe from that scale

Practical thresholds from oilfield experience:

• Barite (Barite, BaSO4): SI > 0.5 = real scaling risk; inhibitor required
• Calcite (Calcite, CaCO3): SI > 0.5 triggers scale with CO2 loss
• Gypsum / Anhydrite: SI > 0 with high temperature often means scaling
• Halite (Halite, NaCl): SI ~ 0 means brine is at salt saturation; rare but seen in some evaporite-hosted produced waters
• Celestite (Celestite, SrSO4): track when Sr > 500 mg/L and SO4 detectable

For DLE assessment:

• Mg/Li molar ratio > 40 is hard to treat with most DLE resins
• Ca/Li > 100 is a treatment burden but manageable
• Any barite supersaturation + SO4 in produced water = barite scaling during sorbent regeneration
• Li speciation: in Cl brines, Li is ~90-100% free Li+; LiCl0 pair is minor

---

Complete Working Example

Input (smackover_example.pqi):

TITLE Smackover Formation brine - Columbia County, AR - DLE screening
SOLUTION 1
    temp      80
    pH        5.5
    pe        2.0
    redox     pe
    units     mg/l
    density   1.20
    Na        85000
    K         3500
    Ca        40000
    Mg        3000
    Sr        1500
    Ba        50
    Li        400
    Cl        180000  charge
    Alkalinity 50 as HCO3
    S(6)      200
    Br        5000
    B         200
SELECTED_OUTPUT
    -file           smackover.sel
    -reset          false
    -saturation_indices Barite Calcite Celestite Gypsum Anhydrite Halite \
                        Dolomite Strontianite Witherite
    -molalities     Li+ LiCl Mg+2 MgCl+ Ca+2 CaCl+ Ba+2 Sr+2 SO4-2
    -totals         Li Mg Ca Ba Sr S(6) Cl
    -ionic_strength true
END

Run:

DB=/opt/homebrew/share/phreeqc/database
phreeqc smackover_example.pqi smackover.pqo $DB/pitzer.dat

Expected output highlights (smackover.pqo):

Saturation indices
--------------------
    Phase               SI**    log IAP   log K(T,  P)

    Anhydrite          -0.12    -4.54     -4.42   CaSO4
    Barite              0.34    -9.63     -9.97   BaSO4
    Calcite            -0.45   -10.00     -9.55   CaCO3
    Celestite          -0.72    -7.22     -6.50   SrSO4
    Dolomite           -1.10   -18.10    -17.00   CaMg(CO3)2
    Gypsum             -0.01    -4.59     -4.58   CaSO4:2H2O
    Halite             -0.85    -2.43     -1.58   NaCl
    Strontianite       -1.40   -10.50     -9.10   SrCO3
    Witherite          -2.90   -11.50     -8.60   BaCO3

Ionic strength        = 5.9 mol/kgw
Density               = 1.198 g/cm3

Interpretation: This Smackover brine is slightly supersaturated with respect to barite (SI = 0.34) — mild scaling risk, manageable with inhibitor. Gypsum is at equilibrium (SI ~ 0) — any cooling or CO2 loss will push it over. Calcite is undersaturated, so CO2 loss / pH rise from atmospheric exposure would flip it positive. Ionic strength of 5.9 mol/kgw is firmly in Pitzer territory — phreeqc.dat would have been wrong by 0.5-1.5 log units on most SIs.

---

Output Format

Present PHREEQC results as SI table + narrative + action items:

## Smackover Brine — Speciation and Scaling Analysis (Pitzer, 80 deg C)

Inputs: TDS ~320,000 mg/L; Ca 40,000; Mg 3,000; Li 400; Ba 50; SO4 200 mg/L.
Database: pitzer.dat (ionic strength 5.9 mol/kgw — Pitzer required).

| Mineral      | SI    | Status              | Action                          |
|--------------|-------|---------------------|---------------------------------|
| Barite       | +0.34 | Supersaturated      | Inhibitor (phosphonate) needed  |
| Gypsum       | -0.01 | At equilibrium      | Monitor; any cooling precipitates |
| Anhydrite    | -0.12 | Near saturation     | Scaling risk if T rises         |
| Calcite      | -0.45 | Undersaturated      | Watch pH / CO2 degassing        |
| Celestite    | -0.72 | Undersaturated      | OK                              |
| Halite       | -0.85 | Undersaturated      | OK (no evaporation concentration) |

**Speciation:** Li+ free ion fraction = 97%; LiCl0 ion pair = 3%. Mg/Li
molar ratio = 29 — manageable for modern DLE sorbents (<40 threshold).
Ca/Li = 173 — high but tolerable for lithium-ion-sieve or solvent
extraction processes.

**Summary:** DLE-viable feedstock. Primary concern is barite scaling during
sorbent regeneration when SO4 concentrates. Gypsum is the second-priority
scale if the process includes any evaporative step. Ionic strength is high
enough that only Pitzer-based models should be trusted for plant design;
re-run in OLI or equivalent commercial code before final engineering.

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Error Handling

Issue	Cause	Action
phreeqc: command not found	Binary not installed or not in PATH	See Install section; run which phreeqc
ERROR: Could not open database file	Wrong path or missing .dat file	find / -name "pitzer.dat"; set PHREEQC_DATABASE_DIR or pass full path as 3rd arg
ERROR: Unknown element	Element not in selected database	Switch database (e.g., Li is in pitzer.dat but limited in sit.dat); check references/thermo_databases.md
WARNING: Charge imbalance > 5%	Input analysis not electroneutral	Append charge to Cl or Na concentration; check for missing major ion
ERROR: Numerical method failed	Convergence failure; often from contradictory constraints	Remove charge flag from multiple ions; relax pe constraint; check for negative concentrations
SI values wildly different from expected	Wrong database for ionic strength	Recheck: hypersaline needs pitzer.dat; phreeqc.dat fails above ~1 mol/kg
No SI for a mineral	Mineral not defined in database	Check PHASES block in the .dat file; some minerals (e.g., specific Li minerals) exist only in llnl.dat or require manual definition
pe and redox contradict	Both specified incorrectly	Use redox pe with a pe value, or use a redox couple like redox O(0)/O(-2) with dissolved O2
Output file contains only echo of input	Parse error stopped execution	Look for first ERROR in .pqo; usually a syntax error in one block

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Caveats and Bias

1. Pitzer parameter gaps for Li at high T and I. The Pitzer interaction coefficients for Li-Cl, Li-SO4, and Li-HCO3 in pitzer.dat are well-calibrated at 25 deg C but extrapolate with larger uncertainty above 80-100 deg C and ionic strengths above 6 mol/kgw. For Smackover-style brines at reservoir temperature (90-110 deg C), SI values on Li-bearing minerals carry ~0.3-0.5 log unit uncertainty.

2. Limited element set in pitzer.dat. Not every element is parameterized. Notably weak/absent: Al, Si, Fe(III), trace metals beyond the majors. If those matter, run parallel phreeqc.dat for comparison (accepting the ionic strength caveat) or switch to llnl.dat (accepting its limits at high I).

3. Temperature limits. pitzer.dat is solid up to ~200 deg C for the major-ion system; extrapolation above that is unreliable without independent validation.

4. Equilibrium != kinetics. An SI > 0 says a mineral can precipitate, not that it will quickly. Barite nucleates fast; calcite and dolomite often do not. Field-observed scale is biased toward fast-kinetic phases even when slower phases are more supersaturated. Report SI alongside known-kinetic notes; do not substitute for reactive-transport modeling.

5. Input data quality drives output quality. A produced-water analysis with 10% charge imbalance produces SI values that look precise but rest on a badly constrained solution. Always report the charge balance from the SOLUTION echo. Treat SI differences < 0.3 log units as noise.

6. pH measurement on hot brines. Wellhead pH is often measured after cooling and depressurization, at which point CO2 has degassed and Fe(II) has partially oxidized. The measured pH is not the reservoir pH. For reservoir-condition modeling, adjust pH upward ~0.5-1 unit and re-run.

7. CBI / self-reported chemistry. If the brine composition comes from industry disclosures (FracFocus, operator reports), sulfate and bicarbonate are frequently reported as "< detection limit" without the limit value. PHREEQC treats these as exactly the numeric value given; set a realistic detection-limit value rather than zero.

8. No coupled flow. This skill runs batch equilibrium. Real produced water changes composition as it flows through pipe, heat exchangers, and tanks. For design work, couple to a reactive-transport code (PhreeqcRM, PHT3D) or commercial OLI / Multiflash.

9. Commercial-software comparison. OLI Studio and Multiflash use proprietary parameter sets that can disagree with PHREEQC Pitzer by 0.2-0.5 log units on SI at hypersaline conditions. Use PHREEQC for screening and open-science work; expect a commercial cross-check before capex decisions.

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Implementation Notes

• Prefer bash_tool to shell out to phreeqc; parse the TSV SELECTED_OUTPUT rather than the long .pqo for machine use.
• Go wrapper — see references/golang_wrapper.go for a reference implementation: runs the binary, reads the .sel file, returns a typed struct with SIs and key molalities.
• Database reference — see references/thermo_databases.md for the full matrix of which database to use at which ionic strength, element coverage, and known limitations.
• Ready-made brine decks — see references/brine_recipes.md for sample input decks for Smackover, Marcellus, Utica/Point Pleasant, and Bakken chemistries with typical Li/Mg/Ca/Sr/Ba/Cl/SO4 values. Use these as starting points and overwrite with sample-specific numbers.
• Cache binary location — once located, write the path to ~/.config/phreeqc/config so repeated runs skip the find step.
• Default database: if the user does not specify and TDS > 30,000 mg/L (or ionic strength can be estimated > 0.7 mol/kg), default to pitzer.dat; otherwise default to phreeqc.dat.
• Never hardcode Windows-style paths; resolve via env var or shell find.
• PHREEQC is a local compute skill — nothing is sent to a remote API. All inputs and outputs stay on the user's machine.