Getting started

Bring-up & first test

A checklist to walk a freshly built analyzer from power-on to a trusted result.

1. Power and buses

sudo systemctl status pigpiod openreef
i2cdetect -y 1          # expect 0x20 (MCP23017), 0x39 (AS7341), 0x63 (EZO-pH)
ls /sys/bus/w1/devices/ # expect 28-xxxxxxxxxxxx (DS18B20)
journalctl -u openreef -f

2. Dry checks (no liquids)

Hardware → Pumps: each peristaltic pump turns the right way (fill pumps push toward the cell, level/drain pumps pull from it). Swap the motor leads if not.
Home all syringes: each carriage retracts to its switch, backs off 0.5 mm and re-homes slowly. If a pump runs into the far end, flip that pump’s DIR sense by swapping one motor coil pair.
Sensors: pH in air reads anything stable; spectral dark counts < 50 with the holder closed; white LED on gives 20 000–40 000 counts on f5_555 through an empty cuvette (adjust gain if clipping at 65 535).
Trip the leak sensor with a wet finger: the dashboard status goes red and the alarm relay clicks.

3. Wet checks

Put the intake in a glass of tank water and the drain in a cup. Run Flush. Cell A should fill, level to 20 mL and drain fully twice; same for Cell B.
Weigh the retained volume after a fill+level: adjust tube depth until 20.0 ± 0.2 g and 10.0 ± 0.1 g.
Prime each syringe pump; confirm drops appear at the correct drip tip.

4. First alkalinity run

Start a test from Overview. Watch the live log: initial_dose, then approach steps of 200 µL until pH < 4.3, then titrate steps of 60 µL. Open the result’s raw data: r2 should be > 0.999 and dic_est_mmol_l between 1.5 and 3.5. If v_eq_outside_expected is flagged, the first dose was too large — lower initial_dose_ul for the first run (later runs size it from the previous result).

5. First colorimetric run

Run phosphate. In the raw data, channels_abs.nir should be positive and f8_680 about 0.65× of it (shape check). A negative absorbance means bubbles on the cuvette wall: increase the settle time or the post-fill stir.

6. Calibrate

Follow Calibration before you act on any number.