From 15b1562f04e18dc91503c5d02723d883d7394e33 Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Fri, 11 Apr 2025 10:59:12 +0200
Subject: [PATCH 01/47] Implement basic zoom; TODO: fix angle in skewT

---
 .../src/components/plots/ChartContainer.tsx   | 51 +++++++++++++++++--
 .../class-solid/src/components/plots/Line.tsx |  1 +
 .../src/components/plots/skewTlogP.tsx        | 11 ----
 3 files changed, 48 insertions(+), 15 deletions(-)

diff --git a/apps/class-solid/src/components/plots/ChartContainer.tsx b/apps/class-solid/src/components/plots/ChartContainer.tsx
index f8a3cf3..ea08e96 100644
--- a/apps/class-solid/src/components/plots/ChartContainer.tsx
+++ b/apps/class-solid/src/components/plots/ChartContainer.tsx
@@ -35,6 +35,7 @@ interface Chart {
   formatX: (value: number) => string;
   formatY: (value: number) => string;
   transformX?: (x: number, y: number, scaleY: SupportedScaleTypes) => number;
+  zoom: number;
 }
 type SetChart = SetStoreFunction<Chart>;
 const ChartContext = createContext<[Chart, SetChart]>();
@@ -65,24 +66,45 @@ export function ChartContainer(props: {
     scaleY: initialScale,
     formatX: d3.format(".4"),
     formatY: d3.format(".4"),
+    zoom: 1,
   });
+
+  // Update scaleXInstance when scaleX props change
   createEffect(() => {
-    // Update scaleXInstance when scaleX props change
+    const fullExtent =
+      chart.scalePropsX.domain[1] - chart.scalePropsX.domain[0];
+    const centerExtent = chart.scalePropsX.domain[0] + fullExtent / 2;
+    const zoomedExtent = fullExtent / chart.zoom;
+    const zoomedDomain = [
+      centerExtent - zoomedExtent / 2,
+      centerExtent + zoomedExtent / 2,
+    ];
+
     const scaleX = supportedScales[chart.scalePropsX.type]()
       .range(chart.scalePropsX.range)
-      .domain(chart.scalePropsX.domain);
+      .domain(zoomedDomain);
     // .nice(); // TODO: could use this instead of getNiceAxisLimits but messes up skewT
     updateChart("scaleX", () => scaleX);
   });
 
+  // Update scaleYInstance when scaleY props change
   createEffect(() => {
-    // Update scaleYInstance when scaleY props change
+    const fullExtent =
+      chart.scalePropsY.domain[1] - chart.scalePropsY.domain[0];
+    const centerExtent = chart.scalePropsY.domain[0] + fullExtent / 2;
+    const zoomedExtent = fullExtent / chart.zoom;
+    const zoomedDomain = [
+      centerExtent - zoomedExtent / 2,
+      centerExtent + zoomedExtent / 2,
+    ];
+
     const scaleY = supportedScales[chart.scalePropsY.type]()
       .range(chart.scalePropsY.range)
-      .domain(chart.scalePropsY.domain);
+      .domain(zoomedDomain);
     // .nice();
     updateChart("scaleY", () => scaleY);
   });
+
   return (
     <ChartContext.Provider value={[chart, updateChart]}>
       <figure>{props.children}</figure>
@@ -125,6 +147,14 @@ export function Chart(props: {
     setCoords([chart.scaleX.invert(x), chart.scaleY.invert(y)]);
   };
 
+  const onWheel = (e: WheelEvent) => {
+    e.preventDefault();
+    const zoomFactor = 1.1;
+    updateChart("zoom", (prev) =>
+      e.deltaY < 0 ? prev * zoomFactor : prev / zoomFactor,
+    );
+  };
+
   const renderXCoord = () =>
     hovering() ? `x: ${chart.formatX(coords()[0])}` : "";
   const renderYCoord = () =>
@@ -138,6 +168,7 @@ export function Chart(props: {
       onmouseover={() => setHovering(true)}
       onmousemove={onMouseMove}
       onmouseout={() => setHovering(false)}
+      onwheel={onWheel}
     >
       <title>{title}</title>
       <g transform={`translate(${marginLeft},${marginTop})`}>
@@ -149,6 +180,7 @@ export function Chart(props: {
           {renderYCoord()}
         </text>
       </g>
+      <ClipPath />
     </svg>
   );
 }
@@ -163,6 +195,17 @@ export function useChartContext() {
   return context;
 }
 
+// To constrain lines and other elements to the axes' extent
+function ClipPath() {
+  const [chart, _updateChart] = useChartContext();
+
+  return (
+    <clipPath id="clipper">
+      <rect x="0" y="0" width={chart.innerWidth} height={chart.innerHeight} />
+    </clipPath>
+  );
+}
+
 export interface ChartData<T> {
   label: string;
   color: string;
diff --git a/apps/class-solid/src/components/plots/Line.tsx b/apps/class-solid/src/components/plots/Line.tsx
index 0320a2d..23d3579 100644
--- a/apps/class-solid/src/components/plots/Line.tsx
+++ b/apps/class-solid/src/components/plots/Line.tsx
@@ -21,6 +21,7 @@ export function Line(d: ChartData<Point>) {
 
   return (
     <path
+      clip-path="url(#clipper)"
       onMouseEnter={() => setHovered(true)}
       onMouseLeave={() => setHovered(false)}
       fill="none"
diff --git a/apps/class-solid/src/components/plots/skewTlogP.tsx b/apps/class-solid/src/components/plots/skewTlogP.tsx
index 26bb985..1f98603 100644
--- a/apps/class-solid/src/components/plots/skewTlogP.tsx
+++ b/apps/class-solid/src/components/plots/skewTlogP.tsx
@@ -26,16 +26,6 @@ function getTempAtCursor(x: number, y: number, scaleY: SupportedScaleTypes) {
   return x + 0.5 - (scaleY(basep) - y) / tan;
 }
 
-function ClipPath() {
-  const [chart, updateChart] = useChartContext();
-
-  return (
-    <clipPath id="clipper">
-      <rect x="0" y="0" width={chart.innerWidth} height={chart.innerHeight} />
-    </clipPath>
-  );
-}
-
 function SkewTGridLine(temperature: number) {
   const [chart, updateChart] = useChartContext();
   const x = (temp: number) => chart.scaleX(temp);
@@ -201,7 +191,6 @@ export function SkewTPlot(props: { data: () => ChartData<SoundingRecord>[] }) {
           tickValues={pressureLines}
           label="Pressure [hPa]"
         />
-        <ClipPath />
         <For each={temperatureLines}>{(t) => SkewTGridLine(t)}</For>
         <For each={pressureLines}>{(p) => LogPGridLine(p)}</For>
         <For each={dryAdiabats}>{(d) => <DryAdiabat {...d} />}</For>

From 4b9625c9f07da8f0c23e3cb6aec80ce55b1b4e7f Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Fri, 11 Apr 2025 11:16:28 +0200
Subject: [PATCH 02/47] Add logarithmic zoom for skew-T diagram; TODO: T
 calculations should use real axis extent rather than fixes base/top pressure

---
 .../src/components/plots/ChartContainer.tsx   | 56 +++++++++++++------
 1 file changed, 38 insertions(+), 18 deletions(-)

diff --git a/apps/class-solid/src/components/plots/ChartContainer.tsx b/apps/class-solid/src/components/plots/ChartContainer.tsx
index ea08e96..527dad7 100644
--- a/apps/class-solid/src/components/plots/ChartContainer.tsx
+++ b/apps/class-solid/src/components/plots/ChartContainer.tsx
@@ -71,37 +71,31 @@ export function ChartContainer(props: {
 
   // Update scaleXInstance when scaleX props change
   createEffect(() => {
-    const fullExtent =
-      chart.scalePropsX.domain[1] - chart.scalePropsX.domain[0];
-    const centerExtent = chart.scalePropsX.domain[0] + fullExtent / 2;
-    const zoomedExtent = fullExtent / chart.zoom;
-    const zoomedDomain = [
-      centerExtent - zoomedExtent / 2,
-      centerExtent + zoomedExtent / 2,
-    ];
+    const [min, max] = chart.scalePropsX.domain;
+    const zoom = chart.zoom;
+    const zoomedDomain = linearZoom(min, max, zoom);
 
     const scaleX = supportedScales[chart.scalePropsX.type]()
       .range(chart.scalePropsX.range)
       .domain(zoomedDomain);
-    // .nice(); // TODO: could use this instead of getNiceAxisLimits but messes up skewT
+
     updateChart("scaleX", () => scaleX);
   });
 
   // Update scaleYInstance when scaleY props change
   createEffect(() => {
-    const fullExtent =
-      chart.scalePropsY.domain[1] - chart.scalePropsY.domain[0];
-    const centerExtent = chart.scalePropsY.domain[0] + fullExtent / 2;
-    const zoomedExtent = fullExtent / chart.zoom;
-    const zoomedDomain = [
-      centerExtent - zoomedExtent / 2,
-      centerExtent + zoomedExtent / 2,
-    ];
+    const [min, max] = chart.scalePropsY.domain;
+    const zoom = chart.zoom;
+
+    const zoomedDomain =
+      chart.scalePropsY.type === "log"
+        ? logarithmicZoom(min, max, zoom)
+        : linearZoom(min, max, zoom);
 
     const scaleY = supportedScales[chart.scalePropsY.type]()
       .range(chart.scalePropsY.range)
       .domain(zoomedDomain);
-    // .nice();
+
     updateChart("scaleY", () => scaleY);
   });
 
@@ -221,3 +215,29 @@ export function highlight(hex: string) {
       .padStart(2, "0");
   return `#${b(hex, 1)}${b(hex, 3)}${b(hex, 5)}`;
 }
+
+function linearZoom(
+  min: number,
+  max: number,
+  zoomFactor: number,
+): [number, number] {
+  const center = (min + max) / 2;
+  const halfExtent = (max - min) / (2 * zoomFactor);
+  return [center - halfExtent, center + halfExtent];
+}
+
+function logarithmicZoom(
+  min: number,
+  max: number,
+  zoomFactor: number,
+): [number, number] {
+  const logMin = Math.log10(min);
+  const logMax = Math.log10(max);
+  const center = (logMin + logMax) / 2;
+  const halfExtent = (logMax - logMin) / (2 * zoomFactor);
+
+  const newLogMin = center - halfExtent;
+  const newLogMax = center + halfExtent;
+
+  return [10 ** newLogMin, 10 ** newLogMax];
+}

From 89f028b0230bb8e6ca2c041c789f643537b1521f Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Fri, 11 Apr 2025 16:02:29 +0200
Subject: [PATCH 03/47] Fix skew-T lines responding to original extent instead
 of actual; now they don't tilt anymore

---
 .../src/components/plots/skewTlogP.tsx        | 32 ++++++++++++-------
 1 file changed, 21 insertions(+), 11 deletions(-)

diff --git a/apps/class-solid/src/components/plots/skewTlogP.tsx b/apps/class-solid/src/components/plots/skewTlogP.tsx
index 1f98603..a9cfc72 100644
--- a/apps/class-solid/src/components/plots/skewTlogP.tsx
+++ b/apps/class-solid/src/components/plots/skewTlogP.tsx
@@ -19,21 +19,22 @@ interface SoundingRecord {
 
 const deg2rad = Math.PI / 180;
 const tan = Math.tan(55 * deg2rad);
-const basep = 1050;
-const topPressure = 100;
 
 function getTempAtCursor(x: number, y: number, scaleY: SupportedScaleTypes) {
-  return x + 0.5 - (scaleY(basep) - y) / tan;
+  const basep = () => scaleY.domain()[0];
+  return x - (scaleY(basep()) - y) / tan;
 }
 
 function SkewTGridLine(temperature: number) {
   const [chart, updateChart] = useChartContext();
   const x = (temp: number) => chart.scaleX(temp);
   const y = (pres: number) => chart.scaleY(pres);
+  const basep = () => chart.scaleY.domain()[0];
+  const topPressure = () => chart.scaleY.domain()[1];
   return (
     <line
-      x1={x(temperature) - 0.5 + (y(basep) - y(100)) / tan}
-      x2={x(temperature) - 0.5}
+      x1={x(temperature) + (y(basep()) - y(topPressure())) / tan}
+      x2={x(temperature)}
       y1="0"
       y2={chart.innerHeight}
       clip-path="url(#clipper)"
@@ -57,6 +58,7 @@ function LogPGridLine(pressure: number) {
       stroke="#dfdfdf"
       stroke-width="0.75px"
       fill="none"
+      clip-path="url(#clipper)"
     />
   );
 }
@@ -66,13 +68,13 @@ function DryAdiabat(d: [number, number][]) {
   const [chart, updateChart] = useChartContext();
   const x = (temp: number) => chart.scaleX(temp);
   const y = (pres: number) => chart.scaleY(pres);
-
+  const basep = () => chart.scaleY.domain()[0];
   const dryline = d3
     .line()
     .x(
       (d) =>
         x((273.15 + d[1]) / (1000 / d[0]) ** 0.286 - 273.15) +
-        (y(basep) - y(d[0])) / tan,
+        (y(basep()) - y(d[0])) / tan,
     )
     .y((d) => y(d[0]));
   return (
@@ -93,15 +95,16 @@ function Sounding(data: ChartData<SoundingRecord>) {
   // Scales and axes. Note the inverted domain for the y-scale: bigger is up!
   const x = (temp: number) => chart.scaleX(temp);
   const y = (pres: number) => chart.scaleY(pres);
+  const basep = () => chart.scaleY.domain()[0];
 
   const temperatureLine = d3
     .line<SoundingRecord>()
-    .x((d) => x(d.T - 273.15) + (y(basep) - y(d.p)) / tan)
+    .x((d) => x(d.T - 273.15) + (y(basep()) - y(d.p)) / tan)
     .y((d) => y(d.p));
 
   const dewpointLine = d3
     .line<SoundingRecord>()
-    .x((d) => x(d.Td - 273.15) + (y(basep) - y(d.p)) / tan)
+    .x((d) => x(d.Td - 273.15) + (y(basep()) - y(d.p)) / tan)
     .y((d) => y(d.p));
 
   const titleT = () => `${data.label} T`;
@@ -144,7 +147,14 @@ export function SkewTPlot(props: { data: () => ChartData<SoundingRecord>[] }) {
   const pressureLines = [1000, 850, 700, 500, 300, 200, 100];
   const temperatureLines = d3.range(-100, 45, 10);
 
-  const pressureGrid = d3.range(topPressure, basep + 1, 10);
+  const initialBasePressure = 1050;
+  const initialTopPressure = 100;
+
+  const pressureGrid = d3.range(
+    initialTopPressure,
+    initialBasePressure + 1,
+    10,
+  );
   const temperatureGrid = d3.range(-30, 240, 20);
   const dryAdiabats: [number, number][][] = temperatureGrid.map((temperature) =>
     pressureGrid.map((pressure) => [pressure, temperature]),
@@ -187,7 +197,7 @@ export function SkewTPlot(props: { data: () => ChartData<SoundingRecord>[] }) {
         />
         <AxisLeft
           type="log"
-          domain={() => [basep, topPressure]}
+          domain={() => [initialBasePressure, initialTopPressure]}
           tickValues={pressureLines}
           label="Pressure [hPa]"
         />

From 8e29a5aff49979ac9cd91f8d748dd49d7c57b0f2 Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Fri, 11 Apr 2025 17:08:31 +0200
Subject: [PATCH 04/47] Add panning effect, but it is stroboscopic and doesn't
 work for skewT yet

---
 .../src/components/plots/ChartContainer.tsx   | 84 ++++++++++++++-----
 1 file changed, 64 insertions(+), 20 deletions(-)

diff --git a/apps/class-solid/src/components/plots/ChartContainer.tsx b/apps/class-solid/src/components/plots/ChartContainer.tsx
index 527dad7..46f7587 100644
--- a/apps/class-solid/src/components/plots/ChartContainer.tsx
+++ b/apps/class-solid/src/components/plots/ChartContainer.tsx
@@ -36,6 +36,7 @@ interface Chart {
   formatY: (value: number) => string;
   transformX?: (x: number, y: number, scaleY: SupportedScaleTypes) => number;
   zoom: number;
+  pan: [number, number];
 }
 type SetChart = SetStoreFunction<Chart>;
 const ChartContext = createContext<[Chart, SetChart]>();
@@ -67,13 +68,15 @@ export function ChartContainer(props: {
     formatX: d3.format(".4"),
     formatY: d3.format(".4"),
     zoom: 1,
+    pan: [0, 0],
   });
 
   // Update scaleXInstance when scaleX props change
   createEffect(() => {
     const [min, max] = chart.scalePropsX.domain;
+    const pan = chart.pan[0];
     const zoom = chart.zoom;
-    const zoomedDomain = linearZoom(min, max, zoom);
+    const zoomedDomain = getZoomedAndPannedDomainLinear(min, max, pan, zoom);
 
     const scaleX = supportedScales[chart.scalePropsX.type]()
       .range(chart.scalePropsX.range)
@@ -82,15 +85,16 @@ export function ChartContainer(props: {
     updateChart("scaleX", () => scaleX);
   });
 
-  // Update scaleYInstance when scaleY props change
+  // Update scales when props change
   createEffect(() => {
     const [min, max] = chart.scalePropsY.domain;
+    const pan = chart.pan[1];
     const zoom = chart.zoom;
 
     const zoomedDomain =
       chart.scalePropsY.type === "log"
-        ? logarithmicZoom(min, max, zoom)
-        : linearZoom(min, max, zoom);
+        ? getZoomedAndPannedDomainLog(min, max, pan, zoom)
+        : getZoomedAndPannedDomainLinear(min, max, pan, zoom);
 
     const scaleY = supportedScales[chart.scalePropsY.type]()
       .range(chart.scalePropsY.range)
@@ -115,10 +119,12 @@ export function Chart(props: {
   transformX?: (x: number, y: number, scaleY: SupportedScaleTypes) => number;
 }) {
   const [hovering, setHovering] = createSignal(false);
-  const [coords, setCoords] = createSignal<[number, number]>([0, 0]);
+  const [panning, setPanning] = createSignal(false);
+  const [dataCoords, setDataCoords] = createSignal<[number, number]>([0, 0]);
   const [chart, updateChart] = useChartContext();
   const title = props.title || "Default chart";
   const [marginTop, _, __, marginLeft] = chart.margin;
+  let panstart = [0, 0];
 
   if (props.formatX) {
     updateChart("formatX", () => props.formatX);
@@ -130,7 +136,8 @@ export function Chart(props: {
     updateChart("transformX", () => props.transformX);
   }
 
-  const onMouseMove = (e: MouseEvent) => {
+  // Utility function to calculate coordinates from mouse event
+  const getDataCoordsFromEvent = (e: MouseEvent) => {
     let x = e.offsetX - marginLeft;
     const y = e.offsetY - marginTop;
 
@@ -138,7 +145,38 @@ export function Chart(props: {
       x = chart.transformX(x, y, chart.scaleY);
     }
 
-    setCoords([chart.scaleX.invert(x), chart.scaleY.invert(y)]);
+    return [chart.scaleX.invert(x), chart.scaleY.invert(y)];
+  };
+
+  const onMouseDown = (e: MouseEvent) => {
+    setPanning(true);
+    panstart = getDataCoordsFromEvent(e);
+  };
+
+  let animationFrameId: number | null = null;
+  const onMouseMove = (e: MouseEvent) => {
+    // If an animation frame is already scheduled, cancel it to prevent multiple frames being scheduled unnecessarily
+    if (animationFrameId) {
+      cancelAnimationFrame(animationFrameId);
+    }
+
+    // Request a new animation frame for the next paint cycle
+    animationFrameId = requestAnimationFrame(() => handlePanMove(e));
+  };
+
+  const handlePanMove = (e: MouseEvent) => {
+    const [x, y] = getDataCoordsFromEvent(e);
+
+    if (panning()) {
+      const [startX, startY] = panstart;
+      const dx = x - startX;
+      const dy = y - startY;
+      panstart = [x, y];
+      updateChart("pan", (prev) => [prev[0] - dx, prev[1] - dy]);
+    } else {
+      // Update the coordinate tracker in the plot when not panning
+      setDataCoords([x, y]);
+    }
   };
 
   const onWheel = (e: WheelEvent) => {
@@ -150,9 +188,9 @@ export function Chart(props: {
   };
 
   const renderXCoord = () =>
-    hovering() ? `x: ${chart.formatX(coords()[0])}` : "";
+    hovering() ? `x: ${chart.formatX(dataCoords()[0])}` : "";
   const renderYCoord = () =>
-    hovering() ? `y: ${chart.formatY(coords()[1])}` : "";
+    hovering() ? `y: ${chart.formatY(dataCoords()[1])}` : "";
 
   return (
     <svg
@@ -160,8 +198,11 @@ export function Chart(props: {
       height={chart.height}
       class="text-slate-500 text-xs tracking-wide"
       onmouseover={() => setHovering(true)}
-      onmousemove={onMouseMove}
       onmouseout={() => setHovering(false)}
+      onmousedown={onMouseDown}
+      onmouseup={() => setPanning(false)}
+      onmousemove={onMouseMove}
+      onmouseleave={() => setPanning(false)}
       onwheel={onWheel}
     >
       <title>{title}</title>
@@ -216,28 +257,31 @@ export function highlight(hex: string) {
   return `#${b(hex, 1)}${b(hex, 3)}${b(hex, 5)}`;
 }
 
-function linearZoom(
+function getZoomedAndPannedDomainLinear(
   min: number,
   max: number,
-  zoomFactor: number,
+  pan: number,
+  zoom: number,
 ): [number, number] {
-  const center = (min + max) / 2;
-  const halfExtent = (max - min) / (2 * zoomFactor);
+  const center = (min + max) / 2 + pan;
+  const halfExtent = (max - min) / (2 * zoom);
   return [center - halfExtent, center + halfExtent];
 }
 
-function logarithmicZoom(
+function getZoomedAndPannedDomainLog(
   min: number,
   max: number,
-  zoomFactor: number,
+  pan: number,
+  zoom: number,
 ): [number, number] {
   const logMin = Math.log10(min);
   const logMax = Math.log10(max);
-  const center = (logMin + logMax) / 2;
-  const halfExtent = (logMax - logMin) / (2 * zoomFactor);
 
-  const newLogMin = center - halfExtent;
-  const newLogMax = center + halfExtent;
+  const logCenter = (logMin + logMax) / 2 + pan;
+  const halfExtent = (logMax - logMin) / (2 * zoom);
+
+  const newLogMin = logCenter - halfExtent;
+  const newLogMax = logCenter + halfExtent;
 
   return [10 ** newLogMin, 10 ** newLogMax];
 }

From 53f2cb19b5e6a0d2b14849101d76b20438eb31a2 Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Fri, 11 Apr 2025 17:14:05 +0200
Subject: [PATCH 05/47] combine side-effects for both axes in a single callback

---
 .../src/components/plots/ChartContainer.tsx   | 34 +++++++++----------
 1 file changed, 16 insertions(+), 18 deletions(-)

diff --git a/apps/class-solid/src/components/plots/ChartContainer.tsx b/apps/class-solid/src/components/plots/ChartContainer.tsx
index 46f7587..e9251e4 100644
--- a/apps/class-solid/src/components/plots/ChartContainer.tsx
+++ b/apps/class-solid/src/components/plots/ChartContainer.tsx
@@ -71,35 +71,33 @@ export function ChartContainer(props: {
     pan: [0, 0],
   });
 
-  // Update scaleXInstance when scaleX props change
+  // Update scales when props change
   createEffect(() => {
-    const [min, max] = chart.scalePropsX.domain;
-    const pan = chart.pan[0];
+    const [minX, maxX] = chart.scalePropsX.domain;
+    const [minY, maxY] = chart.scalePropsY.domain;
+    const [panX, panY] = chart.pan;
     const zoom = chart.zoom;
-    const zoomedDomain = getZoomedAndPannedDomainLinear(min, max, pan, zoom);
 
+    const zoomedXDomain = getZoomedAndPannedDomainLinear(
+      minX,
+      maxX,
+      panX,
+      zoom,
+    );
     const scaleX = supportedScales[chart.scalePropsX.type]()
       .range(chart.scalePropsX.range)
-      .domain(zoomedDomain);
-
-    updateChart("scaleX", () => scaleX);
-  });
+      .domain(zoomedXDomain);
 
-  // Update scales when props change
-  createEffect(() => {
-    const [min, max] = chart.scalePropsY.domain;
-    const pan = chart.pan[1];
-    const zoom = chart.zoom;
-
-    const zoomedDomain =
+    const zoomedYDomain =
       chart.scalePropsY.type === "log"
-        ? getZoomedAndPannedDomainLog(min, max, pan, zoom)
-        : getZoomedAndPannedDomainLinear(min, max, pan, zoom);
+        ? getZoomedAndPannedDomainLog(minY, maxY, panY, zoom)
+        : getZoomedAndPannedDomainLinear(minY, maxY, panY, zoom);
 
     const scaleY = supportedScales[chart.scalePropsY.type]()
       .range(chart.scalePropsY.range)
-      .domain(zoomedDomain);
+      .domain(zoomedYDomain);
 
+    updateChart("scaleX", () => scaleX);
     updateChart("scaleY", () => scaleY);
   });
 

From ca46f1fd3cde488ae1a250747e94bf6c642d80ba Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Fri, 18 Apr 2025 10:07:11 +0200
Subject: [PATCH 06/47] Remove animationframe

---
 .../src/components/plots/ChartContainer.tsx         | 13 +------------
 1 file changed, 1 insertion(+), 12 deletions(-)

diff --git a/apps/class-solid/src/components/plots/ChartContainer.tsx b/apps/class-solid/src/components/plots/ChartContainer.tsx
index e9251e4..41ea82d 100644
--- a/apps/class-solid/src/components/plots/ChartContainer.tsx
+++ b/apps/class-solid/src/components/plots/ChartContainer.tsx
@@ -151,18 +151,7 @@ export function Chart(props: {
     panstart = getDataCoordsFromEvent(e);
   };
 
-  let animationFrameId: number | null = null;
   const onMouseMove = (e: MouseEvent) => {
-    // If an animation frame is already scheduled, cancel it to prevent multiple frames being scheduled unnecessarily
-    if (animationFrameId) {
-      cancelAnimationFrame(animationFrameId);
-    }
-
-    // Request a new animation frame for the next paint cycle
-    animationFrameId = requestAnimationFrame(() => handlePanMove(e));
-  };
-
-  const handlePanMove = (e: MouseEvent) => {
     const [x, y] = getDataCoordsFromEvent(e);
 
     if (panning()) {
@@ -172,7 +161,7 @@ export function Chart(props: {
       panstart = [x, y];
       updateChart("pan", (prev) => [prev[0] - dx, prev[1] - dy]);
     } else {
-      // Update the coordinate tracker in the plot when not panning
+      // Update the coordinate tracker in the plot
       setDataCoords([x, y]);
     }
   };

From 8be96356c597732bbf11a00ac10aff885b820bd0 Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Fri, 18 Apr 2025 10:14:34 +0200
Subject: [PATCH 07/47] Use produce to update both scales in a single call

---
 .../src/components/plots/ChartContainer.tsx            | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/apps/class-solid/src/components/plots/ChartContainer.tsx b/apps/class-solid/src/components/plots/ChartContainer.tsx
index 41ea82d..0e1a73a 100644
--- a/apps/class-solid/src/components/plots/ChartContainer.tsx
+++ b/apps/class-solid/src/components/plots/ChartContainer.tsx
@@ -6,7 +6,7 @@ import {
   createSignal,
   useContext,
 } from "solid-js";
-import { type SetStoreFunction, createStore } from "solid-js/store";
+import { type SetStoreFunction, createStore, produce } from "solid-js/store";
 
 export type SupportedScaleTypes =
   | d3.ScaleLinear<number, number, never>
@@ -97,8 +97,12 @@ export function ChartContainer(props: {
       .range(chart.scalePropsY.range)
       .domain(zoomedYDomain);
 
-    updateChart("scaleX", () => scaleX);
-    updateChart("scaleY", () => scaleY);
+    updateChart(
+      produce((prev) => {
+        prev.scaleX = scaleX;
+        prev.scaleY = scaleY;
+      }),
+    );
   });
 
   return (

From 859557b4a527f17691fc84bc99af9cc50189588e Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Fri, 18 Apr 2025 10:19:24 +0200
Subject: [PATCH 08/47] Don't update panstart; this fixes the jittering

---
 apps/class-solid/src/components/plots/ChartContainer.tsx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/apps/class-solid/src/components/plots/ChartContainer.tsx b/apps/class-solid/src/components/plots/ChartContainer.tsx
index 0e1a73a..a778998 100644
--- a/apps/class-solid/src/components/plots/ChartContainer.tsx
+++ b/apps/class-solid/src/components/plots/ChartContainer.tsx
@@ -162,7 +162,7 @@ export function Chart(props: {
       const [startX, startY] = panstart;
       const dx = x - startX;
       const dy = y - startY;
-      panstart = [x, y];
+      // panstart = [x, y];
       updateChart("pan", (prev) => [prev[0] - dx, prev[1] - dy]);
     } else {
       // Update the coordinate tracker in the plot

From 9c32384520fcca6ab637b367d87d12ca9a84ac15 Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Fri, 18 Apr 2025 10:31:51 +0200
Subject: [PATCH 09/47] Also work in log space

---
 .../src/components/plots/ChartContainer.tsx          | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/apps/class-solid/src/components/plots/ChartContainer.tsx b/apps/class-solid/src/components/plots/ChartContainer.tsx
index a778998..0cc427c 100644
--- a/apps/class-solid/src/components/plots/ChartContainer.tsx
+++ b/apps/class-solid/src/components/plots/ChartContainer.tsx
@@ -144,6 +144,7 @@ export function Chart(props: {
     const y = e.offsetY - marginTop;
 
     if (chart.transformX) {
+      // Correct for skewed lines in thermodynamic diagram
       x = chart.transformX(x, y, chart.scaleY);
     }
 
@@ -161,8 +162,15 @@ export function Chart(props: {
     if (panning()) {
       const [startX, startY] = panstart;
       const dx = x - startX;
-      const dy = y - startY;
-      // panstart = [x, y];
+      let dy: number;
+
+      if (chart.scalePropsY.type === "log") {
+        const logStartY = Math.log10(startY);
+        const logY = Math.log10(y);
+        dy = logY - logStartY;
+      } else {
+        dy = y - startY;
+      }
       updateChart("pan", (prev) => [prev[0] - dx, prev[1] - dy]);
     } else {
       // Update the coordinate tracker in the plot

From d3fae43694231c07a0874090f3b07e6eaeb761d7 Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Fri, 18 Apr 2025 10:36:57 +0200
Subject: [PATCH 10/47] Make consistent for x-direction

---
 .../src/components/plots/ChartContainer.tsx   | 21 ++++++++++---------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/apps/class-solid/src/components/plots/ChartContainer.tsx b/apps/class-solid/src/components/plots/ChartContainer.tsx
index 0cc427c..e422c36 100644
--- a/apps/class-solid/src/components/plots/ChartContainer.tsx
+++ b/apps/class-solid/src/components/plots/ChartContainer.tsx
@@ -161,16 +161,17 @@ export function Chart(props: {
 
     if (panning()) {
       const [startX, startY] = panstart;
-      const dx = x - startX;
-      let dy: number;
-
-      if (chart.scalePropsY.type === "log") {
-        const logStartY = Math.log10(startY);
-        const logY = Math.log10(y);
-        dy = logY - logStartY;
-      } else {
-        dy = y - startY;
-      }
+
+      const dx =
+        chart.scalePropsX.type === "log"
+          ? Math.log10(x) - Math.log10(startX)
+          : x - startX;
+
+      const dy =
+        chart.scalePropsY.type === "log"
+          ? Math.log10(y) - Math.log10(startY)
+          : y - startY;
+
       updateChart("pan", (prev) => [prev[0] - dx, prev[1] - dy]);
     } else {
       // Update the coordinate tracker in the plot

From ea696fc77e6dca63a7d0c659ffdab4cd86465df2 Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Fri, 18 Apr 2025 11:23:42 +0200
Subject: [PATCH 11/47] zoom towards cursor

---
 .../src/components/plots/ChartContainer.tsx   | 35 +++++++++++++++++--
 1 file changed, 33 insertions(+), 2 deletions(-)

diff --git a/apps/class-solid/src/components/plots/ChartContainer.tsx b/apps/class-solid/src/components/plots/ChartContainer.tsx
index e422c36..a3df2ec 100644
--- a/apps/class-solid/src/components/plots/ChartContainer.tsx
+++ b/apps/class-solid/src/components/plots/ChartContainer.tsx
@@ -180,10 +180,41 @@ export function Chart(props: {
   };
 
   const onWheel = (e: WheelEvent) => {
+    // Zoom towards cursor
     e.preventDefault();
     const zoomFactor = 1.1;
-    updateChart("zoom", (prev) =>
-      e.deltaY < 0 ? prev * zoomFactor : prev / zoomFactor,
+    const zoomDirection = e.deltaY < 0 ? 1 : -1;
+    const zoomChange = zoomFactor ** zoomDirection;
+
+    const [cursorX, cursorY] = getDataCoordsFromEvent(e);
+
+    updateChart(
+      produce((draft) => {
+        const { scalePropsX, scalePropsY, pan } = draft;
+        const [panX, panY] = pan;
+
+        // Calculate x-pan (linear only for now)
+        const [xmin, xmax] = scalePropsX.domain;
+        const centerX = (xmin + xmax) / 2 + panX;
+        const dx = cursorX - centerX;
+
+        // Calculate y-pan
+        const [ymin, ymax] = scalePropsY.domain;
+        let dy: number;
+        if (scalePropsY.type === "log") {
+          const logCursor = Math.log10(Math.max(cursorY, 1e-10));
+          const logCenter = (Math.log10(ymin) + Math.log10(ymax)) / 2 + panY;
+          dy = logCursor - logCenter;
+        } else {
+          const centerY = (ymin + ymax) / 2 + panY;
+          dy = cursorY - centerY;
+        }
+
+        // Update the chart (mutating plays nicely with produce)
+        draft.zoom *= zoomChange;
+        draft.pan[0] += dx * (1 - 1 / zoomChange);
+        draft.pan[1] += dy * (1 - 1 / zoomChange);
+      }),
     );
   };
 

From b65f5161d95d16028cb3315b581f2a73972f7bb3 Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Fri, 18 Apr 2025 13:00:37 +0200
Subject: [PATCH 12/47] Add reset plot button

---
 apps/class-solid/src/components/Analysis.tsx  | 18 ++++++++++++----
 apps/class-solid/src/components/icons.tsx     | 21 +++++++++++++++++++
 .../src/components/plots/ChartContainer.tsx   | 13 ++++++++++++
 .../src/components/plots/skewTlogP.tsx        |  6 +++++-
 4 files changed, 53 insertions(+), 5 deletions(-)

diff --git a/apps/class-solid/src/components/Analysis.tsx b/apps/class-solid/src/components/Analysis.tsx
index 6685914..d1ee9d2 100644
--- a/apps/class-solid/src/components/Analysis.tsx
+++ b/apps/class-solid/src/components/Analysis.tsx
@@ -12,6 +12,7 @@ import {
   Switch,
   createEffect,
   createMemo,
+  createSignal,
   createUniqueId,
 } from "solid-js";
 import { createStore } from "solid-js/store";
@@ -31,7 +32,7 @@ import {
   experiments,
   updateAnalysis,
 } from "~/lib/store";
-import { MdiCamera, MdiDelete } from "./icons";
+import { MaterialSymbolsLightResetImage, MdiCamera, MdiDelete } from "./icons";
 import { AxisBottom, AxisLeft, getNiceAxisLimits } from "./plots/Axes";
 import { Chart, ChartContainer } from "./plots/ChartContainer";
 import { Legend } from "./plots/Legend";
@@ -162,7 +163,7 @@ export function TimeSeriesPlot({ analysis }: { analysis: TimeseriesAnalysis }) {
       {/* TODO: get label for yVariable from model config */}
       <ChartContainer>
         <Legend entries={chartData} toggles={toggles} onChange={toggleLine} />
-        <Chart title="Timeseries plot" formatX={formatSeconds}>
+        <Chart id={analysis.id} title="Timeseries plot" formatX={formatSeconds}>
           <AxisBottom domain={xLim} label="Time [s]" />
           <AxisLeft domain={yLim} label={analysis.yVariable} />
           <For each={chartData()}>
@@ -269,7 +270,7 @@ export function VerticalProfilePlot({
             toggles={toggles}
             onChange={toggleLine}
           />
-          <Chart title="Vertical profile plot">
+          <Chart id={analysis.id} title="Vertical profile plot">
             <AxisBottom domain={xLim} label={analysis.variable} />
             <AxisLeft domain={yLim} label="Height[m]" />
             <For each={profileData()}>
@@ -394,7 +395,10 @@ export function ThermodynamicPlot({ analysis }: { analysis: SkewTAnalysis }) {
 
   return (
     <>
-      <SkewTPlot data={() => [...skewTData(), ...observations()]} />
+      <SkewTPlot
+        id={analysis.id}
+        data={() => [...skewTData(), ...observations()]}
+      />
       {TimeSlider(
         () => analysis.time,
         uniqueTimes,
@@ -443,6 +447,9 @@ async function takeScreenshot(event: MouseEvent, analyse: Analysis) {
   saveAs(file);
 }
 
+// Emit a signal when plot reset button is pressed
+export const [resetPlot, setResetPlot] = createSignal("", { equals: false });
+
 export function AnalysisCard(analysis: Analysis) {
   const id = createUniqueId();
   return (
@@ -451,6 +458,9 @@ export function AnalysisCard(analysis: Analysis) {
         {/* TODO: make name & description editable */}
         <CardTitle id={id}>{analysis.name}</CardTitle>
         <div class="flex gap-1">
+          <Button variant="outline" onclick={() => setResetPlot(analysis.id)}>
+            <MaterialSymbolsLightResetImage />
+          </Button>
           <Button
             variant="outline"
             onClick={(e: MouseEvent) => takeScreenshot(e, analysis)}
diff --git a/apps/class-solid/src/components/icons.tsx b/apps/class-solid/src/components/icons.tsx
index 6c74859..f11ec13 100644
--- a/apps/class-solid/src/components/icons.tsx
+++ b/apps/class-solid/src/components/icons.tsx
@@ -355,3 +355,24 @@ export function MdiCamera(props: JSX.IntrinsicElements["svg"]) {
     </svg>
   );
 }
+
+export function MaterialSymbolsLightResetImage(
+  props: JSX.IntrinsicElements["svg"],
+) {
+  // Icon from Material Symbols Light by Google - https://github.com/google/material-design-icons/blob/master/LICENSE
+  return (
+    <svg
+      xmlns="http://www.w3.org/2000/svg"
+      width="1em"
+      height="1em"
+      viewBox="0 0 24 24"
+      {...props}
+    >
+      <title>Reset plot</title>
+      <path
+        fill="currentColor"
+        d="M4 9.77V5h1v3.235q1-1.896 2.851-3.066T12 4q2.739 0 4.849 1.627t2.824 4.142h-1.06q-.696-2.108-2.486-3.438T12 5Q9.979 5 8.36 6.044T5.909 8.77H8.77v1zm3.5 7.73h9.154l-2.827-3.77l-2.615 3.308l-1.75-2.115zM5.616 21q-.672 0-1.144-.472T4 19.385v-6.77h1v6.77q0 .269.173.442t.443.173h12.769q.269 0 .442-.173t.173-.442v-6.77h1v6.77q0 .67-.472 1.143q-.472.472-1.143.472z"
+      />
+    </svg>
+  );
+}
diff --git a/apps/class-solid/src/components/plots/ChartContainer.tsx b/apps/class-solid/src/components/plots/ChartContainer.tsx
index a3df2ec..3ad9ed0 100644
--- a/apps/class-solid/src/components/plots/ChartContainer.tsx
+++ b/apps/class-solid/src/components/plots/ChartContainer.tsx
@@ -7,6 +7,7 @@ import {
   useContext,
 } from "solid-js";
 import { type SetStoreFunction, createStore, produce } from "solid-js/store";
+import { resetPlot } from "../Analysis";
 
 export type SupportedScaleTypes =
   | d3.ScaleLinear<number, number, never>
@@ -115,6 +116,7 @@ export function ChartContainer(props: {
 /** Container for chart elements such as axes and lines */
 export function Chart(props: {
   children: JSX.Element;
+  id: string;
   title?: string;
   formatX?: (value: number) => string;
   formatY?: (value: number) => string;
@@ -128,6 +130,17 @@ export function Chart(props: {
   const [marginTop, _, __, marginLeft] = chart.margin;
   let panstart = [0, 0];
 
+  createEffect(() => {
+    if (resetPlot() === props.id) {
+      updateChart(
+        produce((prev) => {
+          prev.zoom = 1;
+          prev.pan = [0, 0];
+        }),
+      );
+    }
+  });
+
   if (props.formatX) {
     updateChart("formatX", () => props.formatX);
   }
diff --git a/apps/class-solid/src/components/plots/skewTlogP.tsx b/apps/class-solid/src/components/plots/skewTlogP.tsx
index a9cfc72..88d4260 100644
--- a/apps/class-solid/src/components/plots/skewTlogP.tsx
+++ b/apps/class-solid/src/components/plots/skewTlogP.tsx
@@ -143,7 +143,10 @@ function Sounding(data: ChartData<SoundingRecord>) {
 
 // Note: using temperatures in Kelvin as that's easiest to get from CLASS, but
 // perhaps not the most interoperable with other sounding data sources.
-export function SkewTPlot(props: { data: () => ChartData<SoundingRecord>[] }) {
+export function SkewTPlot(props: {
+  data: () => ChartData<SoundingRecord>[];
+  id: string;
+}) {
   const pressureLines = [1000, 850, 700, 500, 300, 200, 100];
   const temperatureLines = d3.range(-100, 45, 10);
 
@@ -185,6 +188,7 @@ export function SkewTPlot(props: { data: () => ChartData<SoundingRecord>[] }) {
     <ChartContainer>
       <Legend entries={props.data} toggles={toggles} onChange={toggleLine} />
       <Chart
+        id={props.id}
         title="Thermodynamic diagram"
         formatX={d3.format(".0d")}
         formatY={d3.format(".0d")}

From 69e93d4ce8659e41e1a63dfb37a3b9d6f827239c Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Fri, 18 Apr 2025 11:25:40 +0200
Subject: [PATCH 13/47] Thinner lines

---
 apps/class-solid/src/components/plots/Line.tsx      | 2 +-
 apps/class-solid/src/components/plots/skewTlogP.tsx | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/apps/class-solid/src/components/plots/Line.tsx b/apps/class-solid/src/components/plots/Line.tsx
index 23d3579..65cce5b 100644
--- a/apps/class-solid/src/components/plots/Line.tsx
+++ b/apps/class-solid/src/components/plots/Line.tsx
@@ -27,7 +27,7 @@ export function Line(d: ChartData<Point>) {
       fill="none"
       stroke={stroke()}
       stroke-dasharray={d.linestyle}
-      stroke-width="3"
+      stroke-width="2"
       d={l(d.data) || ""}
     >
       <title>{d.label}</title>
diff --git a/apps/class-solid/src/components/plots/skewTlogP.tsx b/apps/class-solid/src/components/plots/skewTlogP.tsx
index 88d4260..20a8d83 100644
--- a/apps/class-solid/src/components/plots/skewTlogP.tsx
+++ b/apps/class-solid/src/components/plots/skewTlogP.tsx
@@ -122,7 +122,7 @@ function Sounding(data: ChartData<SoundingRecord>) {
         clip-path="url(#clipper)"
         stroke={stroke()}
         stroke-dasharray={data.linestyle}
-        stroke-width={3}
+        stroke-width={2}
         fill="none"
       >
         <title>{titleT()}</title>
@@ -132,7 +132,7 @@ function Sounding(data: ChartData<SoundingRecord>) {
         clip-path="url(#clipper)"
         stroke={stroke()}
         stroke-dasharray="5,5"
-        stroke-width={3}
+        stroke-width={2}
         fill="none"
       >
         <title>{titleTd()}</title>

From 1ca0f6883242b90f582b1c2d3fce5e005a0e5a9c Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Fri, 18 Apr 2025 11:31:20 +0200
Subject: [PATCH 14/47] Higher resolution plot

---
 apps/class-solid/src/components/Analysis.tsx | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/apps/class-solid/src/components/Analysis.tsx b/apps/class-solid/src/components/Analysis.tsx
index d1ee9d2..67ca305 100644
--- a/apps/class-solid/src/components/Analysis.tsx
+++ b/apps/class-solid/src/components/Analysis.tsx
@@ -418,8 +418,9 @@ async function takeScreenshot(event: MouseEvent, analyse: Analysis) {
     return;
   }
 
-  // TODO Make screenshot bigger than the original?
-  const scale = 1;
+  // Make screenshot bigger than the original
+  const scale = 10;
+
   // Can not use toSvg as legend is written in HTML
   // generated svg document contains foreignObject with html tag
   // which can only be rendered using web browser, not Inkscape or PowerPoint

From 8953c43574a123492f447590261b45c2a985758c Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Fri, 18 Apr 2025 11:57:35 +0200
Subject: [PATCH 15/47] Round time to steps of 10 minutes

---
 apps/class-solid/src/components/Analysis.tsx   | 2 +-
 apps/class-solid/src/components/plots/Axes.tsx | 5 +++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/apps/class-solid/src/components/Analysis.tsx b/apps/class-solid/src/components/Analysis.tsx
index 67ca305..27aad5a 100644
--- a/apps/class-solid/src/components/Analysis.tsx
+++ b/apps/class-solid/src/components/Analysis.tsx
@@ -128,7 +128,7 @@ export function TimeSeriesPlot({ analysis }: { analysis: TimeseriesAnalysis }) {
       e.output ? e.output[analysis.yVariable] : [],
     );
 
-  const xLim = () => getNiceAxisLimits(allX());
+  const xLim = () => getNiceAxisLimits(allX(), 0, 600);
   const yLim = () => getNiceAxisLimits(allY());
 
   const chartData = () =>
diff --git a/apps/class-solid/src/components/plots/Axes.tsx b/apps/class-solid/src/components/plots/Axes.tsx
index e624d4c..9131de3 100644
--- a/apps/class-solid/src/components/plots/Axes.tsx
+++ b/apps/class-solid/src/components/plots/Axes.tsx
@@ -79,6 +79,7 @@ export const AxisLeft = (props: AxisProps) => {
 export function getNiceAxisLimits(
   data: number[],
   extraMargin = 0,
+  roundTo?: number, // Optional rounding step, e.g. 600 for 10 minutes
 ): [number, number] {
   const max = Math.max(...data);
   const min = Math.min(...data);
@@ -87,7 +88,7 @@ export function getNiceAxisLimits(
   // Avoid NaNs on axis for constant values
   if (range === 0) return [min - 1, max + 1];
 
-  const step = 10 ** Math.floor(Math.log10(range));
+  const step = roundTo ?? 10 ** Math.floor(Math.log10(range));
 
   const niceMin = Math.floor(min / step) * step - extraMargin * step;
   const niceMax = Math.ceil(max / step) * step + extraMargin * step;
@@ -99,4 +100,4 @@ export function getNiceAxisLimits(
 const generateTicks = (domain = [0, 1], tickCount = 5) => {
   const step = (domain[1] - domain[0]) / (tickCount - 1);
   return [...Array(10).keys()].map((i) => domain[0] + i * step);
-};
+};
\ No newline at end of file

From 0d72ef178c93983eba7d373f25fd44626fbb5562 Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Fri, 18 Apr 2025 15:09:51 +0200
Subject: [PATCH 16/47] Use runClass from package, skipping BMI altogher + rich
 metadata for output vars; however, app/model hangs on second or third run

---
 apps/class-solid/src/lib/runner.ts | 15 ++---
 apps/class-solid/src/lib/store.ts  |  6 +-
 apps/class-solid/src/lib/worker.ts |  4 +-
 packages/class/src/runner.ts       | 98 +++++++++++++++++++++++++++---
 4 files changed, 100 insertions(+), 23 deletions(-)

diff --git a/apps/class-solid/src/lib/runner.ts b/apps/class-solid/src/lib/runner.ts
index b1a29ed..75fed44 100644
--- a/apps/class-solid/src/lib/runner.ts
+++ b/apps/class-solid/src/lib/runner.ts
@@ -1,22 +1,15 @@
-import { BmiClass } from "@classmodel/class/bmi";
 import type { Config } from "@classmodel/class/config";
-import type { ClassOutput } from "@classmodel/class/runner";
-import { parse } from "@classmodel/class/validate";
+import type { ClassOutput, runClass } from "@classmodel/class/runner";
 import { wrap } from "comlink";
 
 const worker = new Worker(new URL("./worker.ts", import.meta.url), {
   type: "module",
 });
-export const AsyncBmiClass = wrap<typeof BmiClass>(worker);
 
-export async function runClass(config: Config): Promise<ClassOutput> {
+export async function runClassAsync(config: Config): Promise<ClassOutput> {
+  const asyncRunner = wrap<typeof runClass>(worker);
   try {
-    const parsedConfig: Config = parse(config);
-    const model = await new AsyncBmiClass();
-    await model.initialize(parsedConfig);
-    const output = await model.run({
-      var_names: new BmiClass().get_output_var_names(),
-    });
+    const output = asyncRunner(config)
     return output;
   } catch (error) {
     console.error({ config, error });
diff --git a/apps/class-solid/src/lib/store.ts b/apps/class-solid/src/lib/store.ts
index 82d7404..d737a15 100644
--- a/apps/class-solid/src/lib/store.ts
+++ b/apps/class-solid/src/lib/store.ts
@@ -12,7 +12,7 @@ import { decodeAppState } from "./encode";
 import { parseExperimentConfig } from "./experiment_config";
 import type { ExperimentConfig } from "./experiment_config";
 import { findPresetByName } from "./presets";
-import { runClass } from "./runner";
+import { runClassAsync } from "./runner";
 
 interface ExperimentOutput {
   reference?: ClassOutput;
@@ -38,7 +38,7 @@ export async function runExperiment(id: number) {
 
   // Run reference
   const referenceConfig = unwrap(exp.config.reference);
-  const newOutput = await runClass(referenceConfig);
+  const newOutput = await runClassAsync(referenceConfig);
 
   setExperiments(id, "output", "reference", newOutput);
 
@@ -50,7 +50,7 @@ export async function runExperiment(id: number) {
       referenceConfig,
       permConfig,
     ) as Config;
-    const newOutput = await runClass(combinedConfig);
+    const newOutput = await runClassAsync(combinedConfig);
     setExperiments(id, "output", "permutations", permCounter, newOutput);
     permCounter++;
   }
diff --git a/apps/class-solid/src/lib/worker.ts b/apps/class-solid/src/lib/worker.ts
index c1549b7..e66de6b 100644
--- a/apps/class-solid/src/lib/worker.ts
+++ b/apps/class-solid/src/lib/worker.ts
@@ -1,4 +1,4 @@
-import { BmiClass } from "@classmodel/class/bmi";
+import { runClass } from "@classmodel/class/runner";
 import { expose } from "comlink";
 
-expose(BmiClass);
+expose(runClass);
diff --git a/packages/class/src/runner.ts b/packages/class/src/runner.ts
index 6d7e563..a98583a 100644
--- a/packages/class/src/runner.ts
+++ b/packages/class/src/runner.ts
@@ -7,22 +7,106 @@ import { CLASS } from "./class.js";
 import type { Config } from "./config.js";
 import { parse } from "./validate.js";
 
-export type ClassOutput = Record<string, number[]>;
+export interface OutputVariable {
+  key: string;
+  title: string;
+  unit: string;
+  symbol?: string
+}
+
+export const outputVariables: OutputVariable[] = [
+  {
+    key: "t",
+    title: "Time",
+    unit: "s",
+    symbol: "t",
+  },
+  {
+    key: "h",
+    title: "ABL height",
+    unit: "m",
+    symbol: "h",
+  },
+  {
+    key: "theta",
+    title: "Potential temperature",
+    unit: "K",
+    symbol: "θ",
+  },
+  {
+    key: "dtheta",
+    title: "Potential temperature jump",
+    unit: "K",
+    symbol: "Δθ",
+  },
+  {
+    key: "q",
+    title: "Specific humidity",
+    unit: "kg kg⁻¹",
+    symbol: "q",
+  },
+  {
+    key: "dq",
+    title: "Specific humidity jump",
+    unit: "kg kg⁻¹",
+    symbol: "Δq",
+  },
+  {
+    key: "dthetav",
+    title: "Virtual temperature jump at h",
+    unit: "K",
+    symbol: "Δθ<sub>v</sub>",
+  },
+  {
+    key: "we",
+    title: "Entrainment velocity",
+    unit: "m s⁻¹",
+    symbol: "w<sub>e</sub>",
+  },
+  {
+    key: "ws",
+    title: "Large-scale vertical velocity",
+    unit: "m s⁻¹",
+    symbol: "w<sub>s</sub>",
+  },
+  {
+    key: "wthetave",
+    title: "Entrainment virtual heat flux",
+    unit: "K m s⁻¹",
+    symbol: "(w'θ')<sub>ve</sub>",
+  },
+  {
+    key: "wthetav",
+    title: "Surface virtual heat flux",
+    unit: "K m s⁻¹",
+    symbol: "(w'θ')<sub>vs</sub>",
+  },
+];
+
+export type ClassOutput = {
+  [K in (typeof outputVariables)[number]['key']]: number[];
+};
+
 
 export function runClass(config: Config): ClassOutput {
-  // TODO should we do validation/coercion here, in form, or both?
+  
   const validatedConfig = parse(config);
   const model = new CLASS(validatedConfig);
-  const output: ClassOutput = { t: [], h: [] };
+
+  const output = Object.fromEntries(
+    outputVariables.map(v => [v.key, []])
+  ) as ClassOutput;
 
   while (model.t < config.runtime) {
     model.update();
 
-    if (model.t % 60 === 0) {
-      output.t.push(model.t);
-      output.h.push(model.h);
+    if (model.t % 600 === 0) {
+      for (const v of outputVariables) {
+          output[v.key].push(model[v.key as keyof CLASS] as number);
+        output[v.key].push();
+      }
     }
   }
 
   return output;
-}
+}
\ No newline at end of file

From d072e561721a60692ba11d0f664b8b338449ada9 Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Fri, 18 Apr 2025 15:15:55 +0200
Subject: [PATCH 17/47] Fix hanging issue: wrap only once...

---
 apps/class-solid/src/lib/runner.ts | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/apps/class-solid/src/lib/runner.ts b/apps/class-solid/src/lib/runner.ts
index 75fed44..a7b53a9 100644
--- a/apps/class-solid/src/lib/runner.ts
+++ b/apps/class-solid/src/lib/runner.ts
@@ -6,8 +6,9 @@ const worker = new Worker(new URL("./worker.ts", import.meta.url), {
   type: "module",
 });
 
+const asyncRunner = wrap<typeof runClass>(worker);
+
 export async function runClassAsync(config: Config): Promise<ClassOutput> {
-  const asyncRunner = wrap<typeof runClass>(worker);
   try {
     const output = asyncRunner(config)
     return output;

From cd10da814e7d8053ffa1eb60d18d3b6f2c6ecd7d Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Fri, 18 Apr 2025 15:21:31 +0200
Subject: [PATCH 18/47] Make sure initial state is included in output

---
 packages/class/src/runner.ts | 20 +++++++++++++++-----
 1 file changed, 15 insertions(+), 5 deletions(-)

diff --git a/packages/class/src/runner.ts b/packages/class/src/runner.ts
index a98583a..ec29bd9 100644
--- a/packages/class/src/runner.ts
+++ b/packages/class/src/runner.ts
@@ -89,22 +89,32 @@ export type ClassOutput = {
 
 
 export function runClass(config: Config): ClassOutput {
-  
   const validatedConfig = parse(config);
   const model = new CLASS(validatedConfig);
 
+  const writeOutput = () => {
+    for (const v of outputVariables) {
+      const value = model[v.key as keyof CLASS] ?? (v.key === "t" ? model.t : undefined);
+      if (value !== undefined) {
+        (output[v.key] as number[]).push(value as number);
+      }
+    }
+  };
+
+
   const output = Object.fromEntries(
     outputVariables.map(v => [v.key, []])
   ) as ClassOutput;
 
+  // Initial time
+  writeOutput();
+
+  // Update loop
   while (model.t < config.runtime) {
     model.update();
 
     if (model.t % 600 === 0) {
-      for (const v of outputVariables) {
-          output[v.key].push(model[v.key as keyof CLASS] as number);
-        output[v.key].push();
-      }
+      writeOutput();
     }
   }
 

From f085554c87b725590a4cf1a46f04c5fa8f6124ff Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Fri, 18 Apr 2025 15:39:18 +0200
Subject: [PATCH 19/47] Reset pan/zoom when variable changes

---
 apps/class-solid/src/components/Analysis.tsx | 23 ++++++++++++++++----
 1 file changed, 19 insertions(+), 4 deletions(-)

diff --git a/apps/class-solid/src/components/Analysis.tsx b/apps/class-solid/src/components/Analysis.tsx
index 27aad5a..35b6efb 100644
--- a/apps/class-solid/src/components/Analysis.tsx
+++ b/apps/class-solid/src/components/Analysis.tsx
@@ -158,6 +158,16 @@ export function TimeSeriesPlot({ analysis }: { analysis: TimeseriesAnalysis }) {
     setToggles(label, value);
   }
 
+  const setXVar = (v: string) => {
+    updateAnalysis(analysis, { xVariable: v });
+    setResetPlot(analysis.id);
+  };
+
+  const setYVar = (v: string) => {
+    updateAnalysis(analysis, { yVariable: v });
+    setResetPlot(analysis.id);
+  };
+
   return (
     <>
       {/* TODO: get label for yVariable from model config */}
@@ -178,13 +188,13 @@ export function TimeSeriesPlot({ analysis }: { analysis: TimeseriesAnalysis }) {
       <div class="flex justify-around">
         <Picker
           value={() => analysis.xVariable}
-          setValue={(v) => updateAnalysis(analysis, { xVariable: v })}
+          setValue={(v) => setXVar(v)}
           options={xVariableOptions}
           label="x-axis"
         />
         <Picker
           value={() => analysis.yVariable}
-          setValue={(v) => updateAnalysis(analysis, { yVariable: v })}
+          setValue={(v) => setYVar(v)}
           options={yVariableOptions}
           label="y-axis"
         />
@@ -261,6 +271,11 @@ export function VerticalProfilePlot({
     setToggles(label, value);
   }
 
+  function changeVar(v: string) {
+    updateAnalysis(analysis, { variable: v });
+    setResetPlot(analysis.id);
+  }
+
   return (
     <>
       <div class="flex flex-col gap-2">
@@ -291,7 +306,7 @@ export function VerticalProfilePlot({
         </ChartContainer>
         <Picker
           value={() => analysis.variable}
-          setValue={(v) => updateAnalysis(analysis, { variable: v })}
+          setValue={(v) => changeVar(v)}
           options={Object.keys(variableOptions)}
           label="variable: "
         />
@@ -307,7 +322,7 @@ export function VerticalProfilePlot({
 
 type PickerProps = {
   value: Accessor<string>;
-  setValue: Setter<string>;
+  setValue: (value: string) => void;
   options: string[];
   label?: string;
 };

From 202d144c333d6e4a5224c2373db89f471e15b8be Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Fri, 18 Apr 2025 15:39:30 +0200
Subject: [PATCH 20/47] formatting

---
 apps/class-solid/src/components/plots/Axes.tsx |  2 +-
 apps/class-solid/src/lib/runner.ts             |  2 +-
 packages/class/src/runner.ts                   | 13 ++++++-------
 3 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/apps/class-solid/src/components/plots/Axes.tsx b/apps/class-solid/src/components/plots/Axes.tsx
index 9131de3..76a3a25 100644
--- a/apps/class-solid/src/components/plots/Axes.tsx
+++ b/apps/class-solid/src/components/plots/Axes.tsx
@@ -100,4 +100,4 @@ export function getNiceAxisLimits(
 const generateTicks = (domain = [0, 1], tickCount = 5) => {
   const step = (domain[1] - domain[0]) / (tickCount - 1);
   return [...Array(10).keys()].map((i) => domain[0] + i * step);
-};
\ No newline at end of file
+};
diff --git a/apps/class-solid/src/lib/runner.ts b/apps/class-solid/src/lib/runner.ts
index a7b53a9..3dcf765 100644
--- a/apps/class-solid/src/lib/runner.ts
+++ b/apps/class-solid/src/lib/runner.ts
@@ -10,7 +10,7 @@ const asyncRunner = wrap<typeof runClass>(worker);
 
 export async function runClassAsync(config: Config): Promise<ClassOutput> {
   try {
-    const output = asyncRunner(config)
+    const output = asyncRunner(config);
     return output;
   } catch (error) {
     console.error({ config, error });
diff --git a/packages/class/src/runner.ts b/packages/class/src/runner.ts
index ec29bd9..e52216d 100644
--- a/packages/class/src/runner.ts
+++ b/packages/class/src/runner.ts
@@ -11,7 +11,7 @@ export interface OutputVariable {
   key: string;
   title: string;
   unit: string;
-  symbol?: string
+  symbol?: string;
 }
 
 export const outputVariables: OutputVariable[] = [
@@ -84,26 +84,25 @@ export const outputVariables: OutputVariable[] = [
 ];
 
 export type ClassOutput = {
-  [K in (typeof outputVariables)[number]['key']]: number[];
+  [K in (typeof outputVariables)[number]["key"]]: number[];
 };
 
-
 export function runClass(config: Config): ClassOutput {
   const validatedConfig = parse(config);
   const model = new CLASS(validatedConfig);
 
   const writeOutput = () => {
     for (const v of outputVariables) {
-      const value = model[v.key as keyof CLASS] ?? (v.key === "t" ? model.t : undefined);
+      const value =
+        model[v.key as keyof CLASS] ?? (v.key === "t" ? model.t : undefined);
       if (value !== undefined) {
         (output[v.key] as number[]).push(value as number);
       }
     }
   };
 
-
   const output = Object.fromEntries(
-    outputVariables.map(v => [v.key, []])
+    outputVariables.map((v) => [v.key, []]),
   ) as ClassOutput;
 
   // Initial time
@@ -119,4 +118,4 @@ export function runClass(config: Config): ClassOutput {
   }
 
   return output;
-}
\ No newline at end of file
+}

From 1e1399afc143e61ff1df8bed52c8c79d8b7b981b Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Fri, 18 Apr 2025 17:24:21 +0200
Subject: [PATCH 21/47] Use output metadata in plot labels and variable pickers

---
 apps/class-solid/src/components/Analysis.tsx  | 46 +++++++++++++------
 .../src/components/plots/ChartContainer.tsx   | 21 +++++----
 .../src/components/plots/skewTlogP.tsx        |  4 +-
 packages/class/src/runner.ts                  | 12 ++---
 4 files changed, 52 insertions(+), 31 deletions(-)

diff --git a/apps/class-solid/src/components/Analysis.tsx b/apps/class-solid/src/components/Analysis.tsx
index 35b6efb..3d15906 100644
--- a/apps/class-solid/src/components/Analysis.tsx
+++ b/apps/class-solid/src/components/Analysis.tsx
@@ -1,6 +1,6 @@
-import { BmiClass } from "@classmodel/class/bmi";
 import type { Config } from "@classmodel/class/config";
-import type { ClassOutput } from "@classmodel/class/runner";
+import { type ClassOutput, outputVariables } from "@classmodel/class/runner";
+import * as d3 from "d3";
 import { saveAs } from "file-saver";
 import { toBlob } from "html-to-image";
 import {
@@ -115,9 +115,15 @@ const uniqueTimes = () => [...new Set(_allTimes())].sort((a, b) => a - b);
 
 // TODO: could memoize all reactive elements here, would it make a difference?
 export function TimeSeriesPlot({ analysis }: { analysis: TimeseriesAnalysis }) {
-  const xVariableOptions = ["t"]; // TODO: separate plot types for timeseries and x-vs-y? Use time axis?
-  // TODO: add nice description from config as title and dropdown option for the variable picker.
-  const yVariableOptions = new BmiClass().get_output_var_names();
+  const symbols = Object.fromEntries(
+    outputVariables.map((v) => [v.key, v.symbol]),
+  );
+  const getKey = Object.fromEntries(
+    outputVariables.map((v) => [v.symbol, v.key]),
+  );
+  const labels = Object.fromEntries(
+    outputVariables.map((v) => [v.key, `${v.symbol} [${v.unit}]`]),
+  );
 
   const allX = () =>
     flatExperiments().flatMap((e) =>
@@ -158,24 +164,34 @@ export function TimeSeriesPlot({ analysis }: { analysis: TimeseriesAnalysis }) {
     setToggles(label, value);
   }
 
-  const setXVar = (v: string) => {
-    updateAnalysis(analysis, { xVariable: v });
+  const setXVar = (symbol: string) => {
+    updateAnalysis(analysis, { xVariable: getKey[symbol] });
     setResetPlot(analysis.id);
   };
 
-  const setYVar = (v: string) => {
-    updateAnalysis(analysis, { yVariable: v });
+  const setYVar = (symbol: string) => {
+    updateAnalysis(analysis, { yVariable: getKey[symbol] });
     setResetPlot(analysis.id);
   };
 
+  const formatX = () =>
+    analysis.xVariable === "t" ? formatSeconds : d3.format(".4");
+  const formatY = () =>
+    analysis.yVariable === "t" ? formatSeconds : d3.format(".4");
+
   return (
     <>
       {/* TODO: get label for yVariable from model config */}
       <ChartContainer>
         <Legend entries={chartData} toggles={toggles} onChange={toggleLine} />
-        <Chart id={analysis.id} title="Timeseries plot" formatX={formatSeconds}>
+        <Chart
+          id={analysis.id}
+          title="Timeseries plot"
+          formatX={formatX}
+          formatY={formatY}
+        >
           <AxisBottom domain={xLim} label="Time [s]" />
-          <AxisLeft domain={yLim} label={analysis.yVariable} />
+          <AxisLeft domain={yLim} label={labels[analysis.yVariable]} />
           <For each={chartData()}>
             {(d) => (
               <Show when={toggles[d.label]}>
@@ -187,15 +203,15 @@ export function TimeSeriesPlot({ analysis }: { analysis: TimeseriesAnalysis }) {
       </ChartContainer>
       <div class="flex justify-around">
         <Picker
-          value={() => analysis.xVariable}
+          value={() => symbols[analysis.xVariable]}
           setValue={(v) => setXVar(v)}
-          options={xVariableOptions}
+          options={Object.values(symbols)}
           label="x-axis"
         />
         <Picker
-          value={() => analysis.yVariable}
+          value={() => symbols[analysis.yVariable]}
           setValue={(v) => setYVar(v)}
-          options={yVariableOptions}
+          options={Object.values(symbols)}
           label="y-axis"
         />
       </div>
diff --git a/apps/class-solid/src/components/plots/ChartContainer.tsx b/apps/class-solid/src/components/plots/ChartContainer.tsx
index 3ad9ed0..ed3ddb1 100644
--- a/apps/class-solid/src/components/plots/ChartContainer.tsx
+++ b/apps/class-solid/src/components/plots/ChartContainer.tsx
@@ -118,8 +118,8 @@ export function Chart(props: {
   children: JSX.Element;
   id: string;
   title?: string;
-  formatX?: (value: number) => string;
-  formatY?: (value: number) => string;
+  formatX?: () => (value: number) => string;
+  formatY?: () => (value: number) => string;
   transformX?: (x: number, y: number, scaleY: SupportedScaleTypes) => number;
 }) {
   const [hovering, setHovering] = createSignal(false);
@@ -141,12 +141,17 @@ export function Chart(props: {
     }
   });
 
-  if (props.formatX) {
-    updateChart("formatX", () => props.formatX);
-  }
-  if (props.formatY) {
-    updateChart("formatY", () => props.formatY);
-  }
+  createEffect(() => {
+    if (props.formatX) {
+      updateChart("formatX", () => props.formatX?.());
+    }
+  });
+  createEffect(() => {
+    if (props.formatY) {
+      updateChart("formatY", () => props.formatY?.());
+    }
+  });
+
   if (props.transformX) {
     updateChart("transformX", () => props.transformX);
   }
diff --git a/apps/class-solid/src/components/plots/skewTlogP.tsx b/apps/class-solid/src/components/plots/skewTlogP.tsx
index 20a8d83..7b7eed5 100644
--- a/apps/class-solid/src/components/plots/skewTlogP.tsx
+++ b/apps/class-solid/src/components/plots/skewTlogP.tsx
@@ -190,8 +190,8 @@ export function SkewTPlot(props: {
       <Chart
         id={props.id}
         title="Thermodynamic diagram"
-        formatX={d3.format(".0d")}
-        formatY={d3.format(".0d")}
+        formatX={() => d3.format(".0d")}
+        formatY={() => d3.format(".0d")}
         transformX={getTempAtCursor}
       >
         <AxisBottom
diff --git a/packages/class/src/runner.ts b/packages/class/src/runner.ts
index e52216d..d075e7b 100644
--- a/packages/class/src/runner.ts
+++ b/packages/class/src/runner.ts
@@ -11,7 +11,7 @@ export interface OutputVariable {
   key: string;
   title: string;
   unit: string;
-  symbol?: string;
+  symbol: string;
 }
 
 export const outputVariables: OutputVariable[] = [
@@ -55,31 +55,31 @@ export const outputVariables: OutputVariable[] = [
     key: "dthetav",
     title: "Virtual temperature jump at h",
     unit: "K",
-    symbol: "Δθ<sub>v</sub>",
+    symbol: "Δθᵥ",
   },
   {
     key: "we",
     title: "Entrainment velocity",
     unit: "m s⁻¹",
-    symbol: "w<sub>e</sub>",
+    symbol: "wₑ",
   },
   {
     key: "ws",
     title: "Large-scale vertical velocity",
     unit: "m s⁻¹",
-    symbol: "w<sub>s</sub>",
+    symbol: "wₛ",
   },
   {
     key: "wthetave",
     title: "Entrainment virtual heat flux",
     unit: "K m s⁻¹",
-    symbol: "(w'θ')<sub>ve</sub>",
+    symbol: "(w'θ')ᵥₑ",
   },
   {
     key: "wthetav",
     title: "Surface virtual heat flux",
     unit: "K m s⁻¹",
-    symbol: "(w'θ')<sub>vs</sub>",
+    symbol: "(w'θ')ᵥ",
   },
 ];
 

From eeb62df1ad63768675a300fb191f95bb5c8cc539 Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Fri, 18 Apr 2025 17:32:52 +0200
Subject: [PATCH 22/47] ditch BMI

---
 README.md                      |   4 +-
 packages/class/package.json    |   6 --
 packages/class/src/bmi.test.ts |  19 ----
 packages/class/src/bmi.ts      | 162 ---------------------------------
 4 files changed, 1 insertion(+), 190 deletions(-)
 delete mode 100644 packages/class/src/bmi.test.ts
 delete mode 100644 packages/class/src/bmi.ts

diff --git a/README.md b/README.md
index c0184d4..27fc3eb 100644
--- a/README.md
+++ b/README.md
@@ -117,10 +117,8 @@ by [Kobalte](https://kobalte.dev/docs/core/overview/introduction) and
 application and tweaked further as seen fit. It can also do charts, using
 [chart.js](https://www.chartjs.org/), though we might deviate from that later.
 
-To expose the model in a standard way we use the [Basic Model Interface (BMI)](https://bmi.readthedocs.io/).
-
 To prevent the user interface from getting blocked by running the model we use a [Web worker](https://developer.mozilla.org/en-US/docs/Web/API/Worker) to run the computation in a background task/thread.
-A Web worker uses messages passing to communicate, this does not fit with the Basic Model Interface so we use [comlink](https://github.com/GoogleChromeLabs/comlink) to wrap the Web Worker in a BMI class.
+We use [comlink](https://github.com/GoogleChromeLabs/comlink) to wrap the Web Worker so it behaves the same as if the runner was used directly inside the main thread.
 
 To format and lint the code, we use [biome](https://biomejs.dev/) as it combines eslint, prettier in one package.
 
diff --git a/packages/class/package.json b/packages/class/package.json
index c2e756a..4f3c14c 100644
--- a/packages/class/package.json
+++ b/packages/class/package.json
@@ -36,12 +36,6 @@
         "types": "./dist/runner.d.ts"
       }
     },
-    "./bmi": {
-      "import": {
-        "default": "./dist/bmi.js",
-        "types": "./dist/bmi.d.ts"
-      }
-    },
     "./validate": {
       "import": {
         "default": "./dist/validate.js",
diff --git a/packages/class/src/bmi.test.ts b/packages/class/src/bmi.test.ts
deleted file mode 100644
index c108f60..0000000
--- a/packages/class/src/bmi.test.ts
+++ /dev/null
@@ -1,19 +0,0 @@
-import assert from "node:assert/strict";
-import { before, describe, test } from "node:test";
-import { BmiClass } from "./bmi.js";
-
-describe("BmiClass", () => {
-  let bmi: BmiClass;
-  before(() => {
-    bmi = new BmiClass();
-  });
-
-  describe("get_component_name", () => {
-    test("returns the component name", () => {
-      assert.strictEqual(
-        bmi.get_component_name(),
-        "Chemistry Land-surface Atmosphere Soil Slab model",
-      );
-    });
-  });
-});
diff --git a/packages/class/src/bmi.ts b/packages/class/src/bmi.ts
deleted file mode 100644
index 0c29ee6..0000000
--- a/packages/class/src/bmi.ts
+++ /dev/null
@@ -1,162 +0,0 @@
-/**
- * This module contains the Basic Modelling Interface class.
- * @module
- */
-import { CLASS } from "./class.js";
-import type { Config } from "./config.js";
-import { parse } from "./validate.js";
-
-/**
- * A lightweight [Basic Modelling Interface (BMI)](https://bmi.readthedocs.io) like interface for the CLASS model.
- *
- * Inspiration https://github.com/uihilab/BMI-JS/blob/main/bmijs/bmi.js
- *
- * Deviations from the BMI standard
- * - accessors do not use dest argument
- * - initialize() accepts object instead of string
- * - parameters() returns default config
- * - run() as extra method
- */
-interface BmiLight<Config> {
-  initialize(config: Config): void;
-  update(): void;
-  get_component_name(): string;
-  get_output_item_count(): number;
-  get_output_var_names(): string[];
-  get_var_grid(name: string): number;
-  get_var_type(name: string): string;
-  get_var_location(name: string): string;
-  get_current_time(): number;
-  get_end_time(): number;
-  get_time_units(): string;
-  get_time_step(): number;
-  get_value(name: string): number[];
-  get_grid_type(): string;
-}
-
-const ouput_var_names: string[] = [
-  "h",
-  "theta",
-  "dtheta",
-  "q",
-  "dq",
-  "dthetav",
-  "we",
-  "ws",
-  "wthetave",
-  "wthetav",
-] as const;
-
-/**
- * Class representing a BMI (Basic Model Interface) implementation for the CLASS model.
- * This class provides methods to initialize, update, and retrieve information from the model.
- */
-export class BmiClass implements BmiLight<Config> {
-  config: Config = parse({});
-  model: CLASS = new CLASS(this.config);
-
-  // Model control functions
-
-  initialize(config: Config) {
-    this.config = config;
-    this.model = new CLASS(config);
-  }
-
-  update() {
-    this.model.update();
-  }
-
-  // Model information functions
-
-  get_component_name() {
-    return "Chemistry Land-surface Atmosphere Soil Slab model";
-  }
-
-  get_output_item_count() {
-    return ouput_var_names.length;
-  }
-
-  get_output_var_names() {
-    return ouput_var_names;
-  }
-
-  // Variable information functions
-
-  get_var_grid(name: string) {
-    return 1;
-  }
-
-  get_var_type(name: string) {
-    return "float";
-  }
-
-  get_var_location(name: string) {
-    return "node";
-  }
-
-  // Time functions
-  get_current_time() {
-    return this.model.t;
-  }
-
-  get_end_time() {
-    return this.config.runtime;
-  }
-
-  get_time_units() {
-    return "s";
-  }
-
-  get_time_step() {
-    return this.config.dt;
-  }
-
-  // Variable getter and setter functions
-
-  get_value(name: string) {
-    if (ouput_var_names.includes(name)) {
-      return [this.model[name as keyof CLASS]] as [number];
-    }
-    throw new Error(`Variable ${name} not found`);
-  }
-
-  // Model grid functions
-
-  get_grid_type() {
-    return "scalar";
-  }
-
-  // Extra methods
-
-  /**
-   * Runs the model till the end and returns the output data.
-   *
-   * @param options - The options for running the model.
-   * @param options.freq - The frequency at which to record the output data. Default is 60 seconds.
-   * @param options.var_names - For which output variables to record the data. Default is all output variables.
-   * @returns The output data, including the time values in t key and the values of the output variables.
-   */
-  run<T extends string[]>({
-    freq = 600,
-    var_names = ouput_var_names as T,
-  }: {
-    freq?: number;
-    var_names?: T;
-  }): { t: number[] } & { [K in T[number]]: number[] } {
-    const output: { t: number[] } & { [K in T[number]]: number[] } =
-      Object.fromEntries([["t", []], ...var_names.map((name) => [name, []])]);
-    while (this.model.t <= this.config.runtime) {
-      if (this.model.t % freq === 0) {
-        output.t.push(this.model.t);
-        for (const name of var_names) {
-          const value = this.model[name as keyof CLASS] as number;
-          output[name as T[number]].push(value);
-        }
-        // TODO progress callback?
-        // Initial attempt failed with "could not be cloned" error
-      }
-      this.update();
-    }
-    return output;
-  }
-}

From 8e9dddfd687b32959785c8514efc5f099725339a Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Tue, 22 Apr 2025 10:13:52 +0200
Subject: [PATCH 23/47] Fix xlabel in timeseries plot; fix axes extent for
 non-time on x-axis

---
 apps/class-solid/src/components/Analysis.tsx | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/apps/class-solid/src/components/Analysis.tsx b/apps/class-solid/src/components/Analysis.tsx
index 3d15906..c3a3309 100644
--- a/apps/class-solid/src/components/Analysis.tsx
+++ b/apps/class-solid/src/components/Analysis.tsx
@@ -134,7 +134,8 @@ export function TimeSeriesPlot({ analysis }: { analysis: TimeseriesAnalysis }) {
       e.output ? e.output[analysis.yVariable] : [],
     );
 
-  const xLim = () => getNiceAxisLimits(allX(), 0, 600);
+  const granularity = () => (analysis.xVariable === "t" ? 600 : undefined);
+  const xLim = () => getNiceAxisLimits(allX(), 0, granularity());
   const yLim = () => getNiceAxisLimits(allY());
 
   const chartData = () =>
@@ -190,7 +191,7 @@ export function TimeSeriesPlot({ analysis }: { analysis: TimeseriesAnalysis }) {
           formatX={formatX}
           formatY={formatY}
         >
-          <AxisBottom domain={xLim} label="Time [s]" />
+          <AxisBottom domain={xLim} label={labels[analysis.xVariable]} />
           <AxisLeft domain={yLim} label={labels[analysis.yVariable]} />
           <For each={chartData()}>
             {(d) => (

From 638ccfc7312e46028e6d0fdeb8d55615e63bd5db Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Tue, 22 Apr 2025 10:40:24 +0200
Subject: [PATCH 24/47] Remove config.JSON everywhere; only keep the embedded
 version

---
 apps/class-solid/README.md         |   2 +-
 packages/class/README.md           |  12 +-
 packages/class/package.json        |  11 +-
 packages/class/scripts/json2ts.mjs | 135 ----------------------
 packages/class/src/config.json     | 179 -----------------------------
 packages/class/src/config.ts       |  63 +++++-----
 6 files changed, 35 insertions(+), 367 deletions(-)
 delete mode 100644 packages/class/scripts/json2ts.mjs
 delete mode 100644 packages/class/src/config.json

diff --git a/apps/class-solid/README.md b/apps/class-solid/README.md
index ae888fa..c834443 100644
--- a/apps/class-solid/README.md
+++ b/apps/class-solid/README.md
@@ -54,7 +54,7 @@ This allows you to trigger tests from the [playwright ui](https://playwright.dev
 An experiment can get started from a preset.
 
 The presets are stored in the `src/lib/presets/` directory.
-The format is JSON with content adhering to the [JSON schema](https://github.com/classmodel/class-web/blob/main/packages/class/src/config.json).
+The format is JSON with content adhering to the [JSON schema](https://github.com/classmodel/class-web/blob/main/packages/class/src/config.ts).
 
 The `src/lib/presets.ts` is used as an index of presets.
 If you add a preset the `src/lib/presets.ts` file needs to be updated.
diff --git a/packages/class/README.md b/packages/class/README.md
index 2c33ce4..7950a56 100644
--- a/packages/class/README.md
+++ b/packages/class/README.md
@@ -70,20 +70,10 @@ This package is part of a [monorepo](https://github.com/classmodel/class-web) wi
 
 ### JSON schema
 
-The Class model uses a JSON schema to validate the input configuration. The schema is defined in the `@classmodel/class` package and can be found at [src/config.json](https://github.com/classmodel/class-web/blob/main/packages/class/src/config.json) (in [repo](./src/config.json)). The schema is used to validate the input configuration and to generate a form to input the configuration.
+The Class model uses a JSON schema to validate the input configuration. The schema is defined in the `@classmodel/class` package and can be found at [src/config.ts](https://github.com/classmodel/class-web/blob/main/packages/class/src/config.ts) (in [repo](./src/config.ts)). The schema is used to validate the input configuration and to generate a form to input the configuration.
 
 The `src/config.ts` file contains the embedded JSON schema and its Typescript type definition.
 
-<!-- When runnning `pnpm dev` or `pnpm build` the `src/config.ts` file is generated from the `src/config.json` file.
-
-To manually generate the `src/config.ts` file run the following command:
-
-```shell
-pnpm json2ts
-``` -->
-
-At the moment you manually have to keep the `src/config.ts` file in sync with the `src/config.json` file. By copying the content over and updating the TypeScript Config type.
-
 See the [form package](../form/README.md#json-schema) for additional keywords in the JSON schema.
 
 #### Conditional properties
diff --git a/packages/class/package.json b/packages/class/package.json
index 4f3c14c..4168f07 100644
--- a/packages/class/package.json
+++ b/packages/class/package.json
@@ -23,7 +23,6 @@
         "types": "./dist/config.d.ts"
       }
     },
-    "./config.json": "./dist/config.json",
     "./config_utils": {
       "import": {
         "default": "./dist/config_utils.js",
@@ -54,23 +53,17 @@
   "files": ["dist"],
   "license": "GPL-3.0-only",
   "scripts": {
-    "dev": "concurrently -n \"tsc,json2ts\" -c \"blue,green\" \"pnpm dev:tsc\" \"pnpm json2ts --watch\"",
-    "dev:tsc": "tsc --watch",
-    "build:tsc": "tsc",
-    "build:config": "cp src/config.json dist/config.json",
-    "build": "pnpm json2ts && pnpm build:tsc && pnpm build:config",
+    "dev": "tsc --watch",
+    "build": "tsc",
     "prepack": "pnpm build",
     "test": "tsx --test src/*.test.ts",
     "typecheck": "tsc --noEmit",
-    "json2ts": "node scripts/json2ts.mjs",
     "docs": "typedoc",
     "clean": "rm -rf dist"
   },
   "bin": "./dist/cli.js",
   "devDependencies": {
     "@types/node": "^20.13.1",
-    "concurrently": "^9.0.1",
-    "json-schema-to-typescript": "^15.0.2",
     "tsx": "^4.16.5",
     "typedoc": "^0.26.10",
     "typescript": "^5.3.3"
diff --git a/packages/class/scripts/json2ts.mjs b/packages/class/scripts/json2ts.mjs
deleted file mode 100644
index 4ce7482..0000000
--- a/packages/class/scripts/json2ts.mjs
+++ /dev/null
@@ -1,135 +0,0 @@
-/**
- * Convert JSON schema file to TypeScript file with embedded JSON schema and type definition.
- *
- * Some Javascript runtimes cannot import JSON files as ES module, so embedding the JSON schema is a workaround.
- */
-import { exec as cbExec } from "node:child_process";
-import { watch } from "node:fs";
-import { readFile, writeFile } from "node:fs/promises";
-import { basename, extname, join } from "node:path";
-import { promisify } from "node:util";
-
-import { Command } from "@commander-js/extra-typings";
-import { compileFromFile } from "json-schema-to-typescript";
-
-async function format(schemaTsPath) {
-  // Format the generated TypeScript file
-  // Expect this script to be run from packages/class
-  const exec = promisify(cbExec);
-  const biomeHome = join(process.cwd(), "../..");
-  const { stdout, stderr } = await exec(
-    `pnpm biome format --write packages/class/${schemaTsPath}`,
-    {
-      cwd: biomeHome,
-    },
-  );
-  console.log(stdout);
-  console.error(stderr);
-}
-
-async function readJsonSchema(jsonSchemaPath) {
-  const jsonSchema = await readFile(jsonSchemaPath, "utf-8");
-  const trimmedJsonSchema = jsonSchema.trim();
-  return trimmedJsonSchema;
-}
-
-function prefixOfJsonSchema(jsonSchemaPath) {
-  const fn = basename(jsonSchemaPath, extname(jsonSchemaPath));
-  // json-schema-to-typescript generates type names with base of filename with the first letter capitalized
-  const prefix = fn.charAt(0).toUpperCase() + fn.slice(1);
-  return prefix;
-}
-
-/**
- *
- * @param {string} jsonSchemaPath
- * @param {string} schemaTsPath
- */
-async function json2ts(jsonSchemaPath, schemaTsPath) {
-  // Geneerate TypeScript type definition from JSON schema
-  const tsOfJsonSchema = await compileFromFile(jsonSchemaPath, {
-    format: false,
-    bannerComment: "",
-  });
-
-  // Modular forms does not like interface definitions
-  // See https://github.com/fabian-hiller/modular-forms/issues/2
-  // and https://github.com/bcherny/json-schema-to-typescript/issues/307
-  // So, replace interface with type
-  // for example "interface Foo {" becomes "type Foo = {"
-  const tsOfJsonSchemaTypesOnly = tsOfJsonSchema.replaceAll(
-    /interface\s+(\w+) {/g,
-    "type $1 = {",
-  );
-
-  const prefix = prefixOfJsonSchema(jsonSchemaPath);
-
-  // Read JSON schema file
-  const trimmedJsonSchema = await readJsonSchema(jsonSchemaPath);
-
-  // Combine types and JSON schema into a single TypeScript file
-  const body = `\
-/**
- * This file was automatically generated by "../scripts/json2ts.mjs" script.
- * DO NOT MODIFY IT BY HAND. Instead, modify the JSON schema file "${jsonSchemaPath}",
- * and run "pnpm json2ts" to regenerate this file.
- */  
-import type { JSONSchemaType } from "ajv/dist/2019.js";
-${tsOfJsonSchemaTypesOnly}
-export type JsonSchemaOf${prefix} = JSONSchemaType<${prefix}>;
-/**
- * JSON schema of ${jsonSchemaPath} embedded in a TypeScript file.
- */
-export const jsonSchemaOf${prefix} = ${trimmedJsonSchema} as unknown as JsonSchemaOf${prefix};
-`;
-  await writeFile(schemaTsPath, body, { flag: "w" });
-
-  await format(schemaTsPath);
-}
-
-function watchJsonSchema(jsonSchemaPath, schemaTsPath) {
-  console.log(`Watching ${jsonSchemaPath} for changes`);
-  watch(jsonSchemaPath, (event) => {
-    if (event !== "change") {
-      return;
-    }
-    console.log(
-      `File ${jsonSchemaPath} has been changed, regenerating ${schemaTsPath}`,
-    );
-    json2ts(jsonSchemaPath, schemaTsPath).catch((err) => {
-      console.error(err);
-    });
-  });
-}
-
-function main() {
-  const program = new Command()
-    .name("json2ts")
-    .description(
-      "Convert JSON schema file to TypeScript file with embedded JSON schema and type definition",
-    )
-    .option(
-      "-i, --input <jsonSchemaPath>",
-      "JSON schema file",
-      "src/config.json",
-    )
-    .option("-o, --output <schemaTsPath>", "Output file path", "src/config.ts")
-    .option("--watch", "Watch mode")
-    .parse();
-  const options = program.opts();
-  const jsonSchemaPath = options.input;
-  const schemaTsPath = options.output;
-
-  if (options.watch) {
-    watchJsonSchema(jsonSchemaPath, schemaTsPath);
-  } else {
-    console.log(`Generating ${schemaTsPath} from ${jsonSchemaPath}`);
-    json2ts(jsonSchemaPath, schemaTsPath).catch((err) => {
-      console.error(err);
-      process.exit(1);
-    });
-  }
-}
-
-// TODO disabled as json-schema-to-typescript can not handle if/then/else
-// main();
diff --git a/packages/class/src/config.json b/packages/class/src/config.json
deleted file mode 100644
index d771abe..0000000
--- a/packages/class/src/config.json
+++ /dev/null
@@ -1,179 +0,0 @@
-{
-  "$schema": "https://json-schema.org/draft/2020-12/schema",
-  "type": "object",
-  "properties": {
-    "name": {
-      "type": "string",
-      "title": "Name",
-      "default": ""
-    },
-    "description": {
-      "type": "string",
-      "title": "Description",
-      "default": "",
-      "ui:widget": "textarea"
-    },
-    "dt": {
-      "type": "integer",
-      "unit": "s",
-      "minimum": 1,
-      "default": 60,
-      "title": "Time step",
-      "ui:group": "Time Control"
-    },
-    "runtime": {
-      "type": "integer",
-      "unit": "s",
-      "minimum": 1,
-      "title": "Total run time",
-      "default": 43200,
-      "ui:group": "Time Control"
-    },
-    "sw_ml": {
-      "type": "boolean",
-      "ui:group": "Mixed layer",
-      "title": "Mixed-layer switch",
-      "default": true
-    }
-  },
-  "required": ["name", "dt", "runtime"],
-  "allOf": [
-    {
-      "if": {
-        "properties": {
-          "sw_ml": {
-            "const": true
-          }
-        }
-      },
-      "then": {
-        "properties": {
-          "h_0": {
-            "symbol": "h",
-            "type": "number",
-            "title": "ABL height",
-            "unit": "m",
-            "default": 200,
-            "ui:group": "Mixed layer"
-          },
-          "theta_0": {
-            "symbol": "θ",
-            "type": "number",
-            "ui:group": "Mixed layer",
-            "title": "Potential temperature",
-            "minimum": 1,
-            "default": 288,
-            "description": "The potential temperature of the mixed layer at the initial time.",
-            "unit": "K"
-          },
-          "dtheta_0": {
-            "symbol": "Δθ",
-            "type": "number",
-            "title": "Temperature jump at h",
-            "ui:group": "Mixed layer",
-            "default": 1,
-            "unit": "K"
-          },
-          "q_0": {
-            "symbol": "q",
-            "type": "number",
-            "ui:group": "Mixed layer",
-            "unit": "kg kg-1",
-            "default": 0.008,
-            "title": "Mixed-layer specific humidity"
-          },
-          "dq_0": {
-            "symbol": "Δq",
-            "type": "number",
-            "description": "Specific humidity jump at h",
-            "unit": "kg kg-1",
-            "default": -0.001,
-            "ui:group": "Mixed layer"
-          },
-          "wtheta": {
-            "symbol": "(w'θ')ₛ",
-            "type": "array",
-            "items": {
-              "type": "number"
-            },
-            "ui:group": "Mixed layer",
-            "unit": "K m s-1",
-            "title": "Surface kinematic heat flux",
-            "default": [0.1],
-            "minItems": 1
-          },
-          "advtheta": {
-            "symbol": "adv(θ)",
-            "type": "number",
-            "ui:group": "Mixed layer",
-            "unit": "K s-1",
-            "default": 0,
-            "title": "Advection of heat"
-          },
-          "gammatheta": {
-            "symbol": "γ<sub>θ</sub>",
-            "type": "number",
-            "ui:group": "Mixed layer",
-            "unit": "K m-1",
-            "default": 0.006,
-            "title": "Free atmosphere potential temperature lapse rate"
-          },
-          "wq": {
-            "symbol": "(w'q')ₛ",
-            "type": "number",
-            "ui:group": "Mixed layer",
-            "unit": "kg kg-1 m s-1",
-            "default": 0.0001,
-            "title": "Surface kinematic moisture flux"
-          },
-          "advq": {
-            "symbol": "adv(q)",
-            "type": "number",
-            "ui:group": "Mixed layer",
-            "unit": "kg kg-1 s-1",
-            "default": 0,
-            "title": "Advection of moisture"
-          },
-          "gammaq": {
-            "symbol": "γ<sub>q</sub>",
-            "type": "number",
-            "ui:group": "Mixed layer",
-            "unit": "kg kg-1 m-1",
-            "default": 0,
-            "title": "Free atmosphere specific humidity lapse rate"
-          },
-          "divU": {
-            "symbol": "div(Uₕ)",
-            "type": "number",
-            "ui:group": "Mixed layer",
-            "default": 0,
-            "unit": "s-1",
-            "title": "Horizontal large-scale divergence of wind"
-          },
-          "beta": {
-            "symbol": "β",
-            "type": "number",
-            "ui:group": "Mixed layer",
-            "default": 0.2,
-            "title": "Entrainment ratio for virtual heat"
-          }
-        },
-        "required": [
-          "h_0",
-          "theta_0",
-          "dtheta_0",
-          "q_0",
-          "dq_0",
-          "wtheta",
-          "advtheta",
-          "gammatheta",
-          "wq",
-          "advq",
-          "gammaq",
-          "divU",
-          "beta"
-        ]
-      }
-    }
-  ]
-}
diff --git a/packages/class/src/config.ts b/packages/class/src/config.ts
index 1046b54..e3a04d4 100644
--- a/packages/class/src/config.ts
+++ b/packages/class/src/config.ts
@@ -1,34 +1,5 @@
 import type { JSONSchemaType } from "ajv/dist/2020.js";
 
-// TODO generate this from ./config.schema.json
-// at the momemt json-schema-to-typescript does not understand if/then/else
-// and cannot generate such minimalistic types
-export type Config = {
-  name: string;
-  description?: string;
-  dt: number;
-  runtime: number;
-} & ( // Mixed layer
-  | {
-      sw_ml: true;
-      h_0: number;
-      theta_0: number;
-      dtheta_0: number;
-      q_0: number;
-      dq_0: number;
-      wtheta: number[];
-      advtheta: number;
-      gammatheta: number;
-      wq: number;
-      advq: number;
-      gammaq: number;
-      divU: number;
-      beta: number;
-    }
-  // Else, sw_ml key should be absent or false
-  | { sw_ml?: false }
-);
-
 /*
 Notes for JSON schema
 put here because JSON does not support comments
@@ -41,9 +12,7 @@ put here because JSON does not support comments
 TODO move notes to documentation/issues
 */
 
-export type JsonSchemaOfConfig = JSONSchemaType<Config>;
-
-// TODO unable to use import with assert in app, so made copy of ./config.json here
+// Unable to use import with assert in app, so embedded JSON schema here instead
 const untypedSchema = {
   $schema: "https://json-schema.org/draft/2020-12/schema",
   type: "object",
@@ -227,5 +196,35 @@ const untypedSchema = {
   ],
 };
 
+// TODO generate this from ./config.schema.json
+// at the momemt json-schema-to-typescript does not understand if/then/else
+// and cannot generate such minimalistic types
+export type Config = {
+  name: string;
+  description?: string;
+  dt: number;
+  runtime: number;
+} & ( // Mixed layer
+  | {
+      sw_ml: true;
+      h_0: number;
+      theta_0: number;
+      dtheta_0: number;
+      q_0: number;
+      dq_0: number;
+      wtheta: number[];
+      advtheta: number;
+      gammatheta: number;
+      wq: number;
+      advq: number;
+      gammaq: number;
+      divU: number;
+      beta: number;
+    }
+  // Else, sw_ml key should be absent or false
+  | { sw_ml?: false }
+);
+
+export type JsonSchemaOfConfig = JSONSchemaType<Config>;
 export const jsonSchemaOfConfig =
   untypedSchema as unknown as JsonSchemaOfConfig;

From 5faf60c1da3ab58882ea9345fe1f7d4b7388c697 Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Tue, 22 Apr 2025 10:45:30 +0200
Subject: [PATCH 25/47] Change units to use superscript

---
 packages/class/src/config.ts | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/packages/class/src/config.ts b/packages/class/src/config.ts
index e3a04d4..209d941 100644
--- a/packages/class/src/config.ts
+++ b/packages/class/src/config.ts
@@ -96,7 +96,7 @@ const untypedSchema = {
             symbol: "q",
             type: "number",
             "ui:group": "Mixed layer",
-            unit: "kg kg-1",
+            unit: "kg kg⁻¹",
             default: 0.008,
             title: "Mixed-layer specific humidity",
           },
@@ -104,7 +104,7 @@ const untypedSchema = {
             symbol: "Δq",
             type: "number",
             description: "Specific humidity jump at h",
-            unit: "kg kg-1",
+            unit: "kg kg⁻¹",
             default: -0.001,
             "ui:group": "Mixed layer",
           },
@@ -115,7 +115,7 @@ const untypedSchema = {
               type: "number",
             },
             "ui:group": "Mixed layer",
-            unit: "K m s-1",
+            unit: "K m s⁻¹",
             title: "Surface kinematic heat flux",
             default: [0.1],
             minItems: 1,
@@ -124,7 +124,7 @@ const untypedSchema = {
             symbol: "adv(θ)", // _adv not possible in unicode
             type: "number",
             "ui:group": "Mixed layer",
-            unit: "K s-1",
+            unit: "K s⁻¹",
             default: 0,
             title: "Advection of heat",
           },
@@ -132,7 +132,7 @@ const untypedSchema = {
             symbol: "γ<sub>θ</sub>",
             type: "number",
             "ui:group": "Mixed layer",
-            unit: "K m-1",
+            unit: "K m⁻¹",
             default: 0.006,
             title: "Free atmosphere potential temperature lapse rate",
           },
@@ -140,7 +140,7 @@ const untypedSchema = {
             symbol: "(w'q')ₛ",
             type: "number",
             "ui:group": "Mixed layer",
-            unit: "kg kg-1 m s-1",
+            unit: "kg kg⁻¹ m s⁻¹",
             default: 0.0001,
             title: "Surface kinematic moisture flux",
           },
@@ -148,7 +148,7 @@ const untypedSchema = {
             symbol: "adv(q)", // _adv not possible in unicode
             type: "number",
             "ui:group": "Mixed layer",
-            unit: "kg kg-1 s-1",
+            unit: "kg kg⁻¹ s⁻¹",
             default: 0,
             title: "Advection of moisture",
           },
@@ -156,7 +156,7 @@ const untypedSchema = {
             symbol: "γ<sub>q</sub>",
             type: "number",
             "ui:group": "Mixed layer",
-            unit: "kg kg-1 m-1",
+            unit: "kg kg⁻¹ m⁻¹",
             default: 0,
             title: "Free atmosphere specific humidity lapse rate",
           },
@@ -165,7 +165,7 @@ const untypedSchema = {
             type: "number",
             "ui:group": "Mixed layer",
             default: 0,
-            unit: "s-1",
+            unit: "s⁻¹",
             title: "Horizontal large-scale divergence of wind",
           },
           beta: {

From f48fec059af9c0417cfe9827dcfc99d32f026b96 Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Tue, 22 Apr 2025 11:18:46 +0200
Subject: [PATCH 26/47] Drop _0 for initial fields

---
 .../src/lib/presets/death-valley.json         |  10 +-
 apps/class-solid/tests/big-app-state.json     | 110 +++++++++---------
 packages/class/src/class.test.ts              |   2 +-
 packages/class/src/class.ts                   |  10 +-
 packages/class/src/config.ts                  |  30 ++---
 packages/class/src/validate.test.ts           |  24 ++--
 6 files changed, 93 insertions(+), 93 deletions(-)

diff --git a/apps/class-solid/src/lib/presets/death-valley.json b/apps/class-solid/src/lib/presets/death-valley.json
index 17f3f85..4ab4efb 100644
--- a/apps/class-solid/src/lib/presets/death-valley.json
+++ b/apps/class-solid/src/lib/presets/death-valley.json
@@ -1,11 +1,11 @@
 {
   "name": "Death Valley",
   "description": "Preset with Death Valley conditions",
-  "theta_0": 323,
-  "h_0": 200,
-  "dtheta_0": 1,
-  "q_0": 0.008,
-  "dq_0": -0.001,
+  "theta": 323,
+  "h": 200,
+  "dtheta": 1,
+  "q": 0.008,
+  "dq": -0.001,
   "dt": 60,
   "runtime": 43200,
   "wtheta": [0.1],
diff --git a/apps/class-solid/tests/big-app-state.json b/apps/class-solid/tests/big-app-state.json
index b06ff28..0d3bd4c 100644
--- a/apps/class-solid/tests/big-app-state.json
+++ b/apps/class-solid/tests/big-app-state.json
@@ -3,11 +3,11 @@
   "description": "",
   "reference": {
     "initialState": {
-      "h_0": 200,
-      "theta_0": 288,
-      "dtheta_0": 1,
-      "q_0": 0.008,
-      "dq_0": -0.001
+      "h": 200,
+      "theta": 288,
+      "dtheta": 1,
+      "q": 0.008,
+      "dq": -0.001
     },
     "timeControl": {
       "dt": 60,
@@ -26,10 +26,10 @@
   },
   "permutations": [
     {
-      "name": "h_0=100, beta=0.1",
+      "name": "h=100, beta=0.1",
       "config": {
         "initialState": {
-          "h_0": 100
+          "h": 100
         },
         "mixedLayer": {
           "beta": 0.1
@@ -37,10 +37,10 @@
       }
     },
     {
-      "name": "h_0=100, beta=0.3",
+      "name": "h=100, beta=0.3",
       "config": {
         "initialState": {
-          "h_0": 100
+          "h": 100
         },
         "mixedLayer": {
           "beta": 0.3
@@ -48,10 +48,10 @@
       }
     },
     {
-      "name": "h_0=100, beta=0.4",
+      "name": "h=100, beta=0.4",
       "config": {
         "initialState": {
-          "h_0": 100
+          "h": 100
         },
         "mixedLayer": {
           "beta": 0.4
@@ -59,10 +59,10 @@
       }
     },
     {
-      "name": "h_0=100, beta=0.5",
+      "name": "h=100, beta=0.5",
       "config": {
         "initialState": {
-          "h_0": 100
+          "h": 100
         },
         "mixedLayer": {
           "beta": 0.5
@@ -70,10 +70,10 @@
       }
     },
     {
-      "name": "h_0=100, beta=0.6",
+      "name": "h=100, beta=0.6",
       "config": {
         "initialState": {
-          "h_0": 100
+          "h": 100
         },
         "mixedLayer": {
           "beta": 0.6
@@ -81,10 +81,10 @@
       }
     },
     {
-      "name": "h_0=300, beta=0.1",
+      "name": "h=300, beta=0.1",
       "config": {
         "initialState": {
-          "h_0": 300
+          "h": 300
         },
         "mixedLayer": {
           "beta": 0.1
@@ -92,10 +92,10 @@
       }
     },
     {
-      "name": "h_0=300, beta=0.3",
+      "name": "h=300, beta=0.3",
       "config": {
         "initialState": {
-          "h_0": 300
+          "h": 300
         },
         "mixedLayer": {
           "beta": 0.3
@@ -103,10 +103,10 @@
       }
     },
     {
-      "name": "h_0=300, beta=0.4",
+      "name": "h=300, beta=0.4",
       "config": {
         "initialState": {
-          "h_0": 300
+          "h": 300
         },
         "mixedLayer": {
           "beta": 0.4
@@ -114,10 +114,10 @@
       }
     },
     {
-      "name": "h_0=300, beta=0.5",
+      "name": "h=300, beta=0.5",
       "config": {
         "initialState": {
-          "h_0": 300
+          "h": 300
         },
         "mixedLayer": {
           "beta": 0.5
@@ -125,10 +125,10 @@
       }
     },
     {
-      "name": "h_0=300, beta=0.6",
+      "name": "h=300, beta=0.6",
       "config": {
         "initialState": {
-          "h_0": 300
+          "h": 300
         },
         "mixedLayer": {
           "beta": 0.6
@@ -136,10 +136,10 @@
       }
     },
     {
-      "name": "h_0=400, beta=0.1",
+      "name": "h=400, beta=0.1",
       "config": {
         "initialState": {
-          "h_0": 400
+          "h": 400
         },
         "mixedLayer": {
           "beta": 0.1
@@ -147,10 +147,10 @@
       }
     },
     {
-      "name": "h_0=400, beta=0.3",
+      "name": "h=400, beta=0.3",
       "config": {
         "initialState": {
-          "h_0": 400
+          "h": 400
         },
         "mixedLayer": {
           "beta": 0.3
@@ -158,10 +158,10 @@
       }
     },
     {
-      "name": "h_0=400, beta=0.4",
+      "name": "h=400, beta=0.4",
       "config": {
         "initialState": {
-          "h_0": 400
+          "h": 400
         },
         "mixedLayer": {
           "beta": 0.4
@@ -169,10 +169,10 @@
       }
     },
     {
-      "name": "h_0=400, beta=0.5",
+      "name": "h=400, beta=0.5",
       "config": {
         "initialState": {
-          "h_0": 400
+          "h": 400
         },
         "mixedLayer": {
           "beta": 0.5
@@ -180,10 +180,10 @@
       }
     },
     {
-      "name": "h_0=400, beta=0.6",
+      "name": "h=400, beta=0.6",
       "config": {
         "initialState": {
-          "h_0": 400
+          "h": 400
         },
         "mixedLayer": {
           "beta": 0.6
@@ -191,10 +191,10 @@
       }
     },
     {
-      "name": "h_0=500, beta=0.1",
+      "name": "h=500, beta=0.1",
       "config": {
         "initialState": {
-          "h_0": 500
+          "h": 500
         },
         "mixedLayer": {
           "beta": 0.1
@@ -202,10 +202,10 @@
       }
     },
     {
-      "name": "h_0=500, beta=0.3",
+      "name": "h=500, beta=0.3",
       "config": {
         "initialState": {
-          "h_0": 500
+          "h": 500
         },
         "mixedLayer": {
           "beta": 0.3
@@ -213,10 +213,10 @@
       }
     },
     {
-      "name": "h_0=500, beta=0.4",
+      "name": "h=500, beta=0.4",
       "config": {
         "initialState": {
-          "h_0": 500
+          "h": 500
         },
         "mixedLayer": {
           "beta": 0.4
@@ -224,10 +224,10 @@
       }
     },
     {
-      "name": "h_0=500, beta=0.5",
+      "name": "h=500, beta=0.5",
       "config": {
         "initialState": {
-          "h_0": 500
+          "h": 500
         },
         "mixedLayer": {
           "beta": 0.5
@@ -235,10 +235,10 @@
       }
     },
     {
-      "name": "h_0=500, beta=0.6",
+      "name": "h=500, beta=0.6",
       "config": {
         "initialState": {
-          "h_0": 500
+          "h": 500
         },
         "mixedLayer": {
           "beta": 0.6
@@ -246,10 +246,10 @@
       }
     },
     {
-      "name": "h_0=600, beta=0.1",
+      "name": "h=600, beta=0.1",
       "config": {
         "initialState": {
-          "h_0": 600
+          "h": 600
         },
         "mixedLayer": {
           "beta": 0.1
@@ -257,10 +257,10 @@
       }
     },
     {
-      "name": "h_0=600, beta=0.3",
+      "name": "h=600, beta=0.3",
       "config": {
         "initialState": {
-          "h_0": 600
+          "h": 600
         },
         "mixedLayer": {
           "beta": 0.3
@@ -268,10 +268,10 @@
       }
     },
     {
-      "name": "h_0=600, beta=0.4",
+      "name": "h=600, beta=0.4",
       "config": {
         "initialState": {
-          "h_0": 600
+          "h": 600
         },
         "mixedLayer": {
           "beta": 0.4
@@ -279,10 +279,10 @@
       }
     },
     {
-      "name": "h_0=600, beta=0.5",
+      "name": "h=600, beta=0.5",
       "config": {
         "initialState": {
-          "h_0": 600
+          "h": 600
         },
         "mixedLayer": {
           "beta": 0.5
@@ -290,10 +290,10 @@
       }
     },
     {
-      "name": "h_0=600, beta=0.6",
+      "name": "h=600, beta=0.6",
       "config": {
         "initialState": {
-          "h_0": 600
+          "h": 600
         },
         "mixedLayer": {
           "beta": 0.6
diff --git a/packages/class/src/class.test.ts b/packages/class/src/class.test.ts
index 6876c3d..6b30209 100644
--- a/packages/class/src/class.test.ts
+++ b/packages/class/src/class.test.ts
@@ -14,7 +14,7 @@ describe("CLASS model", () => {
     if (!model._cfg.sw_ml) {
       throw new Error("sw_ml not set");
     }
-    assert.strictEqual(model._cfg.h_0, 200);
+    assert.strictEqual(model._cfg.h, 200);
     assert.strictEqual(model._cfg.dt, 60);
     assert.deepEqual(model._cfg.wtheta, [0.1]);
     assert.strictEqual(model._cfg.wq, 0.0001);
diff --git a/packages/class/src/class.ts b/packages/class/src/class.ts
index 10e81a1..a0ad9fd 100644
--- a/packages/class/src/class.ts
+++ b/packages/class/src/class.ts
@@ -34,11 +34,11 @@ export class CLASS {
   constructor(config: Config) {
     this._cfg = config;
     if (config.sw_ml) {
-      this.h = config.h_0;
-      this.theta = config.theta_0;
-      this.dtheta = config.dtheta_0;
-      this.q = config.q_0;
-      this.dq = config.dq_0;
+      this.h = config.h;
+      this.theta = config.theta;
+      this.dtheta = config.dtheta;
+      this.q = config.q;
+      this.dq = config.dq;
     } else {
       // TODO dont have defaults here, but have it work without this else block
       this.h = 200;
diff --git a/packages/class/src/config.ts b/packages/class/src/config.ts
index 209d941..c1c3df8 100644
--- a/packages/class/src/config.ts
+++ b/packages/class/src/config.ts
@@ -64,7 +64,7 @@ const untypedSchema = {
       // biome-ignore lint/suspicious/noThenProperty: part of JSON Schema
       then: {
         properties: {
-          h_0: {
+          h: {
             symbol: "h",
             type: "number",
             title: "ABL height",
@@ -72,7 +72,7 @@ const untypedSchema = {
             default: 200,
             "ui:group": "Mixed layer",
           },
-          theta_0: {
+          theta: {
             symbol: "θ",
             type: "number",
             "ui:group": "Mixed layer",
@@ -84,7 +84,7 @@ const untypedSchema = {
               "The potential temperature of the mixed layer at the initial time.",
             unit: "K",
           },
-          dtheta_0: {
+          dtheta: {
             symbol: "Δθ",
             type: "number",
             title: "Temperature jump at h",
@@ -92,7 +92,7 @@ const untypedSchema = {
             default: 1,
             unit: "K",
           },
-          q_0: {
+          q: {
             symbol: "q",
             type: "number",
             "ui:group": "Mixed layer",
@@ -100,7 +100,7 @@ const untypedSchema = {
             default: 0.008,
             title: "Mixed-layer specific humidity",
           },
-          dq_0: {
+          dq: {
             symbol: "Δq",
             type: "number",
             description: "Specific humidity jump at h",
@@ -177,11 +177,11 @@ const untypedSchema = {
           },
         },
         required: [
-          "h_0",
-          "theta_0",
-          "dtheta_0",
-          "q_0",
-          "dq_0",
+          "h",
+          "theta",
+          "dtheta",
+          "q",
+          "dq",
           "wtheta",
           "advtheta",
           "gammatheta",
@@ -207,11 +207,11 @@ export type Config = {
 } & ( // Mixed layer
   | {
       sw_ml: true;
-      h_0: number;
-      theta_0: number;
-      dtheta_0: number;
-      q_0: number;
-      dq_0: number;
+      h: number;
+      theta: number;
+      dtheta: number;
+      q: number;
+      dq: number;
       wtheta: number[];
       advtheta: number;
       gammatheta: number;
diff --git a/packages/class/src/validate.test.ts b/packages/class/src/validate.test.ts
index e3bd01f..acc632a 100644
--- a/packages/class/src/validate.test.ts
+++ b/packages/class/src/validate.test.ts
@@ -35,11 +35,11 @@ describe("validate", () => {
   );
 
   test("given string should coerce to number", () => {
-    const input = { sw_ml: true, h_0: "42" };
+    const input = { sw_ml: true, h: "42" };
 
     validate(input);
 
-    assert.ok(typeof input.h_0 === "number");
+    assert.ok(typeof input.h === "number");
   });
 });
 
@@ -53,11 +53,11 @@ describe("parse", () => {
       name: "",
       description: "",
       sw_ml: true,
-      h_0: 200,
-      theta_0: 288,
-      dtheta_0: 1,
-      q_0: 0.008,
-      dq_0: -0.001,
+      h: 200,
+      theta: 288,
+      dtheta: 1,
+      q: 0.008,
+      dq: -0.001,
       dt: 60,
       runtime: 43200,
       wtheta: [0.1],
@@ -73,7 +73,7 @@ describe("parse", () => {
   });
 
   test("given partial config should return full config", () => {
-    const input = { h_0: 100, sw_ml: true };
+    const input = { h: 100, sw_ml: true };
 
     const output = parse(input);
 
@@ -81,12 +81,12 @@ describe("parse", () => {
     if (!expected.sw_ml) {
       throw new Error("sw_ml is enabled");
     }
-    expected.h_0 = 100;
+    expected.h = 100;
     assert.deepEqual(output, expected);
   });
 
   test("given partial string config should return full coerced config", () => {
-    const input = { h_0: "100", sw_ml: true };
+    const input = { h: "100", sw_ml: true };
 
     const output = parse(input);
 
@@ -94,12 +94,12 @@ describe("parse", () => {
     if (!expected.sw_ml) {
       throw new Error("sw_ml is enabled");
     }
-    expected.h_0 = 100;
+    expected.h = 100;
     assert.deepEqual(output, expected);
   });
 
   test("given emptry string should return default", () => {
-    const input = { h_0: "", sw_ml: true };
+    const input = { h: "", sw_ml: true };
 
     const output = parse(input);
 

From 63cea842a06280bb956c6da35269d30e97486f59 Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Tue, 22 Apr 2025 11:25:06 +0200
Subject: [PATCH 27/47] Make wq number array in form/config; TODO: interpolate
 value in model

---
 apps/class-solid/src/lib/presets/death-valley.json |  2 +-
 apps/class-solid/tests/big-app-state.json          |  2 +-
 packages/class/src/class.ts                        |  6 ++++--
 packages/class/src/config.ts                       | 10 +++++++---
 4 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/apps/class-solid/src/lib/presets/death-valley.json b/apps/class-solid/src/lib/presets/death-valley.json
index 4ab4efb..49295de 100644
--- a/apps/class-solid/src/lib/presets/death-valley.json
+++ b/apps/class-solid/src/lib/presets/death-valley.json
@@ -11,7 +11,7 @@
   "wtheta": [0.1],
   "advtheta": 0,
   "gammatheta": 0.006,
-  "wq": 0.0001,
+  "wq": [0.0001],
   "advq": 0,
   "gammaq": 0,
   "divU": 0,
diff --git a/apps/class-solid/tests/big-app-state.json b/apps/class-solid/tests/big-app-state.json
index 0d3bd4c..d7475e6 100644
--- a/apps/class-solid/tests/big-app-state.json
+++ b/apps/class-solid/tests/big-app-state.json
@@ -17,7 +17,7 @@
       "wtheta": 0.1,
       "advtheta": 0,
       "gammatheta": 0.006,
-      "wq": 0.0001,
+      "wq": [0.0001],
       "advq": 0,
       "gammaq": 0,
       "divU": 0,
diff --git a/packages/class/src/class.ts b/packages/class/src/class.ts
index a0ad9fd..68e87b6 100644
--- a/packages/class/src/class.ts
+++ b/packages/class/src/class.ts
@@ -103,7 +103,8 @@ export class CLASS {
   /** Tendency of mixed-layer specific humidity [kg kg-1 s-1] */
   get qtend(): number {
     this.hasMixedLayer();
-    return (this._cfg.wq - this.wqe) / this.h + this._cfg.advq;
+    const wq = this._cfg.wq[0]; // TODO: interpolate
+    return (wq - this.wqe) / this.h + this._cfg.advq;
   }
 
   /** Tendency of specific humidity jump at h[kg kg-1 s-1] */
@@ -159,6 +160,7 @@ export class CLASS {
   get wthetav(): number {
     this.hasMixedLayer();
     const wtheta = this.interpolatedWtheta();
-    return wtheta + 0.61 * this.theta * this._cfg.wq;
+    const wq = this._cfg.wq[0]; // TODO: interpolate
+    return wtheta + 0.61 * this.theta * wq;
   }
 }
diff --git a/packages/class/src/config.ts b/packages/class/src/config.ts
index c1c3df8..3164f71 100644
--- a/packages/class/src/config.ts
+++ b/packages/class/src/config.ts
@@ -138,10 +138,14 @@ const untypedSchema = {
           },
           wq: {
             symbol: "(w'q')ₛ",
-            type: "number",
+            type: "array",
+            items: {
+              type: "number",
+            },
             "ui:group": "Mixed layer",
             unit: "kg kg⁻¹ m s⁻¹",
-            default: 0.0001,
+            default: [0.0001],
+            minItems: 1,
             title: "Surface kinematic moisture flux",
           },
           advq: {
@@ -215,7 +219,7 @@ export type Config = {
       wtheta: number[];
       advtheta: number;
       gammatheta: number;
-      wq: number;
+      wq: number[];
       advq: number;
       gammaq: number;
       divU: number;

From d91d8757cd5da4d460f3293e7b19fd5ba5f517e1 Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Tue, 22 Apr 2025 11:41:28 +0200
Subject: [PATCH 28/47] Make gammaq and gammatheta arrays; TODO: fix profiles
 in app, use in model

---
 .../src/lib/presets/death-valley.json         |  4 ++--
 apps/class-solid/tests/big-app-state.json     |  4 ++--
 packages/class/src/class.ts                   |  6 ++++--
 packages/class/src/config.ts                  | 20 +++++++++++++------
 4 files changed, 22 insertions(+), 12 deletions(-)

diff --git a/apps/class-solid/src/lib/presets/death-valley.json b/apps/class-solid/src/lib/presets/death-valley.json
index 49295de..440c683 100644
--- a/apps/class-solid/src/lib/presets/death-valley.json
+++ b/apps/class-solid/src/lib/presets/death-valley.json
@@ -10,10 +10,10 @@
   "runtime": 43200,
   "wtheta": [0.1],
   "advtheta": 0,
-  "gammatheta": 0.006,
+  "gammatheta": [0.006],
   "wq": [0.0001],
   "advq": 0,
-  "gammaq": 0,
+  "gammaq": [0],
   "divU": 0,
   "beta": 0.2
 }
diff --git a/apps/class-solid/tests/big-app-state.json b/apps/class-solid/tests/big-app-state.json
index d7475e6..a61213e 100644
--- a/apps/class-solid/tests/big-app-state.json
+++ b/apps/class-solid/tests/big-app-state.json
@@ -16,10 +16,10 @@
     "mixedLayer": {
       "wtheta": 0.1,
       "advtheta": 0,
-      "gammatheta": 0.006,
+      "gammatheta": [0.006],
       "wq": [0.0001],
       "advq": 0,
-      "gammaq": 0,
+      "gammaq": [0],
       "divU": 0,
       "beta": 0.2
     }
diff --git a/packages/class/src/class.ts b/packages/class/src/class.ts
index 68e87b6..c6cc952 100644
--- a/packages/class/src/class.ts
+++ b/packages/class/src/class.ts
@@ -97,7 +97,8 @@ export class CLASS {
   get dthetatend(): number {
     this.hasMixedLayer();
     const w_th_ft = 0.0; // TODO: add free troposphere switch
-    return this._cfg.gammatheta * this.we - this.thetatend + w_th_ft;
+    const gammatheta = this._cfg.gammatheta[0]; // TODO: make conditional on h and z_ft_theta
+    return gammatheta * this.we - this.thetatend + w_th_ft;
   }
 
   /** Tendency of mixed-layer specific humidity [kg kg-1 s-1] */
@@ -111,7 +112,8 @@ export class CLASS {
   get dqtend(): number {
     this.hasMixedLayer();
     const w_q_ft = 0; // TODO: add free troposphere switch
-    return this._cfg.gammaq * this.we - this.qtend + w_q_ft;
+    const gammaq = this._cfg.gammaq[0]; // TODO: make conditional on h and z_ft_theta
+    return gammaq * this.we - this.qtend + w_q_ft;
   }
 
   /** Entrainment velocity [m s-1]. */
diff --git a/packages/class/src/config.ts b/packages/class/src/config.ts
index 3164f71..87cfa1b 100644
--- a/packages/class/src/config.ts
+++ b/packages/class/src/config.ts
@@ -130,10 +130,14 @@ const untypedSchema = {
           },
           gammatheta: {
             symbol: "γ<sub>θ</sub>",
-            type: "number",
+            type: "array",
+            items: {
+              type: "number",
+            },
+            minItems: 1,
             "ui:group": "Mixed layer",
             unit: "K m⁻¹",
-            default: 0.006,
+            default: [0.006],
             title: "Free atmosphere potential temperature lapse rate",
           },
           wq: {
@@ -158,10 +162,14 @@ const untypedSchema = {
           },
           gammaq: {
             symbol: "γ<sub>q</sub>",
-            type: "number",
+            type: "array",
+            items: {
+              type: "number",
+            },
+            minItems: 1,
             "ui:group": "Mixed layer",
             unit: "kg kg⁻¹ m⁻¹",
-            default: 0,
+            default: [0],
             title: "Free atmosphere specific humidity lapse rate",
           },
           divU: {
@@ -218,10 +226,10 @@ export type Config = {
       dq: number;
       wtheta: number[];
       advtheta: number;
-      gammatheta: number;
+      gammatheta: number[];
       wq: number[];
       advq: number;
-      gammaq: number;
+      gammaq: number[];
       divU: number;
       beta: number;
     }

From cc78b88ee9749b300458b31d542f4e31ced8561f Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Tue, 22 Apr 2025 11:55:37 +0200
Subject: [PATCH 29/47] Add free-troposphere anchor points for theta and q;
 TODO: use in model and app; update reference/default/test configs

---
 packages/class/src/config.ts | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/packages/class/src/config.ts b/packages/class/src/config.ts
index 87cfa1b..98160d1 100644
--- a/packages/class/src/config.ts
+++ b/packages/class/src/config.ts
@@ -187,6 +187,34 @@ const untypedSchema = {
             default: 0.2,
             title: "Entrainment ratio for virtual heat",
           },
+          z_theta: {
+            symbol: "z<sub>θ</sub>",
+            type: "array",
+            items: {
+              type: "number",
+            },
+            minItems: 1,
+            "ui:group": "Mixed layer",
+            unit: "m",
+            default: [5000],
+            title: "Anchor point(s) for γ_θ",
+            description:
+              "Each value specifies the end of the corresponding segment in γ_θ",
+          },
+          z_q: {
+            symbol: "z<sub>q</sub>",
+            type: "array",
+            items: {
+              type: "number",
+            },
+            minItems: 1,
+            "ui:group": "Mixed layer",
+            unit: "m",
+            default: [5000],
+            title: "Anchor point(s) for γ_q",
+            description:
+              "Each value specifies the end of the corresponding segment in γ_q",
+          },
         },
         required: [
           "h",
@@ -202,6 +230,8 @@ const untypedSchema = {
           "gammaq",
           "divU",
           "beta",
+          "z_theta",
+          "z_q",
         ],
       },
     },
@@ -232,6 +262,8 @@ export type Config = {
       gammaq: number[];
       divU: number;
       beta: number;
+      z_theta: number[];
+      z_q: number[];
     }
   // Else, sw_ml key should be absent or false
   | { sw_ml?: false }

From 47c343975da7359262f326fb0f20d5a43fcda8a5 Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Tue, 22 Apr 2025 12:26:49 +0200
Subject: [PATCH 30/47] Add wind variables to config. TODO: use in model /
 display profiles in app?

---
 packages/class/src/config.ts | 123 ++++++++++++++++++++++++++++++++++-
 1 file changed, 122 insertions(+), 1 deletion(-)

diff --git a/packages/class/src/config.ts b/packages/class/src/config.ts
index 98160d1..f691e9b 100644
--- a/packages/class/src/config.ts
+++ b/packages/class/src/config.ts
@@ -50,6 +50,12 @@ const untypedSchema = {
       title: "Mixed-layer switch",
       default: true,
     },
+    sw_wind: {
+      type: "boolean",
+      "ui:group": "Wind",
+      title: "Wind switch",
+      default: false,
+    },
   },
   required: ["name", "dt", "runtime"],
   allOf: [
@@ -235,6 +241,107 @@ const untypedSchema = {
         ],
       },
     },
+    {
+      if: {
+        properties: {
+          sw_wind: {
+            const: true,
+          },
+        },
+      },
+      // biome-ignore lint/suspicious/noThenProperty: part of JSON Schema
+      then: {
+        properties: {
+          u: {
+            symbol: "u",
+            type: "number",
+            unit: "m s-1",
+            default: 0,
+            title: "Mixed-layer u-wind speed",
+            "ui:group": "Wind",
+          },
+          du: {
+            symbol: "Δu",
+            type: "number",
+            unit: "m s-1",
+            default: 0,
+            title: "U-wind jump at h",
+            "ui:group": "Wind",
+          },
+          gamma_u: {
+            symbol: "γ<sub>u</sub>",
+            type: "array",
+            items: {
+              type: "number",
+            },
+            minItems: 1,
+            unit: "s-1",
+            default: [0],
+            title: "Free atmosphere u-wind speed lapse rate",
+            description: "Specify one or multiple segments",
+            "ui:group": "Wind",
+          },
+          z_u: {
+            symbol: "z_u",
+            type: "array",
+            items: {
+              type: "number",
+            },
+            minItems: 1,
+            unit: "m",
+            default: [0],
+            title: "Anchor point(s) for γ_u",
+            description:
+              "Each value specifies the end of the corresponding segment in γ_u",
+            "ui:group": "Wind",
+          },
+          v: {
+            symbol: "v",
+            type: "number",
+            unit: "m s-1",
+            default: 0,
+            title: "Mixed-layer v-wind speed",
+            "ui:group": "Wind",
+          },
+          dv: {
+            symbol: "Δv",
+            type: "number",
+            unit: "m s-1",
+            default: 0,
+            title: "V-wind jump at h",
+            "ui:group": "Wind",
+          },
+          gamma_v: {
+            symbol: "γ<sub>v</sub>",
+            type: "array",
+            items: {
+              type: "number",
+            },
+            minItems: 1,
+            unit: "s-1",
+            default: [0],
+            title: "Free atmosphere v-wind speed lapse rate",
+            description: "Specify one or multiple segments",
+            "ui:group": "Wind",
+          },
+          z_v: {
+            symbol: "z_v",
+            type: "array",
+            items: {
+              type: "number",
+            },
+            minItems: 1,
+            unit: "m",
+            default: [0],
+            title: "Anchor point(s) for γ_v",
+            description:
+              "Each value specifies the end of the corresponding segment in γ_v",
+            "ui:group": "Wind",
+          },
+        },
+        required: ["u", "du", "gamma_u", "z_u", "v", "dv", "gamma_v", "z_v"],
+      },
+    },
   ],
 };
 
@@ -267,7 +374,21 @@ export type Config = {
     }
   // Else, sw_ml key should be absent or false
   | { sw_ml?: false }
-);
+) & // Wind
+  (
+    | {
+        sw_wind: true;
+        u: number;
+        du: number;
+        gamma_u: number[];
+        z_u: number[];
+        v: number;
+        dv: number;
+        gamma_v: number[];
+        z_v: number[];
+      } // Else, sw_wind key should be absent or false
+    | { sw_wind?: true }
+  );
 
 export type JsonSchemaOfConfig = JSONSchemaType<Config>;
 export const jsonSchemaOfConfig =

From b8f3863ce32f47c0ac0bc6f2613c413b84501524 Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Tue, 22 Apr 2025 13:35:22 +0200
Subject: [PATCH 31/47] Implement hourly interpolation of surface fluxes + add
 them to output + move output spec to separate module

---
 apps/class-solid/src/components/Analysis.tsx |  2 +-
 apps/class-solid/src/lib/download.ts         |  2 +-
 apps/class-solid/src/lib/profiles.ts         |  2 +-
 apps/class-solid/src/lib/runner.ts           |  3 +-
 apps/class-solid/src/lib/store.ts            |  2 +-
 packages/class/package.json                  |  6 ++
 packages/class/src/class.ts                  | 32 ++++---
 packages/class/src/cli.ts                    |  2 +-
 packages/class/src/config.ts                 |  4 +-
 packages/class/src/output.ts                 | 91 ++++++++++++++++++++
 packages/class/src/runner.ts                 | 81 +----------------
 packages/class/src/utils.ts                  | 20 +++++
 12 files changed, 142 insertions(+), 105 deletions(-)
 create mode 100644 packages/class/src/output.ts
 create mode 100644 packages/class/src/utils.ts

diff --git a/apps/class-solid/src/components/Analysis.tsx b/apps/class-solid/src/components/Analysis.tsx
index c3a3309..cf2af99 100644
--- a/apps/class-solid/src/components/Analysis.tsx
+++ b/apps/class-solid/src/components/Analysis.tsx
@@ -1,5 +1,5 @@
 import type { Config } from "@classmodel/class/config";
-import { type ClassOutput, outputVariables } from "@classmodel/class/runner";
+import { type ClassOutput, outputVariables } from "@classmodel/class/output";
 import * as d3 from "d3";
 import { saveAs } from "file-saver";
 import { toBlob } from "html-to-image";
diff --git a/apps/class-solid/src/lib/download.ts b/apps/class-solid/src/lib/download.ts
index aa58c30..f512e7e 100644
--- a/apps/class-solid/src/lib/download.ts
+++ b/apps/class-solid/src/lib/download.ts
@@ -1,4 +1,4 @@
-import type { ClassOutput } from "@classmodel/class/runner";
+import type { ClassOutput } from "@classmodel/class/output";
 import { BlobReader, BlobWriter, ZipWriter } from "@zip.js/zip.js";
 import { toPartial } from "./encode";
 import type { ExperimentConfig } from "./experiment_config";
diff --git a/apps/class-solid/src/lib/profiles.ts b/apps/class-solid/src/lib/profiles.ts
index 4d82375..b3db9ee 100644
--- a/apps/class-solid/src/lib/profiles.ts
+++ b/apps/class-solid/src/lib/profiles.ts
@@ -1,5 +1,5 @@
 import type { Config } from "@classmodel/class/config";
-import type { ClassOutput } from "@classmodel/class/runner";
+import type { ClassOutput } from "@classmodel/class/output";
 import type { Point } from "~/components/plots/Line";
 import type { Observation } from "./experiment_config";
 
diff --git a/apps/class-solid/src/lib/runner.ts b/apps/class-solid/src/lib/runner.ts
index 3dcf765..bae7006 100644
--- a/apps/class-solid/src/lib/runner.ts
+++ b/apps/class-solid/src/lib/runner.ts
@@ -1,5 +1,6 @@
 import type { Config } from "@classmodel/class/config";
-import type { ClassOutput, runClass } from "@classmodel/class/runner";
+import type { ClassOutput } from "@classmodel/class/output";
+import type { runClass } from "@classmodel/class/runner";
 import { wrap } from "comlink";
 
 const worker = new Worker(new URL("./worker.ts", import.meta.url), {
diff --git a/apps/class-solid/src/lib/store.ts b/apps/class-solid/src/lib/store.ts
index d737a15..2e02555 100644
--- a/apps/class-solid/src/lib/store.ts
+++ b/apps/class-solid/src/lib/store.ts
@@ -2,7 +2,7 @@ import { createUniqueId } from "solid-js";
 import { createStore, produce, unwrap } from "solid-js/store";
 
 import type { Config } from "@classmodel/class/config";
-import type { ClassOutput } from "@classmodel/class/runner";
+import type { ClassOutput } from "@classmodel/class/output";
 
 import {
   mergeConfigurations,
diff --git a/packages/class/package.json b/packages/class/package.json
index 4168f07..ef35c62 100644
--- a/packages/class/package.json
+++ b/packages/class/package.json
@@ -35,6 +35,12 @@
         "types": "./dist/runner.d.ts"
       }
     },
+    "./output": {
+      "import": {
+        "default": "./dist/output.js",
+        "types": "./dist/output.d.ts"
+      }
+    },
     "./validate": {
       "import": {
         "default": "./dist/validate.js",
diff --git a/packages/class/src/class.ts b/packages/class/src/class.ts
index c6cc952..7555c46 100644
--- a/packages/class/src/class.ts
+++ b/packages/class/src/class.ts
@@ -3,10 +3,7 @@
  * @module
  */
 import type { Config } from "./config.js";
-
-// Constants
-const rho = 1.2; /** Density of air [kg m-3] */
-const cp = 1005.0; /** Specific heat of dry air [J kg-1 K-1] */
+import { interpolateHourly } from "./utils.js";
 
 /**
  * CLASS model definition
@@ -75,12 +72,6 @@ export class CLASS {
     }
   }
 
-  private interpolatedWtheta(): number {
-    this.hasMixedLayer();
-    // TODO interpolated based on this.t / this.runtime and the wtheta values
-    return this._cfg.wtheta[0];
-  }
-
   /** Tendency of CLB [m s-1]*/
   get htend(): number {
     return this.we + this.ws;
@@ -89,8 +80,7 @@ export class CLASS {
   /** Tendency of mixed-layer potential temperature [K s-1] */
   get thetatend(): number {
     this.hasMixedLayer();
-    const wtheta = this.interpolatedWtheta();
-    return (wtheta - this.wthetae) / this.h + this._cfg.advtheta;
+    return (this.wtheta - this.wthetae) / this.h + this._cfg.advtheta;
   }
 
   /** Tendency of potential temperature jump at h [K s-1] */
@@ -104,8 +94,7 @@ export class CLASS {
   /** Tendency of mixed-layer specific humidity [kg kg-1 s-1] */
   get qtend(): number {
     this.hasMixedLayer();
-    const wq = this._cfg.wq[0]; // TODO: interpolate
-    return (wq - this.wqe) / this.h + this._cfg.advq;
+    return (this.wq - this.wqe) / this.h + this._cfg.advq;
   }
 
   /** Tendency of specific humidity jump at h[kg kg-1 s-1] */
@@ -158,11 +147,20 @@ export class CLASS {
     );
   }
 
+  get wtheta(): number {
+    this.hasMixedLayer();
+    return interpolateHourly(this._cfg.wtheta, this.t)
+  }
+
+  get wq(): number {
+    this.hasMixedLayer();
+    return interpolateHourly(this._cfg.wq, this.t)
+  }
+
   /** Surface kinematic virtual heat flux [K m s-1]. */
   get wthetav(): number {
     this.hasMixedLayer();
-    const wtheta = this.interpolatedWtheta();
-    const wq = this._cfg.wq[0]; // TODO: interpolate
-    return wtheta + 0.61 * this.theta * wq;
+    return this.wtheta + 0.61 * this.theta * this.wq;
   }
 }
+
diff --git a/packages/class/src/cli.ts b/packages/class/src/cli.ts
index 583081b..0be76aa 100755
--- a/packages/class/src/cli.ts
+++ b/packages/class/src/cli.ts
@@ -6,7 +6,7 @@
 import { readFile, writeFile } from "node:fs/promises";
 import { EOL } from "node:os";
 import { Command, Option } from "@commander-js/extra-typings";
-import type { ClassOutput } from "./runner.js";
+import type { ClassOutput } from "./output.js";
 import { runClass } from "./runner.js";
 import { parse } from "./validate.js";
 
diff --git a/packages/class/src/config.ts b/packages/class/src/config.ts
index f691e9b..7b1686a 100644
--- a/packages/class/src/config.ts
+++ b/packages/class/src/config.ts
@@ -123,7 +123,7 @@ const untypedSchema = {
             "ui:group": "Mixed layer",
             unit: "K m s⁻¹",
             title: "Surface kinematic heat flux",
-            default: [0.1],
+            default: [0.1, 0.2, 0.3, 0.4, 0.3, 0.2, 0.1],
             minItems: 1,
           },
           advtheta: {
@@ -154,7 +154,7 @@ const untypedSchema = {
             },
             "ui:group": "Mixed layer",
             unit: "kg kg⁻¹ m s⁻¹",
-            default: [0.0001],
+            default: [0.0001, 0.0001, 0.0001, 0.0001, 0.0001],
             minItems: 1,
             title: "Surface kinematic moisture flux",
           },
diff --git a/packages/class/src/output.ts b/packages/class/src/output.ts
new file mode 100644
index 0000000..433991e
--- /dev/null
+++ b/packages/class/src/output.ts
@@ -0,0 +1,91 @@
+export interface OutputVariable {
+  key: string;
+  title: string;
+  unit: string;
+  symbol: string;
+}
+
+export const outputVariables: OutputVariable[] = [
+  {
+    key: "t",
+    title: "Time",
+    unit: "s",
+    symbol: "t",
+  },
+  {
+    key: "h",
+    title: "ABL height",
+    unit: "m",
+    symbol: "h",
+  },
+  {
+    key: "theta",
+    title: "Potential temperature",
+    unit: "K",
+    symbol: "θ",
+  },
+  {
+    key: "dtheta",
+    title: "Potential temperature jump",
+    unit: "K",
+    symbol: "Δθ",
+  },
+  {
+    key: "q",
+    title: "Specific humidity",
+    unit: "kg kg⁻¹",
+    symbol: "q",
+  },
+  {
+    key: "dq",
+    title: "Specific humidity jump",
+    unit: "kg kg⁻¹",
+    symbol: "Δq",
+  },
+  {
+    key: "dthetav",
+    title: "Virtual temperature jump at h",
+    unit: "K",
+    symbol: "Δθᵥ",
+  },
+  {
+    key: "we",
+    title: "Entrainment velocity",
+    unit: "m s⁻¹",
+    symbol: "wₑ",
+  },
+  {
+    key: "ws",
+    title: "Large-scale vertical velocity",
+    unit: "m s⁻¹",
+    symbol: "wₛ",
+  },
+  {
+    key: "wthetave",
+    title: "Entrainment virtual heat flux",
+    unit: "K m s⁻¹",
+    symbol: "(w'θ')ᵥₑ",
+  },
+  {
+    key: "wthetav",
+    title: "Surface virtual heat flux",
+    unit: "K m s⁻¹",
+    symbol: "(w'θ')ᵥ",
+  },
+  {
+    key: "wtheta",
+    title: "Surface kinematic heat flux",
+    unit: "K m s⁻¹",
+    symbol: "(w'θ')ₛ",
+  },
+  {
+    key: "wq",
+    title: "Surface kinematic heat flux",
+    unit: "kg kg⁻¹ m s⁻¹",
+    symbol: "(w'q')ₛ",
+  },
+];
+
+export type ClassOutput = {
+  [K in (typeof outputVariables)[number]["key"]]: number[];
+};
\ No newline at end of file
diff --git a/packages/class/src/runner.ts b/packages/class/src/runner.ts
index d075e7b..d5b9bc7 100644
--- a/packages/class/src/runner.ts
+++ b/packages/class/src/runner.ts
@@ -5,88 +5,9 @@
  */
 import { CLASS } from "./class.js";
 import type { Config } from "./config.js";
+import { type ClassOutput, outputVariables } from "./output.js";
 import { parse } from "./validate.js";
 
-export interface OutputVariable {
-  key: string;
-  title: string;
-  unit: string;
-  symbol: string;
-}
-
-export const outputVariables: OutputVariable[] = [
-  {
-    key: "t",
-    title: "Time",
-    unit: "s",
-    symbol: "t",
-  },
-  {
-    key: "h",
-    title: "ABL height",
-    unit: "m",
-    symbol: "h",
-  },
-  {
-    key: "theta",
-    title: "Potential temperature",
-    unit: "K",
-    symbol: "θ",
-  },
-  {
-    key: "dtheta",
-    title: "Potential temperature jump",
-    unit: "K",
-    symbol: "Δθ",
-  },
-  {
-    key: "q",
-    title: "Specific humidity",
-    unit: "kg kg⁻¹",
-    symbol: "q",
-  },
-  {
-    key: "dq",
-    title: "Specific humidity jump",
-    unit: "kg kg⁻¹",
-    symbol: "Δq",
-  },
-  {
-    key: "dthetav",
-    title: "Virtual temperature jump at h",
-    unit: "K",
-    symbol: "Δθᵥ",
-  },
-  {
-    key: "we",
-    title: "Entrainment velocity",
-    unit: "m s⁻¹",
-    symbol: "wₑ",
-  },
-  {
-    key: "ws",
-    title: "Large-scale vertical velocity",
-    unit: "m s⁻¹",
-    symbol: "wₛ",
-  },
-  {
-    key: "wthetave",
-    title: "Entrainment virtual heat flux",
-    unit: "K m s⁻¹",
-    symbol: "(w'θ')ᵥₑ",
-  },
-  {
-    key: "wthetav",
-    title: "Surface virtual heat flux",
-    unit: "K m s⁻¹",
-    symbol: "(w'θ')ᵥ",
-  },
-];
-
-export type ClassOutput = {
-  [K in (typeof outputVariables)[number]["key"]]: number[];
-};
-
 export function runClass(config: Config): ClassOutput {
   const validatedConfig = parse(config);
   const model = new CLASS(validatedConfig);
diff --git a/packages/class/src/utils.ts b/packages/class/src/utils.ts
new file mode 100644
index 0000000..7070d47
--- /dev/null
+++ b/packages/class/src/utils.ts
@@ -0,0 +1,20 @@
+
+/**
+ * Interpolate between hourly reference values based on current runtime
+ * Padding is applied if not all hours are provided
+ * 
+ * @param arr array with hourly reference values for variable
+ * @param t time in seconds
+ * @param pad fill value if t/3600 exceeds array length
+ * @returns interpolated value
+ */
+export function interpolateHourly(arr: number[], t: number, pad=0){
+const maxIndex = arr.length - 1
+const i = Math.floor(t/3600)
+const p = t % 3600 / 3600
+
+const left = i <= maxIndex ? arr[i] : pad
+const right = i+1 <= maxIndex ? arr[i+1] : pad
+return left + p * (right - left);
+
+}
\ No newline at end of file

From dc2b595d5437883f906e1bfc29e7278af48c7867 Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Tue, 22 Apr 2025 14:00:01 +0200
Subject: [PATCH 32/47] Implement piecewise lapse rate in model

---
 packages/class/src/class.ts | 24 +++++++++++++++++++-----
 packages/class/src/utils.ts | 17 ++++++++++++++++-
 2 files changed, 35 insertions(+), 6 deletions(-)

diff --git a/packages/class/src/class.ts b/packages/class/src/class.ts
index 7555c46..dfde513 100644
--- a/packages/class/src/class.ts
+++ b/packages/class/src/class.ts
@@ -3,7 +3,7 @@
  * @module
  */
 import type { Config } from "./config.js";
-import { interpolateHourly } from "./utils.js";
+import { findInsertIndex, interpolateHourly } from "./utils.js";
 
 /**
  * CLASS model definition
@@ -83,12 +83,27 @@ export class CLASS {
     return (this.wtheta - this.wthetae) / this.h + this._cfg.advtheta;
   }
 
+  /** Free atmosphere potential temperature lapse rate */
+  get gammatheta(): number {
+    this.hasMixedLayer();
+    const { z_theta, gammatheta } = this._cfg;
+    const i = findInsertIndex(z_theta, this.h);
+    return gammatheta[i] ?? 0;
+  }
+
+  /** Free atmosphere specific humidity lapse rate */
+  get gammaq(): number {
+    this.hasMixedLayer();
+    const { z_q, gammaq } = this._cfg;
+    const i = findInsertIndex(z_q, this.h);
+    return gammaq[i] ?? 0;
+  }
+
   /** Tendency of potential temperature jump at h [K s-1] */
   get dthetatend(): number {
     this.hasMixedLayer();
     const w_th_ft = 0.0; // TODO: add free troposphere switch
-    const gammatheta = this._cfg.gammatheta[0]; // TODO: make conditional on h and z_ft_theta
-    return gammatheta * this.we - this.thetatend + w_th_ft;
+    return this.gammatheta * this.we - this.thetatend + w_th_ft;
   }
 
   /** Tendency of mixed-layer specific humidity [kg kg-1 s-1] */
@@ -101,8 +116,7 @@ export class CLASS {
   get dqtend(): number {
     this.hasMixedLayer();
     const w_q_ft = 0; // TODO: add free troposphere switch
-    const gammaq = this._cfg.gammaq[0]; // TODO: make conditional on h and z_ft_theta
-    return gammaq * this.we - this.qtend + w_q_ft;
+    return this.gammaq * this.we - this.qtend + w_q_ft;
   }
 
   /** Entrainment velocity [m s-1]. */
diff --git a/packages/class/src/utils.ts b/packages/class/src/utils.ts
index 7070d47..d812fa2 100644
--- a/packages/class/src/utils.ts
+++ b/packages/class/src/utils.ts
@@ -17,4 +17,19 @@ const left = i <= maxIndex ? arr[i] : pad
 const right = i+1 <= maxIndex ? arr[i+1] : pad
 return left + p * (right - left);
 
-}
\ No newline at end of file
+}
+
+/**
+ * Find the position in an array where value should be inserted to maintain sorted order.
+ * 
+ * @param arr Sorted array
+ * @param value Value that should be inserted
+ * @returns index where value should be inserted to maintain sorted array
+ */
+export function findInsertIndex(arr: number[], value: number) {
+    let i = 0;
+    while (i < arr.length && value >= arr[i]) {
+      i++;
+    }
+    return i;
+  }
\ No newline at end of file

From 431c93898644c254ffba82b3a1fa828d5243459f Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Tue, 22 Apr 2025 14:00:12 +0200
Subject: [PATCH 33/47] formatting

---
 packages/class/src/class.ts  |  5 ++---
 packages/class/src/output.ts |  2 +-
 packages/class/src/utils.ts  | 32 +++++++++++++++-----------------
 3 files changed, 18 insertions(+), 21 deletions(-)

diff --git a/packages/class/src/class.ts b/packages/class/src/class.ts
index dfde513..64969e1 100644
--- a/packages/class/src/class.ts
+++ b/packages/class/src/class.ts
@@ -163,12 +163,12 @@ export class CLASS {
 
   get wtheta(): number {
     this.hasMixedLayer();
-    return interpolateHourly(this._cfg.wtheta, this.t)
+    return interpolateHourly(this._cfg.wtheta, this.t);
   }
 
   get wq(): number {
     this.hasMixedLayer();
-    return interpolateHourly(this._cfg.wq, this.t)
+    return interpolateHourly(this._cfg.wq, this.t);
   }
 
   /** Surface kinematic virtual heat flux [K m s-1]. */
@@ -177,4 +177,3 @@ export class CLASS {
     return this.wtheta + 0.61 * this.theta * this.wq;
   }
 }
-
diff --git a/packages/class/src/output.ts b/packages/class/src/output.ts
index 433991e..e74b90e 100644
--- a/packages/class/src/output.ts
+++ b/packages/class/src/output.ts
@@ -88,4 +88,4 @@ export const outputVariables: OutputVariable[] = [
 
 export type ClassOutput = {
   [K in (typeof outputVariables)[number]["key"]]: number[];
-};
\ No newline at end of file
+};
diff --git a/packages/class/src/utils.ts b/packages/class/src/utils.ts
index d812fa2..894948d 100644
--- a/packages/class/src/utils.ts
+++ b/packages/class/src/utils.ts
@@ -1,35 +1,33 @@
-
 /**
  * Interpolate between hourly reference values based on current runtime
  * Padding is applied if not all hours are provided
- * 
+ *
  * @param arr array with hourly reference values for variable
  * @param t time in seconds
  * @param pad fill value if t/3600 exceeds array length
  * @returns interpolated value
  */
-export function interpolateHourly(arr: number[], t: number, pad=0){
-const maxIndex = arr.length - 1
-const i = Math.floor(t/3600)
-const p = t % 3600 / 3600
-
-const left = i <= maxIndex ? arr[i] : pad
-const right = i+1 <= maxIndex ? arr[i+1] : pad
-return left + p * (right - left);
+export function interpolateHourly(arr: number[], t: number, pad = 0) {
+  const maxIndex = arr.length - 1;
+  const i = Math.floor(t / 3600);
+  const p = (t % 3600) / 3600;
 
+  const left = i <= maxIndex ? arr[i] : pad;
+  const right = i + 1 <= maxIndex ? arr[i + 1] : pad;
+  return left + p * (right - left);
 }
 
 /**
  * Find the position in an array where value should be inserted to maintain sorted order.
- * 
+ *
  * @param arr Sorted array
  * @param value Value that should be inserted
  * @returns index where value should be inserted to maintain sorted array
  */
 export function findInsertIndex(arr: number[], value: number) {
-    let i = 0;
-    while (i < arr.length && value >= arr[i]) {
-      i++;
-    }
-    return i;
-  }
\ No newline at end of file
+  let i = 0;
+  while (i < arr.length && value >= arr[i]) {
+    i++;
+  }
+  return i;
+}

From 7ef439d14759c9523650e538c362155e6e82e1fc Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Tue, 22 Apr 2025 14:40:33 +0200
Subject: [PATCH 34/47] Fix display of piecewise lapse rate in web app

---
 apps/class-solid/src/lib/profiles.ts | 67 +++++++++++++++++++++-------
 packages/class/package.json          |  6 +++
 2 files changed, 57 insertions(+), 16 deletions(-)

diff --git a/apps/class-solid/src/lib/profiles.ts b/apps/class-solid/src/lib/profiles.ts
index b3db9ee..87aa325 100644
--- a/apps/class-solid/src/lib/profiles.ts
+++ b/apps/class-solid/src/lib/profiles.ts
@@ -1,5 +1,6 @@
 import type { Config } from "@classmodel/class/config";
 import type { ClassOutput } from "@classmodel/class/output";
+import { findInsertIndex } from "@classmodel/class/utils";
 import type { Point } from "~/components/plots/Line";
 import type { Observation } from "./experiment_config";
 
@@ -15,30 +16,64 @@ export function getVerticalProfiles(
     return [];
   }
 
-  // Extract height profile
-  const height = output.h.slice(t)[0];
-  const dh = 1600; // how much free troposphere to display?
-  const hProfile = [0, height, height, height + dh];
   if (variable === "theta") {
-    // Extract potential temperature profile
-    const theta = output.theta.slice(t)[0];
+    let z = output.h.slice(t)[0];
+    let theta = output.theta.slice(t)[0];
     const dtheta = output.dtheta.slice(t)[0];
     const gammatheta = config.gammatheta;
-    const thetaProfile = [
-      theta,
-      theta,
-      theta + dtheta,
-      theta + dtheta + dh * gammatheta,
+    const z_theta = config.z_theta;
+    const maxHeight = z_theta.slice(-1)[0];
+
+    // Mixed layer
+    const profile = [
+      { x: theta, y: 0 },
+      { x: theta, y: z },
     ];
-    return hProfile.map((h, i) => ({ x: thetaProfile[i], y: h }));
+
+    // Inversion
+    theta += dtheta;
+    profile.push({ x: theta, y: z });
+
+    // Free troposphere
+    while (z < maxHeight) {
+      const idx = findInsertIndex(z_theta, z);
+      const lapse_rate = gammatheta[idx] ?? 0;
+      const dz = z_theta[idx] - z;
+      z += dz;
+      theta += lapse_rate * dz;
+      console.log(theta, z, dz);
+      profile.push({ x: theta, y: z });
+    }
+    return profile;
   }
   if (variable === "q") {
-    // Extract humidity profile
-    const q = output.q.slice(t)[0];
+    let z = output.h.slice(t)[0];
+    let q = output.q.slice(t)[0];
     const dq = output.dq.slice(t)[0];
     const gammaq = config.gammaq;
-    const qProfile = [q, q, q + dq, q + dq + dh * gammaq];
-    return hProfile.map((h, i) => ({ x: qProfile[i], y: h }));
+    const z_q = config.z_q;
+    const maxHeight = z_q.slice(-1)[0];
+
+    // Mixed layer
+    const profile = [
+      { x: q, y: 0 },
+      { x: q, y: z },
+    ];
+
+    // Inversion
+    q += dq;
+    profile.push({ x: q, y: z });
+
+    // Free troposphere
+    while (z < maxHeight) {
+      const idx = findInsertIndex(z_q, z);
+      const lapse_rate = gammaq[idx] ?? 0;
+      const dz = z_q[idx] - z;
+      z += dz;
+      q += lapse_rate * dz;
+      profile.push({ x: q, y: z });
+    }
+    return profile;
   }
   return [];
 }
diff --git a/packages/class/package.json b/packages/class/package.json
index ef35c62..c90038d 100644
--- a/packages/class/package.json
+++ b/packages/class/package.json
@@ -41,6 +41,12 @@
         "types": "./dist/output.d.ts"
       }
     },
+    "./utils": {
+      "import": {
+        "default": "./dist/utils.js",
+        "types": "./dist/utils.d.ts"
+      }
+    },
     "./validate": {
       "import": {
         "default": "./dist/validate.js",

From 1c0c869410115f38c930e3629464e67748444347 Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Tue, 22 Apr 2025 20:26:56 +0200
Subject: [PATCH 35/47] Add basic wind logistics; rethink optional variable
 groups; use getValue rather than direct getters to access nested object
 groups; TODO in config only allow wind if mixed layer is on; TODO complete
 wind implementation

---
 apps/class-solid/src/lib/profiles.ts |   1 -
 packages/class/src/class.ts          | 239 ++++++++++++++++++---------
 packages/class/src/config.ts         |  86 +++++-----
 packages/class/src/runner.ts         |   3 +-
 4 files changed, 208 insertions(+), 121 deletions(-)

diff --git a/apps/class-solid/src/lib/profiles.ts b/apps/class-solid/src/lib/profiles.ts
index 87aa325..2f2940a 100644
--- a/apps/class-solid/src/lib/profiles.ts
+++ b/apps/class-solid/src/lib/profiles.ts
@@ -41,7 +41,6 @@ export function getVerticalProfiles(
       const dz = z_theta[idx] - z;
       z += dz;
       theta += lapse_rate * dz;
-      console.log(theta, z, dz);
       profile.push({ x: theta, y: z });
     }
     return profile;
diff --git a/packages/class/src/class.ts b/packages/class/src/class.ts
index 64969e1..e7720bf 100644
--- a/packages/class/src/class.ts
+++ b/packages/class/src/class.ts
@@ -2,26 +2,29 @@
  * This module contains the CLASS model implementation.
  * @module
  */
-import type { Config } from "./config.js";
+import type { Config, MixedLayerConfig, WindConfig } from "./config.js";
 import { findInsertIndex, interpolateHourly } from "./utils.js";
 
-/**
- * CLASS model definition
- * @property _cfg: object containing the model settings
- * @property h: ABL height [m]
- * @property theta: Mixed-layer potential temperature [K]
- * @property dtheta: Temperature jump at h [K]
- * @property q: Mixed-layer specific humidity [kg kg-1]
- * @property dq: Specific humidity jump at h [kg kg-1]
- * @property t: Model time [s]
- */
-export class CLASS {
-  _cfg: Config;
+// Group related variables so we can require them as complete sets
+type Wind = {
+  u: number;
+  v: number;
+  du: number;
+  dv: number;
+}
+
+type MixedLayer = {
   h: number;
   theta: number;
   dtheta: number;
   q: number;
   dq: number;
+}
+
+export class CLASS {
+  _cfg: Config;
+  ml?: MixedLayer;
+  wind?: Wind;
   t = 0;
 
   /**
@@ -30,46 +33,61 @@ export class CLASS {
    */
   constructor(config: Config) {
     this._cfg = config;
+    // Initialize state variables from config
     if (config.sw_ml) {
-      this.h = config.h;
-      this.theta = config.theta;
-      this.dtheta = config.dtheta;
-      this.q = config.q;
-      this.dq = config.dq;
-    } else {
-      // TODO dont have defaults here, but have it work without this else block
-      this.h = 200;
-      this.theta = 288;
-      this.dtheta = 1;
-      this.q = 0.008;
-      this.dq = -0.001;
-    }
+      const { h, theta, dtheta, q, dq } = config;
+      this.ml = { h, theta, dtheta, q, dq };
+      
+      if (config.sw_wind){
+        const {u, v, du, dv} = config
+        this.wind = {u, v, du, dv}
+      }
+    }    
   }
+
   /**
    * Integrate mixed layer
    */
   update() {
     const dt = this._cfg.dt;
-    this.h += dt * this.htend;
-    this.theta += dt * this.thetatend;
-    this.dtheta += dt * this.dthetatend;
-    this.q += dt * this.qtend;
-    this.dq += dt * this.dqtend;
+    if (this.ml){
+      this.ml.h += dt * this.htend;
+      this.ml.theta += dt * this.thetatend;
+      this.ml.dtheta += dt * this.dthetatend;
+      this.ml.q += dt * this.qtend;
+      this.ml.dq += dt * this.dqtend;
+      if (this.wind){
+        this.wind.u += dt * this.utend
+        this.wind.v += dt * this.vtend
+        this.wind.du += dt * this.dutend
+        this.wind.dv += dt * this.dvtend
+      }
+    }
     this.t += dt;
   }
 
-  /**
-   * Type guard assertion function that checks if mixed layer mode is enabled in the configuration.
-   * @throws {Error} When mixed layer is not enabled in the configuration.
-   * @typeAssertion {CLASS & {_cfg: Config & {sw_ml: true}}} - Asserts that this instance has mixed layer enabled
-   * @private
-   */
-  private hasMixedLayer(): asserts this is CLASS & {
-    _cfg: Config & { sw_ml: true };
-  } {
-    if (!this._cfg.sw_ml) {
-      throw new Error("Mixed layer is not enabled");
-    }
+  get utend(): number {
+    this.assertWind();
+    // TODO make sure all variables are available
+    // return -this.fc * this.wind.dv + (this.uw + this.we * this.wind.du) / this.ml.h + this.advu
+    return 0
+  }
+  
+  get vtend(): number {
+    this.assertWind();
+    // TODO make sure all variables are available
+    // return this.fc * this.wind.du + (this.vw + this.we * this.wind.dv) / this.ml.h + this.advv
+    return 0
+  }
+
+  get dutend(): number {
+    this.assertWind();
+    return this.gamma_u * this.we - this.utend
+  }
+
+  get dvtend(): number {
+    this.assertWind();
+    return this.gamma_v * this.we - this.vtend
   }
 
   /** Tendency of CLB [m s-1]*/
@@ -79,42 +97,26 @@ export class CLASS {
 
   /** Tendency of mixed-layer potential temperature [K s-1] */
   get thetatend(): number {
-    this.hasMixedLayer();
-    return (this.wtheta - this.wthetae) / this.h + this._cfg.advtheta;
-  }
-
-  /** Free atmosphere potential temperature lapse rate */
-  get gammatheta(): number {
-    this.hasMixedLayer();
-    const { z_theta, gammatheta } = this._cfg;
-    const i = findInsertIndex(z_theta, this.h);
-    return gammatheta[i] ?? 0;
-  }
-
-  /** Free atmosphere specific humidity lapse rate */
-  get gammaq(): number {
-    this.hasMixedLayer();
-    const { z_q, gammaq } = this._cfg;
-    const i = findInsertIndex(z_q, this.h);
-    return gammaq[i] ?? 0;
+    this.assertMixedLayer();
+    return (this.wtheta - this.wthetae) / this.ml.h + this._cfg.advtheta;
   }
 
   /** Tendency of potential temperature jump at h [K s-1] */
   get dthetatend(): number {
-    this.hasMixedLayer();
+    this.assertMixedLayer();
     const w_th_ft = 0.0; // TODO: add free troposphere switch
     return this.gammatheta * this.we - this.thetatend + w_th_ft;
   }
 
   /** Tendency of mixed-layer specific humidity [kg kg-1 s-1] */
   get qtend(): number {
-    this.hasMixedLayer();
-    return (this.wq - this.wqe) / this.h + this._cfg.advq;
+    this.assertMixedLayer();
+    return (this.wq - this.wqe) / this.ml.h + this._cfg.advq;
   }
 
   /** Tendency of specific humidity jump at h[kg kg-1 s-1] */
   get dqtend(): number {
-    this.hasMixedLayer();
+    this.assertMixedLayer();
     const w_q_ft = 0; // TODO: add free troposphere switch
     return this.gammaq * this.we - this.qtend + w_q_ft;
   }
@@ -133,47 +135,128 @@ export class CLASS {
 
   /** Large-scale vertical velocity [m s-1]. */
   get ws(): number {
-    this.hasMixedLayer();
-    return -this._cfg.divU * this.h;
+    this.assertMixedLayer();
+    return -this._cfg.divU * this.ml.h;
   }
 
   /** Entrainment kinematic heat flux [K m s-1]. */
   get wthetae(): number {
-    return -this.we * this.dtheta;
+    this.assertMixedLayer();
+    return -this.we * this.ml.dtheta;
   }
-
+  
   /** Entrainment moisture flux [kg kg-1 m s-1]. */
   get wqe(): number {
-    return -this.we * this.dq;
+    this.assertMixedLayer();
+    return -this.we * this.ml.dq;
   }
 
   /** Entrainment kinematic virtual heat flux [K m s-1]. */
   get wthetave(): number {
-    this.hasMixedLayer();
+    this.assertMixedLayer();
     return -this._cfg.beta * this.wthetav;
   }
 
   /** Virtual temperature jump at h [K]. */
   get dthetav(): number {
+    this.assertMixedLayer()
     return (
-      (this.theta + this.dtheta) * (1.0 + 0.61 * (this.q + this.dq)) -
-      this.theta * (1.0 + 0.61 * this.q)
+      (this.ml.theta + this.ml.dtheta) * (1.0 + 0.61 * (this.ml.q + this.ml.dq)) -
+      this.ml.theta * (1.0 + 0.61 * this.ml.q)
     );
   }
 
   get wtheta(): number {
-    this.hasMixedLayer();
+    this.assertMixedLayer();
     return interpolateHourly(this._cfg.wtheta, this.t);
   }
 
   get wq(): number {
-    this.hasMixedLayer();
+    this.assertMixedLayer();
     return interpolateHourly(this._cfg.wq, this.t);
   }
 
   /** Surface kinematic virtual heat flux [K m s-1]. */
   get wthetav(): number {
-    this.hasMixedLayer();
-    return this.wtheta + 0.61 * this.theta * this.wq;
+    this.assertMixedLayer();
+    return this.wtheta + 0.61 * this.ml.theta * this.wq;
   }
-}
+
+  // Lapse rates
+
+  /** Free atmosphere potential temperature lapse rate */
+  get gammatheta(): number {
+    this.assertMixedLayer();
+    const { z_theta, gammatheta } = this._cfg;
+    const i = findInsertIndex(z_theta, this.ml.h);
+    return gammatheta[i] ?? 0;
+  }
+
+  /** Free atmosphere specific humidity lapse rate */
+  get gammaq(): number {
+    this.assertMixedLayer();
+    const { z_q, gammaq } = this._cfg;
+    const i = findInsertIndex(z_q, this.ml.h);
+    return gammaq[i] ?? 0;
+  }
+
+  /** Free atmosphere u-wind lapse rate */
+  get gamma_u(): number {
+    this.assertWind();
+    const { z_u, gamma_u } = this._cfg;
+    const i = findInsertIndex(z_u, this.ml.h);
+    return gamma_u[i] ?? 0;
+  }
+
+  /** Free atmosphere v-wind lapse rate */
+  get gamma_v(): number {
+    this.assertWind();
+    const { z_v, gamma_v } = this._cfg;
+    const i = findInsertIndex(z_v, this.ml.h);
+    return gamma_v[i] ?? 0;
+  }
+
+  // Type guards
+  private assertMixedLayer(): asserts this is CLASS & {
+    _cfg: MixedLayerConfig;
+    ml: MixedLayer;
+  } {
+    if (!this._cfg.sw_ml || this.ml === undefined) {
+      throw new Error("Mixed layer is not enabled in config");
+    }
+  }
+
+  private assertWind(): asserts this is CLASS & {
+    _cfg: MixedLayerConfig & WindConfig;
+    ml: MixedLayer;
+    wind: Wind;
+  } {
+    this.assertMixedLayer();
+    if (!this._cfg.sw_wind || this.wind === undefined) {
+      throw new Error("Wind is not enabled in config or wind state is not initialized.");
+    }
+  }
+
+  get q(){
+    return this.ml?.q || 999
+  }
+  
+  /**
+   * Retrieve a value by name, treating nested state (wind, ml) as if it's flat.
+   * 
+   * Lookup order:
+   *  1. Property on the class instance itself.
+   *  2. Property on `wind`, if available.
+   *  3. Property on `ml`, if available.
+   * 
+   * Returns `999` if the property is not found in any of the above.
+   */
+  getValue(name: string): number {
+    // biome-ignore lint/suspicious/noExplicitAny: <explanation>
+    const self = this as any;
+    if (name in self && typeof self[name]==="number") return self[name];
+    if (this.wind && name in this.wind) return this.wind[name as keyof Wind];
+    if (this.ml && name in this.ml) return this.ml[name as keyof MixedLayer];
+    return 999;
+  }
+}
\ No newline at end of file
diff --git a/packages/class/src/config.ts b/packages/class/src/config.ts
index 7b1686a..26cb86f 100644
--- a/packages/class/src/config.ts
+++ b/packages/class/src/config.ts
@@ -345,50 +345,56 @@ const untypedSchema = {
   ],
 };
 
-// TODO generate this from ./config.schema.json
-// at the momemt json-schema-to-typescript does not understand if/then/else
-// and cannot generate such minimalistic types
-export type Config = {
+
+type GeneralConfig = {
   name: string;
   description?: string;
   dt: number;
   runtime: number;
-} & ( // Mixed layer
-  | {
-      sw_ml: true;
-      h: number;
-      theta: number;
-      dtheta: number;
-      q: number;
-      dq: number;
-      wtheta: number[];
-      advtheta: number;
-      gammatheta: number[];
-      wq: number[];
-      advq: number;
-      gammaq: number[];
-      divU: number;
-      beta: number;
-      z_theta: number[];
-      z_q: number[];
-    }
-  // Else, sw_ml key should be absent or false
-  | { sw_ml?: false }
-) & // Wind
-  (
-    | {
-        sw_wind: true;
-        u: number;
-        du: number;
-        gamma_u: number[];
-        z_u: number[];
-        v: number;
-        dv: number;
-        gamma_v: number[];
-        z_v: number[];
-      } // Else, sw_wind key should be absent or false
-    | { sw_wind?: true }
-  );
+}
+
+export type WindConfig = {
+  sw_wind: true;
+  u: number;
+  v: number;
+  du: number;
+  dv: number;
+  gamma_u: number[];
+  z_u: number[];
+  gamma_v: number[];
+  z_v: number[];
+};
+type NoWindConfig = {
+  sw_wind?: false;
+};
+
+export type MixedLayerConfig = {
+  sw_ml: true;
+  h: number;
+  theta: number;
+  dtheta: number;
+  q: number;
+  dq: number;
+  wtheta: number[];
+  advtheta: number;
+  gammatheta: number[];
+  wq: number[];
+  advq: number;
+  gammaq: number[];
+  divU: number;
+  beta: number;
+  z_theta: number[];
+  z_q: number[];
+}
+type NoMixedLayerConfig = {
+  sw_ml?: false 
+}
+
+export type Config = (
+  GeneralConfig 
+  & (MixedLayerConfig | NoMixedLayerConfig) 
+  & (WindConfig | NoWindConfig)
+);
 
 export type JsonSchemaOfConfig = JSONSchemaType<Config>;
 export const jsonSchemaOfConfig =
diff --git a/packages/class/src/runner.ts b/packages/class/src/runner.ts
index d5b9bc7..8697ae5 100644
--- a/packages/class/src/runner.ts
+++ b/packages/class/src/runner.ts
@@ -14,8 +14,7 @@ export function runClass(config: Config): ClassOutput {
 
   const writeOutput = () => {
     for (const v of outputVariables) {
-      const value =
-        model[v.key as keyof CLASS] ?? (v.key === "t" ? model.t : undefined);
+      const value = model.getValue(v.key);
       if (value !== undefined) {
         (output[v.key] as number[]).push(value as number);
       }

From 8cd8061bed9211bb3b7deddb87cc49fc2f62fd61 Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Tue, 22 Apr 2025 21:37:04 +0200
Subject: [PATCH 36/47] Complete wind implementation in model; include it in
 timeseries plot for validation

---
 packages/class/src/class.ts  | 91 ++++++++++++++++++++++++------------
 packages/class/src/config.ts | 85 +++++++++++++++++++++++----------
 packages/class/src/output.ts | 12 +++++
 3 files changed, 133 insertions(+), 55 deletions(-)

diff --git a/packages/class/src/class.ts b/packages/class/src/class.ts
index e7720bf..c3f4a25 100644
--- a/packages/class/src/class.ts
+++ b/packages/class/src/class.ts
@@ -5,13 +5,18 @@
 import type { Config, MixedLayerConfig, WindConfig } from "./config.js";
 import { findInsertIndex, interpolateHourly } from "./utils.js";
 
+// Constants
+const CONSTANTS = {
+  fc: 1e-4, // Coriolis parameter [m s-1]
+};
+
 // Group related variables so we can require them as complete sets
 type Wind = {
   u: number;
   v: number;
   du: number;
   dv: number;
-}
+};
 
 type MixedLayer = {
   h: number;
@@ -19,7 +24,7 @@ type MixedLayer = {
   dtheta: number;
   q: number;
   dq: number;
-}
+};
 
 export class CLASS {
   _cfg: Config;
@@ -37,12 +42,12 @@ export class CLASS {
     if (config.sw_ml) {
       const { h, theta, dtheta, q, dq } = config;
       this.ml = { h, theta, dtheta, q, dq };
-      
-      if (config.sw_wind){
-        const {u, v, du, dv} = config
-        this.wind = {u, v, du, dv}
+
+      if (config.sw_wind) {
+        const { u, v, du, dv } = config;
+        this.wind = { u, v, du, dv };
       }
-    }    
+    }
   }
 
   /**
@@ -50,17 +55,17 @@ export class CLASS {
    */
   update() {
     const dt = this._cfg.dt;
-    if (this.ml){
+    if (this.ml) {
       this.ml.h += dt * this.htend;
       this.ml.theta += dt * this.thetatend;
       this.ml.dtheta += dt * this.dthetatend;
       this.ml.q += dt * this.qtend;
       this.ml.dq += dt * this.dqtend;
-      if (this.wind){
-        this.wind.u += dt * this.utend
-        this.wind.v += dt * this.vtend
-        this.wind.du += dt * this.dutend
-        this.wind.dv += dt * this.dvtend
+      if (this.wind) {
+        this.wind.u += dt * this.utend;
+        this.wind.v += dt * this.vtend;
+        this.wind.du += dt * this.dutend;
+        this.wind.dv += dt * this.dvtend;
       }
     }
     this.t += dt;
@@ -69,25 +74,46 @@ export class CLASS {
   get utend(): number {
     this.assertWind();
     // TODO make sure all variables are available
-    // return -this.fc * this.wind.dv + (this.uw + this.we * this.wind.du) / this.ml.h + this.advu
-    return 0
+    return (
+      -CONSTANTS.fc * this.wind.dv +
+      (this.uw + this.we * this.wind.du) / this.ml.h +
+      this._cfg.advu
+    );
+    // return 0
   }
-  
+
   get vtend(): number {
     this.assertWind();
     // TODO make sure all variables are available
-    // return this.fc * this.wind.du + (this.vw + this.we * this.wind.dv) / this.ml.h + this.advv
-    return 0
+    return (
+      CONSTANTS.fc * this.wind.du +
+      (this.vw + this.we * this.wind.dv) / this.ml.h +
+      this._cfg.advv
+    );
   }
 
   get dutend(): number {
     this.assertWind();
-    return this.gamma_u * this.we - this.utend
+    return this.gamma_u * this.we - this.utend;
   }
 
   get dvtend(): number {
     this.assertWind();
-    return this.gamma_v * this.we - this.vtend
+    return this.gamma_v * this.we - this.vtend;
+  }
+
+  get uw(): number {
+    this.assertWind();
+    const { u, v } = this.wind;
+    const { ustar } = this._cfg;
+    return -Math.sign(u) * (ustar ** 4 / (v ** 2 / u ** 2 + 1)) ** 0.5;
+  }
+
+  get vw(): number {
+    this.assertWind();
+    const { u, v } = this.wind;
+    const { ustar } = this._cfg;
+    return -Math.sign(v) * (ustar ** 4 / (u ** 2 / v ** 2 + 1)) ** 0.5;
   }
 
   /** Tendency of CLB [m s-1]*/
@@ -144,7 +170,7 @@ export class CLASS {
     this.assertMixedLayer();
     return -this.we * this.ml.dtheta;
   }
-  
+
   /** Entrainment moisture flux [kg kg-1 m s-1]. */
   get wqe(): number {
     this.assertMixedLayer();
@@ -159,9 +185,10 @@ export class CLASS {
 
   /** Virtual temperature jump at h [K]. */
   get dthetav(): number {
-    this.assertMixedLayer()
+    this.assertMixedLayer();
     return (
-      (this.ml.theta + this.ml.dtheta) * (1.0 + 0.61 * (this.ml.q + this.ml.dq)) -
+      (this.ml.theta + this.ml.dtheta) *
+        (1.0 + 0.61 * (this.ml.q + this.ml.dq)) -
       this.ml.theta * (1.0 + 0.61 * this.ml.q)
     );
   }
@@ -233,30 +260,32 @@ export class CLASS {
   } {
     this.assertMixedLayer();
     if (!this._cfg.sw_wind || this.wind === undefined) {
-      throw new Error("Wind is not enabled in config or wind state is not initialized.");
+      throw new Error(
+        "Wind is not enabled in config or wind state is not initialized.",
+      );
     }
   }
 
-  get q(){
-    return this.ml?.q || 999
+  get q() {
+    return this.ml?.q || 999;
   }
-  
+
   /**
    * Retrieve a value by name, treating nested state (wind, ml) as if it's flat.
-   * 
+   *
    * Lookup order:
    *  1. Property on the class instance itself.
    *  2. Property on `wind`, if available.
    *  3. Property on `ml`, if available.
-   * 
+   *
    * Returns `999` if the property is not found in any of the above.
    */
   getValue(name: string): number {
     // biome-ignore lint/suspicious/noExplicitAny: <explanation>
     const self = this as any;
-    if (name in self && typeof self[name]==="number") return self[name];
+    if (name in self && typeof self[name] === "number") return self[name];
     if (this.wind && name in this.wind) return this.wind[name as keyof Wind];
     if (this.ml && name in this.ml) return this.ml[name as keyof MixedLayer];
     return 999;
   }
-}
\ No newline at end of file
+}
diff --git a/packages/class/src/config.ts b/packages/class/src/config.ts
index 26cb86f..c5822fb 100644
--- a/packages/class/src/config.ts
+++ b/packages/class/src/config.ts
@@ -255,19 +255,27 @@ const untypedSchema = {
           u: {
             symbol: "u",
             type: "number",
-            unit: "m s-1",
-            default: 0,
+            unit: "m s⁻¹",
+            default: 6,
             title: "Mixed-layer u-wind speed",
             "ui:group": "Wind",
           },
           du: {
             symbol: "Δu",
             type: "number",
-            unit: "m s-1",
-            default: 0,
+            unit: "m s⁻¹",
+            default: 4,
             title: "U-wind jump at h",
             "ui:group": "Wind",
           },
+          advu: {
+            symbol: "adv(u)", // _adv not possible in unicode
+            type: "number",
+            "ui:group": "Wind",
+            unit: "m s⁻²",
+            default: 0,
+            title: "Advection of u-wind",
+          },
           gamma_u: {
             symbol: "γ<sub>u</sub>",
             type: "array",
@@ -275,7 +283,7 @@ const untypedSchema = {
               type: "number",
             },
             minItems: 1,
-            unit: "s-1",
+            unit: "s⁻¹",
             default: [0],
             title: "Free atmosphere u-wind speed lapse rate",
             description: "Specify one or multiple segments",
@@ -289,7 +297,7 @@ const untypedSchema = {
             },
             minItems: 1,
             unit: "m",
-            default: [0],
+            default: [5000],
             title: "Anchor point(s) for γ_u",
             description:
               "Each value specifies the end of the corresponding segment in γ_u",
@@ -298,19 +306,27 @@ const untypedSchema = {
           v: {
             symbol: "v",
             type: "number",
-            unit: "m s-1",
-            default: 0,
+            unit: "m s⁻¹",
+            default: -4,
             title: "Mixed-layer v-wind speed",
             "ui:group": "Wind",
           },
           dv: {
             symbol: "Δv",
             type: "number",
-            unit: "m s-1",
-            default: 0,
+            unit: "m s⁻¹",
+            default: 4,
             title: "V-wind jump at h",
             "ui:group": "Wind",
           },
+          advv: {
+            symbol: "adv(v)", // _adv not possible in unicode
+            type: "number",
+            "ui:group": "Wind",
+            unit: "m s⁻²",
+            default: 0,
+            title: "Advection of v-wind",
+          },
           gamma_v: {
             symbol: "γ<sub>v</sub>",
             type: "array",
@@ -318,7 +334,7 @@ const untypedSchema = {
               type: "number",
             },
             minItems: 1,
-            unit: "s-1",
+            unit: "s⁻¹",
             default: [0],
             title: "Free atmosphere v-wind speed lapse rate",
             description: "Specify one or multiple segments",
@@ -332,26 +348,45 @@ const untypedSchema = {
             },
             minItems: 1,
             unit: "m",
-            default: [0],
+            default: [5000],
             title: "Anchor point(s) for γ_v",
             description:
               "Each value specifies the end of the corresponding segment in γ_v",
             "ui:group": "Wind",
           },
+          ustar: {
+            symbol: "u*",
+            type: "number",
+            unit: "m s⁻¹",
+            title: "Surface friction velocity",
+            "ui:group": "Wind",
+            default: 0.3,
+          },
         },
-        required: ["u", "du", "gamma_u", "z_u", "v", "dv", "gamma_v", "z_v"],
+        required: [
+          "u",
+          "du",
+          "advu",
+          "gamma_u",
+          "z_u",
+          "v",
+          "dv",
+          "advv",
+          "gamma_v",
+          "z_v",
+          "ustar",
+        ],
       },
     },
   ],
 };
 
-
 type GeneralConfig = {
   name: string;
   description?: string;
   dt: number;
   runtime: number;
-}
+};
 
 export type WindConfig = {
   sw_wind: true;
@@ -359,10 +394,13 @@ export type WindConfig = {
   v: number;
   du: number;
   dv: number;
+  advu: number;
+  advv: number;
   gamma_u: number[];
-  z_u: number[];
   gamma_v: number[];
+  z_u: number[];
   z_v: number[];
+  ustar: number;
 };
 type NoWindConfig = {
   sw_wind?: false;
@@ -385,16 +423,15 @@ export type MixedLayerConfig = {
   beta: number;
   z_theta: number[];
   z_q: number[];
-}
+};
 type NoMixedLayerConfig = {
-  sw_ml?: false 
-}
+  sw_ml?: false;
+};
 
-export type Config = (
-  GeneralConfig 
-  & (MixedLayerConfig | NoMixedLayerConfig) 
-  & (WindConfig | NoWindConfig)
-);
+// TODO: Don't allow WindConfig with NoMixedLayerConfig
+export type Config = GeneralConfig &
+  (MixedLayerConfig | NoMixedLayerConfig) &
+  (WindConfig | NoWindConfig);
 
 export type JsonSchemaOfConfig = JSONSchemaType<Config>;
 export const jsonSchemaOfConfig =
diff --git a/packages/class/src/output.ts b/packages/class/src/output.ts
index e74b90e..0af2cf9 100644
--- a/packages/class/src/output.ts
+++ b/packages/class/src/output.ts
@@ -84,6 +84,18 @@ export const outputVariables: OutputVariable[] = [
     unit: "kg kg⁻¹ m s⁻¹",
     symbol: "(w'q')ₛ",
   },
+  {
+    key: "u",
+    title: "Mixed-layer u-wind component",
+    unit: "m s⁻¹",
+    symbol: "u",
+  },
+  {
+    key: "v",
+    title: "Mixed-layer v-wind component",
+    unit: "m s⁻¹",
+    symbol: "v",
+  },
 ];
 
 export type ClassOutput = {

From 8afe676b297c18dc681b1e965993f36a62a384a8 Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Tue, 22 Apr 2025 22:03:58 +0200
Subject: [PATCH 37/47] Add varnavas reference config as preset

---
 apps/class-solid/src/lib/presets.ts           |  2 +
 .../class-solid/src/lib/presets/varnavas.json | 42 +++++++++++++++++++
 2 files changed, 44 insertions(+)
 create mode 100644 apps/class-solid/src/lib/presets/varnavas.json

diff --git a/apps/class-solid/src/lib/presets.ts b/apps/class-solid/src/lib/presets.ts
index ace4524..2dfce3f 100644
--- a/apps/class-solid/src/lib/presets.ts
+++ b/apps/class-solid/src/lib/presets.ts
@@ -8,6 +8,7 @@ import { overwriteDefaultsInJsonSchema } from "@classmodel/form/utils";
 import type { DefinedError, JSONSchemaType, ValidateFunction } from "ajv";
 // TODO replace with preset of a forest fire
 import deathValley from "./presets/death-valley.json";
+import varnavas from "./presets/varnavas.json";
 
 const presetConfigs = [
   {
@@ -15,6 +16,7 @@ const presetConfigs = [
     description: "The classic default configuration",
   },
   deathValley,
+  varnavas,
 ] as const;
 
 export interface Preset {
diff --git a/apps/class-solid/src/lib/presets/varnavas.json b/apps/class-solid/src/lib/presets/varnavas.json
new file mode 100644
index 0000000..14f0213
--- /dev/null
+++ b/apps/class-solid/src/lib/presets/varnavas.json
@@ -0,0 +1,42 @@
+{
+  "name": "Varnavas",
+  "description": "EWED Reference configuration",
+  "h": 665.4086303710938,
+  "theta": 301.971435546875,
+  "dtheta": 0.889312744140625,
+  "gammatheta": [0.0015336532378569245, 0.006792282219976187],
+  "z_theta": [1667.025390625, 2500],
+  "q": 0.010794480331242085,
+  "dq": -0.001073240302503109,
+  "gammaq": [-2.382889988439274e-6, -2.5458646177867195e-6],
+  "z_q": [1360.52392578125, 2500],
+  "divU": 1.0981982995872386e-5,
+  "u": -1.6769592761993408,
+  "du": -1.1726601123809814,
+  "gamma_u": [-0.001995581667870283, -0.002064943080767989],
+  "z_u": [1573.5614013671875, 2500],
+  "v": -10.087028503417969,
+  "dv": -1.5727958679199219,
+  "gamma_v": [-0.0005029001622460783, 0.004509935155510902],
+  "z_v": [3037.957763671875, 2500],
+  "wtheta": [
+    0.33137200988670706, 0.28088430353706567, 0.21148639643745845,
+    0.1354453158978963, 0.0558820378352221, 0.0001602229911650289, 0.0, 0.0,
+    0.0, 0.0, 0.0, 0.0
+  ],
+  "wq": [
+    1.9756698748096824e-5, 2.111953654093668e-5, 2.2018328309059143e-5,
+    2.2002774130669422e-5, 1.9648385205073282e-5, 1.6331905499100685e-5,
+    1.3947577826911584e-5, 1.2534562301880214e-5, 1.1651739441731479e-5,
+    1.1526963135111146e-5, 1.3352756468520965e-5, 1.3273539479996543e-5
+  ],
+  "sw_wind": true,
+  "advtheta": 0,
+  "advq": 0,
+  "advu": 0,
+  "advv": 0,
+  "beta": 0.2,
+  "ustar": 0.3,
+  "dt": 60,
+  "runtime": 43200
+}

From a54c64db7ffe8cea516efac5d0b3c2b1a968d828 Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Tue, 22 Apr 2025 22:18:16 +0200
Subject: [PATCH 38/47] Add u and v to profile plots

---
 apps/class-solid/src/components/Analysis.tsx |  2 +
 apps/class-solid/src/lib/profiles.ts         | 62 ++++++++++++++++++++
 packages/class/src/output.ts                 | 12 ++++
 3 files changed, 76 insertions(+)

diff --git a/apps/class-solid/src/components/Analysis.tsx b/apps/class-solid/src/components/Analysis.tsx
index cf2af99..75578a1 100644
--- a/apps/class-solid/src/components/Analysis.tsx
+++ b/apps/class-solid/src/components/Analysis.tsx
@@ -226,6 +226,8 @@ export function VerticalProfilePlot({
   const variableOptions = {
     "Potential temperature [K]": "theta",
     "Specific humidity [kg/kg]": "q",
+    "u-wind component [m/s]": "u",
+    "v-wind component [m/s]": "v",
   };
 
   const classVariable = () =>
diff --git a/apps/class-solid/src/lib/profiles.ts b/apps/class-solid/src/lib/profiles.ts
index 2f2940a..ba2a015 100644
--- a/apps/class-solid/src/lib/profiles.ts
+++ b/apps/class-solid/src/lib/profiles.ts
@@ -45,6 +45,7 @@ export function getVerticalProfiles(
     }
     return profile;
   }
+
   if (variable === "q") {
     let z = output.h.slice(t)[0];
     let q = output.q.slice(t)[0];
@@ -74,6 +75,67 @@ export function getVerticalProfiles(
     }
     return profile;
   }
+
+  if (config.sw_wind && variable === "u") {
+    let z = output.h.slice(t)[0];
+    let u = output.u.slice(t)[0];
+    const du = output.du.slice(t)[0];
+    const gammau = config.gamma_u;
+    const z_u = config.z_u;
+    const maxHeight = z_u.slice(-1)[0];
+
+    // Mixed layer
+    const profile = [
+      { x: u, y: 0 },
+      { x: u, y: z },
+    ];
+
+    // Inversion
+    u += du;
+    profile.push({ x: u, y: z });
+
+    // Free troposphere
+    while (z < maxHeight) {
+      const idx = findInsertIndex(z_u, z);
+      const lapse_rate = gammau[idx] ?? 0;
+      const dz = z_u[idx] - z;
+      z += dz;
+      u += lapse_rate * dz;
+      profile.push({ x: u, y: z });
+    }
+    return profile;
+  }
+
+  if (config.sw_wind && variable === "v") {
+    let z = output.h.slice(t)[0];
+    let v = output.v.slice(t)[0];
+    const dv = output.dv.slice(t)[0];
+    const gammav = config.gamma_v;
+    const z_v = config.z_v;
+    const maxHeight = z_v.slice(-1)[0];
+
+    // Mixed layer
+    const profile = [
+      { x: v, y: 0 },
+      { x: v, y: z },
+    ];
+
+    // Inversion
+    v += dv;
+    profile.push({ x: v, y: z });
+
+    // Free troposphere
+    while (z < maxHeight) {
+      const idx = findInsertIndex(z_v, z);
+      const lapse_rate = gammav[idx] ?? 0;
+      const dz = z_v[idx] - z;
+      z += dz;
+      v += lapse_rate * dz;
+      profile.push({ x: v, y: z });
+    }
+    return profile;
+  }
+
   return [];
 }
 
diff --git a/packages/class/src/output.ts b/packages/class/src/output.ts
index 0af2cf9..f6a7137 100644
--- a/packages/class/src/output.ts
+++ b/packages/class/src/output.ts
@@ -96,6 +96,18 @@ export const outputVariables: OutputVariable[] = [
     unit: "m s⁻¹",
     symbol: "v",
   },
+  {
+    key: "du",
+    title: "U-wind jump at h",
+    unit: "m s⁻¹",
+    symbol: "u",
+  },
+  {
+    key: "dv",
+    title: "V-wind jump at h",
+    unit: "m s⁻¹",
+    symbol: "v",
+  },
 ];
 
 export type ClassOutput = {

From 6e5ca4ee98d7912ba4884e7a7b1729440b8224d7 Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Tue, 22 Apr 2025 22:27:26 +0200
Subject: [PATCH 39/47] Make sure thermodynamic plot works with piecewise lapse
 rate

---
 apps/class-solid/src/lib/profiles.ts | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/apps/class-solid/src/lib/profiles.ts b/apps/class-solid/src/lib/profiles.ts
index ba2a015..39e44fd 100644
--- a/apps/class-solid/src/lib/profiles.ts
+++ b/apps/class-solid/src/lib/profiles.ts
@@ -238,6 +238,8 @@ export function getThermodynamicProfiles(
   const h = output.h.slice(t)[0];
   const gammaTheta = config.gammatheta;
   const gammaq = config.gammaq;
+  const z_theta = config.z_theta;
+  const z_q = config.z_q;
 
   const nz = 25;
   let dz = h / nz;
@@ -265,11 +267,18 @@ export function getThermodynamicProfiles(
   soundingData.push({ p, T, Td });
 
   // Free troposphere
+  let z = zArrayMixedLayer.slice(-1)[0];
   dz = 200;
   while (p > 100) {
-    theta += dz * gammaTheta;
-    q += dz * gammaq;
+    // Note: idx can exceed length of anchor points, then lapse becomes undefined and profile stops
+    const idx_th = findInsertIndex(z_theta, z);
+    const lapse_theta = gammaTheta[idx_th];
+    const idx_q = findInsertIndex(z_q, z);
+    const lapse_q = gammaq[idx_q];
+    theta += dz * lapse_theta;
+    q += dz * lapse_q;
     p += pressureDiff(T, q, p, dz);
+    z += dz;
     T = thetaToT(theta, p);
     Td = dewpoint(q, p);
 

From 678ffdc57a126ec801843ea03e5618a088bccd9f Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Tue, 22 Apr 2025 22:39:26 +0200
Subject: [PATCH 40/47] Determine axis extents of profile plots posterior to
 generating the profiles, so lapse part is fully included

---
 apps/class-solid/src/components/Analysis.tsx | 32 ++++++++------------
 1 file changed, 13 insertions(+), 19 deletions(-)

diff --git a/apps/class-solid/src/components/Analysis.tsx b/apps/class-solid/src/components/Analysis.tsx
index 75578a1..3f3f11e 100644
--- a/apps/class-solid/src/components/Analysis.tsx
+++ b/apps/class-solid/src/components/Analysis.tsx
@@ -235,26 +235,7 @@ export function VerticalProfilePlot({
 
   const observations = () =>
     flatObservations().map((o) => observationsForProfile(o, classVariable()));
-  const obsAllX = () =>
-    observations().flatMap((obs) => obs.data.map((d) => d.x));
-  const obsAllY = () =>
-    observations().flatMap((obs) => obs.data.map((d) => d.y));
-
-  const allValues = () => [
-    ...flatExperiments().flatMap((e) =>
-      e.output ? e.output[classVariable()] : [],
-    ),
-    ...obsAllX(),
-  ];
-  const allHeights = () => [
-    ...flatExperiments().flatMap((e) => (e.output ? e.output.h : [])),
-    ...obsAllY(),
-  ];
 
-  // TODO: better to include jump at top in extent calculation rather than adding random margin.
-  const xLim = () => getNiceAxisLimits(allValues(), 1);
-  const yLim = () =>
-    [0, getNiceAxisLimits(allHeights(), 0)[1]] as [number, number];
   const profileData = () =>
     flatExperiments().map((e) => {
       const { config, output, ...formatting } = e;
@@ -273,6 +254,19 @@ export function VerticalProfilePlot({
       };
     });
 
+  const allX = () => [
+    ...profileData().flatMap((p) => p.data.map((d) => d.x)),
+    ...observations().flatMap((obs) => obs.data.map((d) => d.x)),
+  ];
+  const allY = () => [
+    ...profileData().flatMap((p) => p.data.map((d) => d.y)),
+    ...observations().flatMap((obs) => obs.data.map((d) => d.y)),
+  ];
+
+  // TODO: better to include jump at top in extent calculation rather than adding random margin.
+  const xLim = () => getNiceAxisLimits(allX(), 1);
+  const yLim = () => [0, getNiceAxisLimits(allY(), 0)[1]] as [number, number];
+
   function chartData() {
     return [...profileData(), ...observations()];
   }

From ca9e2017f4c2d6771f4b4120cb7270d78c75c8d7 Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Tue, 22 Apr 2025 22:49:11 +0200
Subject: [PATCH 41/47] Fix tests, set some values back to their previous
 default

---
 packages/class/src/class.test.ts    |  2 +-
 packages/class/src/config.ts        |  4 ++--
 packages/class/src/validate.test.ts | 30 +++++++++++++++++++++--------
 3 files changed, 25 insertions(+), 11 deletions(-)

diff --git a/packages/class/src/class.test.ts b/packages/class/src/class.test.ts
index 6b30209..9c1da65 100644
--- a/packages/class/src/class.test.ts
+++ b/packages/class/src/class.test.ts
@@ -17,7 +17,7 @@ describe("CLASS model", () => {
     assert.strictEqual(model._cfg.h, 200);
     assert.strictEqual(model._cfg.dt, 60);
     assert.deepEqual(model._cfg.wtheta, [0.1]);
-    assert.strictEqual(model._cfg.wq, 0.0001);
+    assert.deepEqual(model._cfg.wq, [0.0001]);
   });
 
   test("calling update advances the model time", () => {
diff --git a/packages/class/src/config.ts b/packages/class/src/config.ts
index c5822fb..480735d 100644
--- a/packages/class/src/config.ts
+++ b/packages/class/src/config.ts
@@ -123,7 +123,7 @@ const untypedSchema = {
             "ui:group": "Mixed layer",
             unit: "K m s⁻¹",
             title: "Surface kinematic heat flux",
-            default: [0.1, 0.2, 0.3, 0.4, 0.3, 0.2, 0.1],
+            default: [0.1],
             minItems: 1,
           },
           advtheta: {
@@ -154,7 +154,7 @@ const untypedSchema = {
             },
             "ui:group": "Mixed layer",
             unit: "kg kg⁻¹ m s⁻¹",
-            default: [0.0001, 0.0001, 0.0001, 0.0001, 0.0001],
+            default: [0.0001],
             minItems: 1,
             title: "Surface kinematic moisture flux",
           },
diff --git a/packages/class/src/validate.test.ts b/packages/class/src/validate.test.ts
index acc632a..e125466 100644
--- a/packages/class/src/validate.test.ts
+++ b/packages/class/src/validate.test.ts
@@ -50,24 +50,38 @@ describe("parse", () => {
     const output = parse(input);
 
     const expected = {
-      name: "",
-      description: "",
-      sw_ml: true,
       h: 200,
       theta: 288,
       dtheta: 1,
       q: 0.008,
       dq: -0.001,
-      dt: 60,
-      runtime: 43200,
       wtheta: [0.1],
       advtheta: 0,
-      gammatheta: 0.006,
-      wq: 0.0001,
+      gammatheta: [0.006],
+      wq: [0.0001],
       advq: 0,
-      gammaq: 0,
+      gammaq: [0],
       divU: 0,
       beta: 0.2,
+      z_theta: [5000],
+      z_q: [5000],
+      u: 6,
+      du: 4,
+      advu: 0,
+      gamma_u: [0],
+      z_u: [5000],
+      v: -4,
+      dv: 4,
+      advv: 0,
+      gamma_v: [0],
+      z_v: [5000],
+      ustar: 0.3,
+      name: "",
+      description: "",
+      dt: 60,
+      runtime: 43200,
+      sw_ml: true,
+      sw_wind: false,
     };
     assert.deepEqual(output, expected);
   });

From 119a01144412664c550949ed73b4be2ff00c9b2f Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Tue, 22 Apr 2025 23:00:20 +0200
Subject: [PATCH 42/47] Make wind from observations also visible in profile
 plots

---
 apps/class-solid/src/lib/profiles.ts | 31 +++++++++++++++++++++++++---
 1 file changed, 28 insertions(+), 3 deletions(-)

diff --git a/apps/class-solid/src/lib/profiles.ts b/apps/class-solid/src/lib/profiles.ts
index 39e44fd..62f4170 100644
--- a/apps/class-solid/src/lib/profiles.ts
+++ b/apps/class-solid/src/lib/profiles.ts
@@ -299,10 +299,23 @@ export function observationsForProfile(obs: Observation, variable = "theta") {
       const p = obs.pressure[i];
       const theta = tToTheta(T, p);
       const q = calculateSpecificHumidity(T, p, rh);
-      if (variable === "theta") {
-        return { y: h, x: theta };
+      const { u, v } = windSpeedDirectionToUV(
+        obs.windSpeed[i],
+        obs.windDirection[i],
+      );
+
+      switch (variable) {
+        case "theta":
+          return { y: h, x: theta };
+        case "q":
+          return { y: h, x: q };
+        case "u":
+          return { y: h, x: u };
+        case "v":
+          return { y: h, x: v };
+        default:
+          throw new Error(`Unknown variable '${variable}'`);
       }
-      return { y: h, x: q };
     }),
   };
 }
@@ -322,3 +335,15 @@ export function observationsForSounding(obs: Observation) {
     linestyle: "none",
   };
 }
+
+function windSpeedDirectionToUV(
+  speed: number,
+  directionDeg: number,
+): { u: number; v: number } {
+  const directionRad = (directionDeg * Math.PI) / 180;
+
+  const u = -speed * Math.sin(directionRad); // zonal (east-west)
+  const v = -speed * Math.cos(directionRad); // meridional (north-south)
+
+  return { u, v };
+}

From e60ef79821bcdf2dbea4de15fb7cb5ad4eb656ee Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Wed, 23 Apr 2025 11:54:23 +0200
Subject: [PATCH 43/47] Added Varnavas config with observations to test folder
 + increased max height in preset

---
 .../class-solid/src/lib/presets/varnavas.json |   8 +-
 apps/class-solid/tests/varnavas.json          | 128 ++++++++++++++++++
 2 files changed, 132 insertions(+), 4 deletions(-)
 create mode 100644 apps/class-solid/tests/varnavas.json

diff --git a/apps/class-solid/src/lib/presets/varnavas.json b/apps/class-solid/src/lib/presets/varnavas.json
index 14f0213..1fecfad 100644
--- a/apps/class-solid/src/lib/presets/varnavas.json
+++ b/apps/class-solid/src/lib/presets/varnavas.json
@@ -5,20 +5,20 @@
   "theta": 301.971435546875,
   "dtheta": 0.889312744140625,
   "gammatheta": [0.0015336532378569245, 0.006792282219976187],
-  "z_theta": [1667.025390625, 2500],
+  "z_theta": [1667.025390625, 3720],
   "q": 0.010794480331242085,
   "dq": -0.001073240302503109,
   "gammaq": [-2.382889988439274e-6, -2.5458646177867195e-6],
-  "z_q": [1360.52392578125, 2500],
+  "z_q": [1360.52392578125, 3720],
   "divU": 1.0981982995872386e-5,
   "u": -1.6769592761993408,
   "du": -1.1726601123809814,
   "gamma_u": [-0.001995581667870283, -0.002064943080767989],
-  "z_u": [1573.5614013671875, 2500],
+  "z_u": [1573.5614013671875, 3720],
   "v": -10.087028503417969,
   "dv": -1.5727958679199219,
   "gamma_v": [-0.0005029001622460783, 0.004509935155510902],
-  "z_v": [3037.957763671875, 2500],
+  "z_v": [3037.957763671875, 3720],
   "wtheta": [
     0.33137200988670706, 0.28088430353706567, 0.21148639643745845,
     0.1354453158978963, 0.0558820378352221, 0.0001602229911650289, 0.0, 0.0,
diff --git a/apps/class-solid/tests/varnavas.json b/apps/class-solid/tests/varnavas.json
new file mode 100644
index 0000000..87cbfba
--- /dev/null
+++ b/apps/class-solid/tests/varnavas.json
@@ -0,0 +1,128 @@
+{
+  "reference": {
+    "name": "Varnavas",
+    "description": "Varnavas wildfire case with observations"
+  },
+  "preset": "Varnavas",
+  "permutations": [],
+  "observations": [
+    {
+      "name": "2024-08-11_2144.sounding",
+      "height": [
+        20, 40, 60, 80, 100, 120, 140, 160, 180, 200, 220, 240, 260, 280, 300,
+        320, 340, 360, 380, 400, 420, 440, 460, 480, 500, 520, 540, 560, 580,
+        600, 620, 640, 660, 680, 700, 720, 740, 760, 780, 800, 820, 840, 860,
+        880, 900, 920, 940, 960, 980, 1000, 1020, 1040, 1060, 1080, 1100, 1120,
+        1140, 1160, 1180, 1200, 1220, 1240, 1260, 1280, 1300, 1320, 1340, 1360,
+        1380, 1400, 1420, 1440, 1460, 1480, 1500, 1520, 1540, 1560, 1580, 1600,
+        1620, 1640, 1660, 1680, 1700, 1720, 1740, 1760, 1780, 1800, 1820, 1840,
+        1860, 1880, 1900, 1920, 1940, 1960, 1980, 2000, 2020, 2040, 2060, 2080,
+        2100, 2120, 2140, 2160, 2180, 2200, 2220, 2240, 2260, 2280, 2300, 2320,
+        2340, 2360, 2380, 2400, 2420, 2440, 2460, 2480, 2500, 2520, 2540, 2560,
+        2580, 2600, 2620, 2640, 2660, 2680, 2700, 2720, 2740, 2760, 2780, 2800,
+        2820, 2840, 2860, 2880, 2900, 2920, 2940, 2960, 2980, 3000, 3020, 3040,
+        3060, 3080, 3100, 3120, 3140, 3160, 3180, 3200, 3220, 3240, 3260, 3280,
+        3300, 3320, 3340, 3360, 3380, 3400, 3420, 3440, 3460, 3480, 3500, 3520,
+        3540, 3560, 3580, 3600, 3620, 3640, 3660, 3680, 3700, 3720
+      ],
+      "pressure": [
+        958.2, 956.04, 953.88, 951.73, 949.58, 947.43, 945.29, 943.16, 941.02,
+        938.89, 936.77, 934.64, 932.53, 930.41, 928.3, 926.19, 924.09, 921.99,
+        919.89, 917.8, 915.71, 913.63, 911.55, 909.47, 907.4, 905.33, 903.26,
+        901.2, 899.14, 897.08, 895.03, 892.98, 890.93, 888.89, 886.85, 884.82,
+        882.79, 880.77, 878.75, 876.73, 874.72, 872.71, 870.7, 868.69, 866.69,
+        864.7, 862.7, 860.71, 858.72, 856.74, 854.76, 852.78, 850.81, 848.84,
+        846.87, 844.91, 842.95, 840.99, 839.04, 837.09, 835.14, 833.2, 831.26,
+        829.32, 827.39, 825.46, 823.53, 821.61, 819.69, 817.77, 815.85, 813.94,
+        812.04, 810.15, 808.26, 806.38, 804.5, 802.62, 800.75, 798.87, 797.01,
+        795.15, 793.29, 791.44, 789.59, 787.75, 785.9, 784.07, 782.23, 780.4,
+        778.57, 776.75, 774.93, 773.11, 771.29, 769.48, 767.67, 765.87, 764.06,
+        762.27, 760.47, 758.68, 756.9, 755.11, 753.33, 751.56, 749.79, 748.02,
+        746.26, 744.5, 742.74, 740.99, 739.24, 737.49, 735.75, 734.01, 732.27,
+        730.54, 728.81, 727.09, 725.37, 723.65, 721.94, 720.23, 718.52, 716.82,
+        715.12, 713.43, 711.74, 710.05, 708.37, 706.69, 705.01, 703.34, 701.67,
+        700, 698.34, 696.68, 695.02, 693.36, 691.71, 690.06, 688.42, 686.77,
+        685.13, 683.49, 681.86, 680.23, 678.6, 676.97, 675.35, 673.73, 672.12,
+        670.5, 668.89, 667.29, 665.68, 664.08, 662.48, 660.89, 659.3, 657.71,
+        656.12, 654.54, 652.96, 651.38, 649.81, 648.24, 646.67, 645.1, 643.55,
+        642, 640.45, 638.91, 637.37, 635.83, 634.3, 632.77, 631.24, 629.72,
+        628.2, 626.68, 625.17, 623.66, 622.15, 620.65
+      ],
+      "temperature": [
+        26.25, 26.32, 26.31, 26.22, 26.04, 25.84, 25.68, 25.56, 25.42, 25.28,
+        25.15, 24.98, 24.85, 24.67, 24.51, 24.39, 24.25, 24.11, 23.93, 23.78,
+        23.69, 23.58, 23.43, 23.25, 23.05, 22.85, 22.58, 22.34, 22.15, 21.99,
+        21.84, 21.75, 21.7, 21.66, 21.6, 21.57, 21.57, 21.46, 21.3, 21.06,
+        20.81, 20.64, 20.44, 20.31, 20.16, 19.98, 19.78, 19.58, 19.31, 19.1,
+        18.92, 18.71, 18.56, 18.49, 18.43, 18.32, 18.19, 18.04, 17.87, 17.65,
+        17.42, 17.2, 17.02, 16.82, 16.58, 16.36, 16.19, 15.88, 15.48, 15.23,
+        14.99, 14.84, 15.84, 16.99, 17.14, 17.4, 17.61, 17.71, 17.7, 17.61,
+        17.49, 17.38, 17.23, 17.07, 16.92, 16.75, 16.62, 16.49, 16.35, 16.19,
+        16.02, 15.85, 15.66, 15.47, 15.29, 15.12, 14.97, 14.86, 14.81, 14.82,
+        14.84, 14.79, 14.72, 14.67, 14.65, 14.61, 14.5, 14.38, 14.3, 14.25,
+        14.16, 14.03, 13.89, 13.76, 13.7, 13.68, 13.61, 13.51, 13.46, 13.52,
+        13.65, 13.74, 13.75, 13.71, 13.63, 13.52, 13.44, 13.38, 13.31, 13.19,
+        13.06, 12.92, 12.77, 12.63, 12.5, 12.37, 12.21, 12.03, 11.88, 11.69,
+        11.51, 11.31, 11.09, 10.89, 10.7, 10.56, 10.49, 10.41, 10.3, 10.14,
+        9.99, 9.86, 9.71, 9.5, 9.31, 9.17, 9.01, 8.86, 8.72, 8.6, 8.52, 8.45,
+        8.34, 8.2, 8.05, 7.86, 7.69, 7.54, 7.43, 7.47, 7.96, 8.46, 8.92, 8.94,
+        8.84, 8.72, 8.65, 8.6, 8.49, 8.35, 8.23, 8.11, 8, 7.89, 7.78, 7.65
+      ],
+      "relativeHumidity": [
+        44.5, 44, 43.9, 43.9, 44.2, 44.5, 44.8, 45, 45.2, 45.3, 45.5, 45.8, 46,
+        46.3, 46.6, 46.8, 47, 47.2, 47.6, 47.8, 48, 48.2, 48.4, 48.7, 49.2,
+        49.6, 50.2, 50.8, 51.3, 51.7, 52, 52.1, 51.8, 51.6, 51.6, 51.4, 51.3,
+        51.2, 51.4, 51.9, 52.5, 52.9, 53.3, 53.5, 53.9, 54.3, 54.7, 55.1, 55.7,
+        56.2, 56.7, 57.1, 57.5, 57.5, 57.4, 57.4, 57.6, 57.8, 58.1, 58.6, 59.3,
+        60.1, 60.8, 61.5, 62.3, 62.9, 63.3, 64.3, 65.6, 66.8, 68, 68.7, 58,
+        44.8, 41.2, 36.5, 33.1, 31.2, 30.4, 30.4, 30.3, 30.1, 30, 30.1, 30.4,
+        30.8, 30.8, 30.9, 31, 31.2, 31.5, 31.8, 32.2, 32.5, 32.8, 33.2, 33.6,
+        33.8, 33.7, 33.2, 32.1, 30.3, 28.7, 27.3, 26, 25.2, 24.8, 24.6, 24,
+        23.2, 22.6, 22.3, 22.2, 21.6, 20.7, 19.7, 18.7, 17.9, 17.1, 16.3, 16,
+        16.1, 16.2, 16.3, 16.4, 16.5, 16.6, 16.5, 16.3, 16.4, 16.6, 16.6, 16.4,
+        16.3, 16.2, 16.2, 16.2, 16.2, 16.2, 16.2, 16.3, 16.5, 16.7, 16.9, 17,
+        16.7, 16.2, 16, 16.9, 18.4, 19.4, 19.8, 19.9, 20, 20.1, 20.1, 20, 19.9,
+        19.4, 17.7, 15.1, 12.7, 10.3, 8.9, 8.4, 8.6, 9, 9.8, 11.7, 14.1, 16.6,
+        16.4, 13, 11.5, 11, 10.4, 9.5, 8.7, 8, 7.4, 7.1, 6.6, 6.1, 5.6, 5.2, 5
+      ],
+      "windSpeed": [
+        4.57, 5.3, 6.04, 6.97, 7.68, 7.88, 7.92, 7.77, 7.54, 7.61, 8.15, 8.6,
+        9.31, 9.57, 9.78, 9.85, 9.87, 9.96, 10.22, 10.3, 10.21, 9.79, 9.56, 9.2,
+        9.27, 9.32, 9.68, 9.59, 9.68, 9.97, 11.23, 12.99, 14.43, 15.11, 15.27,
+        14.77, 14.22, 13.93, 13.63, 13.19, 12.94, 12.47, 12.39, 12.45, 12.98,
+        13.79, 15.16, 16.56, 17.42, 17.95, 18.31, 18.57, 18.54, 18.28, 17.7,
+        17.22, 16.81, 16.76, 16.96, 17.35, 17.72, 18.16, 18.47, 18.84, 19.39,
+        20.02, 20.05, 20.04, 20, 20.19, 20.27, 20.61, 20.33, 19.9, 18.8, 17.97,
+        17.21, 16.66, 16.17, 15.86, 15.58, 15.16, 14.73, 14.37, 13.99, 13.72,
+        13.43, 13.16, 12.82, 12.44, 12.13, 11.84, 11.69, 11.5, 11.33, 11.06,
+        10.73, 10.35, 10.02, 9.74, 9.65, 9.64, 9.66, 9.67, 9.63, 9.49, 9.36,
+        9.14, 8.92, 8.82, 8.88, 9.02, 9.28, 9.62, 9.96, 10.48, 11.04, 11.66,
+        12.09, 12.44, 12.63, 12.63, 12.53, 12.4, 12.13, 11.76, 11.35, 10.84,
+        10.49, 10.24, 10.01, 9.7, 9.45, 9.14, 8.87, 8.76, 8.69, 8.7, 8.7, 8.63,
+        8.56, 8.48, 8.39, 8.24, 8.11, 7.95, 7.96, 8.01, 8.21, 8.44, 8.61, 8.68,
+        8.77, 8.79, 8.71, 8.6, 8.51, 8.42, 8.29, 8.2, 8.09, 7.95, 7.82, 7.81,
+        7.9, 7.98, 7.94, 7.97, 7.98, 7.98, 8.98, 9.39, 10.08, 10.79, 11.34,
+        11.9, 12.38, 12.87, 13.25, 13.63, 13.96, 14.26, 14.62, 14.91, 15.1,
+        15.28
+      ],
+      "windDirection": [
+        355.8, 358, 359.9, 2.3, 3.5, 5, 6.7, 5.3, 359.1, 353.6, 356.6, 359.9,
+        4.2, 9.5, 13.1, 13.5, 13.7, 13.9, 13.5, 13.7, 15.3, 17.1, 21.7, 29.2,
+        33.1, 31.5, 32.2, 35.2, 34.2, 34.4, 37, 35.4, 27.4, 24.5, 25.3, 26.5,
+        27.9, 30.5, 32.9, 33.8, 33.4, 33.3, 37.9, 42.6, 47, 48.4, 49.6, 50.5,
+        51.7, 53.3, 52.6, 50.4, 51.5, 54, 54.7, 51.2, 47, 44.1, 43.1, 42.3,
+        41.9, 40.7, 39.9, 38.7, 35.9, 32.3, 29.8, 26.5, 23.4, 23.5, 26.1, 28.3,
+        30.4, 31.3, 31.2, 31, 30.9, 30.7, 29.7, 29.2, 29.1, 28.9, 28.6, 28.4,
+        29.1, 30.2, 31.4, 32.2, 33.4, 34.4, 34.5, 34.2, 34.5, 34.5, 34.4, 34,
+        33.9, 33.6, 33.4, 34.5, 35.8, 36.6, 37.8, 39.7, 41.8, 43.1, 43.9, 45.8,
+        48.4, 50.9, 52.1, 52.9, 53.3, 53.3, 52.9, 52.9, 51.9, 50.6, 48.7, 48.2,
+        49.2, 51, 52, 53.1, 53.9, 54.2, 53, 52.3, 53.4, 56.6, 57.9, 58.4, 58.4,
+        58.7, 59.4, 59.9, 60, 59.9, 60.3, 60.4, 60.1, 58.3, 55.6, 53.2, 50.6,
+        48.8, 48.4, 48.1, 46.3, 43.9, 42.8, 43.4, 44.7, 45.8, 46.8, 48.4, 48.9,
+        47.4, 45.7, 43.1, 40.8, 39.6, 39.3, 37.7, 35.4, 35.1, 34.8, 32.7, 29.3,
+        27.6, 34.8, 42.1, 49.6, 51.9, 53.8, 55.7, 56.7, 57.3, 56.9, 57.5, 57.7,
+        58.2, 57.8, 57.4, 57.1, 56.4
+      ]
+    }
+  ]
+}

From 36baad4e9310692f804392f9e98615efcdd098ae Mon Sep 17 00:00:00 2001
From: sverhoeven <s.verhoeven@esciencecenter.nl>
Date: Thu, 24 Apr 2025 11:52:57 +0200
Subject: [PATCH 44/47] Make labels of du and dv unique

---
 packages/class/src/output.ts | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/packages/class/src/output.ts b/packages/class/src/output.ts
index f6a7137..1fc455f 100644
--- a/packages/class/src/output.ts
+++ b/packages/class/src/output.ts
@@ -100,13 +100,13 @@ export const outputVariables: OutputVariable[] = [
     key: "du",
     title: "U-wind jump at h",
     unit: "m s⁻¹",
-    symbol: "u",
+    symbol: "Δu",
   },
   {
     key: "dv",
     title: "V-wind jump at h",
     unit: "m s⁻¹",
-    symbol: "v",
+    symbol: "Δv",
   },
 ];
 

From a92ff90431bdf034ec5f019941ef33c16c968da0 Mon Sep 17 00:00:00 2001
From: sverhoeven <s.verhoeven@esciencecenter.nl>
Date: Thu, 24 Apr 2025 13:00:43 +0200
Subject: [PATCH 45/47] Combine tooltip and label + for number[] input show
 extra description about comma seperator

---
 packages/form/src/Form.tsx | 44 ++++++++++++++++++++++++++++----------
 1 file changed, 33 insertions(+), 11 deletions(-)

diff --git a/packages/form/src/Form.tsx b/packages/form/src/Form.tsx
index ec23104..68483fc 100644
--- a/packages/form/src/Form.tsx
+++ b/packages/form/src/Form.tsx
@@ -346,25 +346,42 @@ function createLabel(item: Base) {
   });
 }
 
-const DescriptionTooltip: Component<{ schema: SchemaOfProperty }> = (props) => {
+const LabelWithTooltip: Component<{
+  schema: SchemaOfProperty;
+  label: string;
+  extraDescription?: string;
+  for: string;
+}> = (props) => {
   const UiComponents = useFormContext().uiComponents;
   return (
     <Show
       when={
-        (props.schema.symbol && !props.schema.title) || props.schema.description
+        (props.schema.symbol && props.schema.title) ||
+        props.schema.description ||
+        props.extraDescription
+      }
+      fallback={
+        <UiComponents.Label
+          for={props.for}
+          class="h-auto p-2"
+          innerHTML={props.label}
+        />
       }
     >
       <UiComponents.Tooltip>
         <UiComponents.TooltipTrigger
-          as={Button<"button">}
+          as={UiComponents.Button<"button">}
           variant="ghost"
-          class="ml-2 size-8 rounded-full"
+          class="h-auto p-2"
         >
-          ?
+          <UiComponents.Label for={props.for} innerHTML={props.label} />
         </UiComponents.TooltipTrigger>
         <UiComponents.TooltipContent>
           <p>{!props.schema.symbol || props.schema.title}</p>
           <p>{props.schema.description}</p>
+          <Show when={props.extraDescription}>
+            <p>{props.extraDescription}</p>
+          </Show>
         </UiComponents.TooltipContent>
       </UiComponents.Tooltip>
     </Show>
@@ -433,6 +450,7 @@ interface ValueGetSet {
    */
   // TODO if error is truthy also update AccordionTrigger to havea an error badge
   error?: string;
+  extraDescription?: string;
 }
 
 const TextFieldWrapperControlled: ParentComponent<
@@ -443,6 +461,7 @@ const TextFieldWrapperControlled: ParentComponent<
   const UiComponents = useFormContext().uiComponents;
   return (
     <UiComponents.TextField
+      id={props.item.key}
       name={props.item.key}
       value={props.value}
       onChange={props.onChange}
@@ -452,8 +471,12 @@ const TextFieldWrapperControlled: ParentComponent<
     >
       <div class="flex items-center gap-2">
         <div class="basis-1/2">
-          <UiComponents.TextFieldLabel innerHTML={label()} />
-          <DescriptionTooltip schema={props.item.schema} />
+          <LabelWithTooltip
+            for={`${props.item.key}-input`}
+            schema={props.item.schema}
+            extraDescription={props.extraDescription}
+            label={label()}
+          />
         </div>
         <Show
           when={props.item.schema.unit}
@@ -550,8 +573,7 @@ const InputBoolean: Component<PropFieldProps> = (props) => {
   return (
     <div class="flex items-center space-x-2">
       <div class="basis-1/2">
-        <UiComponents.Label for={id}>{label()}</UiComponents.Label>
-        <DescriptionTooltip schema={props.item.schema} />
+        <LabelWithTooltip schema={props.item.schema} for={id} label={label()} />
       </div>
       <UiComponents.Checkbox
         id={id}
@@ -579,8 +601,7 @@ const InputTextEnum: Component<PropFieldProps> = (props) => {
   return (
     <div class="flex items-center gap-2">
       <div class="basis-1/2">
-        <UiComponents.Label for={id}>{label()}</UiComponents.Label>
-        <DescriptionTooltip schema={props.item.schema} />
+        <LabelWithTooltip schema={props.item.schema} for={id} label={label()} />
       </div>
       <UiComponents.RadioGroup
         id={id}
@@ -649,6 +670,7 @@ const InputNumbers: Component<PropFieldProps> = (props) => {
       value={stringVal()}
       onChange={onChange}
       error={error()}
+      extraDescription="Give multiple values seperated by commas"
     >
       <UiComponents.TextFieldInput
         placeholder={numbers2string(props.item.schema.default)}

From 1201de376efe4dab811ec405430da08b573ce036 Mon Sep 17 00:00:00 2001
From: sverhoeven <s.verhoeven@esciencecenter.nl>
Date: Thu, 24 Apr 2025 13:02:21 +0200
Subject: [PATCH 46/47] Fix types in tests

---
 apps/class-solid/tests/experiment.spec.ts | 18 +++++++++---------
 apps/class-solid/tests/share.spec.ts      |  2 +-
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/apps/class-solid/tests/experiment.spec.ts b/apps/class-solid/tests/experiment.spec.ts
index 1725f2d..d2f103f 100644
--- a/apps/class-solid/tests/experiment.spec.ts
+++ b/apps/class-solid/tests/experiment.spec.ts
@@ -48,7 +48,7 @@ test("Duplicate experiment with a permutation", async ({ page }, testInfo) => {
   if (!config1.permutations[0].sw_ml) {
     throw new Error("sw_ml is not defined");
   }
-  expect(config1.permutations[0].h_0).toEqual(800);
+  expect(config1.permutations[0].h).toEqual(800);
 
   // Download configuration of experiment 2
   experiment2.getByRole("button", { name: "Download" }).click();
@@ -62,7 +62,7 @@ test("Duplicate experiment with a permutation", async ({ page }, testInfo) => {
     throw new Error("sw_ml is not defined");
   }
   expect(config2.reference.beta).toEqual(0.3);
-  expect(config2.permutations[0].h_0).toEqual(800);
+  expect(config2.permutations[0].h).toEqual(800);
 
   // visually check that timeseries plot has 4 non-overlapping lines
   await testInfo.attach("timeseries plot with 4 non-overlapping lines", {
@@ -114,7 +114,7 @@ test("Swap permutation with default reference", async ({ page }) => {
   if (!config1.reference.sw_ml) {
     throw new Error("Mixed layer is turned off");
   }
-  expect(config1.reference.h_0).toEqual(800);
+  expect(config1.reference.h).toEqual(800);
 });
 
 test("Swap permutation with custom reference", async ({ page }) => {
@@ -164,9 +164,9 @@ test("Swap permutation with custom reference", async ({ page }) => {
     throw new Error("sw_ml is not defined");
   }
 
-  expect(config1.reference.h_0).toEqual(800);
-  expect(config1.reference.dtheta_0).toEqual(0.8);
-  expect(config1.permutations[0].h_0).toEqual(400);
+  expect(config1.reference.h).toEqual(800);
+  expect(config1.reference.dtheta).toEqual(0.8);
+  expect(config1.permutations[0].h).toEqual(400);
 });
 
 test("Promote permutation to a new experiment", async ({ page }) => {
@@ -211,7 +211,7 @@ test("Promote permutation to a new experiment", async ({ page }) => {
   if (!config2.reference.sw_ml) {
     throw new Error("sw_ml is not defined");
   }
-  expect(config2.reference.h_0).toEqual(800);
+  expect(config2.reference.h).toEqual(800);
   expect(config2.permutations.length).toEqual(0);
 });
 
@@ -265,6 +265,6 @@ test("Duplicate permutation", async ({ page }) => {
   if (!config1.permutations[0].sw_ml || !config1.permutations[1].sw_ml) {
     throw new Error("sw_ml is not defined");
   }
-  expect(config1.permutations[0].h_0).toEqual(800);
-  expect(config1.permutations[1].h_0).toEqual(400);
+  expect(config1.permutations[0].h).toEqual(800);
+  expect(config1.permutations[1].h).toEqual(400);
 });
diff --git a/apps/class-solid/tests/share.spec.ts b/apps/class-solid/tests/share.spec.ts
index f0580a6..13702e2 100644
--- a/apps/class-solid/tests/share.spec.ts
+++ b/apps/class-solid/tests/share.spec.ts
@@ -40,7 +40,7 @@ test("Create share link from an experiment", async ({ page }) => {
     throw new Error("Mixed layer is turned off");
   }
 
-  expect(config1.reference.h_0).toEqual(800);
+  expect(config1.reference.h).toEqual(800);
 
   // TODO: finalheight is gone; implement alternative check to see that experiment finished
 });

From 3706ee7cb3b524cfdc17a87d08860a27795df784 Mon Sep 17 00:00:00 2001
From: Peter Kalverla <peter.kalverla@gmx.com>
Date: Thu, 24 Apr 2025 16:13:06 +0200
Subject: [PATCH 47/47] fix type issue

---
 apps/class-solid/src/lib/runner.ts | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/apps/class-solid/src/lib/runner.ts b/apps/class-solid/src/lib/runner.ts
index 3dcf765..bae7006 100644
--- a/apps/class-solid/src/lib/runner.ts
+++ b/apps/class-solid/src/lib/runner.ts
@@ -1,5 +1,6 @@
 import type { Config } from "@classmodel/class/config";
-import type { ClassOutput, runClass } from "@classmodel/class/runner";
+import type { ClassOutput } from "@classmodel/class/output";
+import type { runClass } from "@classmodel/class/runner";
 import { wrap } from "comlink";
 
 const worker = new Worker(new URL("./worker.ts", import.meta.url), {