Add vector to scope, fix quantity saving

src/geometry/geom.go

@@ -135,9 +135,7 @@ func (g *Geometry) SetGeom(s shape.Shape) {
 	// M inside geom but previously outside needs to be re-inited
 	needupload := false
 	geomlist := CpuSlice.Host()[0]
-	g.log.Debug("2")
 	mhost := g.mag_slice.HostCopy()
-	g.log.Debug("3")
 	m := mhost.Host()
 	rng := rand.New(rand.NewSource(0))
 	for i := range m[0] {

src/metadata/metadata.go

@@ -53,7 +53,7 @@ func (m *Metadata) Add(key string, val interface{}) {
 		// ignore functions
 		return
 	default:
-		m.log.Debug("Metadata key %s has invalid type %s: %v", key, valType, val)
+		m.log.Warn("Not adding this metadata key %s  because it has an invalid type %s: %v", key, valType, val)
 	}
 }
 

src/saved_quantities/saved_quantities.go

@@ -29,8 +29,11 @@ type SavedQuantity struct {
 	nextTime float64 // Next time when autosave should trigger
 }
 
-func NewSavedQuantity(log *log.Logs, q quantity.Quantity, name string, rchunks chunk.RequestedChunking, period float64) *SavedQuantity {
+func NewSavedQuantity(log *log.Logs, fs *fsutil.FileSystem, solver *solver.Solver, q quantity.Quantity, name string, rchunks chunk.RequestedChunking, period float64) *SavedQuantity {
 	return &SavedQuantity{
+		log:     log,
+		fs:      fs,
+		solver:  solver,
 		name:    name,
 		q:       q,
 		period:  period,
@@ -69,30 +72,34 @@ func (sq *SavedQuantity) save() {
 	sq.q.EvalTo(buffer)
 	defer cuda.Recycle(buffer)
 	dataSlice := buffer.HostCopy()
+	// Saving the step so that it doesn't change during the save process
+	step := len(sq.times) - 1
 	sq.fs.QueueOutput(func() {
-		err := sq.syncSave(dataSlice, sq.name, len(sq.times), sq.chunks)
+		err := sq.syncSave(dataSlice, sq.name, step, sq.chunks)
 		sq.log.PanicIfError(err)
 	})
 }
 
 // syncSave writes the data slice into chunked, compressed files compatible with the Zarr format.
 func (sq *SavedQuantity) syncSave(array *slice.Slice, qname string, step int, chunks chunk.Chunks) error {
+	path := qname + "/.zarray"
 	data := array.Tensors()
 	size := array.Size()
 	ncomp := array.NComp()
 
 	// Save .zarray metadata
 	err := sq.fs.SaveFileZarray(
-		fmt.Sprintf("%s/.zarray", qname),
+		path,
 		size,
 		ncomp,
 		step,
 		chunks.Z.Len, chunks.Y.Len, chunks.X.Len, chunks.C.Len,
 	)
 	if err != nil {
+		sq.log.Err("Error saving .zarray file: %v", err)
 		return err
 	}
-
+	var compressedData []byte
 	// Iterate over chunks and save data
 	for icx := 0; icx < chunks.X.Count; icx++ {
 		for icy := 0; icy < chunks.Y.Count; icy++ {
@@ -108,21 +115,23 @@ func (sq *SavedQuantity) syncSave(array *slice.Slice, qname string, step int, ch
 								for ic := 0; ic < chunks.C.Len; ic++ {
 									c := icc*chunks.C.Len + ic
 									value := data[c][z][y][x]
-									err := binary.Write(&bdata, binary.LittleEndian, value)
+									err = binary.Write(&bdata, binary.LittleEndian, value)
 									if err != nil {
 										return err
 									}
 								}
 							}
 						}
 					}
-					compressedData, err := zstd.Compress(nil, bdata.Bytes())
+					compressedData, err = zstd.Compress(nil, bdata.Bytes())
 					if err != nil {
+						sq.log.Err("Error saving .zarray file: %v", err)
 						return err
 					}
-					filename := fmt.Sprintf("%s/%d.%d.%d.%d.%d", qname, step+1, icz, icy, icx, icc)
+					filename := fmt.Sprintf("%s/%d.%d.%d.%d.%d", qname, step, icz, icy, icx, icc)
 					err = sq.fs.Put(filename, compressedData)
 					if err != nil {
+						sq.log.Err("Error saving .zarray file: %v", err)
 						return err
 					}
 				}
@@ -173,7 +182,7 @@ func (sqs *SavedQuantities) createSavedQuantity(q quantity.Quantity, name string
 	}
 	err := sqs.fs.Mkdir(name)
 	sqs.log.PanicIfError(err)
-	sq := NewSavedQuantity(sqs.log, q, name, rchunks, period)
+	sq := NewSavedQuantity(sqs.log, sqs.fs, sqs.solver, q, name, rchunks, period)
 	sqs.Quantities = append(sqs.Quantities, *sq)
 	return sq
 

src/script/scope.go

@@ -19,6 +19,7 @@ import (
 	"github.com/MathieuMoalic/amumax/src/solver"
 	"github.com/MathieuMoalic/amumax/src/table"
 	"github.com/MathieuMoalic/amumax/src/utils"
+	"github.com/MathieuMoalic/amumax/src/vector"
 	"github.com/MathieuMoalic/amumax/src/window_shift"
 )
 
@@ -149,7 +150,7 @@ func (p *ScriptParser) AddToScopeAll(
 	// p.RegisterFunction("ExpectV", expectV, "Used for automated tests: checks if a vector is close enough to the expected value")
 	// p.RegisterFunction("Fprintln", fprintln, "Print to file")
 	// p.RegisterFunction("Sign", sign, "Signum function")
-	// p.RegisterFunction("Vector", vector, "Constructs a vector with given components")
+	p.RegisterFunction("Vector", vector.New, "Constructs a vector with given components")
 	p.RegisterFunction("Print", p.Print, "Print to standard output")
 	// p.RegisterFunction("LoadFile", loadFile, "Load a zarr data file")
 	// p.RegisterFunction("LoadOvfFile", loadOvfFile, "Load an ovf data file")

src/table/table.go

@@ -109,7 +109,6 @@ func (ts *Table) FlushToFile() error {
 	// Check if the table state has changed
 	currentHash := ts.generateHash()
 	if currentHash == ts.lastSavedHash {
-		ts.log.Debug("Table state has not changed, skipping save.")
 		return nil
 	}
 	for i := range ts.columns {

src/vector/vector.go

@@ -2,6 +2,8 @@ package vector
 
 import "math"
 
+func New(x, y, z float64) Vector { return Vector{x, y, z} }
+
 // 3-component vector
 type Vector [3]float64