// ReadMsh reads .msh file
func ReadMsh(fnk string) (nurbss []*Nurbs) {
// read file
fn := fnk + ".msh"
buf, err := io.ReadFile(fn)
if err != nil {
chk.Panic("ReadMsh cannot read file = '%s', %v'", fn, err)
}
// decode
var dat Data
err = json.Unmarshal(buf, &dat)
if err != nil {
chk.Panic("ReadMsh cannot unmarshal file = '%s', %v'", fn, err)
}
// list of vertices
verts := make([][]float64, len(dat.Verts))
for i, _ := range dat.Verts {
verts[i] = make([]float64, 4)
for j := 0; j < 4; j++ {
verts[i][j] = dat.Verts[i].C[j]
}
}
// allocate NURBSs
nurbss = make([]*Nurbs, len(dat.Nurbss))
for i, v := range dat.Nurbss {
nurbss[i] = new(Nurbs)
nurbss[i].Init(v.Gnd, v.Ords, v.Knots)
nurbss[i].SetControl(verts, v.Ctrls)
}
return
}
func PyFile(filename string) {
b, err := io.ReadFile(filename)
if err != nil {
chk.Panic("PyFile failed:\n%v", err)
}
io.Ff(&bb, string(b))
}
// Read reads configuration parameters from JSON file
func (o *Parameters) Read(filenamepath string) {
o.Default()
b, err := io.ReadFile(filenamepath)
if err != nil {
chk.Panic("cannot read parameters file %q", filenamepath)
}
err = json.Unmarshal(b, o)
if err != nil {
chk.Panic("cannot unmarshal parameters file %q", filenamepath)
}
return
}
// NewData allocates and initialises a new FEM data structure
func NewData(fnkey string, cpu int) *FemData {
// load data
var o FemData
buf, err := io.ReadFile("od-" + fnkey + ".json")
if err != nil {
chk.Panic("cannot load data:\n%v", err)
}
err = json.Unmarshal(buf, &o)
if err != nil {
chk.Panic("cannot unmarshal data:\n%v", err)
}
// load FEM data
o.Analysis = fem.NewMain(fnkey+".sim", io.Sf("cpu%d", cpu), false, false, false, false, false, cpu)
o.Dom = o.Analysis.Domains[0]
o.Sim = o.Dom.Sim
o.Vars = o.Dom.Sim.AdjRandom
// backup dependent variables
for _, prm := range o.Sim.AdjDependent {
prm.S = prm.V // copy V into S
}
// set stage
err = o.Analysis.SetStage(0)
if err != nil {
chk.Panic("cannot set stage:\n%v", err)
}
// equations to track U
verts := o.Dom.Msh.Verts
if o.VtagU < 0 {
verts = o.Dom.Msh.VertTag2verts[o.VtagU]
if len(verts) < 1 {
chk.Panic("cannot find vertices with tag = %d\n", o.VtagU)
}
}
o.EqsU = make([]int, len(verts))
for i, vert := range verts {
eq := o.Dom.Vid2node[vert.Id].GetEq(o.Ukey)
if eq < 0 {
chk.Panic("cannot find equation corresponding to vertex id=%d and ukey=%q", vert.Id, o.Ukey)
}
o.EqsU[i] = eq
}
return &o
}
func read_pyfem_rod_data(fn string) []PyfemRodData {
// read file
b, err := io.ReadFile(fn)
if err != nil {
chk.Panic("%v\n", err.Error())
}
// decode
var dat []PyfemRodData
err = json.Unmarshal(b, &dat)
if err != nil {
chk.Panic("%v\n", err.Error())
}
return dat
}
// ReadJson reads json file
func (o *Path) ReadJson(ndim int, fname string) (err error) {
// read file
b, err := io.ReadFile(fname)
if err != nil {
return chk.Err(_path_err11, fname, err)
}
// decode
err = json.Unmarshal(b, o)
if err != nil {
return chk.Err(_path_err12, fname, err)
}
// set additional information
return o.Init(ndim)
}
func main() {
// filename
filename, fnkey := io.ArgToFilename(0, "sg1121", ".sim", true)
// results
out.Start(filename, 0, 0)
out.Define("A", out.N{30})
out.LoadResults(nil)
// plot FEM results
out.Plot("t", "uy", "A", plt.Fmt{C: "k", Ls: "-", L: "gofem"}, -1)
// old results
b, err := io.ReadFile("cmp/sg1121gofemold.json")
if err != nil {
io.PfRed("cannot read comparison file\n")
return
}
var gofemold struct {
Time, Uy30 []float64
}
err = json.Unmarshal(b, &gofemold)
if err != nil {
io.PfRed("cannot unmarshal comparison file\n")
return
}
// mechsys results
_, res, err := io.ReadTable("cmp/sg1121mechsysN30.cmp")
if err != nil {
io.PfRed("cannot read mechsys comparison file\n")
return
}
// save
plt.SetForPng(0.8, 400, 200)
out.Draw("/tmp", fnkey+".png", false, func(i, j, n int) {
plt.Plot(gofemold.Time, gofemold.Uy30, "'r-', lw=2, label='gofemOld'")
plt.Plot(res["Time"], res["uy"], "'b-', label='mechsys'")
})
}
// ReadMat reads all materials data from a .mat JSON file
// Note: returns nil on errors
func ReadMat(dir, fn string) *MatDb {
// new mat
var o MatDb
// read file
b, err := io.ReadFile(filepath.Join(dir, fn))
if err != nil {
return nil
}
// decode
err = json.Unmarshal(b, &o)
if err != nil {
return nil
}
// results
return &o
}
// ReadMat reads all materials data from a .mat JSON file
// Note: returns nil on errors
func ReadMat(dir, fn string) *MatDb {
// new mat
var o MatDb
// read file
b, err := io.ReadFile(filepath.Join(dir, fn))
if LogErr(err, "mat: cannot open materials file "+dir+"/"+fn) {
return nil
}
// decode
if LogErr(json.Unmarshal(b, &o), "mat: cannot unmarshal materials file "+fn) {
return nil
}
// log
log.Printf("mat: fn=%s nfunctions=%d nmaterials=%d\n", fn, len(o.Functions), len(o.Materials))
return &o
}
// Read reads mesh
func Read(fn string) (o *Mesh, err error) {
// new mesh
o = new(Mesh)
// read file
b, err := io.ReadFile(fn)
if err != nil {
return
}
// decode
err = json.Unmarshal(b, &o)
if err != nil {
return
}
// check
err = o.Check()
return
}
// ReadConfParams reads configuration parameters from JSON file
func ReadConfParams(filenamepath string) *ConfParams {
// new params
var o ConfParams
o.SetDefault()
// read file
b, err := io.ReadFile(filenamepath)
if err != nil {
chk.Panic("cannot read parameters file %q", filenamepath)
}
// decode
err = json.Unmarshal(b, &o)
if err != nil {
chk.Panic("cannot unmarshal parameters file %q", filenamepath)
}
// results
o.CalcDerived()
return &o
}
func Test_step02(tst *testing.T) {
//verbose()
chk.PrintTitle("step02")
buf, err := io.ReadFile("data/beadpanel.step")
if err != nil {
tst.Errorf("cannot read file:\n%v", err)
return
}
dat := string(buf)
var stp STEP
err = stp.ParseDATA(dat)
if err != nil {
tst.Errorf("Parse filed:\n%v", err)
return
}
for _, c := range stp.BScurves {
io.Pforan("c = %v\n", c)
}
}
// MatfileNew2Old converts a new mat file to the old mat file format
// convertsymbols -- convert back symbols with Greek characters to UTF-8
func MatfileNew2Old(dirout string, fnold, fnnew string, convertsymbols bool) {
// read file
b, err := io.ReadFile(fnnew)
if err != nil {
io.PfRed("cannot open file: %v", err.Error())
return
}
// decode
var mats_new MatDb
err = json.Unmarshal(b, &mats_new)
if err != nil {
io.PfRed("cannot unmarshal file: %v", err.Error())
return
}
// oldmatdata implements the old data format
type oldmatdata struct {
Name string
Desc string
Model string
Prms []string
Vals []float64
Units []string
Extra string
}
// convert
var mats_old []oldmatdata
for _, m := range mats_new.Materials {
var oldmat oldmatdata
oldmat.Name = m.Name
oldmat.Desc = m.Desc
oldmat.Model = m.Model
oldmat.Extra = m.Extra
for _, prm := range m.Prms {
name := prm.N
if convertsymbols {
if n, ok := invertedconversiontable[prm.N]; ok {
name = n
}
}
oldmat.Prms = append(oldmat.Prms, name)
oldmat.Vals = append(oldmat.Vals, prm.V)
if len(prm.U) > 0 {
oldmat.Units = append(oldmat.Units, prm.U)
}
}
mats_old = append(mats_old, oldmat)
}
// encode
buf, err := json.MarshalIndent(mats_old, "", " ")
if err != nil {
return
}
// save file
if dirout == "" {
io.WriteFileS(fnold, string(buf))
return
}
io.WriteFileSD(dirout, fnold, string(buf))
}
// MatfileOld2New converts an old mat file to new mat file format
// convertsymbols -- convert symbols with Greek characters to ANSI
func MatfileOld2New(dirout string, fnnew, fnold string, convertsymbols bool) {
// oldmatdata implements the old data format
type oldmatdata struct {
Name string
Desc string
Model string
Prms []string
Vals []float64
Units []string
Extra string
}
// data holder
var mats_old []oldmatdata
// read file
b, err := io.ReadFile(fnold)
if err != nil {
chk.Panic("cannot open file: %v", err.Error())
}
// decode
err = json.Unmarshal(b, &mats_old)
if err != nil {
chk.Panic("cannot unmarshal file: %v", err.Error())
}
// new data holder
var mats_new MatDb
for _, m := range mats_old {
prms := []*fun.Prm{}
has_units := len(m.Units) == len(m.Prms)
for i, prm := range m.Prms {
name := prm
if convertsymbols {
if n, ok := conversiontable[prm]; ok {
name = n
}
}
if has_units {
prms = append(prms, &fun.Prm{N: name, V: m.Vals[i], U: m.Units[i]})
} else {
prms = append(prms, &fun.Prm{N: name, V: m.Vals[i]})
}
}
mat_new := Material{
Name: m.Name,
Desc: m.Desc,
Model: m.Model,
Extra: m.Extra,
Prms: prms,
}
mats_new.Materials = append(mats_new.Materials, &mat_new)
}
// save file
if dirout == "" {
io.WriteFileS(fnnew, mats_new.String())
return
}
io.WriteFileSD(dirout, fnnew, mats_new.String())
}
// NewData allocates and initialises a new FEM data structure
func NewData(filename, fnkey string, cpu int) *FemData {
// load opt data
var o FemData
buf, err := io.ReadFile("od-" + fnkey + ".json")
if err != nil {
chk.Panic("cannot load opt data:\n%v", err)
}
err = json.Unmarshal(buf, &o.Opt)
if err != nil {
chk.Panic("cannot unmarshal opt data:\n%v", err)
}
o.Opt.CalcDerived()
// load FEM data
o.Analysis = fem.NewFEM(filename, io.Sf("cpu%d", cpu), false, false, false, false, false, cpu)
o.Reg = o.Analysis.Sim.Regions[0]
o.Dom = o.Analysis.Domains[0]
// required vertices
for _, vtag := range o.Opt.ReqVtags {
verts := o.Dom.Msh.VertTag2verts[vtag]
for _, vert := range verts {
o.ReqVids = append(o.ReqVids, vert.Id)
}
}
// groups
o.Ncells = len(o.Dom.Msh.Cells)
o.Cid2xid = make([]int, o.Ncells)
if o.Opt.Groups {
o.Nareas = len(o.Dom.Msh.CellTag2cells)
for tag, cells := range o.Dom.Msh.CellTag2cells {
xid := -tag - 1
for _, cell := range cells {
o.Cid2xid[cell.Id] = xid
}
}
} else { // all cells
o.Nareas = o.Ncells
for i, _ := range o.Dom.Msh.Cells {
o.Cid2xid[i] = i
}
}
// vertex to track deflection
o.VidU = -1 // allvertices
if o.Opt.VtagU < 0 {
verts := o.Dom.Msh.VertTag2verts[o.Opt.VtagU]
if len(verts) != 1 {
chk.Panic("cannot set vertex to track deflection: verts = %v", verts)
}
o.VidU = verts[0].Id
}
// compute max weight
o.Analysis.SetStage(0)
for _, elem := range o.Dom.Elems {
ele := elem.(*fem.ElastRod)
o.MaxWeight += ele.Mdl.Rho * ele.Mdl.A * ele.L
}
return &o
}
// ReadMsh reads a mesh for FE analyses
// Note: returns nil on errors
func ReadMsh(dir, fn string) *Mesh {
// new mesh
var o Mesh
// read file
o.FnamePath = filepath.Join(dir, fn)
b, err := io.ReadFile(o.FnamePath)
if LogErr(err, "msh: cannot open mesh file "+o.FnamePath) {
return nil
}
// decode
if LogErr(json.Unmarshal(b, &o), "msh: cannot unmarshal mesh file "+fn+"\n") {
return nil
}
// check
if LogErrCond(len(o.Verts) < 2, "msh: mesh must have at least 2 vertices and 1 cell") {
return nil
}
if LogErrCond(len(o.Cells) < 1, "msh: mesh must have at least 2 vertices and 1 cell") {
return nil
}
// vertex related derived data
o.Ndim = 2
o.Xmin = o.Verts[0].C[0]
o.Ymin = o.Verts[0].C[1]
if len(o.Verts[0].C) > 2 {
o.Zmin = o.Verts[0].C[2]
}
o.Xmax = o.Xmin
o.Ymax = o.Ymin
o.Zmax = o.Zmin
o.VertTag2verts = make(map[int][]*Vert)
for i, v := range o.Verts {
// check vertex id
if LogErrCond(v.Id != i, "msh: vertices must be sequentially numbered. %d != %d\n", v.Id, i) {
return nil
}
// ndim
nd := len(v.C)
if LogErrCond(nd < 2 || nd > 4, "msh: ndim must be 2 or 3\n") {
return nil
}
if nd == 3 {
if math.Abs(v.C[2]) > Ztol {
o.Ndim = 3
}
}
// tags
if v.Tag < 0 {
verts := o.VertTag2verts[v.Tag]
o.VertTag2verts[v.Tag] = append(verts, v)
}
// limits
o.Xmin = min(o.Xmin, v.C[0])
o.Xmax = max(o.Xmax, v.C[0])
o.Ymin = min(o.Ymin, v.C[1])
o.Ymax = max(o.Ymax, v.C[1])
if nd > 2 {
o.Zmin = min(o.Zmin, v.C[2])
o.Zmax = max(o.Zmax, v.C[2])
}
}
// derived data
o.CellTag2cells = make(map[int][]*Cell)
o.FaceTag2cells = make(map[int][]CellFaceId)
o.FaceTag2verts = make(map[int][]int)
o.SeamTag2cells = make(map[int][]CellSeamId)
o.Ctype2cells = make(map[string][]*Cell)
o.Part2cells = make(map[int][]*Cell)
for i, c := range o.Cells {
// check id and tag
if LogErrCond(c.Id != i, "msh: cells must be sequentially numbered. %d != %d\n", c.Id, i) {
return nil
}
if LogErrCond(c.Tag >= 0, "msh: cell tags must be negative\n") {
return nil
}
// face tags
cells := o.CellTag2cells[c.Tag]
o.CellTag2cells[c.Tag] = append(cells, c)
for i, ftag := range c.FTags {
if ftag < 0 {
pairs := o.FaceTag2cells[ftag]
o.FaceTag2cells[ftag] = append(pairs, CellFaceId{c, i})
for _, l := range shp.GetFaceLocalVerts(c.Type, i) {
utl.IntIntsMapAppend(&o.FaceTag2verts, ftag, o.Verts[c.Verts[l]].Id)
}
}
}
// seam tags
if o.Ndim == 3 {
for i, stag := range c.STags {
if stag < 0 {
pairs := o.SeamTag2cells[stag]
o.SeamTag2cells[stag] = append(pairs, CellSeamId{c, i})
}
}
}
// cell type => cells
cells = o.Ctype2cells[c.Type]
o.Ctype2cells[c.Type] = append(cells, c)
// partition => cells
cells = o.Part2cells[c.Part]
o.Part2cells[c.Part] = append(cells, c)
// get shape structure
switch c.Type {
case "joint":
c.IsJoint = true
default:
c.Shp = shp.Get(c.Type)
if LogErrCond(c.Shp == nil, "msh: cannot find shape type == %q\n", c.Type) {
return nil
}
}
}
// remove duplicates
for ftag, verts := range o.FaceTag2verts {
o.FaceTag2verts[ftag] = utl.IntUnique(verts)
}
// log
log.Printf("msh: fn=%s nverts=%d ncells=%d ncelltags=%d nfacetags=%d nseamtags=%d nverttags=%d ncelltypes=%d npart=%d\n", fn, len(o.Verts), len(o.Cells), len(o.CellTag2cells), len(o.FaceTag2cells), len(o.SeamTag2cells), len(o.VertTag2verts), len(o.Ctype2cells), len(o.Part2cells))
return &o
}
// testing_compare_results_u compares results with u-formulation
func TestingCompareResultsU(tst *testing.T, simfname, cmpfname string, tolK, tolu, tols float64, skipK, verbose bool) {
// only root can run this test
if !Global.Root {
return
}
// read summary
sum := ReadSum(Global.Dirout, Global.Fnkey)
if sum == nil {
tst.Error("cannot read summary file for simulation=%q\n", simfname)
return
}
// allocate domain
distr := false
d := NewDomain(Global.Sim.Regions[0], distr)
if !d.SetStage(0, Global.Sim.Stages[0], distr) {
tst.Errorf("TestingCompareResultsU: SetStage failed\n")
return
}
// read file
buf, err := io.ReadFile(cmpfname)
if err != nil {
tst.Errorf("TestingCompareResultsU: ReadFile failed\n")
return
}
// unmarshal json
var cmp_set T_results_set
err = json.Unmarshal(buf, &cmp_set)
if err != nil {
tst.Errorf("TestingCompareResultsU: Unmarshal failed\n")
return
}
// run comparisons
dmult := 1.0
for idx, cmp := range cmp_set {
// displacements multiplier
if idx == 0 && math.Abs(cmp.DispMult) > 1e-10 {
dmult = cmp.DispMult
}
// time index
tidx := idx + 1
if verbose {
io.PfYel("\n\ntidx = %d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .\n", tidx)
}
// load gofem results
if !d.In(sum, tidx, true) {
tst.Errorf("TestingCompareResultsU: reading of results failed\n")
return
}
if verbose {
io.Pfyel("time = %v\n", d.Sol.T)
}
// check K matrices
if !skipK {
if verbose {
io.Pfgreen(". . . checking K matrices . . .\n")
}
for eid, Ksg := range cmp.Kmats {
if e, ok := d.Elems[eid].(*ElemU); ok {
if !e.AddToKb(d.Kb, d.Sol, true) {
tst.Errorf("TestingCompareResultsU: AddToKb failed\n")
return
}
chk.Matrix(tst, io.Sf("K%d", eid), tolK, e.K, Ksg)
}
}
}
// check displacements
if verbose {
io.Pfgreen(". . . checking displacements . . .\n")
}
for nid, usg := range cmp.Disp {
ix := d.Vid2node[nid].Dofs[0].Eq
iy := d.Vid2node[nid].Dofs[1].Eq
chk.AnaNum(tst, "ux", tolu, d.Sol.Y[ix], usg[0]*dmult, verbose)
chk.AnaNum(tst, "uy", tolu, d.Sol.Y[iy], usg[1]*dmult, verbose)
if len(usg) == 3 {
iz := d.Vid2node[nid].Dofs[2].Eq
chk.AnaNum(tst, "uz", tolu, d.Sol.Y[iz], usg[2]*dmult, verbose)
}
}
// check stresses
if true {
if verbose {
io.Pfgreen(". . . checking stresses . . .\n")
}
for eid, sig := range cmp.Sigmas {
if verbose {
io.Pforan("eid = %d\n", eid)
}
if e, ok := d.Cid2elem[eid].(*ElemU); ok {
for ip, val := range sig {
if verbose {
io.Pfgrey2("ip = %d\n", ip)
}
σ := e.States[ip].Sig
if len(val) == 6 {
chk.AnaNum(tst, "sx ", tols, σ[0], val[0], verbose)
chk.AnaNum(tst, "sy ", tols, σ[1], val[1], verbose)
} else {
chk.AnaNum(tst, "sx ", tols, σ[0], val[0], verbose)
chk.AnaNum(tst, "sy ", tols, σ[1], val[1], verbose)
chk.AnaNum(tst, "sxy", tols, σ[3]/SQ2, val[2], verbose)
if len(val) > 3 { // sx, sy, sxy, sz
chk.AnaNum(tst, "sz ", tols, σ[2], val[3], verbose)
}
}
}
}
}
}
}
}
// ReadMsh reads a mesh for FE analyses
// Note: returns nil on errors
func ReadMsh(dir, fn string, goroutineId int) (o *Mesh, err error) {
// new mesh
o = new(Mesh)
// read file
o.FnamePath = filepath.Join(dir, fn)
b, err := io.ReadFile(o.FnamePath)
if err != nil {
return
}
// decode
err = json.Unmarshal(b, &o)
if err != nil {
return
}
// check
if len(o.Verts) < 2 {
err = chk.Err("at least 2 vertices are required in mesh\n")
return
}
if len(o.Cells) < 1 {
err = chk.Err("at least 1 cell is required in mesh\n")
return
}
// variables for NURBS
var controlpts [][]float64
has_nurbs := false
if len(o.Nurbss) > 0 {
controlpts = make([][]float64, len(o.Verts))
has_nurbs = true
}
// vertex related derived data
o.Ndim = 2
o.Xmin = o.Verts[0].C[0]
o.Ymin = o.Verts[0].C[1]
if len(o.Verts[0].C) > 2 {
o.Zmin = o.Verts[0].C[2]
}
o.Xmax = o.Xmin
o.Ymax = o.Ymin
o.Zmax = o.Zmin
o.VertTag2verts = make(map[int][]*Vert)
for i, v := range o.Verts {
// check vertex id
if v.Id != i {
err = chk.Err("vertices ids must coincide with order in \"verts\" list. %d != %d\n", v.Id, i)
return
}
// ndim
nd := len(v.C)
if nd < 2 || nd > 4 {
err = chk.Err("number of space dimensions must be 2, 3 or 4 (NURBS). %d is invalid\n", nd)
return
}
if nd == 3 {
if math.Abs(v.C[2]) > Ztol {
o.Ndim = 3
}
}
// tags
if v.Tag < 0 {
verts := o.VertTag2verts[v.Tag]
o.VertTag2verts[v.Tag] = append(verts, v)
}
// limits
o.Xmin = utl.Min(o.Xmin, v.C[0])
o.Xmax = utl.Max(o.Xmax, v.C[0])
o.Ymin = utl.Min(o.Ymin, v.C[1])
o.Ymax = utl.Max(o.Ymax, v.C[1])
if nd > 2 {
o.Zmin = utl.Min(o.Zmin, v.C[2])
o.Zmax = utl.Max(o.Zmax, v.C[2])
}
// control points to initialise NURBS
if has_nurbs {
controlpts[i] = make([]float64, 4)
for j := 0; j < 4; j++ {
controlpts[i][j] = v.C[j]
}
}
}
// allocate NURBSs
o.PtNurbs = make([]*gm.Nurbs, len(o.Nurbss))
o.NrbFaces = make([][]*gm.Nurbs, len(o.Nurbss))
for i, d := range o.Nurbss {
o.PtNurbs[i] = new(gm.Nurbs)
o.PtNurbs[i].Init(d.Gnd, d.Ords, d.Knots)
o.PtNurbs[i].SetControl(controlpts, d.Ctrls)
o.NrbFaces[i] = o.PtNurbs[i].ExtractSurfaces()
}
// derived data
o.CellTag2cells = make(map[int][]*Cell)
o.FaceTag2cells = make(map[int][]CellFaceId)
o.FaceTag2verts = make(map[int][]int)
o.SeamTag2cells = make(map[int][]CellSeamId)
o.Ctype2cells = make(map[string][]*Cell)
o.Part2cells = make(map[int][]*Cell)
for i, c := range o.Cells {
// check id and tag
if c.Id != i {
err = chk.Err("cells ids must coincide with order in \"verts\" list. %d != %d\n", c.Id, i)
return
}
if c.Tag >= 0 {
err = chk.Err("cells tags must be negative. %d is incorrect\n", c.Tag)
return
}
// get shape structure
switch c.Type {
case "joint":
c.IsJoint = true
case "nurbs":
c.Shp = shp.GetShapeNurbs(o.PtNurbs[c.Nrb], o.NrbFaces[c.Nrb], c.Span)
if c.Shp == nil {
err = chk.Err("cannot allocate \"shape\" structure for cell type = %q\n", c.Type)
return
}
default:
c.Shp = shp.Get(c.Type, goroutineId)
if c.Shp == nil {
err = chk.Err("cannot allocate \"shape\" structure for cell type = %q\n", c.Type)
return
}
}
c.GoroutineId = goroutineId
// face tags
cells := o.CellTag2cells[c.Tag]
o.CellTag2cells[c.Tag] = append(cells, c)
for i, ftag := range c.FTags {
if ftag < 0 {
pairs := o.FaceTag2cells[ftag]
o.FaceTag2cells[ftag] = append(pairs, CellFaceId{c, i})
for _, l := range c.Shp.FaceLocalVerts[i] {
utl.IntIntsMapAppend(&o.FaceTag2verts, ftag, o.Verts[c.Verts[l]].Id)
}
}
}
// seam tags
if o.Ndim == 3 {
for i, stag := range c.STags {
if stag < 0 {
pairs := o.SeamTag2cells[stag]
o.SeamTag2cells[stag] = append(pairs, CellSeamId{c, i})
}
}
}
// cell type => cells
cells = o.Ctype2cells[c.Type]
o.Ctype2cells[c.Type] = append(cells, c)
// partition => cells
cells = o.Part2cells[c.Part]
o.Part2cells[c.Part] = append(cells, c)
}
// remove duplicates
for ftag, verts := range o.FaceTag2verts {
o.FaceTag2verts[ftag] = utl.IntUnique(verts)
}
// results
return
}
// testing_compare_results_u compares results with u-formulation
func TestingCompareResultsU(tst *testing.T, simfilepath, cmpfname, alias string, tolK, tolu, tols float64, skipK, verbose bool) {
// FEM structure
fem := NewFEM(simfilepath, alias, false, false, true, false, verbose, 0)
// set stage
err := fem.SetStage(0)
if err != nil {
chk.Panic("cannot set stage:\n%v", err)
}
// zero solution
err = fem.ZeroStage(0, true)
if err != nil {
chk.Panic("cannot zero stage data:\n%v", err)
}
// read file with comparison results
buf, err := io.ReadFile(cmpfname)
if err != nil {
tst.Errorf("TestingCompareResultsU: ReadFile failed\n")
return
}
// unmarshal json
var cmp_set T_results_set
err = json.Unmarshal(buf, &cmp_set)
if err != nil {
tst.Errorf("TestingCompareResultsU: Unmarshal failed\n")
return
}
// run comparisons
dom := fem.Domains[0]
dmult := 1.0
for idx, cmp := range cmp_set {
// displacements multiplier
if idx == 0 && math.Abs(cmp.DispMult) > 1e-10 {
dmult = cmp.DispMult
}
// time index
tidx := idx + 1
if verbose {
io.PfYel("\n\ntidx = %d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .\n", tidx)
}
// load gofem results
err = dom.Read(fem.Summary, tidx, 0, true)
if err != nil {
chk.Panic("cannot read 'gofem' results:\n%v", err)
}
if verbose {
io.Pfyel("time = %v\n", dom.Sol.T)
}
// check K matrices
if !skipK {
if verbose {
io.Pfgreen(". . . checking K matrices . . .\n")
}
for eid, Ksg := range cmp.Kmats {
if e, ok := dom.Elems[eid].(*ElemU); ok {
err = e.AddToKb(dom.Kb, dom.Sol, true)
if err != nil {
chk.Panic("TestingCompareResultsU: AddToKb failed\n")
}
chk.Matrix(tst, io.Sf("K%d", eid), tolK, e.K, Ksg)
}
if e, ok := dom.Elems[eid].(*Rod); ok {
err = e.AddToKb(dom.Kb, dom.Sol, true)
if err != nil {
chk.Panic("TestingCompareResultsU: AddToKb failed\n")
}
chk.Matrix(tst, io.Sf("K%d", eid), tolK, e.K, Ksg)
}
if e, ok := dom.Elems[eid].(*ElastRod); ok {
err = e.AddToKb(dom.Kb, dom.Sol, true)
if err != nil {
chk.Panic("TestingCompareResultsU: AddToKb failed\n")
}
chk.Matrix(tst, io.Sf("K%d", eid), tolK, e.K, Ksg)
}
}
}
// check displacements
if verbose {
io.Pfgreen(". . . checking displacements . . .\n")
}
for nid, usg := range cmp.Disp {
ix := dom.Vid2node[nid].Dofs[0].Eq
iy := dom.Vid2node[nid].Dofs[1].Eq
chk.AnaNum(tst, "ux", tolu, dom.Sol.Y[ix], usg[0]*dmult, verbose)
chk.AnaNum(tst, "uy", tolu, dom.Sol.Y[iy], usg[1]*dmult, verbose)
if len(usg) == 3 {
iz := dom.Vid2node[nid].Dofs[2].Eq
chk.AnaNum(tst, "uz", tolu, dom.Sol.Y[iz], usg[2]*dmult, verbose)
}
}
// check stresses
if true {
if verbose {
io.Pfgreen(". . . checking stresses . . .\n")
}
for eid, sig := range cmp.Sigmas {
if verbose {
io.Pforan("eid = %d\n", eid)
}
if e, ok := dom.Cid2elem[eid].(*ElemU); ok {
for ip, val := range sig {
if verbose {
io.Pfgrey2("ip = %d\n", ip)
}
σ := e.States[ip].Sig
if len(val) == 6 {
chk.AnaNum(tst, "sx ", tols, σ[0], val[0], verbose)
chk.AnaNum(tst, "sy ", tols, σ[1], val[1], verbose)
} else {
chk.AnaNum(tst, "sx ", tols, σ[0], val[0], verbose)
chk.AnaNum(tst, "sy ", tols, σ[1], val[1], verbose)
chk.AnaNum(tst, "sxy", tols, σ[3]/SQ2, val[2], verbose)
if len(val) > 3 { // sx, sy, sxy, sz
chk.AnaNum(tst, "sz ", tols, σ[2], val[3], verbose)
}
}
}
}
if e, ok := dom.Cid2elem[eid].(*Rod); ok {
for ip, val := range sig {
if verbose {
io.Pfgrey2("ip = %d\n", ip)
}
σ := e.States[ip].Sig
chk.AnaNum(tst, "sig", tols, σ, val[0], verbose)
}
}
if e, ok := dom.Cid2elem[eid].(*ElastRod); ok {
dat := e.OutIpsData()
for ip, val := range sig {
if verbose {
io.Pfgrey2("ip = %d\n", ip)
}
res := dat[ip].Calc(dom.Sol)
σ := res["sig"]
chk.AnaNum(tst, "sig", tols, σ, val[0], verbose)
}
}
}
}
}
}
func test_rwstep01(tst *testing.T) {
verbose()
chk.PrintTitle("rwstep01")
buf, err := io.ReadFile("rw/data/beadpanel.step")
if err != nil {
tst.Errorf("cannot read file:\n%v", err)
return
}
dat := string(buf)
var stp rw.STEP
err = stp.ParseDATA(dat)
if err != nil {
tst.Errorf("Parse filed:\n%v", err)
return
}
var bsplines []*Bspline
for _, scurve := range stp.Scurves {
curve := stp.BScurves[scurve.Curve_3d]
if curve == nil {
continue
}
// collect vertices
nv := len(curve.Control_points_list)
verts := utl.DblsAlloc(nv, 4)
for i, key := range curve.Control_points_list {
if p, ok := stp.Points[key]; ok {
for j := 0; j < 3; j++ {
verts[i][j] = p.Coordinates[j]
}
verts[i][3] = 1.0
} else {
chk.Panic("cannot find point %q", key)
}
}
// collect knots
nk := 0
for _, m := range curve.Knot_multiplicities {
nk += m
}
knots := make([]float64, nk)
k := 0
for i, u := range curve.Knots {
m := curve.Knot_multiplicities[i]
for j := 0; j < m; j++ {
knots[k] = u
k++
}
}
// create B-spline
bsp := new(Bspline)
bsp.Init(knots, curve.Degree)
bsp.SetControl(verts)
bsplines = append(bsplines, bsp)
}
if true {
io.Pforan("n = %v\n", len(bsplines))
for i, bsp := range bsplines {
bsp.Draw3d("", "", 21, i == 0)
}
//plt.Show()
}
}
func Test_sg1121(tst *testing.T) {
//verbose()
chk.PrintTitle("sg1121")
// run simulation
if !Start("data/sg1121.sim", true, chk.Verbose) {
tst.Errorf("test failed\n")
return
}
// make sure to flush log
defer End()
// run simulation
if !Run() {
tst.Errorf("test failed\n")
return
}
// plot
doplot := false
if doplot {
// read summary
sum := ReadSum(Global.Dirout, Global.Fnkey)
// allocate domain
distr := false
d := NewDomain(Global.Sim.Regions[0], distr)
if !d.SetStage(0, Global.Sim.Stages[0], distr) {
tst.Errorf("SetStage failed\n")
return
}
// selected node and dof index
nidx := 30
didx := 1
// new results
ntout := len(sum.OutTimes)
uy := make([]float64, ntout)
for tidx := 0; tidx < ntout; tidx++ {
if !d.ReadSol(sum.Dirout, sum.Fnkey, tidx) {
tst.Errorf("test failed:\n")
return
}
nod := d.Nodes[nidx]
eq := nod.Dofs[didx].Eq
uy[tidx] = d.Sol.Y[eq]
// check
if math.Abs(d.Sol.T-sum.OutTimes[tidx]) > 1e-14 {
tst.Errorf("output times do not match time in solution array")
return
}
}
plt.Plot(sum.OutTimes, uy, "'k*-', clip_on=0, label='gofem'")
// old results
b, err := io.ReadFile("cmp/sg1121gofemold.json")
if err != nil {
tst.Errorf("cannot read comparison file\n")
return
}
var gofemold struct {
Time, Uy30 []float64
}
err = json.Unmarshal(b, &gofemold)
if err != nil {
tst.Errorf("cannot unmarshal comparison file\n")
return
}
plt.Plot(gofemold.Time, gofemold.Uy30, "'ro-', label='gofemOld'")
// mechsys results
_, res, err := io.ReadTable("cmp/sg1121mechsysN30.cmp")
if err != nil {
tst.Errorf("cannot read mechsys comparison file\n")
return
}
plt.Plot(res["Time"], res["uy"], "'b+-', label='mechsys'")
// show figure
plt.Gll("$t$", "$u_y$", "")
plt.Show()
}
}
func main() {
// read README.md file
md, err := io.ReadFile("README.md")
if err != nil {
io.PfRed("cannot read README.md\n")
return
}
// process markdown
//html := string(blackfriday.MarkdownCommon(md))
flags := 0 |
blackfriday.HTML_USE_XHTML |
blackfriday.HTML_USE_SMARTYPANTS |
blackfriday.HTML_SMARTYPANTS_LATEX_DASHES
extensions := 0 |
blackfriday.EXTENSION_NO_INTRA_EMPHASIS |
blackfriday.EXTENSION_TABLES |
blackfriday.EXTENSION_FENCED_CODE |
blackfriday.EXTENSION_AUTOLINK |
blackfriday.EXTENSION_STRIKETHROUGH |
blackfriday.EXTENSION_SPACE_HEADERS |
blackfriday.EXTENSION_HEADER_IDS |
blackfriday.EXTENSION_BACKSLASH_LINE_BREAK |
blackfriday.EXTENSION_DEFINITION_LISTS
renderer := blackfriday.HtmlRenderer(flags, "", "")
html := string(blackfriday.MarkdownOptions(md, renderer, blackfriday.Options{Extensions: extensions}))
// environment variable => figures path
path := os.ExpandEnv("${GOPATH}/src/github.com/cpmech/gofem/")
io.Pforan("path = %v\n", path)
// set path of figures
html = strings.Replace(html, "img src=\"", io.Sf("img src=\"%s/examples/", path), -1)
// set header and footer
html = `<!DOCTYPE HTML>
<html>
<head>
<title>Gofem – Examples</title>
<meta charset="utf-8" />
<style>
h1 {color:#0064cb; font-family:verdana; font-size:200%;}
h2 {color:#0064cb}
h3 {color:#0064cb}
a:hover {background-color:#5397dc;}
#container {
width:500px;
text-align:center;
}
#container img {
max-width:100%;
height:auto;
}
</style>
</head>
<body>
` + html + `
</body>
</html>`
// write file
io.WriteFileVD("/tmp", "gofem-README.html", bytes.NewBuffer([]byte(html)))
//io.WriteFileVD("/tmp", "gofem-README.html", bytes.NewBuffer(html))
}
// ReadSim reads all simulation data from a .sim JSON file
// Notes: 1) this function initialises log file
// 2) returns nil on errors
func ReadSim(dir, fn, logPrefix string, erasefiles bool) *Simulation {
// new sim
var o Simulation
// read file
b, err := io.ReadFile(filepath.Join(dir, fn))
if err != nil {
io.PfRed("sim: cannot read simulation file %s/%s\n%v\n", dir, fn, err)
return nil
}
// set default values
o.Data.SetDefault()
o.Solver.SetDefault()
o.LinSol.SetDefault()
// decode
err = json.Unmarshal(b, &o)
if err != nil {
io.PfRed("sim: cannot unmarshal simulation file %s/%s\n%v\n", dir, fn, err)
return nil
}
// derived data
o.Data.PostProcess(dir, fn, erasefiles)
o.LinSol.PostProcess()
o.Solver.PostProcess()
// init log file
err = InitLogFile(o.Data.DirOut, logPrefix+o.Data.FnameKey)
if err != nil {
io.PfRed("sim: cannot create log file\n%v", err)
return nil
}
// read materials database
o.Mdb = ReadMat(o.Data.FnameDir, o.Data.Matfile)
if LogErrCond(o.Mdb == nil, "sim: cannot read materials file") {
return nil
}
// for all regions
for i, reg := range o.Regions {
// read mesh
reg.Msh = ReadMsh(o.Data.FnameDir, reg.Mshfile)
if LogErrCond(reg.Msh == nil, "cannot read mesh file") {
return nil
}
// dependent variables
reg.etag2idx = make(map[int]int)
for j, ed := range reg.ElemsData {
reg.etag2idx[ed.Tag] = j
}
// get ndim and max elevation
if i == 0 {
o.Ndim = reg.Msh.Ndim
o.MaxElev = reg.Msh.Ymax
if o.Ndim == 3 {
o.MaxElev = reg.Msh.Zmax
}
} else {
if LogErrCond(reg.Msh.Ndim != o.Ndim, "all meshes must have the same ndim. %d != %d") {
return nil
}
if o.Ndim == 2 {
o.MaxElev = max(o.MaxElev, reg.Msh.Ymax)
} else {
o.MaxElev = max(o.MaxElev, reg.Msh.Zmax)
}
}
// get water data
for _, mat := range o.Mdb.Materials {
if mat.Model == "porous" {
if prm := mat.Prms.Find("RhoL0"); prm != nil {
o.WaterRho0 = prm.V
}
if prm := mat.Prms.Find("BulkL"); prm != nil {
o.WaterBulk = prm.V
}
}
}
}
// water level
o.WaterLevel = max(o.Data.Wlevel, o.MaxElev)
// for all stages
var t float64
for i, stg := range o.Stages {
// fix Tf
if stg.Control.Tf < 1e-14 {
stg.Control.Tf = 1
}
// fix Dt
if stg.Control.DtFcn == "" {
if stg.Control.Dt < 1e-14 {
stg.Control.Dt = 1
}
stg.Control.DtFunc = &fun.Cte{C: stg.Control.Dt}
} else {
stg.Control.DtFunc = o.Functions.Get(stg.Control.DtFcn)
if LogErrCond(stg.Control.DtFunc == nil, "sim: cannot get Dt function named %s\n", stg.Control.DtFcn) {
return nil
}
stg.Control.Dt = stg.Control.DtFunc.F(t, nil)
}
// fix DtOut
if stg.Control.DtoFcn == "" {
if stg.Control.DtOut < 1e-14 {
stg.Control.DtOut = stg.Control.Dt
stg.Control.DtoFunc = stg.Control.DtFunc
} else {
if stg.Control.DtOut < stg.Control.Dt {
stg.Control.DtOut = stg.Control.Dt
}
stg.Control.DtoFunc = &fun.Cte{C: stg.Control.DtOut}
}
} else {
stg.Control.DtoFunc = o.Functions.Get(stg.Control.DtoFcn)
if LogErrCond(stg.Control.DtoFunc == nil, "sim: cannot get DtOut function named %s\n", stg.Control.DtoFcn) {
return nil
}
stg.Control.DtOut = stg.Control.DtoFunc.F(t, nil)
}
// first stage
if i == 0 {
// gravity
for _, econd := range stg.EleConds {
for j, key := range econd.Keys {
if key == "g" {
if o.Gfcn == nil {
o.Gfcn = o.Functions.Get(econd.Funcs[j])
if LogErrCond(o.Gfcn == nil, "sim: cannot find gravity function in functions database") {
return nil
}
break
}
}
}
}
if o.Gfcn == nil {
o.Gfcn = &fun.Cte{C: 10}
}
}
// update time
t += stg.Control.Tf
}
// log
log.Printf("sim: file=%s/%s desc=%q nfunctions=%d nregions=%d nstages=%d linsol=%s itol=%g\n", dir, fn, o.Data.Desc, len(o.Functions), len(o.Regions), len(o.Stages), o.LinSol.Name, o.Solver.Itol)
return &o
}
func main() {
// input data file
inpfn := "data/loccmdrv1.inp"
flag.Parse()
if len(flag.Args()) > 0 {
inpfn = flag.Arg(0)
}
if io.FnExt(inpfn) == "" {
inpfn += ".inp"
}
// read and parse input data
var in Input
b, err := io.ReadFile(inpfn)
if err != nil {
io.PfRed("cannot read %s\n", inpfn)
return
}
err = json.Unmarshal(b, &in)
if err != nil {
io.PfRed("cannot parse %s\n", inpfn)
return
}
in.PostProcess()
// print input data
io.Pf("%v\n", in)
// load simulation
sim := inp.ReadSim(in.Dir, in.SimFn, "cmd_", false)
if sim == nil {
io.PfRed("cannot load simulation\n")
return
}
// get material data
mat := sim.Mdb.Get(in.MatName)
if mat == nil {
io.PfRed("cannot get material\n")
return
}
//io.Pfcyan("mat = %v\n", mat)
// get and initialise model
mdl, _ := msolid.GetModel(in.SimFn, in.MatName, mat.Model, false)
if mdl == nil {
io.PfRed("cannot allocate model\n")
return
}
ndim := 3
pstress := false
mdl.Init(ndim, pstress, mat.Prms)
//io.Pforan("mdl = %v\n", mdl)
// load path
var pth msolid.Path
err = pth.ReadJson(ndim, path.Join(in.Dir, in.PathFn))
if err != nil {
io.PfRed("cannot read path file %v\n", err)
return
}
//io.PfYel("pth = %v\n", pth)
// driver
var drv msolid.Driver
drv.InitWithModel(ndim, mdl)
// run
err = drv.Run(&pth)
if err != nil {
io.Pfred("driver: Run failed: %v\n", err)
}
// plot
//if false {
if true {
var plr msolid.Plotter
plr.SetFig(false, in.FigEps, in.FigProp, in.FigWid, "/tmp", "cmd_"+in.SimFn)
var epm msolid.EPmodel
if m, ok := mdl.(msolid.EPmodel); ok {
plr.SetModel(m)
epm = m
}
if epm != nil {
//plr.Phi = epm.Get_phi()
b := epm.Get_bsmp()
epm.Set_bsmp(0)
plr.YsClr0 = "magenta"
plr.Plot(in.PlotSet, drv.Res, nil, true, false)
epm.Set_bsmp(b)
}
plr.YsClr0 = "green"
plr.Plot(in.PlotSet, drv.Res, drv.Eps, false, true)
}
// plot ys
if false {
//if true {
plt.Reset()
m := mdl.(*msolid.SmpInvs)
φ := m.Get_phi()
σcCte := 10.0
M := tsr.Phi2M(φ, "oct")
rmin, rmax := 0.0, 1.28*M*σcCte
nr, nα := 31, 81
//nr, nα := 31, 1001
npolarc := true
simplec := false
only0 := false
grads := false
showpts := false
ferr := 10.0
tsr.PlotOct("fig_isofun02.png", σcCte, rmin, rmax, nr, nα, φ, m.Isof.Fa, m.Isof.Ga,
npolarc, simplec, only0, grads, showpts, true, true, ferr)
}
}
func main() {
// catch errors
defer func() {
if err := recover(); err != nil {
io.PfRed("ERROR: %v\n", err)
}
}()
// input data
mshfn, fnkey := io.ArgToFilename(0, "data/sgm57", ".msh", true)
// old mesh
var old OldMesh
// read file
b, err := io.ReadFile(mshfn)
if err != nil {
chk.Panic("%v", err)
}
// decode
err = json.Unmarshal(b, &old)
if err != nil {
chk.Panic("%v", err)
}
// verts: find largest strings
var ndim int
L := make([]int, 5)
for _, v := range old.Verts {
L[0] = utl.Imax(L[0], len(io.Sf("%d", v.Id)))
L[1] = utl.Imax(L[1], len(io.Sf("%d", v.Tag)))
for j, x := range v.C {
L[2+j] = utl.Imax(L[2+j], len(io.Sf("%g", x)))
}
ndim = len(v.C)
}
S := make([]string, 5)
for i, l := range L {
S[i] = io.Sf("%d", l)
}
// write vertices
buf := new(bytes.Buffer)
io.Ff(buf, "{\n \"verts\":[\n")
for i, v := range old.Verts {
if i > 0 {
io.Ff(buf, ",\n")
}
io.Ff(buf, " {\"i\":%"+S[0]+"d, \"t\":%"+S[1]+"d, \"x\":[", v.Id, v.Tag)
for j, x := range v.C {
if j > 0 {
io.Ff(buf, ", ")
}
io.Ff(buf, "%"+S[2+j]+"g", x)
}
io.Ff(buf, "] }")
}
// cells: find largest strings
n := 30
L = make([]int, n*2)
for _, c := range old.Cells {
L[0] = utl.Imax(L[0], len(io.Sf("%d", c.Id)))
L[1] = utl.Imax(L[1], len(io.Sf("%d", c.Tag)))
L[2] = utl.Imax(L[2], len(io.Sf("%d", c.Part)))
for j, v := range c.Verts {
L[3+j] = utl.Imax(L[3+j], len(io.Sf("%d", v)))
}
}
S = make([]string, n*2)
for i, l := range L {
S[i] = io.Sf("%d", l)
}
io.Ff(buf, "\n ],")
// write cells
io.Ff(buf, "\n \"cells\":[\n")
for i, c := range old.Cells {
if i > 0 {
io.Ff(buf, ",\n")
}
io.Ff(buf, " {\"i\":%"+S[0]+"d, \"t\":%"+S[1]+"d, \"p\":%"+S[2]+"d, \"y\":%q, \"v\":[", c.Id, c.Tag, c.Part, c.Type)
for j, v := range c.Verts {
if j > 0 {
io.Ff(buf, ", ")
}
io.Ff(buf, "%"+S[3+j]+"d", v)
}
io.Ff(buf, "]")
if len(c.FTags) > 0 {
io.Ff(buf, ", ")
if ndim == 2 {
io.Ff(buf, "\"et\":[")
} else {
io.Ff(buf, "\"ft\":[")
}
for j, t := range c.FTags {
if j > 0 {
io.Ff(buf, ", ")
}
io.Ff(buf, "%d", t)
}
io.Ff(buf, "]")
}
io.Ff(buf, " }")
}
io.Ff(buf, "\n ]\n}")
io.WriteFileVD("/tmp/gosl", fnkey+"-new.msh", buf)
// check
m, err := msh.Read("/tmp/gosl/" + fnkey + "-new.msh")
if err != nil {
chk.Panic("cannot read new mesh:\n%v", err)
}
m.Check()
}