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/*
* hydra.i $Id$
* functions to access hydra-generated Silo/PDB files
*/
local hydra ;
/* DOCUMENT hydra.i
defines several functions useful for examining and extracting
data from hydra-generated Silo/PDB dump files:
h_openb -- use instead of openb for hydra files
hydra_xyz -- extracts xyz and boundary arrays
h_data -- extracts data nodal or zonal arrays
h_array -- extracts data nodal or zonal arrays for one ublk
h_mix -- extracts zonal data for mixed zones
h_iparm -- extracts integer parameter values
h_gblk -- extracts information relating hblks to
user blocks
h_collect -- loops on h_array over all times
SEE ALSO: h_openb, hydra_xyz, h_data, h_array, h_mix,
h_iparm, h_fparm, h_gblk
*/
/*
* NOTES:
* (1) legacy format
* support for legacy file format does not allow distributed (.root)
* files, but in principle allows time history families
* (2) ndims
* assume that dimensionality of /hblk0/hydro_mesh_coord0 variable
* in the first file of the family is ndims
* (3) assume the times in a history family are in alphabetical order
* of their filenames, only include files with names alphabetically
* greater than the filename passed to h_openb
*/
/* ------------------------------------------------------------------------ */
func h_openb (name, one=)
/* DOCUMENT f = h_openb(filename)
open a hydra dump file, including 2D families of distributed
history files.
The return value is a list (see _lst function) containing the
currently opened file and the non-PDB data required to navigate
through each file and the entire family.
With one=1 keyword, only one file of a history family is opened.
SEE ALSO: h_close, hydra_xyz, h_data, h_jt, h_jr, h_get_times
*/
{
f = _h_openb(name);
tmp = print(f);
dir = strtok(strtok(tmp(1:2),":")(2,))(1,);
name = dir(1); /* non-directory part of name */
dir = dir(2); /* directory name */
if (numberof(tmp)>2) {
tmp = tmp(3:0);
dir = strpart(dir, 1:-1);
if (numberof(tmp)>1) tmp(1:-1) = strpart(tmp(1:-1), 1:-1);
for (n=1 ; n<=numberof(tmp) ; ++n) dir += tmp(n);
}
tmp = [];
root = (strpart(name,-4:0) == ".root");
if (root) name = strpart(name,1:-5);
_h_legacy = 0; /* 1 to use obsolete hydra format */
if (!root && _h_autodetect)
_h_legacy = noneof((*get_vars(f)(1))=="/Global/");
sfx = strpart(name,-3:0);
n = 0;
if (sread(sfx,n) && swrite(format="%04ld",n)==sfx) {
/* filename (excluding any .root) ends in four digits */
pfx = strpart(name,1:-5); /* suffix is either 4 or 5 digits */
n = strlen(pfx);
fifth = strpart(name,n+1:n+1);
has_five = ((fifth>="0") && (fifth<="9"));
if (!has_five) {
/* if this is obsolete naming style, assume pbnm has 4 characters */
if (n!=3) pfx = strpart(name,1:3);
}
if (n) {
list = lsdir(dir);
if (root && numberof(list)) {
list = list(where(strpart(list,-4:0)==".root"));
if (numberof(list)) list = strpart(list,1:-5);
}
if (numberof(list))
list = list(where((strpart(list,1:strlen(pfx))==pfx) &
(strlen(list)==n+5)));
if (numberof(list) > 1) {
list = list(sort(list));
final = strpart(list,n+1:n+1);
if (has_five) {
/* all new files have five digit numeric suffix, fixed prefix */
list = list(where((final>="0") & (final<="9")));
} else {
/* this is obsolete naming convention */
ok = (final==fifth);
if (nallof(ok)) {
fdigit = (final>="0") & (final<="9");
/* make non-digit fifth character files come first in list */
last = list(where( (!ok) & fdigit ));
list = list(where(ok));
grow, list, last;
/* note that "g" or "opc" or restart have already been
* weeded out by the fact that the filename length
* would be 1 or 3 characters longer than a restart dump */
}
}
if (numberof(list)) {
ok = array(1n, numberof(list));
for (i=n+2 ; i<=n+5 ; i++) {
final = strpart(list, i:i);
ok &= (final>="0") & (final<="9");
}
list = list(where(ok));
}
if (numberof(list) > 1) {
i = where(list==name);
if (numberof(i)) {
/* this file is member of a history family */
if (!one)
name = list(i(1):0); /* only take this file and later */
else
name = list(i(1));
}
}
}
}
}
/* name is now either the original scalar name (excluding any directory)
* or an array of names in a history family
* if name ended in ".root", that is not included in name value(s)
*/
name = dir+name;
/* scan through files to get cycle and time, umap and gmap
* this collects everything necessary to find variables except for
* the dimensionality of the problem (ndims), which cannot be easily
* determined until the first non-root file is read
* all the relevant information in .root files is read here,
* they will not be opened again */
data = array(pointer, 3, numberof(name));
time = array(-1.e20, numberof(name));
ncyc = array(-1, numberof(name));
if (root) {
sfx = ".root";
} else {
sfx = "";
f0 = f;
}
ihist = 1;
for (i=1 ; i<=numberof(name) ; i++) {
if (i>1) f = _h_openb(name(i)+sfx);
data(,i) = _h_read_maps(f, (root?dir:name(i)), root);
if (!numberof(time)) continue;
vars = *(get_vars(f)(1));
if (anyof(vars=="/dtime")) time(i) = get_member(f,"/dtime")(1);
if (anyof(vars=="/cycle")) ncyc(i) = get_member(f,"/cycle")(1);
}
if (numberof(time) && noneof(time > -1.1e20)) time = [];
if (numberof(ncyc) && noneof(ncyc > -1)) ncyc = [];
if (is_void(f0))
f0 = _h_openb((*data(1,1))(1));
/* is this always same as h_iparm(f0, "ndims") ?? */
ndims = dimsof(get_member(f0, "/hblk0/hydro_mesh_coord0"))(1);
return _lst(f0, [1,1,ndims,_h_legacy], data, time, ncyc);
}
func h_close (&f)
/* DOCUMENT h_close, f
close a file F opened with h_openb.
SEE ALSO: h_openb
*/
{
ff = _car(f,1);
_car, f, 1, [];
_car, f, 3, [];
f = [];
if (is_stream(ff)) close, ff;
}
func h_get_times (f)
/* DOCUMENT times = h_get_times(f)
return array of times in hydra history file family F.
SEE ALSO: h_data, h_openb, h_jt, h_jr
*/
{
return _car(f, 4);
}
func h_jt (f, time)
/* DOCUMENT h_jt, f, time
jump to time TIME in hydra history file family F.
SEE ALSO: h_data, h_openb, h_get_times, h_jr, h_collect
*/
{
times = _car(f, 4);
if (is_void(times)) error, "no times in file";
ihist = abs(times-time)(mnx);
flags = _car(f, 2);
if (flags(2) != ihist) {
flags(2) = ihist;
_car, f, 2, flags;
_car, f, 1, [];
}
}
func h_jr (f, irec)
/* DOCUMENT h_jr, f, irec
or nrecs = h_jr(f)
jump to record IREC in hydra history file family F.
In second form, return total number of records in family.
SEE ALSO: h_data, h_openb, h_get_times, h_jt, h_collect
*/
{
nrecs = dimsof(_car(f, 3));
if (nrecs(1)==2) nrecs = nrecs(3);
else nrecs = 0;
if (!is_void(irec)) {
if (irec>nrecs || irec<1)
error, "no such record as "+print(irec)(1)+" in file";
flags = _car(f, 2);
if (flags(2) != irec) {
flags(2) = irec;
_car, f, 2, flags;
_car, f, 1, [];
}
}
return nrecs;
}
func h_show (f)
/* DOCUMENT h_show, f
or varnames = h_show(f)
prints names of variables available for h_data, h_mix, h_array.
SEE ALSO: h_data, h_openb
*/
{
{ local _h_legacy; }
vars = *get_vars(_h_get_file(f, 1, , _h_legacy))(1);
list = where(strpart(vars,1:7)=="/hblk0/");
if (numberof(list)) {
vars = strpart(vars(list),8:0);
vars = vars(where(strlen(vars)>0));
vars = vars(where(!strmatch(vars,"/")));
vars = vars(where(!strmatch(vars,"_")));
vars = vars(sort(vars));
}
if (am_subroutine()) {
write, vars;
nrecs = h_jr(f);
if (nrecs > 1) {
nt = numberof((time=h_get_times(f)));
if (nt)
write, format=" Found %ld history dumps from time=%e to time=%e\n",
nt, time(1), time(0);
else
write, format=" Found %ld history dumps (no times available)\n", nt;
}
}
return vars;
}
func hydra_xyz (f, ublk, i0, j0, k0, face)
/* DOCUMENT mesh = hydra_xyz(f)
or mesh = hydra_xyz(f, ublk, i0, j0, k0, face)
or mesh = hydra_xyz(f, ublk, i0, j0, k0)
read a 3D mesh object from the hydra PDB/Silo file F.
The returned mesh is _lst(xyz, bound, mbnds, blks, start).
Note that the boundary arrays are adjusted to the hex convention
that cells with i=1, j=1, k=1 are missing, rather than the hydra
convention that i=imax, j=jmax, k=kmax are missing.
In the first form, the ray entry search will start on the
first open boundary face in the mesh. If the actual problem
boundary is not convex, you need to identify a surface of
constant i, j, or k in the problem which is convex, and which
all the rays you intend to trace intersect.
UBLK is the user block number (starting from 0),
I0, J0, K0 are the (1-origin) logical coordinates of a
hydra *cell*. Note that unlike hex cells, the hydra
cell bounded by nodes (1,1,1) and (2,2,2) is numbered (1,1,1).
(Hex numbers it (2,2,2).)
FACE is the face number on cell (I0,J0,K0) which you want a
ray to enter. 0 means the -I face, 1 the +I face, 2 the -J
face, 3 the +J face, 4 the -K face, and 5 the +K face.
As you step from this cell to its neighbors, then to their
neighbors, and so on, this face must trace out a convex
surface for the ray entry search. Rays not intersecting
this surface will not enter the problem; the ray trace
will begin at this surface, not at -infinity.
If FACE==-1 or is omitted (as in the third form), then the
given points on the rays are assumed to lie inside the mesh,
and a pseudo ray from the centroid of cell (I0, J0, K0) will be
tracked to the given point on each ray; the ray will be launched
into the cell containing that point.
You can set a hydra_bnd_hook function before calling hydra_xyz
if the boundary conditions for hex need to be different than
for hydra.
SEE ALSO: hydra_bnd_hook, h_data, h_openb
*/
{
{ local mdims, mlens, bnum, _h_legacy, gmap; }
nblk = h_blocks(f, mdims, mlens, _h_legacy, , gmap);
/* compute strides and global offsets for all the mesh blocks */
blo = array(0, 4, nblk);
blo(2:4,) = mdims;
lscratch = hydra_blks(nblk, blo);
/* allocate the global mesh array and read it from disk
* read bc and bnd information at same time to avoid multiple
* loops in the case of multiple files */
if (nblk>1) xyz = array(0., 3, sum(mlens));
else xyz = array(0., 3, grow([3],mdims(,1)));
off = 0;
binfo = array(0, 4, nblk);
bndtmp = array(pointer, nblk);
bctmp = array(pointer, 2, nblk);
for (i=1 ; i<=nblk ; i++) {
ff = _h_get_file(f, i, bnum);
off0 = off+1;
off += mlens(i);
xyz(1,off0:off) =
get_member(ff,swrite(format="/hblk%ld/hydro_mesh_coord0",bnum))(*);
xyz(2,off0:off) =
get_member(ff,swrite(format="/hblk%ld/hydro_mesh_coord1",bnum))(*);
xyz(3,off0:off) =
get_member(ff,swrite(format="/hblk%ld/hydro_mesh_coord2",bnum))(*);
/* read [nbc, nbnd, jp, kp] */
binfo(,i) = get_member(ff,_h_varname(bnum,"hydrodati"))([34,37,21,22]);
n = binfo(2,i);
strides = [1,binfo(3,i),binfo(4,i)];
if (n > 0) {
tmp = array(pointer, 3, n);
bndtmp(i) = &tmp;
for (j=1 ; j<=n ; j++) {
prefix = _h_bndname(bnum,j-1);
pn = get_member(ff,prefix+"pn")(1);
list = where(abs(pn)==strides);
if (!numberof(list)) continue;
pn = sign(pn)*list(1);
tmp(1,j) = &[i, get_member(ff,prefix+"len_nsend1")(1),
pn, get_member(ff,prefix+"blk_send")(1),
get_member(ff,prefix+"bndnbc")(1)];
tmp(2,j) = &long(get_member(ff,prefix+"ndx_send"));
tmp(3,j) = &long(get_member(ff,prefix+"ndx_recv"));
}
}
n = binfo(1,i);
if (n > 0) {
tmp = array(pointer, n);
tmp2 = array(0, 2, n);
bctmp(1,i) = &tmp;
bctmp(2,i) = &tmp2;
for (j=1 ; j<=n ; j++) {
prefix = _h_bcname(bnum,j-1);
pn = get_member(ff,prefix+"pn")(1);
list = where(abs(pn)==strides);
if (!numberof(list)) continue;
pn = sign(pn)*list(1);
tmp2(1,j) = pn;
jj = get_member(ff,prefix+"len")(1); /* unnecessary?? */
tmp(j) = &long(get_member(ff,prefix+"ndx")(1:jj));
tmp2(2,j) = get_member(ff,prefix+"rtype")(1);
}
}
}
bnd_off= binfo(2,cum);
nbnd= max(bnd_off(0),1);
bnd_blk= bnd_len= bnd_pn= bnd_r= bnd_ri= array(0, nbnd);
bnd_ndxs= bnd_ndxr= array(pointer, nbnd);
jj= 0;
for (i=1 ; i<=nblk ; i++) {
n= binfo(2,i);
strides= [1,binfo(3,i),binfo(4,i)];
eq_nocopy, tmp, *bndtmp(i);
for (j=1 ; j<=n ; j++) {
jj++;
eq_nocopy, tmp2, *tmp(1,j);
if (!numberof(tmp2)) continue;
bnd_blk(jj)= tmp2(1);
bnd_len(jj)= tmp2(2);
bnd_pn(jj)= tmp2(3);
bnd_r(jj)= tmp2(4);
bnd_ri(jj)= tmp2(5);
bnd_ndxs(jj)= tmp(2,j);
bnd_ndxr(jj)= tmp(3,j);
}
}
bndtmp = tmp = tmp2 = [];
bnd_r++;
bnd_ri++;
/* allocate the block bound array and construct it from disk data */
bound= array(0, dimsof(xyz));
scratch= array(0, lscratch);
/* number of bnd nodes is sum(bnd_len), which overestimates number
* of faces; take that as a safe length to allocate */
n= bnd_len(sum:1:jj);
mbnds= n? array(HX_blkbnd, n) : [];
for (i=1,ibnd=0 ; i<=jj ; i++) {
if (!bnd_pn(i)) continue;
n= bnd_len(i);
s= bnd_blk(i);
r= bnd_r(i);
ri= bnd_off(r) + bnd_ri(i);
bnds= [bnd_pn(i),binfo(3,s),binfo(4,s)];
bndr= [bnd_pn(ri),binfo(3,r),binfo(4,r)];
jbnd= hydra_bnd(ibnd, bound, scratch, blo(,s), blo(,r),
bnds, bndr, n, *bnd_ndxs(i), bnd_ndxr(ri), &mbnds, r-1);
if (jbnd<0) {
if (hydra_bnd_check) error, "illegal bnd data";
} else {
ibnd = jbnd;
}
}
nbnds= ibnd;
bnd_ndxs= bnd_ndxr= [];
/* remains only to fill in the bcs in bound */
start= -1;
bndr= blor= [0]; /* unused */
for (i=1,off=0 ; i<=nblk ; off+=mlens(i++)) {
n= binfo(1,i);
if (n <= 0) continue;
strides= bnds= [1,binfo(3,i),binfo(4,i)];
blos= blo(,i);
tbound= array(0, 3,mdims(1,i),mdims(2,i),mdims(3,i));
tcheck= array(0, 2,n);
eq_nocopy, tmp, *bctmp(1,i);
eq_nocopy, tmp2, *bctmp(2,i);
for (j=1 ; j<=n ; j++) {
local ndxs;
eq_nocopy, ndxs, *tmp(j);
if (!numberof(ndxs)) continue;
pn = tmp2(1,j);
bnds(1) = pn;
rtype = tmp2(2,j);
if (rtype==0) ibnd= -1; /* open bc */
else if (rtype==1) ibnd= -2; /* reflecting bc */
else if (rtype==3) ibnd= -3; /* zero area bc */
else error, "unknown rtype in bc data";
if (!is_void(hydra_bnd_hook))
ibnd= hydra_bnd_hook(ibnd, pn, i, j, ndxs);
jj = numberof(ndxs);
jj= hydra_mrk(ibnd, tbound, blos, bnds, jj, ndxs);
if (jj < 0) error, "illegal bc data";
tcheck(1,j)= pn;
tcheck(2,j)= jj;
}
jj= hydra_adj(bound, tbound, blos, n, tcheck);
tbound= [];
if (jj>=0 && start<0) start= jj;
}
bctmp = tmp = tmp2 = [];
blks= array(HX_block, nblk);
blks.length= blo(2:4,);
blks.stride(1,)= 1;
blks.stride(2:3,)= blo(2:3,);
blks.first= blo(1,);
blks.final= blo(1,)+blo(4,);
if (is_void(ublk)) {
if (start<0) error, "mesh must have at least one open bc";
} else {
list= where(gmap(1,)==ublk);
if (!numberof(list)) error, "mesh has no user block #"+pr1(ublk);
gmap= gmap(,list);
lst= where((gmap(2,)<=i0) & (gmap(3,)>i0) &
(gmap(4,)<=j0) & (gmap(5,)>j0) &
(gmap(6,)<=k0) & (gmap(7,)>k0));
if (!numberof(lst))
error, "mesh ublk #"+pr1(ublk)+" has no point "+pr1([i0,j0,k0]);
if (numberof(lst)>1)
error, "mesh ublk #"+pr1(ublk)+" has multiple points "+pr1([i0,j0,k0]);
/* could read ireg and check that this cell exists, but don't bother */
lst= lst(1);
/* get 0-origin hex cell ijk within this block, convert to 1D index */
start= [i0,j0,k0] - gmap(2:6:2,lst) + 1;
block= blks(list(lst));
start= block.first + sum(start*block.stride);
if (!is_void(face) && face!=-1) {
if (face<0 || face>5) error, "face must be between 0 and 5 inclusive";
start= 6*start + face;
} else {
start= -1 - start;
}
}
if (nbnds) mbnds= mbnds(1:nbnds);
/* form the mesh */
return _lst(xyz, bound, mbnds, blks, start);
}
if (is_void(h_xyz)) h_xyz = hydra_xyz;
func h_data (f, name)
/* DOCUMENT name_array = h_data(f, name)
or pname_arrays = h_data(f, [name1,name2,...,nameN])
eq_nocopy, name_array1, *pname_arrays(1)
...
eq_nocopy, name_arrayN, *pname_arrays(N)
reads variable NAME from the hydra file F. If F is a multiblock
file, NAME_ARRAY will be 1-D; for single block problems it will
be 3-D. If NAME=="matlist", you get the "Materials_matlist"
array. Coordinates can be obtained using the names x, y or z.
In the second form, NAME1, ..., NAMEN are retrieved simultaneously,
which is useful when F is a large family of files.
Note that zone centered arrays are adjusted to the hex convention
that cells with i=1, j=1, k=1 are missing, rather than the hydra
convention that i=imax, j=jmax, k=kmax are missing.
SEE ALSO: hydra_xyz, h_mix, h_array, h_show
*/
{
{ local mdims, mlens, bnum, _h_legacy, ndims; }
nblk = h_blocks(f, mdims, mlens, _h_legacy, ndims);
dim2 = dim3 = call(2:0);
if (ndims < 3) {
dim3 = 1;
if (ndims < 2) dim2 = 1;
}
/* allocate the global data array and read it from disk */
name = _h_translate(name);
dims = dimsof(name);
nn = numberof(name);
pdata = array(pointer, dims);
data = [];
off = 0;
for (i=1 ; i<=nblk ; i++) {
off0 = off+1;
off += mlens(i);
ff = _h_get_file(f, i, bnum);
for (j=1 ; j<=nn ; j++) {
bdat = get_member(ff,swrite(format="/hblk%ld/%s",bnum,name(j)));
if (numberof(bdat)!=mlens(i)) {
if (dimsof(bdat)(1)==1) {
tmp = array(structof(bdat), mdims(,i)-1);
tmp(*) = bdat;
bdat = tmp;
}
tmp = array(structof(bdat), grow([3],mdims(,i)));
tmp(2:0,dim2,dim3) = bdat;
bdat=tmp; tmp=[];
}
eq_nocopy, data, *pdata(j);
if (is_void(data)) {
if (nblk>1) data = array(structof(bdat), sum(mlens));
else data = array(structof(bdat), grow([ndims],mdims(,1)));
pdata(j) = &data;
}
data(off0:off) = bdat(*);
}
}
return dims(1)? pdata : data;
}
func h_mix (f, &matlist, name, &mixdat)
/* DOCUMENT mixdat = h_mix(f, matlist)
eq_nocopy, mixn, *mixdat(1)
eq_nocopy, mixcell, *mixdat(2)
eq_nocopy, mixnmat, *mixdat(3)
eq_nocopy, mixhist, *mixdat(4)
or mix_array = h_mix(f, mixdat, name)
or pmix_array = h_mix(f, matlist, [name1,...,nameN], mixdat)
eq_nocopy, mix_array1, *pmix_array(1)
...
eq_nocopy, mix_arrayN, *pmix_array(N)
In first form, returns MIXDAT and MATLIST for the hydra file F.
MIXDAT consists of two arrays: MIXN is a list of the number of
mixed cells for each block, and MIXCELL is an index array
into any hex global cell array (as returned by h_data),
MIXNMAT is the number of mix "zones" within each cell,
and MIXHIST is the list required in order to use the
histogram function on a mix array.
In the second form, reads the mix data for the variable NAME
in the hydra file F; the MIXDAT argument must have been returned
by a previous call to h_mix using the first form.
In the third form, MATLIST and MIXDAT are both returned along
with the set of variables NAME1, ..., NAMEN, so that a number of
variables can be retrieved in one call (useful when F is a large
family of files).
For example, to compute the temperature in each cell, using
a mass weighted average in mixed zones, you would do this:
den = h_data(f,"den");
tmat = h_data(f,"tmat");
mixdat = h_mix(f, matlist);
local mixcell, mixhist;
eq_nocopy, mixcell, *mixdat(2);
eq_nocopy, mixhist, *mixdat(4);
denx = h_mix(f, mixdat, "den");
tmatx = h_mix(f, mixdat, "tmat");
vf = h_mix(f, mixdat, "vf");
tavg = tmat;
tavg(mixcell) = histogram(mixhist, tmatx*denx*vf)/den(mixcell);
SEE ALSO: hydra_xyz, h_data, h_array, h_show
*/
{
{ local mdims, mlens, bnum, _h_legacy, ndims; }
nblk = h_blocks(f, mdims, mlens, _h_legacy, ndims);
dim2 = dim3 = call(2:0);
if (ndims < 3) {
dim3 = 1;
if (ndims < 2) dim2 = 1;
}
dims = dimsof(name);
if (is_void(name) || dims(1)) {
/* may as well collect matlist as long as we have to read it */
if (nblk>1) matlist = array(0., sum(mlens));
else matlist = array(0., grow([3],mdims(,1)));
offs = mlens(cum);
if (!is_void(name)) {
nn = numberof(name);
nm = array(string, dims);
for (j=1 ; j<=nn ; j++) {
nami = name(j);
if (nami=="vf") nm(j) = "Materials_mix_vf";
else if (nami=="mat") nm(j) = "Materials_mix_mat";
else nm(j) = nami+"_mix";
}
name = nm;
pdata = array(pointer, dims);
qdata = array(pointer, nblk);
data = [];
}
/* scan blocks for mix data */
nmix = array(0, nblk);
cmix = lmix = array(pointer, nblk);
moff = 0;
for (i=1 ; i<=nblk ; i++) {
ff = _h_get_file(f, i, bnum);
prefix = swrite(format="/hblk%ld/",bnum);
list = get_member(ff, prefix+"Materials_matlist");
dims = grow([ndims],mdims(,i));
tmp = array(0, dims-[0,1,1,1]);
tmp(*) = list(*);
list = array(0, dims);
list(2:0,dim2,dim3) = tmp; tmp = [];
matlist(offs(i)+1:offs(i+1)) = list(*);
cells = where(list<0); /* cells with mixed materials */
if (numberof(cells)) {
start = -list(cells); /* initial indices into mix_next (1-origin) */
mix_next = get_member(ff, prefix+"Materials_mix_next");
/* mix_next is a packed set of sequences of indices into vf,
* with each sequence terminated by a zero
* - apparently, only the zero markers are used by the hydra
* - mix_next is the same shape as the vf or *_mix variables
*
* start is guaranteed to be a monotonically increasing
* (hydra creates it by incrementing through all zones),
* so each contiguous block of vf or the *_mix variables
* represents the next mixed cell in zone order */
stop = where(mix_next<=0);
n = stop - start + 1; /* number of materials per mixed zone */
/* convert cells to global hex cell indices */
cells += offs(i);
} else {
cells = n = [];
}
cmix(i) = &cells;
lmix(i) = &n;
nmix(i) = numberof(cells);
if (nn && numberof(cells)) {
data = array(pointer, nn);
qdata(i) = &data;
for (j=1 ; j<=nn ; j++)
data(j) = &get_member(ff,swrite(format="/hblk%ld/%s",bnum,name(j)));
}
}
n = sum(nmix);
if (n) {
cells = n = array(0, n);
offs = nmix(cum);
for (i=1 ; i<=nblk ; i++) if (nmix(i)) {
cells(offs(i)+1:offs(i+1)) = *cmix(i);
n(offs(i)+1:offs(i+1)) = *lmix(i);
}
imix = n(cum);
marks = array(0, imix(0));
marks(imix(1:-1)+1) = 1;
marks = marks(psum); /* n(1) copies of 1, n(2) copies of 2
* n(3) copies of 3, etc. */
n = imix(offs+1)(dif);
} else {
cells = n = marks = [];
}
mixdat = [&nmix, &cells, &n, &marks];
if (is_void(qdata)) return mixdat;
if (is_void(n)) return pdata;
} else {
n = *matlist(3);
}
if (is_void(n)) return [];
if (is_void(qdata)) {
if (name=="vf") name = "Materials_mix_vf";
else if (name=="mat") name = "Materials_mix_mat";
else name = name+"_mix";
nn = 1;
}
data = pbdat = [];
off = 0;
for (i=1 ; i<=nblk ; i++) {
if (!n(i)) continue;
off0 = off+1;
off += n(i);
if (!is_void(qdata)) eq_nocopy, pbdat, *qdata(i);
for (j=1 ; j<=nn ; j++) {
if (is_void(qdata)) {
ff = _h_get_file(f, i, bnum);
bdat = get_member(ff,swrite(format="/hblk%ld/%s",bnum,name));
} else {
eq_nocopy, bdat, *pbdat(j);
eq_nocopy, data, *pdata(j);
}
if (is_void(data)) {
data = array(structof(bdat), sum(n));
if (!is_void(qdata)) pdata(j) = &data;
}
data(off0:off) = bdat(*);
}
}
return is_void(qdata)? data : pdata;
}
func h_array (f, ublk, name)
/* DOCUMENT name_array = h_array(f, ublk, name)
or pname_arrays = h_array(f, ublk, [name1,name2,...,nameN])
eq_nocopy, name_array1, *pname_arrays(1)
...
eq_nocopy, name_arrayN, *pname_arrays(N)
reads variable array NAME for user block UBLK from the hydra file F.
If NAME=="matlist", you get the "Materials_matlist" array.
Coordinates can be obtained using the names x, y or z.
Ublk numbering starts at 0.
Note that here zone centered arrays are given using the hydra convention
so that i=imax, j=jmax, k=kmax are missing. Thus in order to use the
Yorick plc and plf functions correctly you should index the plotted
variable i.e. for a 2D array.
plf, den(1:-1,1:-1), y, x
SEE ALSO: hydra_xyz, h_data, h_mix, h_show, h_collect
*/
{
{ local mdims, mlens, bnum, _h_legacy, ndims, gmap, umap; }
gnblk = h_blocks(f, mdims, mlens, _h_legacy, ndims, gmap, umap);
unblk = dimsof(umap)(0);
ublk++;
if (ublk > unblk) {
write, format="Error bad ublk number specified - only %ld user blocks,"+
" numbering starts from 0\n", unblk;
return ;
}
/* allocate the global data array and read it from disk */
name = _h_translate(name);
dims = dimsof(name);
nn = numberof(name);
pdata = array(pointer, dims);
data = [];
off= 0;
if (ndims == 1)
udims = [1,umap(3,ublk)];
else if (ndims == 2)
udims = [2,umap(3,ublk),umap(5,ublk)];
else
udims = [3,umap(3,ublk),umap(5,ublk),umap(7,ublk)];
for (i=1 ; i<=gnblk ; i++) {
if ((gmap(1,i)+1) != ublk) continue;
ff = _h_get_file(f, i, bnum);
for (j=1 ; j<=nn ; j++) {
bdat = get_member(ff,swrite(format="/hblk%ld/%s",bnum,name(j)));
eq_nocopy, data, *pdata(j);
if (is_void(data)) {
data = array(structof(bdat), udims);
pdata(j) = &data;
}
dm = dimsof(bdat);
ix = dm(2);
ioff = gmap(2,i)-1;
if (ndims < 2) {
data(ioff+1:ioff+ix) = bdat(*);
} else {
jx = dm(3);
joff = gmap(4,i)-1;
if (ndims < 3) {
data(ioff+1:ioff+ix,joff+1:joff+jx) = bdat;
} else {
kx = dm(4);
koff = gmap(6,i)-1;
data(ioff+1:ioff+ix,joff+1:joff+jx,koff+1:koff+kx) = bdat;
}
}
}
}
return dims(1)? pdata : data;
}
func h_collect (f, ublk, name)
/* DOCUMENT vart = h_collect(f, ublk, name)
returns an array of the variable NAME (a string) from user block
UBLK of hydra file family F. The return value has the leading
dimensions of h_array(f,ublk,name), with a trailing dimension
representing all the times in the family.
SEE ALSO: h_array, h_show
*/
{
nrecs = h_jr(f);
if (nrecs < 1) return h_array(f, ublk, name);
ihist = _car(f, 2)(2);
h_jr, f, 1;
result = array(h_array(f, ublk, name), nrecs);
for (i=1 ; i<=nrecs ; i++) {
h_jr, f, i;
result(..,i) = h_array(f, ublk, name);
}
h_jr, f, ihist;
return result;
}
func h_iparm (f, name)
/* DOCUMENT value = h_iparm(f, name)
or names = h_iparm(f)
returns value of hydra parameter NAME from file F,
or a list of all names in NAME is not supplied.
If NAME is not a string, returns that parameter
or parameters (NAME is index in the returned list of names),
for example h_iparm(f,1:0) returns all parameters.
SEE ALSO: hydra_xyz, h_fparm
*/
{
{ local _h_legacy, lparm; }
f = _h_get_file(f, 1, , _h_legacy);
iparmn0= get_member(f,_h_globname("iparmn")); /* dims may be wrong :(*/
iparmn= _h_parm_fix(iparmn0, lparm);
if (!is_void(name)) {
if (structof(name)==string) {
name= *pointer(name);
n= numberof(name);
if (n>lparm) name= name(1:(n=lparm));
i= where(!(iparmn(1:n,)!=name)(sum,))(1);
} else {
i= name;
}
result= get_member(f,_h_globname("iparmv"))(i);
return result;
} else {
n= numberof(iparmn0)/lparm;
iparmn0= array(string, n);
for (i=1 ; i<=n ; i++) iparmn0(i)= string(&iparmn(,i));
return iparmn0;
}
}
func h_fparm (f, name)
/* DOCUMENT value = h_fparm(f, name)
or names = h_fparm(f)
returns value of hydra parameter NAME from file F,
or a list of all names in NAME is not supplied.
If NAME is not a string, returns that parameter
or parameters (NAME is index in the returned list of names),
for example h_fparm(f,1:0) returns all parameters.
SEE ALSO: hydra_xyz, h_iparm
*/
{
{ local _h_legacy, lparm; }
f = _h_get_file(f, 1, , _h_legacy);
fparmn0= get_member(f,_h_globname("fparmn")); /* dims may be wrong :(*/
fparmn= _h_parm_fix(fparmn0, lparm);
if (!is_void(name)) {
if (structof(name)==string) {
name= *pointer(name);
n= numberof(name);
if (n>lparm) name= name(1:(n=lparm));
i= where(!(fparmn(1:n,)!=name)(sum,))(1);
} else {
i= name;
}
result= get_member(f,_h_globname("fparmv"))(i);
return result;
} else {
n= numberof(fparmn0)/lparm;
fparmn0= array(string, n);
for (i=1 ; i<=n ; i++) fparmn0(i)= string(&fparmn(,i));
return fparmn0;
}
}
func _h_parm_fix (parms, &lparm)
{
/* silo bug reverses order of dimensions of parameter names
* /Global/wordlength if present gives true length of leading dim
* as an easier way to maintain backward compatibility, and
* also to allow for the silo bug being fixed someday,
* hydra guarantees that (1) the first parameter name is <=8 chars,
* and (2) the second parameter name does not begin with <=' '
*/
dims = dimsof(parms);
lparm = numberof(parms);
if (lparm<9 || dims(min:2:0)==1) return [parms(*)];
lparm = 7 + min(where(parms(9:lparm)>' '));
if (dims(2) != lparm) {
dims = array(structof(parms), lparm, numberof(parms)/lparm);
dims(*) = parms(*);
parms = dims;
}
return parms;
}
func h_global (f, name, prefix=)
/* DOCUMENT value = h_global(f, name)
returns value of hydra Global variable NAME from file F.
SEE ALSO: hydra_xyz, h_iparm
*/
{
{ local _h_legacy; }
f = _h_get_file(f, 1, , _h_legacy);
if (!prefix) prefix = "/Global/";
return get_member(f, prefix+name);
}
func h_gblk (f)
/* DOCUMENT gblk = h_gblk(f)
return global block information from the hydra file F (see h_openb).
Each hblk in the mesh corresponds to a particular imin:imax,
jmin:jmax, kmin:kmax in a particular gblk. The return value is
a 2D long array 7-by-numberof(h blocks):
gblk(1,) = user block number for this hblk
gblk(2:3,) = gblk [imin,imax] of this hblk
gblk(4:5,) = gblk [jmin,jmax] of this hblk
gblk(6:7,) = gblk [kmin,kmax] of this hblk
SEE ALSO: hydra_xyz, h_data, h_openb
*/
{
{ local gmap; }
_h_unpack_file, f, , , , , , gmap;
return gmap(1:7,); /* gmap(8,)=hblk number in distributed file */
}
func h_ublk (f)
/* DOCUMENT ublk = h_ublk(f)
return user block information from the hydra file F (see h_openb).
Each hblk in the mesh corresponds to a particular imin:imax,
jmin:jmax, kmin:kmax in a particular ublk. The return value is
a 2D long array 7-by-numberof(h blocks):
ublk(1,) = user block number for this hblk
ublk(2:3,) = ublk [imin,imax] of this hblk
ublk(4:5,) = ublk [jmin,jmax] of this hblk
ublk(6:7,) = ublk [kmin,kmax] of this hblk
SEE ALSO: hydra_xyz, h_data, h_openb
*/
{
{ local umap; }
_h_unpack_file, f, , , , , , , umap;
return umap;
}
/* ------------------------------------------------------------------------ */
/* should this be demoted to an _h internal routine? */
func h_blocks (f, &mdims, &mlens, &legacy, &ndims, &gmap, &umap)
/* DOCUMENT gnblk = h_blocks(f, mdims, mlens)
returns number of blocks GNBLK, block dimensions MDIMS, and
block lengths MLENS for the hydra mesh in file F.
MDIMS is 3-by-NBLK, MLENS is GNBLK elements.
SEE ALSO: hydra_xyz, h_iparm
*/
{
_h_unpack_file, f, , , ndims, legacy, , gmap, umap;
mdims = gmap(3:7:2,) - gmap(2:6:2,) + 1;
if (ndims < 3) {
mdims(3,) = 1;
if (ndims < 2) mdims(2,) = 1;
}
mlens = mdims(1,) * mdims(2,) * mdims(3,);
return numberof(mlens);
}
/* ------------------------------------------------------------------------ */
_h_autodetect = 1; /* set to 0 to skip legacy detection */
func _h_openb (name)
{
yPDBopen = 1; /* open102=1 */
f = open(name, "rb");
if (_not_pdb(f, 0)) {
close, f;
error, name+" missing or not a PDB file";
}
return f;
}
func _h_get_file (f, i, &bnum, &legacy)
{
{ local idistrib, ihist, names, gmap;}
ff = _h_unpack_file(f, idistrib, ihist, , legacy, names, gmap);
name = names(i);
if (!ff || !idistrib || names(idistrib)!=name) {
ff = _h_openb(name);
_car, f, 1, ff;
}
bnum = gmap(8, i);
flags = _car(f, 2);
flags(1) = i;
_car, f, 2, flags;
return ff;
}
func _h_unpack_file (f, &idistrib, &ihist, &ndims, &legacy,
&names, &gmap, &umap, &time, &ncyc)
{
ff = _car(f, 1);
flags = _car(f, 2);
idistrib = flags(1);
ihist = flags(2);
ndims = flags(3);
legacy = flags(4);
data = _car(f, 3);
eq_nocopy, names, *data(1,ihist);
eq_nocopy, gmap, *data(2,ihist);
eq_nocopy, umap, *data(3,ihist);
time = _car(f,4);
ncyc = _car(f,5);
return ff;
}
func _h_translate (name)
{
nm = array(string, dimsof(name));
for (i=1 ; i<=numberof(nm) ; i++) {
nami = name(i);
if (nami=="matlist") nm(i) = "Materials_matlist";
else if (nami=="x") nm(i) = "hydro_mesh_coord0";
else if (nami=="y") nm(i) = "hydro_mesh_coord1";
else if (nami=="z") nm(i) = "hydro_mesh_coord2";
else nm(i) = nami+"_data";
}
return nm;
}
func _h_varname (n,suffix)
{
if (_h_legacy) return swrite(format="/BDATA/hblk%ld/"+suffix,n);
return swrite(format="/hblk%ld/bdata/"+suffix,n);
}
func _h_bndname (n,b)
{
if (_h_legacy) return swrite(format="/BDATA/hblk%ld/bnd%ld/",n,b);
return swrite(format="/hblk%ld/bdata/bnd%ld/",n,b);
}
func _h_bcname (n,b)
{
if (_h_legacy) return swrite(format="/BDATA/hblk%ld/bc%ld/",n,b);
return swrite(format="/hblk%ld/bdata/bc%ld/",n,b);
}
func _h_globname (suffix)
{
if (_h_legacy) return "/BDATA/"+suffix;
return "/Global/"+suffix;
}
func _h_gmapname (n)
{
if (_h_legacy) return swrite(format="/BDATA/gmap%ld",n);
return swrite(format="/Global/Decomposition/gmap%ld/gmap",n);
}
func _h_umapname (n)
{
if (_h_legacy) return swrite(format="/BDATA/umap%ld",n);
return swrite(format="/Global/Decomposition/umap%ld/umap",n);
}
/*
* ublk
* gblk (may be several gblks per ublk each gblk is in one ublk)
*
* distributed file
* gblk (may be several gblks per file)
*
* history family
* either distributed file or not
* names[gnblk] file names (may be repeats)
* blocks[gnblk] block number in file --> append to gmap
* gmap[7,gnblk] (user block and how it fits)
* umap[7,unblk] (user block sizes)
*/
func _h_read_maps (f, name, root)
{
list = [1,4,7,5,8,6,9];
if (root) {
unblk = get_member(f,"/Decomposition/NumBlocks")(1);
umap = array(0, 7, unblk);
for (i=1 ; i<=unblk ; i++) {
nm = swrite(format="/Decomposition/umap%ld/umap",i-1);
umap(,i) = get_member(f, nm)(list);
}
gnblk = get_member(f,"/Decomposition/NumDomains")(1);
names = array(string, gnblk);
toks = [string(0), string(&get_member(f,"/hydro_mesh_meshnames"))];
gmap = array(0, 8, gnblk);
for (i=1 ; i<=gnblk ; i++) {
toks = strtok(toks(2),";");
names(i) = strtok(toks(1),":")(1);
nm = swrite(format="/Decomposition/gmap%ld/gmap",i-1);
gmap(1:7,i) = get_member(f, nm)(list);
}
gmap(8,) = get_member(f,"/DomainFiles")(1:gnblk);
names = name+names;
} else {
iparmnv= get_member(f, _h_globname("iparmn")); /* dims may be wrong :(*/
iparmn= _h_parm_fix(iparmnv);
iparmv = get_member(f, _h_globname("iparmv"));
pname = *pointer("unblk");
i = where(!(iparmn(1:6,)!=pname)(sum,))(1);
unblk = iparmv(i);
umap = array(0, 7, unblk);
for (i=1 ; i<=unblk ; i++)
umap(,i) = get_member(f, _h_umapname(i-1))(list);
pname(1) = 'g'; /* "gnblk" */
i = where(!(iparmn(1:6,)!=pname)(sum,))(1);
gnblk = iparmv(i);
gmap = array(0, 8, gnblk);
for (i=1 ; i<=gnblk ; i++) {
nblk = get_member(f,_h_varname(i-1,"hydrodati"))(36);
gmap(1:7,i) = get_member(f, _h_gmapname(nblk))(list);
}
gmap(8,) = indgen(0:gnblk-1);
names = array(name, gnblk);
}
/* adjust umap, gmap for ghost nodes, 0 vs 1-origin */
umap(2:7,) -= 1;
gmap(2:7,) -= 1;
return [&names, &gmap, &umap];
}
struct HX_block { /* must match hex.h */
long stride(3);
long length(3);
long first;
long final;
}
struct HX_blkbnd { /* must match hex.h */
long block;
long cell;
int orient;
}
/* ------------------------------------------------------------------------ */
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