static PetscErrorCode TSTrajectorySet_Visualization(TSTrajectory tj,TS ts,PetscInt stepnum,PetscReal time,Vec X)
{
PetscViewer viewer;
char filename[PETSC_MAX_PATH_LEN];
PetscReal tprev;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = TSGetTotalSteps(ts,&stepnum);CHKERRQ(ierr);
if (stepnum == 0) {
PetscMPIInt rank;
ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)ts),&rank);CHKERRQ(ierr);
if (!rank) {
ierr = PetscRMTree("Visualization-data");CHKERRQ(ierr);
ierr = PetscMkdir("Visualization-data");CHKERRQ(ierr);
}
ierr = PetscSNPrintf(filename,sizeof(filename),"Visualization-data/SA-%06d.bin",stepnum);CHKERRQ(ierr);
ierr = OutputBIN(filename,&viewer);CHKERRQ(ierr);
ierr = VecView(X,viewer);CHKERRQ(ierr);
ierr = PetscViewerBinaryWrite(viewer,&time,1,PETSC_REAL,PETSC_FALSE);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
ierr = PetscSNPrintf(filename,sizeof(filename),"Visualization-data/SA-%06d.bin",stepnum);CHKERRQ(ierr);
ierr = OutputBIN(filename,&viewer);CHKERRQ(ierr);
ierr = VecView(X,viewer);CHKERRQ(ierr);
ierr = PetscViewerBinaryWrite(viewer,&time,1,PETSC_REAL,PETSC_FALSE);CHKERRQ(ierr);
ierr = TSGetPrevTime(ts,&tprev);CHKERRQ(ierr);
ierr = PetscViewerBinaryWrite(viewer,&tprev,1,PETSC_REAL,PETSC_FALSE);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode PetscDrawSave_SAWs(PetscDraw draw)
{
PetscImageList image;
char body[4096];
size_t len = 0;
PetscErrorCode ierr;
PetscFunctionBegin;
if (!draw->savefilename) PetscFunctionReturn(0);
ierr = PetscImageListAdd(draw->savefilename,draw->saveimageext,draw->savefilecount-1);CHKERRQ(ierr);
image = SAWs_images;
while (image) {
const char *name = image->filename;
const char *ext = image->ext;
if (draw->savesinglefile) {
ierr = PetscSNPrintf(body+len,4086-len,"<img src=\"%s%s\" alt=\"None\">",name,ext);CHKERRQ(ierr);
} else {
ierr = PetscSNPrintf(body+len,4086-len,"<img src=\"%s/%s_%d%s\" alt=\"None\">",name,name,image->count,ext);CHKERRQ(ierr);
}
ierr = PetscStrlen(body,&len);CHKERRQ(ierr);
image = image->next;
}
ierr = PetscStrcat(body,"<br>\n");CHKERRQ(ierr);
if (draw->savefilecount > 0) PetscStackCallSAWs(SAWs_Pop_Body,("index.html",1));
PetscStackCallSAWs(SAWs_Push_Body,("index.html",1,body));
PetscFunctionReturn(0);
}
/* Precondition: blocksize is set to a meaningful value */
static PetscErrorCode SNESMultiblockSetFieldsRuntime_Private(SNES snes)
{
SNES_Multiblock *mb = (SNES_Multiblock *) snes->data;
PetscInt *ifields;
PetscInt i, nfields;
PetscBool flg = PETSC_TRUE;
char optionname[128], name[8];
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscMalloc(mb->bs * sizeof(PetscInt), &ifields);CHKERRQ(ierr);
for (i = 0; ; ++i) {
ierr = PetscSNPrintf(name, sizeof(name), "%D", i);CHKERRQ(ierr);
ierr = PetscSNPrintf(optionname, sizeof(optionname), "-snes_multiblock_%D_fields", i);CHKERRQ(ierr);
nfields = mb->bs;
ierr = PetscOptionsGetIntArray(((PetscObject) snes)->prefix, optionname, ifields, &nfields, &flg);CHKERRQ(ierr);
if (!flg) break;
if (!nfields) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_USER, "Cannot list zero fields");
ierr = SNESMultiblockSetFields(snes, name, nfields, ifields);CHKERRQ(ierr);
}
if (i > 0) {
/* Makes command-line setting of blocks take precedence over setting them in code.
Otherwise subsequent calls to SNESMultiblockSetIS() or SNESMultiblockSetFields() would
create new blocks, which would probably not be what the user wanted. */
mb->defined = PETSC_TRUE;
}
ierr = PetscFree(ifields);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode VecView_Nest(Vec x,PetscViewer viewer)
{
Vec_Nest *bx = (Vec_Nest*)x->data;
PetscBool isascii;
PetscInt i;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&isascii);CHKERRQ(ierr);
if (isascii) {
ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"VecNest, rows=%D, structure: \n",bx->nb);CHKERRQ(ierr);
for (i=0; i<bx->nb; i++) {
VecType type;
char name[256] = "",prefix[256] = "";
PetscInt NR;
ierr = VecGetSize(bx->v[i],&NR);CHKERRQ(ierr);
ierr = VecGetType(bx->v[i],&type);CHKERRQ(ierr);
if (((PetscObject)bx->v[i])->name) {ierr = PetscSNPrintf(name,sizeof(name),"name=\"%s\", ",((PetscObject)bx->v[i])->name);CHKERRQ(ierr);}
if (((PetscObject)bx->v[i])->prefix) {ierr = PetscSNPrintf(prefix,sizeof(prefix),"prefix=\"%s\", ",((PetscObject)bx->v[i])->prefix);CHKERRQ(ierr);}
ierr = PetscViewerASCIIPrintf(viewer,"(%D) : %s%stype=%s, rows=%D \n",i,name,prefix,type,NR);CHKERRQ(ierr);
ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr); /* push1 */
ierr = VecView(bx->v[i],viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr); /* pop1 */
}
ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr); /* pop0 */
}
PetscFunctionReturn(0);
}
dErr dUnitsSetFromOptions(dUnits un)
{
dErr err;
dFunctionBegin;
dValidHeader(un,dUNITS_CLASSID,1);
err = PetscOptionsBegin(((PetscObject)un)->comm,((PetscObject)un)->prefix,"Units manager","dUnits");dCHK(err);
for (dUnitsBaseType btype = 0; btype < dUNITS_MAX; btype++) {
char opt[256],help[256],uspec[256];
dReal commonpersi = 1.0,scale = 1.0;
dBool flg;
err = PetscSNPrintf(opt,sizeof opt,"-units_%s",dUnitsBaseTypes[btype]);dCHK(err);
err = PetscSNPrintf(uspec,sizeof uspec,"%s:%s:%f:%f",dUnitsBaseNamesSI[btype],dUnitsBaseNamesShortSI[btype],commonpersi,scale);
err = PetscSNPrintf(help,sizeof help,"Common name:short name:one common unit of %s expressed in %s:common units per non-dimensionalized",dUnitsBaseTypes[btype],dUnitsBaseNamesSI[btype]);dCHK(err);
err = PetscOptionsString(opt,help,"dUnitsSetBase",uspec,uspec,sizeof uspec,&flg);dCHK(err);
if (flg) {
char *longname,*shortname,*buf1,*buf2;
longname = uspec;
if (!(shortname = strchr(longname,':'))) dERROR(((dObject)un)->comm,PETSC_ERR_USER,"The field specification '%s' is ':' delimited",opt);
*shortname++ = 0;
if (!(buf1 = strchr(shortname,':'))) dERROR(((dObject)un)->comm,PETSC_ERR_USER,"The field specification for '%s' needs four arguments, but only two given",longname);
*buf1++ = 0;
if (!(buf2 = strchr(buf1,':'))) dERROR(((dObject)un)->comm,PETSC_ERR_USER,"The field specification for '%s' needs four arguments, but only three given",longname);
*buf2++ = 0;
if (sscanf(buf1,"%lf",&commonpersi) != 1) dERROR(((dObject)un)->comm,PETSC_ERR_USER,"Size of common unit '%s' could not be parsed from '%s'",longname,buf1);
if (sscanf(buf2,"%lf",&scale) != 1) dERROR(((dObject)un)->comm,PETSC_ERR_USER,"Scale for common unit '%s' could not be parsed from '%s'",longname,buf2);
err = dUnitsSetBase(un,btype,longname,shortname,commonpersi,scale,NULL);dCHK(err);
}
}
err = PetscOptionsEnd();dCHK(err);
dFunctionReturn(0);
}
static PetscErrorCode PetscHTTPBuildRequest(const char type[],const char url[],const char header[],const char ctype[],const char body[],char **outrequest)
{
char *request=0;
char contentlength[40],contenttype[80],*path,*host;
size_t request_len,headlen,bodylen,contentlen,pathlen,hostlen,typelen,contenttypelen = 0;
PetscErrorCode ierr;
PetscBool flg;
PetscFunctionBegin;
ierr = PetscStrallocpy(url,&host);CHKERRQ(ierr);
ierr = PetscStrchr(host,'/',&path);CHKERRQ(ierr);
if (!path) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"url must contain / it is %s",url);
*path = 0;
ierr = PetscStrlen(host,&hostlen);CHKERRQ(ierr);
ierr = PetscStrchr(url,'/',&path);CHKERRQ(ierr);
ierr = PetscStrlen(path,&pathlen);CHKERRQ(ierr);
if (header) {
ierr = PetscStrendswith(header,"\r\n",&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"header must end with \\r\\n");
}
ierr = PetscStrlen(type,&typelen);CHKERRQ(ierr);
if (ctype) {
ierr = PetscSNPrintf(contenttype,80,"Content-Type: %s\r\n",ctype);CHKERRQ(ierr);
ierr = PetscStrlen(contenttype,&contenttypelen);CHKERRQ(ierr);
}
ierr = PetscStrlen(header,&headlen);CHKERRQ(ierr);
ierr = PetscStrlen(body,&bodylen);CHKERRQ(ierr);
ierr = PetscSNPrintf(contentlength,40,"Content-Length: %d\r\n\r\n",(int)bodylen);CHKERRQ(ierr);
ierr = PetscStrlen(contentlength,&contentlen);CHKERRQ(ierr);
/* Now construct our HTTP request */
request_len = typelen + 1 + pathlen + hostlen + 100 + headlen + contenttypelen + contentlen + bodylen + 1;
ierr = PetscMalloc1(request_len,&request);CHKERRQ(ierr);
ierr = PetscStrcpy(request,type);CHKERRQ(ierr);
ierr = PetscStrcat(request," ");CHKERRQ(ierr);
ierr = PetscStrcat(request,path);CHKERRQ(ierr);
ierr = PetscStrcat(request," HTTP/1.1\r\nHost: ");CHKERRQ(ierr);
ierr = PetscStrcat(request,host);CHKERRQ(ierr);
ierr = PetscFree(host);CHKERRQ(ierr);
ierr = PetscStrcat(request,"\r\nUser-Agent:PETScClient\r\n");CHKERRQ(ierr);
ierr = PetscStrcat(request,header);CHKERRQ(ierr);
if (ctype) {
ierr = PetscStrcat(request,contenttype);CHKERRQ(ierr);
}
ierr = PetscStrcat(request,contentlength);CHKERRQ(ierr);
ierr = PetscStrcat(request,body);CHKERRQ(ierr);
ierr = PetscStrlen(request,&request_len);CHKERRQ(ierr);
ierr = PetscInfo1(NULL,"HTTPS request follows: \n%s\n",request);CHKERRQ(ierr);
*outrequest = request;
PetscFunctionReturn(0);
}
PetscErrorCode PetscParseLayerYAML(yaml_parser_t *parser,int *lvl)
{
yaml_event_t event;
int storage = VAR; /* mapping cannot start with VAL definition w/o VAR key */
char key[PETSC_MAX_PATH_LEN],option[PETSC_MAX_PATH_LEN],prefix[PETSC_MAX_PATH_LEN];
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscSNPrintf(option,PETSC_MAX_PATH_LEN,"%s"," ");CHKERRQ(ierr);
do {
yaml_parser_parse(parser,&event);
/* Parse value either as a new leaf in the mapping */
/* or as a leaf value (one of them, in case it's a sequence) */
switch (event.type) {
case YAML_SCALAR_EVENT:
if (storage) {
ierr = PetscSNPrintf(option,PETSC_MAX_PATH_LEN,"-%s %s",key,(char*)event.data.scalar.value);CHKERRQ(ierr);
ierr = PetscOptionsInsertString(option);CHKERRQ(ierr);
} else {
ierr = PetscStrncpy(key,(char*)event.data.scalar.value,event.data.scalar.length+1);CHKERRQ(ierr);
}
storage ^= VAL; /* Flip VAR/VAL switch for the next event */
break;
case YAML_SEQUENCE_START_EVENT:
/* Sequence - all the following scalars will be appended to the last_leaf */
storage = SEQ;
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP ,"Unable to open YAML option file: sequences not supported");
yaml_event_delete(&event);
break;
case YAML_SEQUENCE_END_EVENT:
storage = VAR;
yaml_event_delete(&event);
break;
case YAML_MAPPING_START_EVENT:
ierr = PetscSNPrintf(prefix,PETSC_MAX_PATH_LEN,"%s_",key);CHKERRQ(ierr);
if (*lvl > 0) {
ierr = PetscOptionsPrefixPush(prefix);CHKERRQ(ierr);
}
(*lvl)++;
ierr = PetscParseLayerYAML(parser,lvl);CHKERRQ(ierr);
(*lvl)--;
if (*lvl > 0) {
ierr = PetscOptionsPrefixPop();CHKERRQ(ierr);
}
storage ^= VAL; /* Flip VAR/VAL, w/o touching SEQ */
yaml_event_delete(&event);
break;
default:
break;
}
}
while ((event.type != YAML_MAPPING_END_EVENT) && (event.type != YAML_STREAM_END_EVENT));
PetscFunctionReturn(0);
}
/*@
PetscDrawSave - Saves a drawn image
Collective on PetscDraw
Input Parameters:
. draw - the drawing context
Level: advanced
Notes: this is not normally called by the user, it is called by PetscDrawFlush() to save a sequence of images.
.seealso: PetscDrawSetSave()
@*/
PetscErrorCode PetscDrawSave(PetscDraw draw)
{
PetscInt savecount;
char basename[PETSC_MAX_PATH_LEN];
unsigned char palette[256][3];
unsigned int w,h;
unsigned char *pixels = NULL;
PetscMPIInt rank;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(draw,PETSC_DRAW_CLASSID,1);
if (draw->ops->save) {ierr = (*draw->ops->save)(draw);CHKERRQ(ierr); goto finally;}
if (!draw->savefilename) PetscFunctionReturn(0);
if (!draw->ops->getimage) PetscFunctionReturn(0);
ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)draw),&rank);CHKERRQ(ierr);
savecount = draw->savefilecount++;
if (!rank && !savecount) {
char path[PETSC_MAX_PATH_LEN];
if (draw->savesinglefile) {
ierr = PetscSNPrintf(path,sizeof(path),"%s%s",draw->savefilename,draw->saveimageext);CHKERRQ(ierr);
(void)remove(path);
} else {
ierr = PetscSNPrintf(path,sizeof(path),"%s",draw->savefilename);CHKERRQ(ierr);
ierr = PetscRMTree(path);CHKERRQ(ierr);
ierr = PetscMkdir(path);CHKERRQ(ierr);
}
if (draw->savemovieext) {
ierr = PetscSNPrintf(path,sizeof(path),"%s%s",draw->savefilename,draw->savemovieext);CHKERRQ(ierr);
(void)remove(path);
}
}
if (draw->savesinglefile) {
ierr = PetscSNPrintf(basename,sizeof(basename),"%s",draw->savefilename);CHKERRQ(ierr);
} else {
ierr = PetscSNPrintf(basename,sizeof(basename),"%s/%s_%d",draw->savefilename,draw->savefilename,(int)savecount);CHKERRQ(ierr);
}
/* this call is collective, only the first process gets the image data */
ierr = (*draw->ops->getimage)(draw,palette,&w,&h,&pixels);CHKERRQ(ierr);
/* only the first process handles the saving business */
if (!rank) {ierr = PetscDrawImageSave(basename,draw->saveimageext,palette,w,h,pixels);CHKERRQ(ierr);}
ierr = PetscFree(pixels);CHKERRQ(ierr);
ierr = MPI_Barrier(PetscObjectComm((PetscObject)draw));CHKERRQ(ierr);
finally:
#if defined(PETSC_HAVE_SAWS)
ierr = PetscDrawSave_SAWs(draw);CHKERRQ(ierr);
#endif
PetscFunctionReturn(0);
}
PetscErrorCode PetscGetVersion(char version[], size_t len)
{
PetscErrorCode ierr;
PetscFunctionBegin;
#if (PETSC_VERSION_RELEASE == 1)
ierr = PetscSNPrintf(version,len,"Petsc Release Version %d.%d.%d, %s ",PETSC_VERSION_MAJOR,PETSC_VERSION_MINOR, PETSC_VERSION_SUBMINOR,PETSC_VERSION_DATE);CHKERRQ(ierr);
#else
ierr = PetscSNPrintf(version,len,"Petsc Development GIT revision: %s GIT Date: %s",PETSC_VERSION_GIT, PETSC_VERSION_DATE_GIT);CHKERRQ(ierr);
#endif
PetscFunctionReturn(0);
}
/*@C
DMNetworkMonitorAdd - Adds a new viewer to monitor
Collective on DMNetworkMonitor
Input Parameters:
+ monitor - the monitor
. name - name of viewer
. element - vertex / edge number
. nodes - number of nodes
. start - variable starting offset
. blocksize - variable blocksize
. xmin - xmin (or PETSC_DECIDE) for viewer
. xmax - xmax (or PETSC_DECIDE) for viewer
. ymin - ymin for viewer
. ymax - ymax for viewer
- hold - determines if plot limits should be held
Level: intermediate
Notes:
This is written to be independent of the semantics associated to the variables
at a given network vertex / edge.
Precisely, the parameters nodes, start and blocksize allow you to select a general
strided subarray of the variables to monitor.
.seealso: DMNetworkMonitorCreate(), DMNetworkMonitorDestroy()
@*/
PetscErrorCode DMNetworkMonitorAdd(DMNetworkMonitor monitor,const char *name,PetscInt element,PetscInt nodes,PetscInt start,PetscInt blocksize,PetscReal xmin,PetscReal xmax,PetscReal ymin,PetscReal ymax,PetscBool hold)
{
PetscErrorCode ierr;
PetscDrawLG drawlg;
PetscDrawAxis axis;
PetscMPIInt rank, size;
DMNetworkMonitorList node;
char titleBuffer[64];
PetscInt vStart,vEnd,eStart,eEnd;
PetscFunctionBegin;
ierr = MPI_Comm_rank(monitor->comm, &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(monitor->comm, &size);CHKERRQ(ierr);
ierr = DMNetworkGetVertexRange(monitor->network, &vStart, &vEnd);CHKERRQ(ierr);
ierr = DMNetworkGetEdgeRange(monitor->network, &eStart, &eEnd);CHKERRQ(ierr);
/* Make window title */
if (vStart <= element && element < vEnd) {
ierr = PetscSNPrintf(titleBuffer, 64, "%s @ vertex %d [%d / %d]", name, element - vStart, rank, size-1);CHKERRQ(ierr);
} else if (eStart <= element && element < eEnd) {
ierr = PetscSNPrintf(titleBuffer, 64, "%s @ edge %d [%d / %d]", name, element - eStart, rank, size-1);CHKERRQ(ierr);
} else {
/* vertex / edge is not on local machine, so skip! */
PetscFunctionReturn(0);
}
ierr = PetscMalloc1(1, &node);CHKERRQ(ierr);
/* Setup viewer. */
ierr = PetscViewerDrawOpen(monitor->comm, NULL, titleBuffer, PETSC_DECIDE, PETSC_DECIDE, PETSC_DRAW_QUARTER_SIZE, PETSC_DRAW_QUARTER_SIZE, &(node->viewer));CHKERRQ(ierr);
ierr = PetscViewerPushFormat(node->viewer, PETSC_VIEWER_DRAW_LG_XRANGE);CHKERRQ(ierr);
ierr = PetscViewerDrawGetDrawLG(node->viewer, 0, &drawlg);CHKERRQ(ierr);
ierr = PetscDrawLGGetAxis(drawlg, &axis);CHKERRQ(ierr);
if (xmin != PETSC_DECIDE && xmax != PETSC_DECIDE) {
ierr = PetscDrawAxisSetLimits(axis, xmin, xmax, ymin, ymax);CHKERRQ(ierr);
} else {
ierr = PetscDrawAxisSetLimits(axis, 0, nodes-1, ymin, ymax);CHKERRQ(ierr);
}
ierr = PetscDrawAxisSetHoldLimits(axis, hold);CHKERRQ(ierr);
/* Setup vector storage for drawing. */
ierr = VecCreateSeq(PETSC_COMM_SELF, nodes, &(node->v));CHKERRQ(ierr);
node->element = element;
node->nodes = nodes;
node->start = start;
node->blocksize = blocksize;
node->next = monitor->firstnode;
monitor->firstnode = node;
PetscFunctionReturn(0);
}
EXTERN_C_BEGIN
#undef __FUNCT__
#define __FUNCT__ "SNESMultiblockSetFields_Default"
PetscErrorCode SNESMultiblockSetFields_Default(SNES snes, const char name[], PetscInt n, const PetscInt fields[])
{
SNES_Multiblock *mb = (SNES_Multiblock *) snes->data;
BlockDesc newblock, next = mb->blocks;
char prefix[128];
PetscInt i;
PetscErrorCode ierr;
PetscFunctionBegin;
if (mb->defined) {
ierr = PetscInfo1(snes, "Ignoring new block \"%s\" because the blocks have already been defined\n", name);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
for (i = 0; i < n; ++i) {
if (fields[i] >= mb->bs) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Field %D requested but only %D exist", fields[i], mb->bs);
if (fields[i] < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Negative field %D requested", fields[i]);
}
ierr = PetscNew(struct _BlockDesc, &newblock);CHKERRQ(ierr);
if (name) {
ierr = PetscStrallocpy(name, &newblock->name);CHKERRQ(ierr);
} else {
PetscInt len = floor(log10(mb->numBlocks))+1;
ierr = PetscMalloc((len+1)*sizeof(char), &newblock->name);CHKERRQ(ierr);
ierr = PetscSNPrintf(newblock->name, len, "%s", mb->numBlocks);CHKERRQ(ierr);
}
newblock->nfields = n;
ierr = PetscMalloc(n*sizeof(PetscInt), &newblock->fields);CHKERRQ(ierr);
ierr = PetscMemcpy(newblock->fields, fields, n*sizeof(PetscInt));CHKERRQ(ierr);
newblock->next = PETSC_NULL;
ierr = SNESCreate(((PetscObject) snes)->comm, &newblock->snes);CHKERRQ(ierr);
ierr = PetscObjectIncrementTabLevel((PetscObject) newblock->snes, (PetscObject) snes, 1);CHKERRQ(ierr);
ierr = SNESSetType(newblock->snes, SNESNRICHARDSON);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject) snes, (PetscObject) newblock->snes);CHKERRQ(ierr);
ierr = PetscSNPrintf(prefix, sizeof(prefix), "%smultiblock_%s_", ((PetscObject) snes)->prefix ? ((PetscObject) snes)->prefix : "", newblock->name);CHKERRQ(ierr);
ierr = SNESSetOptionsPrefix(newblock->snes, prefix);CHKERRQ(ierr);
if (!next) {
mb->blocks = newblock;
newblock->previous = PETSC_NULL;
} else {
while (next->next) {
next = next->next;
}
next->next = newblock;
newblock->previous = next;
}
mb->numBlocks++;
PetscFunctionReturn(0);
}
EXTERN_C_END
EXTERN_C_BEGIN
#undef __FUNCT__
#define __FUNCT__ "SNESMultiblockSetIS_Default"
PetscErrorCode SNESMultiblockSetIS_Default(SNES snes, const char name[], IS is)
{
SNES_Multiblock *mb = (SNES_Multiblock *) snes->data;
BlockDesc newblock, next = mb->blocks;
char prefix[128];
PetscErrorCode ierr;
PetscFunctionBegin;
if (mb->defined) {
ierr = PetscInfo1(snes, "Ignoring new block \"%s\" because the blocks have already been defined\n", name);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
ierr = PetscNew(struct _BlockDesc, &newblock);CHKERRQ(ierr);
if (name) {
ierr = PetscStrallocpy(name, &newblock->name);CHKERRQ(ierr);
} else {
PetscInt len = floor(log10(mb->numBlocks))+1;
ierr = PetscMalloc((len+1)*sizeof(char), &newblock->name);CHKERRQ(ierr);
ierr = PetscSNPrintf(newblock->name, len, "%s", mb->numBlocks);CHKERRQ(ierr);
}
newblock->is = is;
ierr = PetscObjectReference((PetscObject) is);CHKERRQ(ierr);
newblock->next = PETSC_NULL;
ierr = SNESCreate(((PetscObject) snes)->comm, &newblock->snes);CHKERRQ(ierr);
ierr = PetscObjectIncrementTabLevel((PetscObject) newblock->snes, (PetscObject) snes, 1);CHKERRQ(ierr);
ierr = SNESSetType(newblock->snes, SNESNRICHARDSON);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject) snes, (PetscObject) newblock->snes);CHKERRQ(ierr);
ierr = PetscSNPrintf(prefix, sizeof(prefix), "%smultiblock_%s_", ((PetscObject) snes)->prefix ? ((PetscObject) snes)->prefix : "", newblock->name);CHKERRQ(ierr);
ierr = SNESSetOptionsPrefix(newblock->snes, prefix);CHKERRQ(ierr);
if (!next) {
mb->blocks = newblock;
newblock->previous = PETSC_NULL;
} else {
while (next->next) {
next = next->next;
}
next->next = newblock;
newblock->previous = next;
}
mb->numBlocks++;
PetscFunctionReturn(0);
}
/*@C
PetscObjectName - Gives an object a name if it does not have one
Collective
Input Parameters:
. obj - the Petsc variable
Thus must be cast with a (PetscObject), for example,
PetscObjectName((PetscObject)mat,name);
Level: developer
Concepts: object name^setting default
Notes: This is used in a small number of places when an object NEEDS a name, for example when it is saved to MATLAB with that variable name.
Use PetscObjectSetName() to set the name of an object to what you want. The SAWs viewer requires that no two published objects
share the same name.
Developer Note: this needs to generate the exact same string on all ranks that share the object. The current algorithm may not always work.
.seealso: PetscObjectGetName(), PetscObjectSetName()
@*/
PetscErrorCode PetscObjectName(PetscObject obj)
{
PetscErrorCode ierr;
PetscCommCounter *counter;
PetscMPIInt flg;
char name[64];
PetscFunctionBegin;
PetscValidHeader(obj,1);
if (!obj->name) {
union {
MPI_Comm comm;
void *ptr;
char raw[sizeof(MPI_Comm)];
} ucomm;
ierr = MPI_Attr_get(obj->comm,Petsc_Counter_keyval,(void*)&counter,&flg);
CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_CORRUPT,"Bad MPI communicator supplied; must be a PETSc communicator");
ucomm.ptr = NULL;
ucomm.comm = obj->comm;
ierr = MPI_Bcast(ucomm.raw,sizeof(MPI_Comm),MPI_BYTE,0,obj->comm);
CHKERRQ(ierr);
/* If the union has extra bytes, their value is implementation-dependent, but they will normally be what we set last
* in 'ucomm.ptr = NULL'. This output is always implementation-defined (and varies from run to run) so the union
* abuse acceptable. */
ierr = PetscSNPrintf(name,64,"%s_%p_%D",obj->class_name,ucomm.ptr,counter->namecount++);
CHKERRQ(ierr);
ierr = PetscStrallocpy(name,&obj->name);
CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode BVResize_Mat(BV bv,PetscInt m,PetscBool copy)
{
PetscErrorCode ierr;
BV_MAT *ctx = (BV_MAT*)bv->data;
PetscScalar *pA,*pnew;
Mat A;
char str[50];
PetscFunctionBegin;
ierr = MatCreateDense(PetscObjectComm((PetscObject)bv->t),bv->n,PETSC_DECIDE,PETSC_DECIDE,m,NULL,&A);CHKERRQ(ierr);
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)bv,(PetscObject)A);CHKERRQ(ierr);
if (((PetscObject)bv)->name) {
ierr = PetscSNPrintf(str,50,"%s_0",((PetscObject)bv)->name);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)A,str);CHKERRQ(ierr);
}
if (copy) {
ierr = MatDenseGetArray(ctx->A,&pA);CHKERRQ(ierr);
ierr = MatDenseGetArray(A,&pnew);CHKERRQ(ierr);
ierr = PetscMemcpy(pnew,pA,PetscMin(m,bv->m)*bv->n*sizeof(PetscScalar));CHKERRQ(ierr);
ierr = MatDenseRestoreArray(ctx->A,&pA);CHKERRQ(ierr);
ierr = MatDenseRestoreArray(A,&pnew);CHKERRQ(ierr);
}
ierr = MatDestroy(&ctx->A);CHKERRQ(ierr);
ctx->A = A;
PetscFunctionReturn(0);
}
PetscErrorCode TSTrajectoryGet_Basic(TSTrajectory tj,TS ts,PetscInt stepnum,PetscReal *t)
{
Vec Sol,*Y;
PetscInt Nr,i;
PetscViewer viewer;
PetscReal timepre;
char filename[PETSC_MAX_PATH_LEN];
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = TSGetTotalSteps(ts,&stepnum);CHKERRQ(ierr);
ierr = PetscSNPrintf(filename,sizeof filename,"SA-data/SA-%06d.bin",stepnum);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,filename,FILE_MODE_READ,&viewer);CHKERRQ(ierr);
ierr = TSGetSolution(ts,&Sol);CHKERRQ(ierr);
ierr = VecLoad(Sol,viewer);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,t,1,NULL,PETSC_REAL);CHKERRQ(ierr);
if (stepnum != 0) {
ierr = TSGetStages(ts,&Nr,&Y);CHKERRQ(ierr);
for (i=0;i<Nr ;i++) {
ierr = VecLoad(Y[i],viewer);CHKERRQ(ierr);
}
ierr = PetscViewerBinaryRead(viewer,&timepre,1,NULL,PETSC_REAL);CHKERRQ(ierr);
ierr = TSSetTimeStep(ts,-(*t)+timepre);CHKERRQ(ierr);
}
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
Use TSMonitorLG to monitor the reactions in a particular cell
*/
static PetscErrorCode MonitorCell(TS ts,User user,PetscInt cell)
{
PetscErrorCode ierr;
TSMonitorLGCtx ctx;
char **snames;
UserLGCtx *uctx;
char label[128];
PetscReal temp,*xc;
PetscMPIInt rank;
PetscFunctionBegin;
ierr = DMDAGetCoordinateArray(user->dm,&xc);CHKERRQ(ierr);
temp = 1.0 + .05*PetscSinScalar(2.*PETSC_PI*xc[cell]); /* Non-dimensionalized by user->Tini */
ierr = DMDARestoreCoordinateArray(user->dm,&xc);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = PetscSNPrintf(label,sizeof(label),"Initial Temperature %g Cell %d Rank %d",(double)user->Tini*temp,(int)cell,rank);CHKERRQ(ierr);
ierr = TSMonitorLGCtxCreate(PETSC_COMM_SELF,NULL,label,PETSC_DECIDE,PETSC_DECIDE,600,400,1,&ctx);CHKERRQ(ierr);
ierr = DMDAGetFieldNames(user->dm,(const char * const **)&snames);CHKERRQ(ierr);
ierr = TSMonitorLGCtxSetVariableNames(ctx,(const char * const *)snames);CHKERRQ(ierr);
ierr = PetscNew(&uctx);CHKERRQ(ierr);
uctx->cell = cell;
uctx->user = user;
ierr = TSMonitorLGCtxSetTransform(ctx,(PetscErrorCode (*)(void*,Vec,Vec*))FormMoleFraction,(PetscErrorCode (*)(void*))MonitorCellDestroy,uctx);CHKERRQ(ierr);
ierr = TSMonitorSet(ts,TSMonitorLGSolution,ctx,(PetscErrorCode (*)(void**))TSMonitorLGCtxDestroy);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode CreateSpectralPlanes(DM dm, PetscInt numPlanes, const PetscInt planeDir[], const PetscReal planeCoord[], AppCtx *user)
{
PetscSection coordSection;
Vec coordinates;
const PetscScalar *coords;
PetscInt dim, p, vStart, vEnd, v;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = DMGetCoordinateDim(dm, &dim);CHKERRQ(ierr);
ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr);
ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
ierr = VecGetArrayRead(coordinates, &coords);CHKERRQ(ierr);
for (p = 0; p < numPlanes; ++p) {
DMLabel label;
char name[PETSC_MAX_PATH_LEN];
ierr = PetscSNPrintf(name, PETSC_MAX_PATH_LEN, "spectral_plane_%D", p);CHKERRQ(ierr);
ierr = DMCreateLabel(dm, name);CHKERRQ(ierr);
ierr = DMGetLabel(dm, name, &label);CHKERRQ(ierr);
ierr = DMLabelAddStratum(label, 1);CHKERRQ(ierr);
for (v = vStart; v < vEnd; ++v) {
PetscInt off;
ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr);
if (PetscAbsReal(planeCoord[p] - PetscRealPart(coords[off+planeDir[p]])) < PETSC_SMALL) {
ierr = DMLabelSetValue(label, v, 1);CHKERRQ(ierr);
}
}
}
ierr = VecRestoreArrayRead(coordinates, &coords);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode PetscDrawDestroy_X(PetscDraw draw)
{
PetscDraw_X *win = (PetscDraw_X*)draw->data;
PetscErrorCode ierr;
#if defined(PETSC_HAVE_POPEN)
char command[PETSC_MAX_PATH_LEN];
PetscMPIInt rank;
FILE *fd;
#endif
PetscFunctionBegin;
ierr = PetscDrawSynchronizedClear(draw);CHKERRQ(ierr);
#if defined(PETSC_HAVE_POPEN)
ierr = MPI_Comm_rank(((PetscObject)draw)->comm,&rank);CHKERRQ(ierr);
if (draw->savefilename && !rank && draw->savefilemovie) {
ierr = PetscSNPrintf(command,PETSC_MAX_PATH_LEN,"ffmpeg -i %s_%%d.Gif %s.m4v",draw->savefilename,draw->savefilename);CHKERRQ(ierr);
ierr = PetscPOpen(((PetscObject)draw)->comm,PETSC_NULL,command,"r",&fd);CHKERRQ(ierr);
ierr = PetscPClose(((PetscObject)draw)->comm,fd,PETSC_NULL);CHKERRQ(ierr);
}
#endif
XFreeGC(win->disp,win->gc.set);
XCloseDisplay(win->disp);
ierr = PetscDrawDestroy(&draw->popup);CHKERRQ(ierr);
ierr = PetscFree(win->font);CHKERRQ(ierr);
ierr = PetscFree(win);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode SetupFE(DM dm, PetscInt Nc, PetscBool simplex, const char name[], PetscErrorCode (*setup)(DM, AppCtx *), void *ctx)
{
AppCtx *user = (AppCtx *) ctx;
DM cdm = dm;
PetscFE fe;
char prefix[PETSC_MAX_PATH_LEN];
PetscInt dim;
PetscErrorCode ierr;
PetscFunctionBegin;
/* Create finite element */
ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
ierr = PetscSNPrintf(prefix, PETSC_MAX_PATH_LEN, "%s_", name);CHKERRQ(ierr);
ierr = PetscFECreateDefault(PetscObjectComm((PetscObject) dm), dim, Nc, simplex, name ? prefix : NULL, -1, &fe);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) fe, name);CHKERRQ(ierr);
/* Set discretization and boundary conditions for each mesh */
ierr = DMSetField(dm, 0, NULL, (PetscObject) fe);CHKERRQ(ierr);
ierr = DMCreateDS(dm);CHKERRQ(ierr);
ierr = (*setup)(dm, user);CHKERRQ(ierr);
while (cdm) {
ierr = DMCopyDisc(dm, cdm);CHKERRQ(ierr);
if (user->useNearNullspace) {ierr = DMSetNearNullSpaceConstructor(cdm, 0, CreateElasticityNullSpace);CHKERRQ(ierr);}
/* TODO: Check whether the boundary of coarse meshes is marked */
ierr = DMGetCoarseDM(cdm, &cdm);CHKERRQ(ierr);
}
ierr = PetscFEDestroy(&fe);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PETSC_EXTERN PetscErrorCode BVCreate_Mat(BV bv)
{
PetscErrorCode ierr;
BV_MAT *ctx;
PetscInt nloc,bs;
PetscBool seq;
char str[50];
PetscFunctionBegin;
ierr = PetscNewLog(bv,&ctx);CHKERRQ(ierr);
bv->data = (void*)ctx;
ierr = PetscObjectTypeCompare((PetscObject)bv->t,VECMPI,&ctx->mpi);CHKERRQ(ierr);
if (!ctx->mpi) {
ierr = PetscObjectTypeCompare((PetscObject)bv->t,VECSEQ,&seq);CHKERRQ(ierr);
if (!seq) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot create a BVMAT from a non-standard template vector");
}
ierr = VecGetLocalSize(bv->t,&nloc);CHKERRQ(ierr);
ierr = VecGetBlockSize(bv->t,&bs);CHKERRQ(ierr);
ierr = MatCreateDense(PetscObjectComm((PetscObject)bv->t),nloc,PETSC_DECIDE,PETSC_DECIDE,bv->m,NULL,&ctx->A);CHKERRQ(ierr);
ierr = MatAssemblyBegin(ctx->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(ctx->A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)bv,(PetscObject)ctx->A);CHKERRQ(ierr);
if (((PetscObject)bv)->name) {
ierr = PetscSNPrintf(str,50,"%s_0",((PetscObject)bv)->name);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)ctx->A,str);CHKERRQ(ierr);
}
if (ctx->mpi) {
ierr = VecCreateMPIWithArray(PetscObjectComm((PetscObject)bv->t),bs,nloc,PETSC_DECIDE,NULL,&bv->cv[0]);CHKERRQ(ierr);
ierr = VecCreateMPIWithArray(PetscObjectComm((PetscObject)bv->t),bs,nloc,PETSC_DECIDE,NULL,&bv->cv[1]);CHKERRQ(ierr);
} else {
ierr = VecCreateSeqWithArray(PetscObjectComm((PetscObject)bv->t),bs,nloc,NULL,&bv->cv[0]);CHKERRQ(ierr);
ierr = VecCreateSeqWithArray(PetscObjectComm((PetscObject)bv->t),bs,nloc,NULL,&bv->cv[1]);CHKERRQ(ierr);
}
bv->ops->mult = BVMult_Mat;
bv->ops->multvec = BVMultVec_Mat;
bv->ops->multinplace = BVMultInPlace_Mat;
bv->ops->multinplacetrans = BVMultInPlaceTranspose_Mat;
bv->ops->axpy = BVAXPY_Mat;
bv->ops->dot = BVDot_Mat;
bv->ops->dotvec = BVDotVec_Mat;
bv->ops->scale = BVScale_Mat;
bv->ops->norm = BVNorm_Mat;
/*bv->ops->orthogonalize = BVOrthogonalize_Mat;*/
bv->ops->matmult = BVMatMult_Mat;
bv->ops->copy = BVCopy_Mat;
bv->ops->resize = BVResize_Mat;
bv->ops->getcolumn = BVGetColumn_Mat;
bv->ops->restorecolumn = BVRestoreColumn_Mat;
bv->ops->getarray = BVGetArray_Mat;
bv->ops->restorearray = BVRestoreArray_Mat;
bv->ops->destroy = BVDestroy_Mat;
if (!ctx->mpi) bv->ops->view = BVView_Mat;
PetscFunctionReturn(0);
}
/*@C
PetscRandomView - Views a random number generator object.
Collective on PetscRandom
Input Parameters:
+ rnd - The random number generator context
- viewer - an optional visualization context
Notes:
The available visualization contexts include
+ PETSC_VIEWER_STDOUT_SELF - standard output (default)
- PETSC_VIEWER_STDOUT_WORLD - synchronized standard
output where only the first processor opens
the file. All other processors send their
data to the first processor to print.
You can change the format the vector is printed using the
option PetscViewerSetFormat().
Level: beginner
.seealso: PetscRealView(), PetscScalarView(), PetscIntView()
@*/
PetscErrorCode PetscRandomView(PetscRandom rnd,PetscViewer viewer)
{
PetscErrorCode ierr;
PetscBool iascii;
#if defined(PETSC_HAVE_SAWS)
PetscBool issaws;
#endif
PetscFunctionBegin;
PetscValidHeaderSpecific(rnd,PETSC_RANDOM_CLASSID,1);
PetscValidType(rnd,1);
if (!viewer) {
ierr = PetscViewerASCIIGetStdout(PetscObjectComm((PetscObject)rnd),&viewer);
CHKERRQ(ierr);
}
PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,2);
PetscCheckSameComm(rnd,1,viewer,2);
ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);
CHKERRQ(ierr);
#if defined(PETSC_HAVE_SAWS)
ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERSAWS,&issaws);
CHKERRQ(ierr);
#endif
if (iascii) {
PetscMPIInt rank;
ierr = PetscObjectPrintClassNamePrefixType((PetscObject)rnd,viewer);
CHKERRQ(ierr);
ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)rnd),&rank);
CHKERRQ(ierr);
ierr = PetscViewerASCIIPushSynchronized(viewer);
CHKERRQ(ierr);
ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Random type %s, seed %D\n",rank,((PetscObject)rnd)->type_name,rnd->seed);
CHKERRQ(ierr);
ierr = PetscViewerFlush(viewer);
CHKERRQ(ierr);
ierr = PetscViewerASCIIPopSynchronized(viewer);
CHKERRQ(ierr);
#if defined(PETSC_HAVE_SAWS)
} else if (issaws) {
PetscMPIInt rank;
const char *name;
ierr = PetscObjectGetName((PetscObject)rnd,&name);
CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);
CHKERRQ(ierr);
if (!((PetscObject)rnd)->amsmem && !rank) {
char dir[1024];
ierr = PetscObjectViewSAWs((PetscObject)rnd,viewer);
CHKERRQ(ierr);
ierr = PetscSNPrintf(dir,1024,"/PETSc/Objects/%s/Low",name);
CHKERRQ(ierr);
PetscStackCallSAWs(SAWs_Register,(dir,&rnd->low,1,SAWs_READ,SAWs_DOUBLE));
}
#endif
}
PetscFunctionReturn(0);
}
PetscErrorCode VTKIO_PVTI_Write(FD3D_Parameters *p, Vec x,const char fieldname[], const char filename[])
{
char vti_filename[PETSC_MAX_PATH_LEN];
char pvti_filename[PETSC_MAX_PATH_LEN];
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = PetscSNPrintf(vti_filename,sizeof(vti_filename),"%s.%04d",filename,p->file_id);CHKERRQ(ierr);
ierr = VTKIO_VTI_appended(p, p->da,x, fieldname, vti_filename);CHKERRQ(ierr);
ierr = PetscSNPrintf(pvti_filename,sizeof(pvti_filename),"%s.%04d",filename, p->file_id);CHKERRQ(ierr);
ierr = VTKIO_VTI_Write(p, p->da,fieldname,pvti_filename,vti_filename);CHKERRQ(ierr);
p->file_id++;
PetscFunctionReturn(0);
}
PetscErrorCode VTKIO_VTI_Write(FD3D_Parameters *p, DM da, const char fieldname[], const char file_prefix[],const char local_file_prefix[])
{
MPI_Comm comm;
PetscMPIInt size,rank;
char vtk_filename[PETSC_MAX_PATH_LEN];
FILE *vtk_fp = NULL;
PetscInt M,N,P,si,sj,sk,nx,ny,nz;
PetscInt i,dofs;
PetscErrorCode ierr;
PetscFunctionBeginUser;
/* only master generates this file */
PetscObjectGetComm((PetscObject)da,&comm);
MPI_Comm_size(comm,&size);
MPI_Comm_rank(comm,&rank);
if (rank != 0) PetscFunctionReturn(0);
/* create file name */
ierr = PetscSNPrintf(vtk_filename,sizeof(vtk_filename),"%s.pvti",file_prefix);CHKERRQ(ierr);
vtk_fp = fopen(vtk_filename,"w");
if (!vtk_fp) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SYS,"Cannot open file = %s \n",vtk_filename);
/* (VTK) generate pvts header */
PetscFPrintf(PETSC_COMM_SELF,vtk_fp,"<?xml version=\"1.0\"?>\n");
#if defined(PETSC_WORDS_BIGENDIAN)
PetscFPrintf(PETSC_COMM_SELF,vtk_fp,"<VTKFile type=\"PImageData\" version=\"0.1\" byte_order=\"BigEndian\">\n");
#else
PetscFPrintf(PETSC_COMM_SELF,vtk_fp,"<VTKFile type=\"PImageData\" version=\"0.1\" byte_order=\"LittleEndian\">\n");
#endif
/* define size of the nodal mesh based on the cell DM */
ierr = DMDAGetInfo(da,0,&M,&N,&P,0,0,0,&dofs,0,0,0,0,0);CHKERRQ(ierr);
ierr = DMDAGetGhostCorners(da,&si,&sj,&sk,&nx,&ny,&nz);CHKERRQ(ierr);
PetscFPrintf(PETSC_COMM_SELF,vtk_fp," <PImageData GhostLevel=\"4\" WholeExtent=\"%d %d %d %d %d %d\" Origin=\"0 0 0\" Spacing=\"%f %f %f\">\n",0,M-1,0,N-1,0,P-1,p->delta_xyz, p->delta_xyz,p->delta_xyz); /* note overlap = 1 for Q1 */
/* DUMP THE CELL REFERENCES */
PetscFPrintf(PETSC_COMM_SELF,vtk_fp," <PCellData>\n");
PetscFPrintf(PETSC_COMM_SELF,vtk_fp," </PCellData>\n");
PetscFPrintf(PETSC_COMM_SELF,vtk_fp," <PPointData>\n");
PetscFPrintf(PETSC_COMM_SELF,vtk_fp," <PDataArray type=\"Float64\" Name=\"%s\" NumberOfComponents=\"1\"/>\n",fieldname);
PetscFPrintf(PETSC_COMM_SELF,vtk_fp," </PPointData>\n");
/* write out the parallel information */
ierr = VTKIO_VTI_PieceExtend(vtk_fp,2,da,local_file_prefix);CHKERRQ(ierr);
/* close the file */
PetscFPrintf(PETSC_COMM_SELF,vtk_fp," </PImageData>\n");
PetscFPrintf(PETSC_COMM_SELF,vtk_fp,"</VTKFile>\n");
if (vtk_fp) {
fclose(vtk_fp);
vtk_fp = NULL;
}
PetscFunctionReturn(0);
}
PETSC_EXTERN PetscErrorCode BVCreate_Contiguous(BV bv)
{
PetscErrorCode ierr;
BV_CONTIGUOUS *ctx;
PetscInt j,nloc,bs;
PetscBool seq;
char str[50];
PetscFunctionBegin;
ierr = PetscNewLog(bv,&ctx);CHKERRQ(ierr);
bv->data = (void*)ctx;
ierr = PetscObjectTypeCompare((PetscObject)bv->t,VECMPI,&ctx->mpi);CHKERRQ(ierr);
if (!ctx->mpi) {
ierr = PetscObjectTypeCompare((PetscObject)bv->t,VECSEQ,&seq);CHKERRQ(ierr);
if (!seq) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot create a contiguous BV from a non-standard template vector");
}
ierr = VecGetLocalSize(bv->t,&nloc);CHKERRQ(ierr);
ierr = VecGetBlockSize(bv->t,&bs);CHKERRQ(ierr);
ierr = PetscMalloc1(bv->m*nloc,&ctx->array);CHKERRQ(ierr);
ierr = PetscMemzero(ctx->array,bv->m*nloc*sizeof(PetscScalar));CHKERRQ(ierr);
ierr = PetscMalloc1(bv->m,&ctx->V);CHKERRQ(ierr);
for (j=0;j<bv->m;j++) {
if (ctx->mpi) {
ierr = VecCreateMPIWithArray(PetscObjectComm((PetscObject)bv->t),bs,nloc,PETSC_DECIDE,ctx->array+j*nloc,ctx->V+j);CHKERRQ(ierr);
} else {
ierr = VecCreateSeqWithArray(PetscObjectComm((PetscObject)bv->t),bs,nloc,ctx->array+j*nloc,ctx->V+j);CHKERRQ(ierr);
}
}
ierr = PetscLogObjectParents(bv,bv->m,ctx->V);CHKERRQ(ierr);
if (((PetscObject)bv)->name) {
for (j=0;j<bv->m;j++) {
ierr = PetscSNPrintf(str,50,"%s_%D",((PetscObject)bv)->name,j);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)ctx->V[j],str);CHKERRQ(ierr);
}
}
bv->ops->mult = BVMult_Contiguous;
bv->ops->multvec = BVMultVec_Contiguous;
bv->ops->multinplace = BVMultInPlace_Contiguous;
bv->ops->multinplacetrans = BVMultInPlaceTranspose_Contiguous;
bv->ops->axpy = BVAXPY_Contiguous;
bv->ops->dot = BVDot_Contiguous;
bv->ops->dotvec = BVDotVec_Contiguous;
bv->ops->scale = BVScale_Contiguous;
bv->ops->norm = BVNorm_Contiguous;
/*bv->ops->orthogonalize = BVOrthogonalize_Contiguous;*/
bv->ops->matmult = BVMatMult_Contiguous;
bv->ops->copy = BVCopy_Contiguous;
bv->ops->resize = BVResize_Contiguous;
bv->ops->getcolumn = BVGetColumn_Contiguous;
bv->ops->getarray = BVGetArray_Contiguous;
bv->ops->destroy = BVDestroy_Contiguous;
PetscFunctionReturn(0);
}
/* Get a parallel dFS for representing the geometry
*
* @note Creates a new one if not yet set, generally based on the nodal locations in the mesh
*/
dErr dFSGetCoordinateFS(dFS fs,dFS *incfs)
{
dErr err;
dFunctionBegin;
if (!fs->geometry.fs) {
dFS cfs;
dMesh mesh;
dJacobi jacobi;
dMeshTag dtag;
char degreename[256],prefix[256];
err = dFSGetMesh(fs,&mesh);
dCHK(err);
err = dFSGetJacobi(fs,&jacobi);
dCHK(err);
err = dFSCreate(((dObject)fs)->comm,&cfs);
dCHK(err);
err = dFSSetMesh(cfs,mesh,fs->set.active);
dCHK(err);
err = dFSSetOrderingType(cfs,fs->orderingtype);
dCHK(err);
err = PetscSNPrintf(degreename,sizeof degreename,"%scfs_degree",dNonNullElse(((dObject)fs)->prefix,""));
dCHK(err);
err = dMeshCreateRuleTagIsotropic(mesh,fs->set.active,degreename,1,&dtag);
dCHK(err);
err = dFSSetDegree(cfs,jacobi,dtag);
dCHK(err);
err = dFSSetBlockSize(cfs,3);
dCHK(err);
err = PetscSNPrintf(prefix,sizeof prefix,"%scoord_",dNonNullElse(((dObject)fs)->prefix,""));
dCHK(err);
err = dFSSetOptionsPrefix(cfs,prefix);
dCHK(err);
err = dFSSetFromOptions(cfs);
dCHK(err);
fs->geometry.fs = cfs;
}
*incfs = fs->geometry.fs;
dFunctionReturn(0);
}
/*@C
PetscViewerDrawGetDraw - Returns PetscDraw object from PetscViewer object.
This PetscDraw object may then be used to perform graphics using
PetscDrawXXX() commands.
Collective on PetscViewer
Input Parameters:
+ viewer - the PetscViewer (created with PetscViewerDrawOpen())
- windownumber - indicates which subwindow (usually 0)
Ouput Parameter:
. draw - the draw object
Level: intermediate
Concepts: drawing^accessing PetscDraw context from PetscViewer
Concepts: graphics
.seealso: PetscViewerDrawGetLG(), PetscViewerDrawGetAxis(), PetscViewerDrawOpen()
@*/
PetscErrorCode PetscViewerDrawGetDraw(PetscViewer viewer,PetscInt windownumber,PetscDraw *draw)
{
PetscViewer_Draw *vdraw;
PetscErrorCode ierr;
PetscBool isdraw;
PetscFunctionBegin;
PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1);
PetscValidLogicalCollectiveInt(viewer,windownumber,2);
if (draw) PetscValidPointer(draw,3);
ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);CHKERRQ(ierr);
if (!isdraw) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Must be draw type PetscViewer");
if (windownumber < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Window number cannot be negative");
vdraw = (PetscViewer_Draw*)viewer->data;
windownumber += vdraw->draw_base;
if (windownumber >= vdraw->draw_max) {
/* allocate twice as many slots as needed */
PetscInt draw_max = vdraw->draw_max;
PetscDraw *tdraw = vdraw->draw;
PetscDrawLG *drawlg = vdraw->drawlg;
PetscDrawAxis *drawaxis = vdraw->drawaxis;
vdraw->draw_max = 2*windownumber;
ierr = PetscCalloc3(vdraw->draw_max,&vdraw->draw,vdraw->draw_max,&vdraw->drawlg,vdraw->draw_max,&vdraw->drawaxis);CHKERRQ(ierr);
ierr = PetscMemcpy(vdraw->draw,tdraw,draw_max*sizeof(PetscDraw));CHKERRQ(ierr);
ierr = PetscMemcpy(vdraw->drawlg,drawlg,draw_max*sizeof(PetscDrawLG));CHKERRQ(ierr);
ierr = PetscMemcpy(vdraw->drawaxis,drawaxis,draw_max*sizeof(PetscDrawAxis));CHKERRQ(ierr);
ierr = PetscFree3(tdraw,drawlg,drawaxis);CHKERRQ(ierr);
}
if (!vdraw->draw[windownumber]) {
char *title = vdraw->title, tmp_str[128];
if (windownumber) {
ierr = PetscSNPrintf(tmp_str,sizeof(tmp_str),"%s:%d",vdraw->title?vdraw->title:"",windownumber);CHKERRQ(ierr);
title = tmp_str;
}
ierr = PetscDrawCreate(PetscObjectComm((PetscObject)viewer),vdraw->display,title,PETSC_DECIDE,PETSC_DECIDE,vdraw->w,vdraw->h,&vdraw->draw[windownumber]);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)viewer,(PetscObject)vdraw->draw[windownumber]);CHKERRQ(ierr);
if (vdraw->drawtype) {
ierr = PetscDrawSetType(vdraw->draw[windownumber],vdraw->drawtype);CHKERRQ(ierr);
}
ierr = PetscDrawSetPause(vdraw->draw[windownumber],vdraw->pause);CHKERRQ(ierr);
ierr = PetscDrawSetOptionsPrefix(vdraw->draw[windownumber],((PetscObject)viewer)->prefix);CHKERRQ(ierr);
ierr = PetscDrawSetFromOptions(vdraw->draw[windownumber]);CHKERRQ(ierr);
}
if (draw) *draw = vdraw->draw[windownumber];
if (draw) PetscValidHeaderSpecific(*draw,PETSC_DRAW_CLASSID,-1);
PetscFunctionReturn(0);
}
/*@
PetscDrawScalePopup - draws a contour scale window.
Collective on PetscDraw
Input Parameters:
+ popup - the window (often a window obtained via PetscDrawGetPopup()
. min - minimum value being plotted
- max - maximum value being plotted
Level: intermediate
Notes: All processors that share the draw MUST call this routine
.seealso: PetscDrawGetPopup(), PetscDrawTensorContour()
@*/
PetscErrorCode PetscDrawScalePopup(PetscDraw popup,PetscReal min,PetscReal max)
{
PetscBool isnull;
PetscReal xl = 0.0,yl = 0.0,xr = 1.0,yr = 1.0;
PetscMPIInt rank;
PetscErrorCode ierr;
int i;
char string[32];
PetscFunctionBegin;
if (!popup) PetscFunctionReturn(0);
PetscValidHeaderSpecific(popup,PETSC_DRAW_CLASSID,1);
ierr = PetscDrawIsNull(popup,&isnull);
CHKERRQ(ierr);
if (isnull) PetscFunctionReturn(0);
ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)popup),&rank);
CHKERRQ(ierr);
ierr = PetscDrawCheckResizedWindow(popup);
CHKERRQ(ierr);
ierr = PetscDrawClear(popup);
CHKERRQ(ierr);
ierr = PetscDrawSetTitle(popup,"Contour Scale");
CHKERRQ(ierr);
ierr = PetscDrawSetCoordinates(popup,xl,yl,xr,yr);
CHKERRQ(ierr);
ierr = PetscDrawCollectiveBegin(popup);
CHKERRQ(ierr);
if (!rank) {
for (i=0; i<10; i++) {
int c = PetscDrawRealToColor((PetscReal)i/9,0,1);
ierr = PetscDrawRectangle(popup,xl,yl,xr,yr,c,c,c,c);
CHKERRQ(ierr);
yl += 0.1;
}
for (i=0; i<10; i++) {
PetscReal value = min + i*(max-min)/9;
/* look for a value that should be zero, but is not due to round-off */
if (PetscAbsReal(value) < 1.e-10 && max-min > 1.e-6) value = 0.0;
ierr = PetscSNPrintf(string,sizeof(string),"%18.16e",(double)value);
CHKERRQ(ierr);
ierr = PetscDrawString(popup,0.2,0.02+i/10.0,PETSC_DRAW_BLACK,string);
CHKERRQ(ierr);
}
}
ierr = PetscDrawCollectiveEnd(popup);
CHKERRQ(ierr);
ierr = PetscDrawFlush(popup);
CHKERRQ(ierr);
ierr = PetscDrawSave(popup);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
dErr dOptionsRealUnits(const char opt[],const char text[],const char man[],dUnit unit,PetscReal defaultv,PetscReal *value,PetscBool *set)
{
char text2[512];
PetscReal default2,value2,one;
dBool set2;
dErr err;
dFunctionBegin;
if (unit) {
default2 = dUnitDimensionalize(unit,defaultv);
one = dUnitDimensionalize(unit,1);
err = PetscSNPrintf(text2,sizeof text2,"%s [%G in %G %s]",text,defaultv,one,dUnitName(unit));dCHK(err);
err = PetscOptionsReal(opt,text2,man,default2,&value2,&set2);dCHK(err);
if (set2) *value = dUnitNonDimensionalize(unit,value2);
if (set) *set = set2;
} else {
err = PetscSNPrintf(text2,sizeof text2,"%s [nondimensional]",text);dCHK(err);
err = PetscOptionsReal(opt,text2,man,defaultv,value,set);dCHK(err);
}
dFunctionReturn(0);
}
PetscErrorCode PetscObjectSAWsViewOff(PetscObject obj)
{
char dir[1024];
PetscErrorCode ierr;
PetscFunctionBegin;
if (obj->classid == PETSC_VIEWER_CLASSID) PetscFunctionReturn(0);
if (!obj->amsmem) PetscFunctionReturn(0);
ierr = PetscSNPrintf(dir,1024,"/PETSc/Objects/%s",obj->name);CHKERRQ(ierr);
PetscStackCallSAWs(SAWs_Delete,(dir));
PetscFunctionReturn(0);
}
/*@C
PetscViewerDrawGetDraw - Returns PetscDraw object from PetscViewer object.
This PetscDraw object may then be used to perform graphics using
PetscDrawXXX() commands.
Not collective (but PetscDraw returned will be parallel object if PetscViewer is)
Input Parameters:
+ viewer - the PetscViewer (created with PetscViewerDrawOpen())
- windownumber - indicates which subwindow (usually 0)
Ouput Parameter:
. draw - the draw object
Level: intermediate
Concepts: drawing^accessing PetscDraw context from PetscViewer
Concepts: graphics
.seealso: PetscViewerDrawGetLG(), PetscViewerDrawGetAxis(), PetscViewerDrawOpen()
@*/
PetscErrorCode PETSC_DLLEXPORT PetscViewerDrawGetDraw(PetscViewer viewer,PetscInt windownumber,PetscDraw *draw)
{
PetscViewer_Draw *vdraw = (PetscViewer_Draw*)viewer->data;
PetscErrorCode ierr;
PetscTruth isdraw;
char *title;
PetscFunctionBegin;
PetscValidHeaderSpecific(viewer,PETSC_VIEWER_COOKIE,1);
if (draw) PetscValidPointer(draw,3);
ierr = PetscTypeCompare((PetscObject)viewer,PETSC_VIEWER_DRAW,&isdraw);CHKERRQ(ierr);
if (!isdraw) {
SETERRQ(PETSC_ERR_ARG_WRONG,"Must be draw type PetscViewer");
}
if (windownumber < 0) {
SETERRQ(PETSC_ERR_ARG_OUTOFRANGE,"Window number cannot be negative");
}
windownumber += vdraw->draw_base;
if (windownumber >= vdraw->draw_max) {
/* allocate twice as many slots as needed */
PetscInt draw_max = vdraw->draw_max;
PetscDraw *tdraw = vdraw->draw;
PetscDrawLG *drawlg = vdraw->drawlg;
PetscDrawAxis *drawaxis = vdraw->drawaxis;
vdraw->draw_max = 2*windownumber;
ierr = PetscMalloc3(vdraw->draw_max,PetscDraw,&vdraw->draw,vdraw->draw_max,PetscDrawLG,&vdraw->drawlg,vdraw->draw_max,PetscDrawAxis,&vdraw->drawaxis);CHKERRQ(ierr);
ierr = PetscMemzero(vdraw->draw,vdraw->draw_max*sizeof(PetscDraw));CHKERRQ(ierr);
ierr = PetscMemzero(vdraw->drawlg,vdraw->draw_max*sizeof(PetscDrawLG));CHKERRQ(ierr);
ierr = PetscMemzero(vdraw->drawaxis,vdraw->draw_max*sizeof(PetscDrawAxis));CHKERRQ(ierr);
ierr = PetscMemcpy(vdraw->draw,tdraw,draw_max*sizeof(PetscDraw));CHKERRQ(ierr);
ierr = PetscMemcpy(vdraw->drawlg,drawlg,draw_max*sizeof(PetscDrawLG));CHKERRQ(ierr);
ierr = PetscMemcpy(vdraw->drawaxis,drawaxis,draw_max*sizeof(PetscDrawAxis));CHKERRQ(ierr);
ierr = PetscFree3(tdraw,drawlg,drawaxis);CHKERRQ(ierr);
}
if (!vdraw->draw[windownumber]) {
if (!windownumber) {
title = vdraw->title;
} else {
char tmp_str[128];
ierr = PetscSNPrintf(tmp_str, 128, "%s:%d", vdraw->title,windownumber);CHKERRQ(ierr);
title = tmp_str;
}
ierr = PetscDrawCreate(((PetscObject)viewer)->comm,vdraw->display,title,PETSC_DECIDE,PETSC_DECIDE,vdraw->w,vdraw->h,&vdraw->draw[windownumber]);CHKERRQ(ierr);
ierr = PetscDrawSetFromOptions(vdraw->draw[windownumber]);CHKERRQ(ierr);
}
if (draw) *draw = vdraw->draw[windownumber];
PetscFunctionReturn(0);
}
