/*
* Test nc_open.
* If in read-only section of tests,
* Try to open a non-existent netCDF file, check error return.
* Open a file that is not a netCDF file, check error return.
* Open a netCDF file with a bad mode argument, check error return.
* Open a netCDF file with NC_NOWRITE mode, try to write, check error.
* Try to open a netcdf twice, check whether returned netcdf ids different.
* If in writable section of tests,
* Open a netCDF file with NC_WRITE mode, write something, close it.
* On exit, any open netCDF files are closed.
*/
void
test_nc_open(void)
{
int err;
int ncid;
int ncid2;
/* Try to open a nonexistent file */
err = nc_open("tooth-fairy.nc", NC_NOWRITE, &ncid);/* should fail */
IF (err == NC_NOERR)
error("nc_open of nonexistent file should have failed");
#ifndef USE_PARALLEL
IF (! NC_ISSYSERR(err))
error("nc_open of nonexistent file should have returned system error");
#endif
/* Open a file that is not a netCDF file. But need a portable
* test that also works for cross-compiles ... */
/* err = nc_open("nc_test.o", NC_NOWRITE, &ncid);/\* should fail *\/ */
/* IF (err != NC_ENOTNC) */
/* error("nc_open of non-netCDF file: status = %d", err); */
/* Open a netCDF file in read-only mode, check that write fails */
err = nc_open(testfile, NC_NOWRITE, &ncid);
IF (err)
error("nc_open: %s", nc_strerror(err));
err = nc_redef(ncid); /* should fail */
IF (err != NC_EPERM)
error("nc_redef of read-only file should fail");
/* Opened OK, see if can open again and get a different netCDF ID */
err = nc_open(testfile, NC_NOWRITE, &ncid2);
IF (err)
error("nc_open: %s", nc_strerror(err));
else {
void R_nc_redef( int *ncid )
{
int err;
err = nc_redef(*ncid);
if( err != NC_NOERR )
REprintf( "Error in R_nc_redef: %s\n",
nc_strerror(err) );
}
/* This internal function adds a new user defined type to the metadata
* of a group of an open file. */
static int
add_user_type(int ncid, size_t size, const char *name, nc_type base_typeid,
nc_type type_class, nc_type *typeidp)
{
NC_HDF5_FILE_INFO_T *h5;
NC_GRP_INFO_T *grp;
char norm_name[NC_MAX_NAME + 1];
int retval;
/* Check and normalize the name. */
if ((retval = nc4_check_name(name, norm_name)))
return retval;
LOG((2, "add_user_type: ncid 0x%x size %d name %s base_typeid %d ",
ncid, size, norm_name, base_typeid));
/* Find group metadata. */
if ((retval = nc4_find_grp_h5(ncid, &grp, &h5)))
return retval;
/* Only netcdf-4 files! */
if (!h5)
return NC_ENOTNC4;
/* Turn on define mode if it is not on. */
if (!(h5->cmode & NC_INDEF))
if ((retval = nc_redef(ncid)))
return retval;
/* No size is provided for vlens or enums, get it from the base type. */
if (type_class == NC_VLEN || type_class == NC_ENUM)
{
if ((retval = nc4_get_typelen_mem(grp->file->nc4_info, base_typeid, 0,
&size)))
return retval;
}
else if (size <= 0)
return NC_EINVAL;
/* Check that this name is not in use as a var, grp, or type. */
if ((retval = nc4_check_dup_name(grp, norm_name)))
return retval;
/* Add to our list of types. */
if ((retval = nc4_type_list_add(&(grp->type), grp->file->nc4_info->next_typeid,
size, norm_name, type_class, base_typeid)))
return retval;
/* Return the typeid to the user. */
if (typeidp)
*typeidp = grp->file->nc4_info->next_typeid;
grp->file->nc4_info->next_typeid++;
return NC_NOERR;
}
int ncd_wdset(int ncid,char *path,char *name, void *val, \
enum ADIOS_TYPES type, int rank, \
struct adios_bp_dimension_struct *dims)
{
int i,valid,retval;
char fullname[100];
char dimname[100];
fullname[0]='\0';
char *result=NULL;
int dimids[2];
dimids[1]=0;
strcpy(fullname,name);
if(start[0]==0)
{
retval=nc_redef(ncid);
sprintf(dimname,"%s_%d",name,0);
retval=nc_inq_unlimdim(ncid,&dimids[1]);
if(dimids[1]==-1)retval=nc_def_dim(ncid,"timesteps",NC_UNLIMITED,&dimids[0]);
retval=nc_def_dim(ncid,dimname,dims[0].local_bound,&dimids[1]);
if(type==adios_real)
retval=nc_def_var(ncid,fullname,NC_FLOAT,2,dimids,&valid);
if(type==adios_integer)
retval=nc_def_var(ncid,fullname,NC_INT,2,dimids,&valid);
if(type==adios_long)
retval=nc_def_var(ncid,fullname,NC_LONG,2,dimids,&valid);
if(type==adios_double)
{
retval=nc_def_var(ncid,fullname,NC_DOUBLE,2,dimids,&valid);
ERR(retval);
}
//printf("\t RANK=%d, DIMS:%s[0]=%d dimids[1]=%d\n",rank,dimname,dims[0].local_bound,dimids[1]);
retval=nc_enddef(ncid);
}
else
retval=nc_inq_varid (ncid, fullname, &valid);
start[1]=0;//dims[0].local_bound;
count[0]=1;
count[1]=dims[0].local_bound;
if(type==adios_double)
retval=nc_put_vara_double(ncid,valid,start,count,val);
if(type==adios_real)
retval=nc_put_vara_float(ncid,valid,start,count,val);
if(type==adios_integer)
retval=nc_put_vara_int(ncid,valid,start,count,val);
if(type==adios_long)
retval=nc_put_vara_long(ncid,valid,start,count,val);
//#if DEBUG
//printf("create dataset:%s\n",fullname);
//printf("start:%dx%d. count:%dx%d\n",start[0],start[1],count[0],count[1]);
//printf("-------------------\n");
//#endif
return;
}
int
ncredef(int ncid)
{
const int status = nc_redef(ncid);
if(status != NC_NOERR)
{
nc_advise("ncredef", status, "ncid %d", ncid);
return -1;
}
return 0;
}
void bi::SMCNetCDFBuffer::create() {
nc_redef(ncid);
nc_put_att(ncid, "libbi_schema", "SMC");
nc_put_att(ncid, "libbi_schema_version", 1);
nc_put_att(ncid, "libbi_version", PACKAGE_VERSION);
lwVar = nc_def_var(ncid, "logweight", NC_REAL, npDim);
nc_enddef(ncid);
}
/* Test a small file with two record vars, which grow, and has
* attributes added. */
static int
test_two_growing_with_att(const char *testfile)
{
int ncid, dimid, varid[NUM_VARS];
char data[MAX_RECS], data_in;
char att_name[NC_MAX_NAME + 1];
size_t start[ONE_DIM], count[ONE_DIM], index[ONE_DIM], len_in;
int v, r;
/* Create a file with one ulimited dimensions, and one var. */
if (nc_create(testfile, NC_CLOBBER, &ncid)) ERR;
if (nc_def_dim(ncid, DIM1_NAME, NC_UNLIMITED, &dimid)) ERR;
if (nc_def_var(ncid, VAR_NAME, NC_CHAR, 1, &dimid, &varid[0])) ERR;
if (nc_def_var(ncid, VAR_NAME2, NC_CHAR, 1, &dimid, &varid[1])) ERR;
if (nc_close(ncid)) ERR;
/* Create some phoney data. */
for (data[0] = 'a', r = 1; r < MAX_RECS; r++)
data[r] = data[r - 1] + 1;
/* Normally one would not close and reopen the file for each
* record, nor add an attribute each time I add a record, but I am
* giving the library a little work-out here... */
for (r = 0; r < MAX_RECS; r++)
{
/* Write one record of var data, a single character. */
if (nc_open(testfile, NC_WRITE, &ncid)) ERR;
count[0] = 1;
start[0] = r;
sprintf(att_name, "a_%d", data[r]);
for (v = 0; v < NUM_VARS; v++)
{
if (nc_put_vara_text(ncid, varid[v], start, count, &data[r])) ERR;
if (nc_redef(ncid)) ERR;
if (nc_put_att_text(ncid, varid[v], att_name, 1, &data[r])) ERR;
if (nc_enddef(ncid)) ERR;
}
if (nc_close(ncid)) ERR;
/* Reopen the file and check it. */
if (nc_open(testfile, NC_NOWRITE, &ncid)) ERR;
if (nc_inq_dimlen(ncid, 0, &len_in)) ERR;
if (len_in != r + 1) ERR;
index[0] = r;
for (v = 0; v < NUM_VARS; v++)
{
if (nc_get_var1_text(ncid, varid[v], index, &data_in)) ERR;
if (data_in != data[r]) ERR;
}
if (nc_close(ncid)) ERR;
} /* Next record. */
return 0;
}
void bi::OptimiserNetCDFBuffer::create() {
nc_redef(ncid);
nc_put_att(ncid, "libbi_schema", "Optimiser");
nc_put_att(ncid, "libbi_schema_version", 2);
nc_put_att(ncid, "libbi_version", PACKAGE_VERSION);
valueVar = nc_def_var(ncid, "optimiser.value", NC_REAL, npDim);
sizeVar = nc_def_var(ncid, "optimiser.size", NC_REAL, npDim);
nc_enddef(ncid);
}
void bi::MCMCNetCDFBuffer::create() {
nc_redef(ncid);
nc_put_att(ncid, "libbi_schema", "MCMC");
nc_put_att(ncid, "libbi_schema_version", 1);
nc_put_att(ncid, "libbi_version", PACKAGE_VERSION);
llVar = nc_def_var(ncid, "loglikelihood", NC_REAL, npDim);
lpVar = nc_def_var(ncid, "logprior", NC_REAL, npDim);
nc_enddef(ncid);
}
NcBool NcFile::define_mode( void )
{
if (! is_valid())
return FALSE;
if (in_define_mode)
return TRUE;
if (NcError::set_err(
nc_redef(the_id)
) != NC_NOERR)
return FALSE;
in_define_mode = 1;
return TRUE;
}
/*********************************************************************
void mpp_redef(int fid)
redef the meta data of netcdf file with fid.
*******************************************************************/
void mpp_redef(int fid) {
int status;
char errmsg[512];
if( mpp_pe() != mpp_root_pe() ) return;
if(fid<0 || fid >=nfiles) mpp_error("mpp_io(mpp_redef): invalid fid number, fid should be "
"a nonnegative integer that less than nfiles");
status = nc_redef(files[fid].ncid);
if(status != NC_NOERR) {
sprintf(errmsg, "mpp_io(mpp_redef): Error in redef the meta data of file %s", files[fid].name );
netcdf_error(errmsg, status);
}
} /* mpp_redef */
//-------------------------------------------------------------------------
// Function to set the netCDF file to be in define mode or data mode
//-------------------------------------------------------------------------
void SetFileState(NcFile* nc,State s)
{
switch(s)
{
case DATA:
try{ncCheck(nc_enddef(nc->getId()),(char*)__FILE__,__LINE__);}
catch(netCDF::exceptions::NcNotInDefineMode){std::cout<<"Already in data mode"<<std::endl;}
break;
case DEFINE:
try{ncCheck(nc_redef(nc->getId()),(char*)__FILE__,__LINE__);}
catch(netCDF::exceptions::NcInDefineMode){std::cout<<"Already in define mode."<<std::endl;}
break;
}
}
NCstate NCdataSetTextAttribute(int ncid, int varid, const char *attName, const char *text) {
int status;
bool redef;
redef = nc_redef(ncid) == NC_NOERR ? true : false;
status = nc_put_att_text(ncid, varid, attName, strlen(text) + 1, text);
if (redef) nc_enddef(ncid);
if (status != NC_NOERR) {
NCprintNCError (status, "NCdataSetTextAttribute");
return (NCfailed);
}
return (NCsucceeded);
}
/*!
This function put a netcdf file into define mode, given its id
\param [in] ncId id of the opening netcdf file to be put into define mode
\return Status code
*/
int CNetCdfInterface::reDef(int ncId)
{
int status = nc_redef(ncId);
if (NC_NOERR != status)
{
StdString errormsg(nc_strerror(status));
StdStringStream sstr;
sstr << "Error when calling function nc_redef(ncId)" << std::endl
<< errormsg << std::endl
<< "Unable to put this file into define mode given its id: " << ncId << std::endl;
StdString e = sstr.str();
throw CNetCdfException(e);
}
return status;
}
int ncd_attr_str_ds (int ncid, char *path, char *name, void *val)
{
int valid,retval;
char *text=(char *)val;
retval=nc_redef(ncid);
retval=nc_inq_varid(ncid,path,&valid);
//printf("varname=%s, valid=%d\n",path,valid);
if(valid>0)
{
retval=nc_put_att_text(ncid,valid,name,strlen(text),text);
ERR(retval);
printf("varname=%s, valid=%d text=%s len=%d\n",path,valid,text,strlen(text));
}
retval=nc_enddef(ncid);
return 0;
}
NCstate NCdataCopyAttributes(int inNCid, int inVarid, int outNCid, int outVarid, bool overwrite) {
bool redef;
int status, att = 0, attId;
char attName[NC_MAX_NAME];
redef = nc_redef(outNCid) == NC_NOERR;
while ((status = nc_inq_attname(inNCid, inVarid, att++, attName)) == NC_NOERR) {
if (overwrite || (nc_inq_attid(outNCid, outVarid, attName, &attId) != NC_NOERR)) {
if ((status = nc_copy_att(inNCid, inVarid, attName, outNCid, outVarid)) != NC_NOERR) {
NCprintNCError (status, "_NCdataCopyAttributes");
return (NCfailed);
}
}
}
if (redef) nc_enddef(outNCid);
return (NCsucceeded);
}
/* Test a diskless file with two record vars, which grow, and has
* attributes added. */
static int
test_two_growing_with_att(const char *testfile)
{
int ncid, dimid, varid[NUM_VARS];
char data[MAX_RECS], data_in;
char att_name[NC_MAX_NAME + 1];
size_t start[ONE_DIM], count[ONE_DIM], index[ONE_DIM], len_in;
int v, r;
/* Create a file with one ulimited dimensions, and one var. */
if((status=nc_create(testfile, diskmode|NC_CLOBBER, &ncid))) ERRSTAT(status);
if((status=nc_def_dim(ncid, DIM1_NAME, NC_UNLIMITED, &dimid))) ERRSTAT(status);
if((status=nc_def_var(ncid, VAR_NAME, NC_CHAR, 1, &dimid, &varid[0]))) ERRSTAT(status);
if((status=nc_def_var(ncid, VAR_NAME2, NC_CHAR, 1, &dimid, &varid[1]))) ERRSTAT(status);
if((status=nc_enddef(ncid))) ERRSTAT(status);
/* Create some phoney data. */
for (data[0] = 'a', r = 1; r < MAX_RECS; r++)
data[r] = data[r - 1] + 1;
for (r = 0; r < MAX_RECS; r++)
{
count[0] = 1;
start[0] = r;
sprintf(att_name, "a_%d", data[r]);
for (v = 0; v < NUM_VARS; v++)
{
if((status=nc_put_vara_text(ncid, varid[v], start, count, &data[r]))) ERRSTAT(status);
if((status=nc_redef(ncid))) ERRSTAT(status);
if((status=nc_put_att_text(ncid, varid[v], att_name, 1, &data[r]))) ERRSTAT(status);
if((status=nc_enddef(ncid))) ERRSTAT(status);
}
/* verify */
if((status=nc_inq_dimlen(ncid, 0, &len_in))) ERRSTAT(status);
if (len_in != r + 1) ERR;
index[0] = r;
for (v = 0; v < NUM_VARS; v++)
{
if((status=nc_get_var1_text(ncid, varid[v], index, &data_in))) ERRSTAT(status);
if (data_in != data[r]) ERR;
}
} /* Next record. */
if((status=nc_close(ncid))) ERRSTAT(status);
return 0;
}
/* Create a group. It's ncid is returned in the new_ncid pointer. */
int
nc_def_grp(int parent_ncid, const char *name, int *new_ncid)
{
NC_GRP_INFO_T *grp, *g;
NC_HDF5_FILE_INFO_T *h5;
char norm_name[NC_MAX_NAME + 1];
int retval;
LOG((2, "nc_def_grp: parent_ncid 0x%x name %s", parent_ncid, name));
/* Find info for this file and group, and set pointer to each. */
if ((retval = nc4_find_grp_h5(parent_ncid, &grp, &h5)))
return retval;
if (!h5)
return NC_ENOTNC4;
/* Check and normalize the name. */
if ((retval = nc4_check_name(name, norm_name)))
return retval;
/* Check that this name is not in use as a var, grp, or type. */
if ((retval = nc4_check_dup_name(grp, norm_name)))
return retval;
/* No groups in netcdf-3! */
if (h5->cmode & NC_CLASSIC_MODEL)
return NC_ESTRICTNC3;
/* If it's not in define mode, switch to define mode. */
if (!(h5->flags & NC_INDEF))
if ((retval = nc_redef(parent_ncid)))
return retval;
/* Update internal lists to reflect new group. The actual HDF5
* group creation will be done when metadata is written by a
* sync. */
if ((retval = nc4_grp_list_add(&(grp->children), h5->next_nc_grpid,
grp, grp->file, norm_name, &g)))
return retval;
if (new_ncid)
*new_ncid = grp->file->ext_ncid | h5->next_nc_grpid;
h5->next_nc_grpid++;
return NC_NOERR;
}
int ncd_wscalar(int ncid,char *path,char *name, void *val, \
enum ADIOS_TYPES type)
{
int i,valid,retval;
char fullname[100];
char dimname[100];
fullname[0]='\0';
char *result=NULL;
int dimids[1];
dimids[0]=0;
strcpy(fullname,name);
if(start[0]==0)
{
retval=nc_redef(ncid);
sprintf(dimname,"%s_%d",name,0);
retval=nc_inq_unlimdim(ncid,&dimids[0]);
if(dimids[0]==-1)retval=nc_def_dim(ncid,"timesteps",NC_UNLIMITED,&dimids[0]);
if(type==adios_real)
retval=nc_def_var(ncid,fullname,NC_FLOAT,1,dimids,&valid);
else if(type==adios_double)
retval=nc_def_var(ncid,fullname,NC_DOUBLE,1,dimids,&valid);
else if(type==adios_integer)
retval=nc_def_var(ncid,fullname,NC_INT,1,dimids,&valid);
else if(type==adios_long)
retval=nc_def_var(ncid,fullname,NC_LONG,1,dimids,&valid);
retval=nc_enddef(ncid);
}
else
retval=nc_inq_varid (ncid, fullname, &valid);
if(type==adios_real)
retval=nc_put_vara_float(ncid,valid,start_scalar,count_scalar,val);
else if(type==bp_double)
retval=nc_put_vara_double(ncid,valid,start_scalar,count_scalar,val);
else if(type==adios_integer)
retval=nc_put_vara_int(ncid,valid,start_scalar,count_scalar,val);
else if(type==adios_long)
retval=nc_put_vara_long(ncid,valid,start_scalar,count_scalar,val);
ERR(retval);
return 0;
}
int ex_create_group (int parent_id, const char *group_name)
{
int exoid = -1;
int status;
char errmsg[MAX_ERR_LENGTH];
exerrval = 0; /* clear error code */
#if defined(NOT_NETCDF4)
exerrval = NC_ENOTNC4;
sprintf(errmsg,
"Error: Group capabilities are not available in this netcdf version--not netcdf4");
ex_err("ex_create_group",errmsg,exerrval);
return (EX_FATAL);
#else
if ((status = nc_redef (parent_id)) != NC_NOERR) {
exerrval = status;
sprintf(errmsg,
"Error: failed to put file id %d into define mode", parent_id);
ex_err("ex_create_group",errmsg,exerrval);
return (EX_FATAL);
}
if ((status = nc_def_grp (parent_id, group_name, &exoid)) != NC_NOERR) {
exerrval = status;
sprintf(errmsg,
"Error: group create failed for %s in file id %d",
group_name, parent_id);
ex_err("ex_create_group",errmsg,exerrval);
return (EX_FATAL);
}
if ((status = nc_enddef (parent_id)) != NC_NOERR) {
exerrval = status;
sprintf(errmsg,
"Error: failed to complete definition for file id %d", exoid);
ex_err("ex_create",errmsg,exerrval);
return (EX_FATAL);
}
#endif
return (exoid);
}
int ncd_wdset1(int ncid,char *path,char *name, void *val, \
enum ADIOS_TYPES type, int rank, \
struct adios_bp_dimension_struct *dims)
{
int i,valid,retval;
char fullname[100];
char dimname[100];
fullname[0]='\0';
char *result=NULL;
int dimids[1];
strcpy(fullname,name);
retval=nc_redef(ncid);
sprintf(dimname,"%s_%d",name,0);
retval=nc_def_dim(ncid,dimname,dims[0].local_bound,&dimids[1]);
if(type==adios_real)
retval=nc_def_var(ncid,fullname,NC_FLOAT,1,dimids,&valid);
if(type==adios_integer)
retval=nc_def_var(ncid,fullname,NC_INT,1,dimids,&valid);
if(type==adios_long)
retval=nc_def_var(ncid,fullname,NC_LONG,1,dimids,&valid);
if(type==adios_double)
{
retval=nc_def_var(ncid,fullname,NC_DOUBLE,1,dimids,&valid);
ERR(retval);
}
retval=nc_enddef(ncid);
size_t a[1],b[1];
a[0]=0;
b[0]=dims[0].local_bound;
if(type==adios_double)
retval=nc_put_vara_double(ncid,valid,a,b,val);
if(type==adios_real)
retval=nc_put_vara_float(ncid,valid,a,b,val);
if(type==adios_integer)
retval=nc_put_vara_int(ncid,valid,a,b,val);
if(type==adios_long)
retval=nc_put_vara_long(ncid,valid,a,b,val);
return;
}
virtual void serialize(const PropertyBag &v)
{
int retval;
/**
* Check if the netcdf file is already in define mode.
* Increase counter every time serialize function is called and no errors occurs.
*/
if ( ncopen ) {
ncopen++;
}
else {
retval = nc_redef(ncid);
if ( retval )
log(Error) << "Could not enter define mode in NetcdfHeaderMarshaller, error "<< retval <<endlog();
else
ncopen++;
}
for (
PropertyBag::const_iterator i = v.getProperties().begin();
i != v.getProperties().end();
i++ )
{
this->serialize(*i);
}
/**
* Decrease counter, if zero enter data mode else stay in define mode
*/
if (--ncopen)
log(Info) << "Serializer still in progress" <<endlog();
else {
retval = nc_enddef(ncid);
if (retval)
log(Error) << "Could not leave define mode, error" << retval <<endlog();
}
}
// NetcdfFile::NC_createReservoir()
int NetcdfFile::NC_createReservoir(bool hasBins, double reservoirT, int iseed,
int& eptotVID, int& binsVID)
{
int dimensionID[1];
dimensionID[0] = frameDID_;
if (ncid_ == -1 || dimensionID[0] == -1) return 1;
// Place file back in define mode
if ( checkNCerr( nc_redef( ncid_ ) ) ) return 1;
// Define eptot, bins, temp0
if ( checkNCerr( nc_def_var(ncid_, NCEPTOT, NC_DOUBLE, 1, dimensionID, &eptotVID)) ) {
mprinterr("Error: defining eptot variable ID.\n");
return 1;
}
if (hasBins) {
if ( checkNCerr( nc_def_var(ncid_, NCBINS, NC_INT, 1, dimensionID, &binsVID)) ) {
mprinterr("Error: defining bins variable ID.\n");
return 1;
}
} else
binsVID = -1;
if (NC_defineTemperature(dimensionID, 0)) return 1;
// Random seed, make global
if ( checkNCerr( nc_put_att_int(ncid_, NC_GLOBAL, "iseed", NC_INT, 1, &iseed) ) ) {
mprinterr("Error: setting random seed attribute.\n");
return 1;
}
// End definitions
if (checkNCerr(nc_enddef(ncid_))) {
mprinterr("NetCDF error on ending definitions.");
return 1;
}
// Write temperature
if (checkNCerr(nc_put_var_double(ncid_,TempVID_,&reservoirT)) ) {
mprinterr("Error: Writing reservoir temperature.\n");
return 1;
}
return 0;
}
void bi::ParticleFilterNetCDFBuffer::create() {
nc_redef(ncid);
if (schema == FLEXI) {
nc_put_att(ncid, "libbi_schema", "FlexiParticleFilter");
nc_put_att(ncid, "libbi_schema_version", 1);
} else {
nc_put_att(ncid, "libbi_schema", "ParticleFilter");
nc_put_att(ncid, "libbi_schema_version", 1);
}
nc_put_att(ncid, "libbi_version", PACKAGE_VERSION);
if (schema == FLEXI) {
aVar = nc_def_var(ncid, "ancestor", NC_INT, nrpDim);
lwVar = nc_def_var(ncid, "logweight", NC_REAL, nrpDim);
} else {
aVar = nc_def_var(ncid, "ancestor", NC_INT, nrDim, npDim);
lwVar = nc_def_var(ncid, "logweight", NC_REAL, nrDim, npDim);
}
llVar = nc_def_var(ncid, "loglikelihood", NC_REAL);
nc_enddef(ncid);
}
NCstate NCtableCommitField (int ncid, char *tablename, NCfield_t *field)
{
int status, dimid, varid;
if (nc_inq_varid(ncid,field->Name,&varid) != NC_NOERR)
{
if(field->Len > 1) return (NCfailed);
if((status = nc_inq_dimid(ncid,tablename,&dimid)) != NC_NOERR)
{ NCprintNCError (status,"NCtableCommitField"); return (NCfailed);}
if((status = nc_redef(ncid) != NC_NOERR))
{ NCprintNCError (status,"NCtableCommitField"); return (NCfailed);}
if ((status = nc_def_var(ncid,field->Name,field->Type,1,&dimid,&varid)) != NC_NOERR)
{ NCprintNCError (status,"NCtableCommitField"); return (NCfailed);}
if((status = nc_enddef(ncid) != NC_NOERR))
{ NCprintNCError (status,"NCtableCommitField"); return (NCfailed);}
}
switch (field->Type)
{
default:
case NC_CHAR:
if((status = nc_put_var_text(ncid,varid,(char *) field->Data)) != NC_NOERR)
{ NCprintNCError (status,"NCtableCommitField"); return (NCfailed);}
break;
case NC_BYTE:
case NC_SHORT:
case NC_INT:
if((status = nc_put_var_int(ncid,varid, (int *) field->Data)) != NC_NOERR)
{ NCprintNCError (status,"NCtableCommitField"); return (NCfailed);}
break;
case NC_FLOAT:
case NC_DOUBLE:
if((status = nc_put_var_double(ncid,varid,(double *) field->Data)) != NC_NOERR)
{ NCprintNCError (status,"NCtableCommitField"); return (NCfailed);}
break;
}
return (NCsucceeded);
}
int ex_put_map_param(int exoid, int num_node_maps, int num_elem_maps)
{
int dim[2], dimid, strdim, varid, status;
int var_nm_id, var_em_id;
int i;
char errmsg[MAX_ERR_LENGTH];
int id_type = NC_INT;
int int_type = NC_INT;
#if NC_HAS_HDF5
int fill = NC_FILL_CHAR;
#endif
EX_FUNC_ENTER();
ex_check_valid_file_id(exoid, __func__);
if (ex_int64_status(exoid) & EX_IDS_INT64_DB) {
id_type = NC_INT64;
}
if (ex_int64_status(exoid) & EX_BULK_INT64_DB) {
int_type = NC_INT64;
}
/* return if these have been defined before */
if ((num_node_maps > 0 && ((nc_inq_dimid(exoid, DIM_NUM_NM, &dimid)) == NC_NOERR)) ||
(num_elem_maps > 0 && ((nc_inq_dimid(exoid, DIM_NUM_EM, &dimid)) == NC_NOERR))) {
snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: number of maps already defined for file id %d", exoid);
ex_err(__func__, errmsg, EX_BADPARAM);
EX_FUNC_LEAVE(EX_FATAL);
}
if ((num_node_maps > 0) || (num_elem_maps > 0)) {
/* inquire previously defined dimensions */
if ((status = nc_inq_dimid(exoid, DIM_STR_NAME, &strdim)) != NC_NOERR) {
snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to get string length in file id %d", exoid);
ex_err(__func__, errmsg, status);
EX_FUNC_LEAVE(EX_FATAL);
}
/* put file into define mode */
if ((status = nc_redef(exoid)) != NC_NOERR) {
snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to put file id %d into define mode", exoid);
ex_err(__func__, errmsg, status);
EX_FUNC_LEAVE(EX_FATAL);
}
/* node maps: */
if (num_node_maps > 0) {
if ((status = nc_def_dim(exoid, DIM_NUM_NM, num_node_maps, &dimid)) != NC_NOERR) {
snprintf(errmsg, MAX_ERR_LENGTH,
"ERROR: failed to define number of node maps in file id %d", exoid);
ex_err(__func__, errmsg, status);
goto error_ret; /* exit define mode and return */
}
/* node maps id array: */
dim[0] = dimid;
if ((status = nc_def_var(exoid, VAR_NM_PROP(1), id_type, 1, dim, &var_nm_id)) != NC_NOERR) {
snprintf(errmsg, MAX_ERR_LENGTH,
"ERROR: failed to create node maps property array in file id %d", exoid);
ex_err(__func__, errmsg, status);
goto error_ret; /* exit define mode and return */
}
/* store property name as attribute of property array variable */
if ((status = nc_put_att_text(exoid, var_nm_id, ATT_PROP_NAME, 3, "ID")) != NC_NOERR) {
snprintf(errmsg, MAX_ERR_LENGTH,
"ERROR: failed to store node map property name %s in file id %d", "ID", exoid);
ex_err(__func__, errmsg, status);
goto error_ret; /* exit define mode and return */
}
/* Node map names... */
dim[0] = dimid;
dim[1] = strdim;
if (nc_def_var(exoid, VAR_NAME_NM, NC_CHAR, 2, dim, &varid) != NC_NOERR) {
snprintf(errmsg, MAX_ERR_LENGTH,
"ERROR: failed to define node map name array in file id %d", exoid);
ex_err(__func__, errmsg, status);
goto error_ret; /* exit define mode and return */
}
#if NC_HAS_HDF5
nc_def_var_fill(exoid, varid, 0, &fill);
#endif
/* determine number of nodes */
if ((status = nc_inq_dimid(exoid, DIM_NUM_NODES, &dimid)) != NC_NOERR) {
snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: couldn't determine number of nodes in file id %d",
exoid);
ex_err(__func__, errmsg, status);
goto error_ret; /* exit define mode and return */
}
dim[0] = dimid;
/* create variable array in which to store the node maps */
for (i = 0; i < num_node_maps; i++) {
if ((status = nc_def_var(exoid, VAR_NODE_MAP(i + 1), int_type, 1, dim, &varid)) !=
NC_NOERR) {
if (status == NC_ENAMEINUSE) {
snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: node map %d already defined in file id %d", i,
exoid);
ex_err(__func__, errmsg, status);
}
else {
snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to create node map %d in file id %d", i,
exoid);
ex_err(__func__, errmsg, status);
}
goto error_ret; /* exit define mode and return */
}
ex_compress_variable(exoid, varid, 1);
}
}
/* element maps: */
if (num_elem_maps > 0) {
if ((status = nc_def_dim(exoid, DIM_NUM_EM, num_elem_maps, &dimid)) != NC_NOERR) {
snprintf(errmsg, MAX_ERR_LENGTH,
"ERROR: failed to define number of element maps in file id %d", exoid);
ex_err(__func__, errmsg, status);
goto error_ret; /* exit define mode and return */
}
/* element maps id array: */
dim[0] = dimid;
if ((status = nc_def_var(exoid, VAR_EM_PROP(1), id_type, 1, dim, &var_em_id)) != NC_NOERR) {
snprintf(errmsg, MAX_ERR_LENGTH,
"ERROR: failed to create element maps property array in file id %d", exoid);
ex_err(__func__, errmsg, status);
goto error_ret; /* exit define mode and return */
}
/* store property name as attribute of property array variable */
if ((status = nc_put_att_text(exoid, var_em_id, ATT_PROP_NAME, 3, "ID")) != NC_NOERR) {
snprintf(errmsg, MAX_ERR_LENGTH,
"ERROR: failed to store element map property name %s in file id %d", "ID", exoid);
ex_err(__func__, errmsg, status);
goto error_ret; /* exit define mode and return */
}
/* Element map names... */
dim[0] = dimid;
dim[1] = strdim;
if ((status = nc_def_var(exoid, VAR_NAME_EM, NC_CHAR, 2, dim, &varid)) != NC_NOERR) {
snprintf(errmsg, MAX_ERR_LENGTH,
"ERROR: failed to define element map name array in file id %d", exoid);
ex_err(__func__, errmsg, status);
goto error_ret; /* exit define mode and return */
}
#if NC_HAS_HDF5
nc_def_var_fill(exoid, varid, 0, &fill);
#endif
/* determine number of elements */
if ((status = nc_inq_dimid(exoid, DIM_NUM_ELEM, &dimid)) != NC_NOERR) {
snprintf(errmsg, MAX_ERR_LENGTH,
"ERROR: couldn't determine number of elements in file id %d", exoid);
ex_err(__func__, errmsg, status);
goto error_ret; /* exit define mode and return */
}
/* create variable array in which to store the element maps */
dim[0] = dimid;
for (i = 0; i < num_elem_maps; i++) {
if ((status = nc_def_var(exoid, VAR_ELEM_MAP(i + 1), int_type, 1, dim, &varid)) !=
NC_NOERR) {
if (status == NC_ENAMEINUSE) {
snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: element map %d already defined in file id %d",
i, exoid);
ex_err(__func__, errmsg, status);
}
else {
snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to create element map %d in file id %d",
i, exoid);
ex_err(__func__, errmsg, status);
}
goto error_ret; /* exit define mode and return */
}
ex_compress_variable(exoid, varid, 1);
}
}
/* leave define mode */
if ((status = nc_enddef(exoid)) != NC_NOERR) {
snprintf(errmsg, MAX_ERR_LENGTH,
"ERROR: failed to complete variable definitions in file id %d", exoid);
ex_err(__func__, errmsg, status);
EX_FUNC_LEAVE(EX_FATAL);
}
/* Fill the id arrays with EX_INVALID_ID */
{
int maxset = num_node_maps > num_elem_maps ? num_node_maps : num_elem_maps;
int *invalid_ids = malloc(maxset * sizeof(int));
if (invalid_ids == NULL) {
snprintf(errmsg, MAX_ERR_LENGTH,
"ERROR: failed to allocate memory for invalid id "
"storage in file id %d",
exoid);
ex_err(__func__, errmsg, EX_MEMFAIL);
EX_FUNC_LEAVE(EX_FATAL);
}
for (i = 0; i < maxset; i++) {
invalid_ids[i] = EX_INVALID_ID;
}
if (num_node_maps > 0) {
status = nc_put_var_int(exoid, var_nm_id, invalid_ids);
assert(status == NC_NOERR);
}
if (num_elem_maps > 0) {
status = nc_put_var_int(exoid, var_em_id, invalid_ids);
assert(status == NC_NOERR);
}
free(invalid_ids);
}
}
EX_FUNC_LEAVE(EX_NOERR);
/* Fatal error: exit definition mode and return */
error_ret:
if ((status = nc_enddef(exoid)) != NC_NOERR) /* exit define mode */
{
snprintf(errmsg, MAX_ERR_LENGTH, "ERROR: failed to complete definition for file id %d", exoid);
ex_err(__func__, errmsg, status);
}
EX_FUNC_LEAVE(EX_FATAL);
}
int ex_put_set_param (int exoid,
ex_entity_type set_type,
int set_id,
int num_entries_in_set,
int num_dist_fact_in_set)
{
int status;
size_t temp;
int dimid, varid, set_id_ndx, dims[1];
size_t start[1];
int num_sets;
int ldum;
int cur_num_sets, set_stat;
char *cdum;
char errmsg[MAX_ERR_LENGTH];
char* dimptr;
char* idsptr;
char* statptr;
char* numentryptr = NULL;
char* numdfptr = NULL;
char* factptr = NULL;
char* entryptr = NULL;
char* extraptr = NULL;
exerrval = 0; /* clear error code */
cdum = 0;
/* setup pointers based on set_type
NOTE: there is another block that sets more stuff later ... */
if (set_type == EX_NODE_SET) {
dimptr = DIM_NUM_NS;
idsptr = VAR_NS_IDS;
statptr = VAR_NS_STAT;
}
else if (set_type == EX_EDGE_SET) {
dimptr = DIM_NUM_ES;
idsptr = VAR_ES_IDS;
statptr = VAR_ES_STAT;
}
else if (set_type == EX_FACE_SET) {
dimptr = DIM_NUM_FS;
idsptr = VAR_FS_IDS;
statptr = VAR_FS_STAT;
}
else if (set_type == EX_SIDE_SET) {
dimptr = DIM_NUM_SS;
idsptr = VAR_SS_IDS;
statptr = VAR_SS_STAT;
}
else if (set_type == EX_ELEM_SET) {
dimptr = DIM_NUM_ELS;
idsptr = VAR_ELS_IDS;
statptr = VAR_ELS_STAT;
}
else {
exerrval = EX_FATAL;
sprintf(errmsg,
"Error: invalid set type (%d)", set_type);
ex_err("ex_put_set_param",errmsg,exerrval);
return (EX_FATAL);
}
/* first check if any of that set type is specified */
if ((status = nc_inq_dimid(exoid, dimptr, &dimid)) != NC_NOERR) {
exerrval = status;
sprintf(errmsg,
"Error: no %ss specified in file id %d", ex_name_of_object(set_type),
exoid);
ex_err("ex_put_set_param",errmsg,exerrval);
return (EX_FATAL);
}
/* Check for duplicate set id entry */
ex_id_lkup(exoid, set_type, set_id);
if (exerrval != EX_LOOKUPFAIL) { /* found the side set id */
sprintf(errmsg,
"Error: %s %d already defined in file id %d", ex_name_of_object(set_type),
set_id,exoid);
ex_err("ex_put_set_param",errmsg,exerrval);
return(EX_FATAL);
}
/* Get number of sets specified for this file */
if ((status = nc_inq_dimlen(exoid,dimid,&temp)) != NC_NOERR) {
exerrval = status;
sprintf(errmsg,
"Error: failed to get number of %ss in file id %d",
ex_name_of_object(set_type), exoid);
ex_err("ex_put_set_param",errmsg,exerrval);
return (EX_FATAL);
}
num_sets = temp;
/* Keep track of the total number of sets defined using a counter stored
in a linked list keyed by exoid.
NOTE: ex_get_file_item finds the maximum number of sets defined
for a specific file and returns that value.
*/
cur_num_sets=ex_get_file_item(exoid, ex_get_counter_list(set_type));
if (cur_num_sets >= num_sets) {
exerrval = EX_FATAL;
sprintf(errmsg,
"Error: exceeded number of %ss (%d) defined in file id %d",
ex_name_of_object(set_type), num_sets,exoid);
ex_err("ex_put_set_param",errmsg,exerrval);
return (EX_FATAL);
}
/* NOTE: ex_inc_file_item finds the current number of sets defined
for a specific file and returns that value incremented. */
cur_num_sets=ex_inc_file_item(exoid, ex_get_counter_list(set_type));
set_id_ndx = cur_num_sets + 1;
/* setup more pointers based on set_type */
if (set_type == EX_NODE_SET) {
numentryptr = DIM_NUM_NOD_NS(set_id_ndx);
entryptr = VAR_NODE_NS(set_id_ndx);
extraptr = NULL;
/* note we are using DIM_NUM_NODE_NS instead of DIM_NUM_DF_NS */
numdfptr = DIM_NUM_NOD_NS(set_id_ndx);
factptr = VAR_FACT_NS(set_id_ndx);
}
else if (set_type == EX_EDGE_SET) {
numentryptr = DIM_NUM_EDGE_ES(set_id_ndx);
entryptr = VAR_EDGE_ES(set_id_ndx);
extraptr = VAR_ORNT_ES(set_id_ndx);
numdfptr = DIM_NUM_DF_ES(set_id_ndx);
factptr = VAR_FACT_ES(set_id_ndx);
}
else if (set_type == EX_FACE_SET) {
numentryptr = DIM_NUM_FACE_FS(set_id_ndx);
entryptr = VAR_FACE_FS(set_id_ndx);
extraptr = VAR_ORNT_FS(set_id_ndx);
numdfptr = DIM_NUM_DF_FS(set_id_ndx);
factptr = VAR_FACT_FS(set_id_ndx);
}
else if (set_type == EX_SIDE_SET) {
numentryptr = DIM_NUM_SIDE_SS(set_id_ndx);
entryptr = VAR_ELEM_SS(set_id_ndx);
extraptr = VAR_SIDE_SS(set_id_ndx);
numdfptr = DIM_NUM_DF_SS(set_id_ndx);
factptr = VAR_FACT_SS(set_id_ndx);
}
if (set_type == EX_ELEM_SET) {
numentryptr = DIM_NUM_ELE_ELS(set_id_ndx);
entryptr = VAR_ELEM_ELS(set_id_ndx);
extraptr = NULL;
numdfptr = DIM_NUM_DF_ELS(set_id_ndx);
factptr = VAR_FACT_ELS(set_id_ndx);
}
/* write out information to previously defined variable */
/* first: get id of set id variable */
if ((status = nc_inq_varid(exoid, idsptr, &varid)) != NC_NOERR) {
exerrval = status;
sprintf(errmsg,
"Error: failed to locate %s %d in file id %d", ex_name_of_object(set_type),
set_id, exoid);
ex_err("ex_put_set_param",errmsg,exerrval);
return (EX_FATAL);
}
/* write out set id */
start[0] = cur_num_sets;
ldum = (int)set_id;
if ((status = nc_put_var1_int(exoid, varid, start, &ldum)) != NC_NOERR) {
exerrval = status;
sprintf(errmsg,
"Error: failed to store %s id %d in file id %d", ex_name_of_object(set_type),
set_id, exoid);
ex_err("ex_put_set_param",errmsg,exerrval);
return (EX_FATAL);
}
if (num_entries_in_set == 0) /* Is this a NULL set? */
set_stat = 0; /* change set status to NULL */
else
set_stat = 1; /* change set status to TRUE */
if ((status = nc_inq_varid(exoid, statptr, &varid)) != NC_NOERR) {
exerrval = status;
sprintf(errmsg,
"Error: failed to locate %s status in file id %d", ex_name_of_object(set_type),
exoid);
ex_err("ex_put_set_param",errmsg,exerrval);
return (EX_FATAL);
}
ldum = (int)set_stat;
if ((status = nc_put_var1_int(exoid, varid, start, &ldum)) != NC_NOERR) {
exerrval = status;
sprintf(errmsg,
"Error: failed to store %s %d status to file id %d", ex_name_of_object(set_type),
set_id, exoid);
ex_err("ex_put_set_param",errmsg,exerrval);
return (EX_FATAL);
}
if (num_entries_in_set == 0) {/* Is this a NULL set? */
return(EX_NOERR);
}
/* put netcdf file into define mode */
if ((status = nc_redef (exoid)) != NC_NOERR) {
exerrval = status;
sprintf(errmsg,
"Error: failed to put file id %d into define mode",
exoid);
ex_err("ex_put_set_param",errmsg,exerrval);
return (EX_FATAL);
}
/* define dimensions and variables */
if ((status = nc_def_dim(exoid, numentryptr,
num_entries_in_set, &dimid)) != NC_NOERR) {
exerrval = status;
if (status == NC_ENAMEINUSE)
{
sprintf(errmsg,
"Error: %s %d size already defined in file id %d",
ex_name_of_object(set_type), set_id,exoid);
ex_err("ex_put_set_param",errmsg,exerrval);
}
else {
sprintf(errmsg,
"Error: failed to define number of entries in %s %d in file id %d",
ex_name_of_object(set_type), set_id,exoid);
ex_err("ex_put_set_param",errmsg,exerrval);
}
goto error_ret;
}
/* create variable array in which to store the entry lists */
dims[0] = dimid;
if ((status = nc_def_var(exoid, entryptr, NC_INT, 1, dims, &varid)) != NC_NOERR) {
exerrval = status;
if (status == NC_ENAMEINUSE) {
sprintf(errmsg,
"Error: entry list already exists for %s %d in file id %d",
ex_name_of_object(set_type), set_id,exoid);
ex_err("ex_put_set_param",errmsg,exerrval);
} else {
sprintf(errmsg,
"Error: failed to create entry list for %s %d in file id %d",
ex_name_of_object(set_type), set_id,exoid);
ex_err("ex_put_set_param",errmsg,exerrval);
}
goto error_ret; /* exit define mode and return */
}
if (extraptr) {
if ((status = nc_def_var(exoid, extraptr, NC_INT, 1, dims, &varid)) != NC_NOERR) {
exerrval = status;
if (status == NC_ENAMEINUSE) {
sprintf(errmsg,
"Error: extra list already exists for %s %d in file id %d",
ex_name_of_object(set_type), set_id, exoid);
ex_err("ex_put_set_param",errmsg,exerrval);
} else {
sprintf(errmsg,
"Error: failed to create extra list for %s %d in file id %d",
ex_name_of_object(set_type), set_id,exoid);
ex_err("ex_put_set_param",errmsg,exerrval);
}
goto error_ret; /* exit define mode and return */
}
}
/* Create distribution factors variable if required */
if (num_dist_fact_in_set > 0) {
if (set_type == EX_NODE_SET) {
/* but num_dist_fact_in_set must equal number of nodes */
if (num_dist_fact_in_set != num_entries_in_set) {
exerrval = EX_FATAL;
sprintf(errmsg,
"Error: # dist fact (%d) not equal to # nodes (%d) in node set %d file id %d",
num_dist_fact_in_set, num_entries_in_set, set_id, exoid);
ex_err("ex_put_set_param",errmsg,exerrval);
goto error_ret; /* exit define mode and return */
}
/* resuse dimid from entry lists */
} else {
if ((status = nc_def_dim(exoid, numdfptr,
num_dist_fact_in_set, &dimid)) != NC_NOERR) {
exerrval = status;
sprintf(errmsg,
"Error: failed to define number of dist factors in %s %d in file id %d",
ex_name_of_object(set_type), set_id,exoid);
ex_err("ex_put_set_param",errmsg,exerrval);
goto error_ret; /* exit define mode and return */
}
}
/* create variable array in which to store the set distribution factors
*/
dims[0] = dimid;
if ((status = nc_def_var(exoid, factptr, nc_flt_code(exoid), 1, dims, &varid)) != NC_NOERR) {
exerrval = status;
if (status == NC_ENAMEINUSE) {
sprintf(errmsg,
"Error: dist factors list already exists for %s %d in file id %d",
ex_name_of_object(set_type), set_id,exoid);
ex_err("ex_put_set_param",errmsg,exerrval);
} else {
sprintf(errmsg,
"Error: failed to create dist factors list for %s %d in file id %d",
ex_name_of_object(set_type), set_id,exoid);
ex_err("ex_put_set_param",errmsg,exerrval);
}
goto error_ret; /* exit define mode and return */
}
}
/* leave define mode */
if ((status = nc_enddef (exoid)) != NC_NOERR) {
exerrval = status;
sprintf(errmsg,
"Error: failed to complete definition in file id %d", exoid);
ex_err("ex_put_set_param",errmsg,exerrval);
return (EX_FATAL);
}
return (EX_NOERR);
/* Fatal error: exit definition mode and return */
error_ret:
if (nc_enddef (exoid) != NC_NOERR) { /* exit define mode */
sprintf(errmsg,
"Error: failed to complete definition for file id %d",
exoid);
ex_err("ex_put_set_param",errmsg,exerrval);
}
return (EX_FATAL);
}
int ex_put_sets (int exoid,
size_t set_count,
const struct ex_set *sets)
{
size_t i;
int needs_define = 0;
int set_stat;
int dimid, varid, status, dims[1];
int set_id_ndx;
size_t start[1];
int cur_num_sets;
char errmsg[MAX_ERR_LENGTH];
int* sets_to_define = NULL;
char* numentryptr = NULL;
char* entryptr = NULL;
char* extraptr = NULL;
char* idsptr = NULL;
char* statptr = NULL;
char* numdfptr = NULL;
char* factptr = NULL;
size_t int_size;
exerrval = 0; /* clear error code */
sets_to_define = malloc(set_count*sizeof(int));
/* Note that this routine can be called:
1) just define the sets
2) just output the set data (after a previous call to define)
3) define and output the set data in one call.
*/
for (i=0; i < set_count; i++) {
/* first check if any sets are specified */
if ((status = nc_inq_dimid(exoid, ex_dim_num_objects(sets[i].type), &dimid)) != NC_NOERR) {
if (status == NC_EBADDIM) {
exerrval = status;
sprintf(errmsg,
"Error: no %ss defined for file id %d", ex_name_of_object(sets[i].type), exoid);
ex_err("ex_put_sets",errmsg,exerrval);
} else {
exerrval = status;
sprintf(errmsg,
"Error: failed to locate %ss defined in file id %d",
ex_name_of_object(sets[i].type), exoid);
ex_err("ex_put_sets",errmsg,exerrval);
}
return (EX_FATAL);
}
set_id_ndx = ex_id_lkup(exoid, sets[i].type, sets[i].id);
if (exerrval != EX_LOOKUPFAIL) { /* found the side set id, so set is already defined... */
sets_to_define[i] = 0;
continue;
} else {
needs_define++;
sets_to_define[i] = 1;
}
}
if (needs_define > 0) {
/* put netcdf file into define mode */
if ((status = nc_redef (exoid)) != NC_NOERR) {
exerrval = status;
sprintf(errmsg,
"Error: failed to put file id %d into define mode",
exoid);
ex_err("ex_put_sets",errmsg,exerrval);
return (EX_FATAL);
}
for (i=0; i < set_count; i++) {
if (sets_to_define[i] == 0)
continue;
/* NOTE: ex_inc_file_item finds the current number of sets defined
for a specific file and returns that value incremented. */
cur_num_sets=ex_inc_file_item(exoid, ex_get_counter_list(sets[i].type));
set_id_ndx = cur_num_sets + 1;
sets_to_define[i] = set_id_ndx;
if (sets[i].num_entry == 0)
continue;
/* setup pointers based on set_type */
if (sets[i].type == EX_NODE_SET) {
numentryptr = DIM_NUM_NOD_NS(set_id_ndx);
entryptr = VAR_NODE_NS(set_id_ndx);
extraptr = NULL;
/* note we are using DIM_NUM_NODE_NS instead of DIM_NUM_DF_NS */
numdfptr = DIM_NUM_NOD_NS(set_id_ndx);
factptr = VAR_FACT_NS(set_id_ndx);
}
else if (sets[i].type == EX_EDGE_SET) {
numentryptr = DIM_NUM_EDGE_ES(set_id_ndx);
entryptr = VAR_EDGE_ES(set_id_ndx);
extraptr = VAR_ORNT_ES(set_id_ndx);
numdfptr = DIM_NUM_DF_ES(set_id_ndx);
factptr = VAR_FACT_ES(set_id_ndx);
}
else if (sets[i].type == EX_FACE_SET) {
numentryptr = DIM_NUM_FACE_FS(set_id_ndx);
entryptr = VAR_FACE_FS(set_id_ndx);
extraptr = VAR_ORNT_FS(set_id_ndx);
numdfptr = DIM_NUM_DF_FS(set_id_ndx);
factptr = VAR_FACT_FS(set_id_ndx);
}
else if (sets[i].type == EX_SIDE_SET) {
numentryptr = DIM_NUM_SIDE_SS(set_id_ndx);
entryptr = VAR_ELEM_SS(set_id_ndx);
extraptr = VAR_SIDE_SS(set_id_ndx);
numdfptr = DIM_NUM_DF_SS(set_id_ndx);
factptr = VAR_FACT_SS(set_id_ndx);
}
else if (sets[i].type == EX_ELEM_SET) {
numentryptr = DIM_NUM_ELE_ELS(set_id_ndx);
entryptr = VAR_ELEM_ELS(set_id_ndx);
extraptr = NULL;
numdfptr = DIM_NUM_DF_ELS(set_id_ndx);
factptr = VAR_FACT_ELS(set_id_ndx);
}
/* define dimensions and variables */
if ((status = nc_def_dim(exoid, numentryptr,
sets[i].num_entry, &dimid)) != NC_NOERR) {
exerrval = status;
if (status == NC_ENAMEINUSE) {
sprintf(errmsg,
"Error: %s %"PRId64" -- size already defined in file id %d",
ex_name_of_object(sets[i].type), sets[i].id,exoid);
ex_err("ex_put_sets",errmsg,exerrval);
}
else {
sprintf(errmsg,
"Error: failed to define number of entries in %s %"PRId64" in file id %d",
ex_name_of_object(sets[i].type), sets[i].id,exoid);
ex_err("ex_put_sets",errmsg,exerrval);
}
goto error_ret;
}
int_size = sizeof(int);
if (ex_int64_status(exoid) & EX_BULK_INT64_DB) {
int_size = sizeof(int64_t);
}
/* create variable array in which to store the entry lists */
dims[0] = dimid;
if ((status = nc_def_var(exoid, entryptr, int_size, 1, dims, &varid)) != NC_NOERR) {
exerrval = status;
if (status == NC_ENAMEINUSE) {
sprintf(errmsg,
"Error: entry list already exists for %s %"PRId64" in file id %d",
ex_name_of_object(sets[i].type), sets[i].id,exoid);
ex_err("ex_put_sets",errmsg,exerrval);
} else {
sprintf(errmsg,
"Error: failed to create entry list for %s %"PRId64" in file id %d",
ex_name_of_object(sets[i].type), sets[i].id,exoid);
ex_err("ex_put_sets",errmsg,exerrval);
}
goto error_ret; /* exit define mode and return */
}
ex_compress_variable(exoid, varid, 1);
if (extraptr) {
if ((status = nc_def_var(exoid, extraptr, int_size, 1, dims, &varid)) != NC_NOERR) {
exerrval = status;
if (status == NC_ENAMEINUSE) {
sprintf(errmsg,
"Error: extra list already exists for %s %"PRId64" in file id %d",
ex_name_of_object(sets[i].type), sets[i].id, exoid);
ex_err("ex_put_sets",errmsg,exerrval);
} else {
sprintf(errmsg,
"Error: failed to create extra list for %s %"PRId64" in file id %d",
ex_name_of_object(sets[i].type), sets[i].id,exoid);
ex_err("ex_put_sets",errmsg,exerrval);
}
goto error_ret; /* exit define mode and return */
}
ex_compress_variable(exoid, varid, 1);
}
/* Create distribution factors variable if required */
if (sets[i].num_distribution_factor > 0) {
if (sets[i].type != EX_SIDE_SET) {
/* but sets[i].num_distribution_factor must equal number of nodes */
if (sets[i].num_distribution_factor != sets[i].num_entry) {
exerrval = EX_FATAL;
sprintf(errmsg,
"Error: # dist fact (%"PRId64") not equal to # nodes (%"PRId64") in node set %"PRId64" file id %d",
sets[i].num_distribution_factor, sets[i].num_entry, sets[i].id, exoid);
ex_err("ex_put_sets",errmsg,exerrval);
goto error_ret; /* exit define mode and return */
}
} else {
/* resuse dimid from entry lists */
if ((status = nc_def_dim(exoid, numdfptr,
sets[i].num_distribution_factor, &dimid)) != NC_NOERR) {
exerrval = status;
sprintf(errmsg,
"Error: failed to define number of dist factors in %s %"PRId64" in file id %d",
ex_name_of_object(sets[i].type), sets[i].id,exoid);
ex_err("ex_put_sets",errmsg,exerrval);
goto error_ret; /* exit define mode and return */
}
}
/* create variable array in which to store the set distribution factors
*/
dims[0] = dimid;
if ((status = nc_def_var(exoid, factptr, nc_flt_code(exoid), 1, dims, &varid)) != NC_NOERR) {
exerrval = status;
if (status == NC_ENAMEINUSE) {
sprintf(errmsg,
"Error: dist factors list already exists for %s %"PRId64" in file id %d",
ex_name_of_object(sets[i].type), sets[i].id,exoid);
ex_err("ex_put_sets",errmsg,exerrval);
} else {
sprintf(errmsg,
"Error: failed to create dist factors list for %s %"PRId64" in file id %d",
ex_name_of_object(sets[i].type), sets[i].id,exoid);
ex_err("ex_put_sets",errmsg,exerrval);
}
goto error_ret; /* exit define mode and return */
}
ex_compress_variable(exoid, varid, 2);
}
}
/* leave define mode */
if ((status = nc_enddef (exoid)) != NC_NOERR) {
exerrval = status;
sprintf(errmsg,
"Error: failed to complete definition in file id %d", exoid);
ex_err("ex_put_sets",errmsg,exerrval);
return (EX_FATAL);
}
/* Output the set ids and status... */
for (i=0; i < set_count; i++) {
/* setup pointers based on sets[i].type */
if (sets[i].type == EX_NODE_SET) {
idsptr = VAR_NS_IDS;
statptr = VAR_NS_STAT;
}
else if (sets[i].type == EX_EDGE_SET) {
idsptr = VAR_ES_IDS;
statptr = VAR_ES_STAT;
}
else if (sets[i].type == EX_FACE_SET) {
idsptr = VAR_FS_IDS;
statptr = VAR_FS_STAT;
}
else if (sets[i].type == EX_SIDE_SET) {
idsptr = VAR_SS_IDS;
statptr = VAR_SS_STAT;
}
else if (sets[i].type == EX_ELEM_SET) {
idsptr = VAR_ELS_IDS;
statptr = VAR_ELS_STAT;
}
/* first: get id of set id variable */
if ((status = nc_inq_varid(exoid, idsptr, &varid)) != NC_NOERR) {
exerrval = status;
sprintf(errmsg,
"Error: failed to locate %s %"PRId64" in file id %d", ex_name_of_object(sets[i].type),
sets[i].id, exoid);
ex_err("ex_put_sets",errmsg,exerrval);
return (EX_FATAL);
}
/* write out set id */
start[0] = sets_to_define[i]-1;
status = nc_put_var1_longlong(exoid, varid, start, (long long*)&sets[i].id);
if (status != NC_NOERR) {
exerrval = status;
sprintf(errmsg,
"Error: failed to store %s id %"PRId64" in file id %d", ex_name_of_object(sets[i].type),
sets[i].id, exoid);
ex_err("ex_put_sets",errmsg,exerrval);
return (EX_FATAL);
}
set_stat = (sets[i].num_entry == 0) ? 0 : 1;
if ((status = nc_inq_varid(exoid, statptr, &varid)) != NC_NOERR) {
exerrval = status;
sprintf(errmsg,
"Error: failed to locate %s status in file id %d", ex_name_of_object(sets[i].type),
exoid);
ex_err("ex_put_sets",errmsg,exerrval);
return (EX_FATAL);
}
if ((status = nc_put_var1_int(exoid, varid, start, &set_stat)) != NC_NOERR) {
exerrval = status;
sprintf(errmsg,
"Error: failed to store %s %"PRId64" status to file id %d", ex_name_of_object(sets[i].type),
sets[i].id, exoid);
ex_err("ex_put_sets",errmsg,exerrval);
return (EX_FATAL);
}
}
free(sets_to_define);
}
/* Sets are now all defined; see if any set data needs to be output... */
status = EX_NOERR;
for (i=0; i < set_count; i++) {
int stat;
if (sets[i].entry_list != NULL || sets[i].extra_list != NULL) {
/* NOTE: ex_put_set will write the warning/error message... */
stat = ex_put_set(exoid, sets[i].type, sets[i].id, sets[i].entry_list, sets[i].extra_list);
if (stat != EX_NOERR) status = EX_FATAL;
}
if (sets[i].distribution_factor_list != NULL) {
/* NOTE: ex_put_set_dist_fact will write the warning/error message... */
stat = ex_put_set_dist_fact(exoid, sets[i].type, sets[i].id, sets[i].distribution_factor_list);
if (stat != EX_NOERR) status = EX_FATAL;
}
}
return (status);
/* Fatal error: exit definition mode and return */
error_ret:
free(sets_to_define);
if (nc_enddef (exoid) != NC_NOERR) { /* exit define mode */
sprintf(errmsg,
"Error: failed to complete definition for file id %d",
exoid);
ex_err("ex_put_sets",errmsg,exerrval);
}
return (EX_FATAL);
}
void ParcelManager::
output(const TimeLevelIndex<2> &timeIdx, int ncId) const {
int parcelDimId, skel1DimId, dimDimId, tracerDimId;
int idVarId;
int cDimIds[2], cVarId;
int hDimIds[3], hVarId;
int mDimIds[2], mVarId;
int sDimIds[3], s1VarId;
#define OUTPUT_TRACER_SHAPE
#ifdef OUTPUT_TRACER_SHAPE
int skel2DimId, s2VarId, numSkel2 = 40;
#endif
char str[100];
int l;
int *intData;
double *doubleData;
nc_redef(ncId);
nc_def_dim(ncId, "parcel", _parcels.size(), &parcelDimId);
nc_def_dim(ncId, "dim", mesh->domain().numDim(), &dimDimId);
nc_def_dim(ncId, "tracer", Tracers::numTracer(), &tracerDimId);
nc_def_dim(ncId, "skel1", SkeletonPoints::numPoint(), &skel1DimId);
#ifdef OUTPUT_TRACER_SHAPE
if (mesh->domain().numDim() == 2) {
// Only output skeleton in 2D domain, since in 3D it could be messy.
nc_def_dim(ncId, "skel2", numSkel2, &skel2DimId);
}
#endif
nc_def_var(ncId, "id", NC_INT, 1, &parcelDimId, &idVarId);
sprintf(str, "parcel identifier");
nc_put_att(ncId, idVarId, "long_name", NC_CHAR, strlen(str), str);
cDimIds[0] = parcelDimId; cDimIds[1] = dimDimId;
nc_def_var(ncId, "c", NC_DOUBLE, 2, cDimIds, &cVarId);
sprintf(str, "parcel centroid coordinates on %s", mesh->domain().brief().c_str());
nc_put_att(ncId, cVarId, "long_name", NC_CHAR, strlen(str), str);
hDimIds[0] = parcelDimId; hDimIds[1] = dimDimId; hDimIds[2] = dimDimId;
nc_def_var(ncId, "h", NC_DOUBLE, 3, hDimIds, &hVarId);
sprintf(str, "parcel linear deformation matrix");
nc_put_att(ncId, hVarId, "long_name", NC_CHAR, strlen(str), str);
mDimIds[0] = parcelDimId; mDimIds[1] = tracerDimId;
nc_def_var(ncId, "m", NC_DOUBLE, 2, mDimIds, &mVarId);
sprintf(str, "tracer mass");
nc_put_att(ncId, mVarId, "long_name", NC_CHAR, strlen(str), str);
sDimIds[0] = parcelDimId; sDimIds[1] = skel1DimId; sDimIds[2] = dimDimId;
nc_def_var(ncId, "s1", NC_DOUBLE, 3, sDimIds, &s1VarId);
sprintf(str, "parcel actual skeleton");
nc_put_att(ncId, s1VarId, "long_name", NC_CHAR, strlen(str), str);
#ifdef OUTPUT_TRACER_SHAPE
if (mesh->domain().numDim() == 2) {
sDimIds[1] = skel2DimId;
nc_def_var(ncId, "s2", NC_DOUBLE, 3, sDimIds, &s2VarId);
sprintf(str, "parcel fitted skeleton");
nc_put_att(ncId, s2VarId, "long_name", NC_CHAR, strlen(str), str);
}
#endif
nc_enddef(ncId);
intData = new int[_parcels.size()];
l = 0;
for (auto parcel : _parcels) {
intData[l++] = parcel->id();
}
nc_put_var(ncId, idVarId, intData);
delete [] intData;
doubleData = new double[_parcels.size()*mesh->domain().numDim()];
l = 0;
for (auto parcel : _parcels) {
for (uword m = 0; m < mesh->domain().numDim(); ++m) {
doubleData[l++] = parcel->x(timeIdx)(m);
}
}
nc_put_var(ncId, cVarId, doubleData);
delete [] doubleData;
doubleData = new double[_parcels.size()*mesh->domain().numDim()*mesh->domain().numDim()];
l = 0;
for (auto parcel : _parcels) {
for (uword m1 = 0; m1 < mesh->domain().numDim(); ++m1) {
for (uword m2 = 0; m2 < mesh->domain().numDim(); ++m2) {
doubleData[l++] = parcel->H(timeIdx)(m1, m2);
}
}
}
nc_put_var(ncId, hVarId, doubleData);
delete [] doubleData;
doubleData = new double[_parcels.size()*Tracers::numTracer()];
l = 0;
for (auto parcel : _parcels) {
for (int t = 0; t < Tracers::numTracer(); ++t) {
doubleData[l++] = parcel->tracers().mass(t);
}
}
nc_put_var(ncId, mVarId, doubleData);
delete [] doubleData;
doubleData = new double[_parcels.size()*SkeletonPoints::numPoint()*mesh->domain().numDim()];
l = 0;
for (auto parcel : _parcels) {
for (auto xs : parcel->skeletonPoints().spaceCoords(timeIdx)) {
for (uword m = 0; m < mesh->domain().numDim(); ++m) {
doubleData[l++] = xs(m);
}
}
}
nc_put_var(ncId, s1VarId, doubleData);
delete [] doubleData;
#ifdef OUTPUT_TRACER_SHAPE
if (mesh->domain().numDim() == 2) {
double dtheta = PI2/numSkel2;
BodyCoord y(2); SpaceCoord x(2);
doubleData = new double[_parcels.size()*numSkel2*mesh->domain().numDim()];
l = 0;
for (auto parcel : _parcels) {
for (int i = 0; i < numSkel2; ++i) {
double theta = i*dtheta;
y(0) = cos(theta);
y(1) = sin(theta);
parcel->calcSpaceCoord(timeIdx, y, x);
for (uword m = 0; m < mesh->domain().numDim(); ++m) {
doubleData[l++] = x(m);
}
}
}
nc_put_var(ncId, s2VarId, doubleData);
delete [] doubleData;
}
#endif
} // output
int ex_put_id_map (int exoid,
ex_entity_type map_type,
const int *map)
{
int dimid, mapid, status, dims[1];
char errmsg[MAX_ERR_LENGTH];
const char* tname;
const char* dnumentries;
const char* vmap;
exerrval = 0; /* clear error code */
switch ( map_type ) {
case EX_NODE_MAP:
tname = "node";
dnumentries = DIM_NUM_NODES;
vmap = VAR_NODE_NUM_MAP;
break;
case EX_EDGE_MAP:
tname = "edge";
dnumentries = DIM_NUM_EDGE;
vmap = VAR_EDGE_NUM_MAP;
break;
case EX_FACE_MAP:
tname = "face";
dnumentries = DIM_NUM_FACE;
vmap = VAR_FACE_NUM_MAP;
break;
case EX_ELEM_MAP:
tname = "element";
dnumentries = DIM_NUM_ELEM;
vmap = VAR_ELEM_NUM_MAP;
break;
default:
exerrval = EX_BADPARAM;
sprintf( errmsg,
"Error: Bad map type (%d) specified for file id %d",
map_type, exoid );
ex_err( "ex_put_id_map", errmsg, exerrval );
return (EX_FATAL);
}
/* Make sure the file contains entries */
if (nc_inq_dimid (exoid, dnumentries, &dimid) != NC_NOERR) {
return (EX_NOERR);
}
/* put netcdf file into define mode */
if (nc_inq_varid (exoid, vmap, &mapid) != NC_NOERR) {
if ((status = nc_redef (exoid)) != NC_NOERR) {
exerrval = status;
sprintf(errmsg,
"Error: failed to put file id %d into define mode",
exoid);
ex_err("ex_put_id_map",errmsg,exerrval);
return (EX_FATAL);
}
/* create a variable array in which to store the id map */
dims[0] = dimid;
if ((status = nc_def_var(exoid, vmap, NC_INT, 1, dims, &mapid)) != NC_NOERR) {
if (status == NC_ENAMEINUSE) {
exerrval = status;
sprintf(errmsg,
"Error: %s numbering map already exists in file id %d",
tname, exoid);
ex_err("ex_put_id_map",errmsg,exerrval);
} else {
exerrval = status;
sprintf(errmsg,
"Error: failed to create %s id map in file id %d",
tname, exoid);
ex_err("ex_put_id_map",errmsg,exerrval);
}
goto error_ret; /* exit define mode and return */
}
/* leave define mode */
if ((status = nc_enddef (exoid)) != NC_NOERR) {
exerrval = status;
sprintf(errmsg,
"Error: failed to complete definition in file id %d",
exoid);
ex_err("ex_put_id_map",errmsg,exerrval);
return (EX_FATAL);
}
}
/* write out the entity numbering map */
status = nc_put_var_int(exoid, mapid, map);
if (status!= NC_NOERR) {
exerrval = status;
sprintf(errmsg,
"Error: failed to store %s numbering map in file id %d",
tname, exoid);
ex_err("ex_put_id_map",errmsg,exerrval);
return (EX_FATAL);
}
return (EX_NOERR);
/* Fatal error: exit definition mode and return */
error_ret:
if (nc_enddef (exoid) != NC_NOERR) /* exit define mode */
{
sprintf(errmsg,
"Error: failed to complete definition for file id %d",
exoid);
ex_err("ex_put_id_map",errmsg,exerrval);
}
return (EX_FATAL);
}
