/** Determine if Netcdf file contains multi-D REMD info. If so set the
* number of replica dimensions (remd_dimension_) and figure out
* the dimension types (remdDim)
*/
int NetcdfFile::SetupMultiD(ReplicaDimArray& remdDim) {
int dimensionDID;
if ( nc_inq_dimid(ncid_, NCREMD_DIMENSION, &dimensionDID) != NC_NOERR)
return 1;
// Although this is a second call to dimid, makes for easier code
if ( (dimensionDID = GetDimInfo(NCREMD_DIMENSION, &remd_dimension_))==-1 )
return -1;
if (ncdebug_ > 0)
mprintf("\tNetcdf file has multi-D REMD info, %i dimensions.\n",remd_dimension_);
// Ensure valid # dimensions
if (remd_dimension_ < 1) {
mprinterr("Error: Number of REMD dimensions is less than 1!\n");
return -1;
}
// Start and count for groupnum and dimtype, allocate mem
start_[0]=0;
start_[1]=0;
start_[2]=0;
count_[0]=remd_dimension_;
count_[1]=0;
count_[2]=0;
int* remd_dimtype = new int[ remd_dimension_ ];
// Get dimension types
int dimtypeVID;
if ( checkNCerr(nc_inq_varid(ncid_, NCREMD_DIMTYPE, &dimtypeVID)) ) {
mprinterr("Error: Getting dimension type variable ID for each dimension.\n");
return -1;
}
if ( checkNCerr(nc_get_vara_int(ncid_, dimtypeVID, start_, count_, remd_dimtype)) ) {
mprinterr("Error: Getting dimension type in each dimension.\n");
return -1;
}
// Get VID for replica indices
if ( checkNCerr(nc_inq_varid(ncid_, NCREMD_INDICES, &indicesVID_)) ) {
mprinterr("Error: Getting replica indices variable ID.\n");
return -1;
}
// Print info for each dimension
for (int dim = 0; dim < remd_dimension_; ++dim)
remdDim.AddRemdDimension( remd_dimtype[dim] );
delete[] remd_dimtype;
return 0;
}
NclFDimRec *GetDimInfo(void* therec, NclQuark dim_name)
{
NclFileGrpNode *grpnode = (NclFileGrpNode *)therec;
NclFileDimNode *dimnode;
NclFDimRec *tmp = NULL;
int n;
if(NULL != grpnode->dim_rec)
{
for(n = 0; n < grpnode->dim_rec->n_dims; n++)
{
dimnode = &(grpnode->dim_rec->dim_node[n]);
if(dimnode->name != dim_name)
continue;
tmp = (NclFDimRec *)NclCalloc(1, sizeof(NclFDimRec));
assert(tmp);
tmp->dim_name_quark = dimnode->name;
tmp->dim_size = dimnode->size;
tmp->is_unlimited = dimnode->is_unlimited;
return tmp;
}
}
if(NULL != grpnode->grp_rec)
{
for(n = 0; n < grpnode->grp_rec->n_grps; n++)
{
tmp = GetDimInfo(grpnode->grp_rec->grp_node[n], dim_name);
if(NULL != tmp)
return tmp;
}
}
return tmp;
}
/** Setup ncatom, ncatom3, atomDID, coordVID, spatialDID, spatialVID,
* velocityVID, frcVID. Check units and spatial dimensions.
*/
int NetcdfFile::SetupCoordsVelo(bool useVelAsCoords) {
int spatial;
atomDID_ = GetDimInfo(NCATOM, &ncatom_);
if (atomDID_==-1) return 1;
ncatom3_ = ncatom_ * 3;
// Get coord info
coordVID_ = -1;
if ( nc_inq_varid(ncid_, NCCOORDS, &coordVID_) == NC_NOERR ) {
if (ncdebug_ > 0) mprintf("\tNetcdf file has coordinates.\n");
std::string attrText = GetAttrText(coordVID_, "units");
if (attrText!="angstrom")
mprintf("Warning: Netcdf file has length units of %s - expected angstrom.\n",
attrText.c_str());
}
// Get spatial info
spatialDID_ = GetDimInfo(NCSPATIAL, &spatial);
if (spatialDID_==-1) return 1;
if (spatial!=3) {
mprinterr("Error: Expected 3 spatial dimensions, got %i\n",spatial);
return 1;
}
if ( checkNCerr(nc_inq_varid(ncid_, NCSPATIAL, &spatialVID_)) ) {
mprintf("Warning: Could not get spatial VID. File may not be Amber NetCDF compliant.\n");
mprintf("Warning: Assuming spatial variables are 'x', 'y', 'z'\n");
} else {
start_[0] = 0;
count_[0] = 3;
char xyz[3];
if (checkNCerr(nc_get_vara_text(ncid_, spatialVID_, start_, count_, xyz))) {
mprinterr("Error: Getting spatial variables.\n");
return 1;
}
if (xyz[0] != 'x' || xyz[1] != 'y' || xyz[2] != 'z') {
mprinterr("Error: NetCDF spatial variables are '%c', '%c', '%c', not 'x', 'y', 'z'\n",
xyz[0], xyz[1], xyz[2]);
return 1;
}
}
// Get velocity info
velocityVID_ = -1;
if ( nc_inq_varid(ncid_, NCVELO, &velocityVID_) == NC_NOERR ) {
if (ncdebug_>0) mprintf("\tNetcdf file has velocities.\n");
}
// Return a error if no coords and no velocity
if ( coordVID_ == -1 && velocityVID_ == -1 ) {
mprinterr("Error: NetCDF file has no coords and no velocities.\n");
return 1;
}
// If using velocities as coordinates, swap them now.
if (useVelAsCoords) {
if (velocityVID_ == -1) {
mprinterr("Error: Cannot use velocities as coordinates; no velocities present.\n");
return 1;
}
mprintf("\tUsing velocities as coordinates.\n");
coordVID_ = velocityVID_;
velocityVID_ = -1;
}
// Get force info
frcVID_ = -1;
if ( nc_inq_varid(ncid_, NCFRC, &frcVID_) == NC_NOERR ) {
if (ncdebug_>0) mprintf("\tNetcdf file has forces.\n");
}
// Get overall replica and coordinate indices
crdidxVID_ = -1;
if ( nc_inq_varid(ncid_, NCREMD_REPIDX, &repidxVID_) == NC_NOERR ) {
//if (ncdebug_ > 0)
mprintf(" Netcdf file has overall replica indices.\n");
if ( checkNCerr(nc_inq_varid(ncid_, NCREMD_CRDIDX, &crdidxVID_)) ) {
mprinterr("Error: Getting overall coordinate index variable ID.\n");
return 1;
}
} else
repidxVID_ = -1;
return 0;
}
/** Get the ensemble dimension ID and size. */
int NetcdfFile::SetupEnsembleDim() {
int ensembleSize = 0;
ensembleDID_ = GetDimInfo( NCENSEMBLE, &ensembleSize );
if (ensembleDID_ == -1) return 0;
return ensembleSize;
}
/** Get the frame dimension ID and # of frames (ncframe). */
int NetcdfFile::SetupFrameDim() {
frameDID_ = GetDimInfo( NCFRAME, &ncframe_ );
if (frameDID_==-1) return 1;
return 0;
}