CoeffsBase::CoeffsBase(
const std::string& label,
const std::vector<std::string>& dimension_labels,
const std::vector<unsigned int>& indices_shape,
const bool use_iteration_counter):
label_(label),
data_label_(label),
coeffs_type_(Generic),
iteration_and_time_active_(use_iteration_counter),
iteration_opt(0),
time_md(-1.0),
active(true),
action_pntr_(NULL),
vesbias_pntr_(NULL),
ndimensions_(0),
indices_shape_(0),
ncoeffs_(0),
coeffs_descriptions_(0),
dimension_labels_(0),
args_(0),
basisf_(0),
multicoeffs_(false),
multicoeffs_args_(0),
multicoeffs_basisf_(0),
field_type_("type"),
field_ndimensions_("ndimensions"),
field_ncoeffs_total_("ncoeffs_total"),
field_shape_prefix_("shape_"),
field_time_("time"),
field_iteration_("iteration"),
output_fmt_("%30.16e")
{
initializeIndices(indices_shape,dimension_labels);
setAllCoeffsDescriptions();
}
CoeffsBase::CoeffsBase(
const std::string& label,
std::vector<std::vector<Value*> >& multicoeffs_args,
std::vector<std::vector<BasisFunctions*> >& multicoeffs_basisf,
const bool use_iteration_counter,
const std::string& multicoeffs_label):
label_(label),
data_label_(label),
coeffs_type_(MultiCoeffs_LinearBasisSet),
iteration_and_time_active_(use_iteration_counter),
iteration_opt(0),
time_md(-1.0),
active(true),
action_pntr_(NULL),
vesbias_pntr_(NULL),
ndimensions_(0),
indices_shape_(0),
ncoeffs_(0),
coeffs_descriptions_(0),
dimension_labels_(0),
args_(0),
basisf_(0),
multicoeffs_(true),
multicoeffs_args_(multicoeffs_args),
multicoeffs_basisf_(multicoeffs_basisf),
field_type_("type"),
field_ndimensions_("ndimensions"),
field_ncoeffs_total_("ncoeffs_total"),
field_shape_prefix_("shape_"),
field_time_("time"),
field_iteration_("iteration"),
output_fmt_("%30.16e")
{
plumed_massert(multicoeffs_args.size()==multicoeffs_basisf.size(),"Multi Coeffs: number of arguments vectors does not match number of basis functions vectors");
unsigned int num_args = multicoeffs_args[0].size();
unsigned int dim = num_args+1;
std::vector<std::string> dimension_labels(dim);
std::vector<unsigned int> indices_shape(dim);
for(unsigned int i=0; i<num_args; i++) {
std::string ip;
Tools::convert(i+1,ip);
dimension_labels[i] = "bf" + ip;
indices_shape[i] = multicoeffs_basisf[0][i]->getNumberOfBasisFunctions();
}
indices_shape[dim-1] = multicoeffs_args.size();
dimension_labels[dim-1] = multicoeffs_label;
for(unsigned int k=0; k<multicoeffs_args.size(); k++) {
plumed_massert(multicoeffs_args[k].size()==num_args && multicoeffs_basisf[k].size()==num_args,"Multi Coeffs: arguments and basis functions vectors for each bias should be of the same size");
for(unsigned int i=0; i<num_args; i++) {
plumed_massert(indices_shape[i]==multicoeffs_basisf[k][i]->getNumberOfBasisFunctions(),"Multi Coeffs: the coeffs shape for each bias should be identical");
}
}
initializeIndices(indices_shape,dimension_labels);
setupBasisFunctionsInfo();
}
inline static
Ptr
create(std::shared_ptr<render::AbstractContext> context,
unsigned int numParallels = 10,
unsigned int numMeridians = 0,
bool withNormals = true)
{
numMeridians = numMeridians != 0 ? numMeridians : numParallels;
auto geom = std::shared_ptr<SphereGeometry>(new SphereGeometry());
geom->initializeVertices(context, numParallels, numMeridians, withNormals);
geom->initializeIndices(context, numParallels, numMeridians);
return geom;
}
CoeffsBase::CoeffsBase(
const std::string& label,
std::vector<Value*>& args,
std::vector<BasisFunctions*>& basisf,
const bool use_iteration_counter):
label_(label),
data_label_(label),
coeffs_type_(LinearBasisSet),
iteration_and_time_active_(use_iteration_counter),
iteration_opt(0),
time_md(-1.0),
active(true),
action_pntr_(NULL),
vesbias_pntr_(NULL),
ndimensions_(0),
indices_shape_(0),
ncoeffs_(0),
coeffs_descriptions_(0),
dimension_labels_(0),
args_(args),
basisf_(basisf),
multicoeffs_(false),
multicoeffs_args_(0),
multicoeffs_basisf_(0),
field_type_("type"),
field_ndimensions_("ndimensions"),
field_ncoeffs_total_("ncoeffs_total"),
field_shape_prefix_("shape_"),
field_time_("time"),
field_iteration_("iteration"),
output_fmt_("%30.16e")
{
plumed_massert(args_.size()==basisf_.size(),"CoeffsBase: number of arguments do not match number of basis functions");
std::vector<std::string> dimension_labels(args_.size());
std::vector<unsigned int> indices_shape(args_.size());
for(unsigned int i=0; i<args_.size(); i++) {
dimension_labels[i]=args_[i]->getName();
indices_shape[i]=basisf_[i]->getNumberOfBasisFunctions();
}
initializeIndices(indices_shape,dimension_labels);
setupBasisFunctionsInfo();
}