diff --git a/src/soap/atomicspectrum.cpp b/src/soap/atomicspectrum.cpp
index 902939bbe92a94764873a5a6cffcf20b24c89079..099344f64dd5c2b3d02409866aa4a32d27d55694 100644
--- a/src/soap/atomicspectrum.cpp
+++ b/src/soap/atomicspectrum.cpp
@@ -159,7 +159,7 @@ void AtomicSpectrum::addQnlmNeighbour(Particle *nb, qnlm_t *nb_expansion) {
return;
}
-void AtomicSpectrum::mergeQnlm(AtomicSpectrum *other, double scale) {
+void AtomicSpectrum::mergeQnlm(AtomicSpectrum *other, double scale, bool gradients) {
// Function used to construct global spectrum as sum over atomic spectra.
// The result is itself an "atomic" spectrum (as data fields are largely identical,
// except for the fact that this summed spectrum does not have a well-defined center.
@@ -186,22 +186,24 @@ void AtomicSpectrum::mergeQnlm(AtomicSpectrum *other, double scale) {
mit->second->add(*density, scale);
}
// Particle-ID-resolved gradients
- map_pid_qnlm_t &map_pid_qnlm_other = other->getPidQnlmMap();
- for (auto it = map_pid_qnlm_other.begin(); it != map_pid_qnlm_other.end(); ++it) {
- int pid = it->first;
- std::string pid_type = it->second.first;
- qnlm_t *density_grad = it->second.second;
- // Already have density gradient for this particle?
- auto mit = _map_pid_qnlm.find(pid);
- if (mit == _map_pid_qnlm.end()) {
- qnlm_t *qnlm = new qnlm_t(_basis);
- // Remember to setup zero matrices to store gradient ...
- qnlm->zeroGradient();
- _map_pid_qnlm[pid] = std::pair<std::string,qnlm_t*>(pid_type, qnlm);
- mit = _map_pid_qnlm.find(pid);
+ if (gradients) {
+ map_pid_qnlm_t &map_pid_qnlm_other = other->getPidQnlmMap();
+ for (auto it = map_pid_qnlm_other.begin(); it != map_pid_qnlm_other.end(); ++it) {
+ int pid = it->first;
+ std::string pid_type = it->second.first;
+ qnlm_t *density_grad = it->second.second;
+ // Already have density gradient for this particle?
+ auto mit = _map_pid_qnlm.find(pid);
+ if (mit == _map_pid_qnlm.end()) {
+ qnlm_t *qnlm = new qnlm_t(_basis);
+ // Remember to setup zero matrices to store gradient ...
+ qnlm->zeroGradient();
+ _map_pid_qnlm[pid] = std::pair<std::string,qnlm_t*>(pid_type, qnlm);
+ mit = _map_pid_qnlm.find(pid);
+ }
+ // Add gradients ...
+ mit->second.second->addGradient(*density_grad);
}
- // Add gradients ...
- mit->second.second->addGradient(*density_grad);
}
return;
}
diff --git a/src/soap/atomicspectrum.hpp b/src/soap/atomicspectrum.hpp
index d840e234c18df76284e8610d198b792eccd30b16..6b9da75826b49d450d5943e18970dbc41c923fa4 100644
--- a/src/soap/atomicspectrum.hpp
+++ b/src/soap/atomicspectrum.hpp
@@ -59,7 +59,7 @@ public:
qnlm_t *getQnlmGeneric() { return _qnlm_generic; }
map_qnlm_t &getQnlmMap() { return _map_qnlm; }
map_pid_qnlm_t &getPidQnlmMap() { return _map_pid_qnlm; }
- void mergeQnlm(AtomicSpectrum *other, double scale);
+ void mergeQnlm(AtomicSpectrum *other, double scale, bool gradients);
// XNKL METHODS
void computePower();
void computePowerGradients();
diff --git a/src/soap/cutoff.cpp b/src/soap/cutoff.cpp
index 6eeb759371bb9e7059e41656cc1da767dd5cd979..93caed10bce88cf70196913b144bf959ec3f3283 100644
--- a/src/soap/cutoff.cpp
+++ b/src/soap/cutoff.cpp
@@ -1,4 +1,8 @@
#include "soap/cutoff.hpp"
+#include <boost/archive/binary_iarchive.hpp>
+#include <boost/archive/binary_oarchive.hpp>
+#include <boost/archive/text_iarchive.hpp>
+#include <boost/archive/text_oarchive.hpp>
namespace soap {
@@ -77,6 +81,7 @@ void CutoffFunctionFactory::registerAll(void) {
CutoffFunctionOutlet().Register<CutoffFunctionHeaviside>("heaviside");
}
-
}
+BOOST_CLASS_EXPORT_IMPLEMENT(soap::CutoffFunctionHeaviside);
+
diff --git a/src/soap/cutoff.hpp b/src/soap/cutoff.hpp
index eb0a0fd577af943f4ede951292873c4cb9ddba8d..ad4b54cda5e8e952ed153180068ffaae0837f75a 100644
--- a/src/soap/cutoff.hpp
+++ b/src/soap/cutoff.hpp
@@ -4,6 +4,8 @@
#include <string>
#include <math.h>
#include <vector>
+#include <boost/serialization/base_object.hpp>
+#include <boost/serialization/export.hpp>
#include "soap/base/exceptions.hpp"
#include "soap/base/objectfactory.hpp"
@@ -93,6 +95,9 @@ inline CutoffFunction *CutoffFunctionFactory::create(const std::string &key) {
}
}
-}
+} /* CLOSE NAMESPACE */
+
+BOOST_CLASS_EXPORT_KEY(soap::CutoffFunction);
+BOOST_CLASS_EXPORT_KEY(soap::CutoffFunctionHeaviside);
#endif
diff --git a/src/soap/options.cpp b/src/soap/options.cpp
index 2e7ca88060db5c9d905100a2c0c8dd36b82bb5cc..9f3eeeab92392fe32ab0ce023ac90673726ede1c 100644
--- a/src/soap/options.cpp
+++ b/src/soap/options.cpp
@@ -96,6 +96,30 @@ bool Options::doExcludeTargetId(int pid) {
return (it == _exclude_target_id.end()) ? false : true;
}
+void Options::generateExclusionLists() {
+ if (!boost::python::len(_exclude_center_list)) {
+ for (auto it = _exclude_center.begin(); it != _exclude_center.end(); ++it) {
+ if (it->second) _exclude_center_list.append(it->first);
+ }
+ }
+ if (!boost::python::len(_exclude_target_list)) {
+ for (auto it = _exclude_target.begin(); it != _exclude_target.end(); ++it) {
+ if (it->second) _exclude_target_list.append(it->first);
+ }
+ }
+ if (!boost::python::len(_exclude_center_id_list)) {
+ for (auto it = _exclude_center_id.begin(); it != _exclude_center_id.end(); ++it) {
+ if (it->second) _exclude_center_id_list.append(it->first);
+ }
+ }
+ if (!boost::python::len(_exclude_target_id_list)) {
+ for (auto it = _exclude_target_id.begin(); it != _exclude_target_id.end(); ++it) {
+ if (it->second) _exclude_target_id_list.append(it->first);
+ }
+ }
+ return;
+}
+
void Options::registerPython() {
using namespace boost::python;
void (Options::*set_int)(std::string, int) = &Options::set;
diff --git a/src/soap/options.hpp b/src/soap/options.hpp
index 8d7b6079ea217b0394ee77a63e27670a6a9c31ff..c396ede3fab61f66f7c88a3710a2f1d92aba01a5 100644
--- a/src/soap/options.hpp
+++ b/src/soap/options.hpp
@@ -47,6 +47,9 @@ public:
boost::python::list getExcludeCenterIdList() { return _exclude_center_id_list; }
boost::python::list getExcludeTargetIdList() { return _exclude_target_id_list; }
+ // USED IN SERIALIZATION-LOAD: std::map TO boost::python::list
+ void generateExclusionLists();
+
// PYTHON
static void registerPython();
@@ -57,13 +60,15 @@ public:
arch & _exclude_center;
arch & _exclude_target;
- arch & _exclude_center_list;
- arch & _exclude_target_list;
+ //arch & _exclude_center_list;
+ //arch & _exclude_target_list;
arch & _exclude_center_id;
arch & _exclude_target_id;
- arch & _exclude_center_id_list;
- arch & _exclude_target_id_list;
+ //arch & _exclude_center_id_list;
+ //arch & _exclude_target_id_list;
+
+ this->generateExclusionLists();
return;
}
diff --git a/src/soap/spectrum.cpp b/src/soap/spectrum.cpp
index 79bcd2536092c3d70d001a65678f172af6efec89..ef33149eebd4168baaa7263a31fc27ca92848e3f 100644
--- a/src/soap/spectrum.cpp
+++ b/src/soap/spectrum.cpp
@@ -129,13 +129,14 @@ AtomicSpectrum *Spectrum::computeGlobal() {
if (_global_atomic) throw soap::base::APIError("<Spectrum::computeGlobal> Already initialised.");
_global_atomic = new AtomicSpectrum(_basis);
GLOG() << "Computing global spectrum ..." << std::endl;
+ bool gradients = _options->get<bool>("spectrum.gradients");
for (auto it = _atomspec_array.begin(); it != _atomspec_array.end(); ++it) {
GLOG() << " Adding center " << (*it)->getCenter()->getId()
<< " (type " << (*it)->getCenter()->getType() << ")" << std::endl;
- _global_atomic->mergeQnlm(*it, 0.5); // <- Scale factor 0.5 necessary in order not to overcount pairs
+ _global_atomic->mergeQnlm(*it, 0.5, gradients); // <- Scale factor 0.5 necessary in order not to overcount pairs
}
_global_atomic->computePower();
- _global_atomic->computePowerGradients();
+ if (gradients) _global_atomic->computePowerGradients();
return _global_atomic;
}