diff --git a/include/tadah/mlip/dataset_readers/castep_castep_reader.h b/include/tadah/mlip/dataset_readers/castep_castep_reader.h
index db0db0143353ca811055bcf8df99f16bc353dd43..794a1144c29a4ed44c7c5abf65a88e26dc90f68c 100644
--- a/include/tadah/mlip/dataset_readers/castep_castep_reader.h
+++ b/include/tadah/mlip/dataset_readers/castep_castep_reader.h
@@ -74,6 +74,7 @@ public:
* @brief Prints a summary of the parsed .castep data.
*/
virtual void print_summary() const override;
+ virtual std::string get_summary() const override;
protected:
std::string raw_data_; /**< Stores raw file data */
diff --git a/include/tadah/mlip/dataset_readers/castep_md_reader.h b/include/tadah/mlip/dataset_readers/castep_md_reader.h
index 147f54d366b75dd50fd8fc2ea24533a8bb06ef5e..8ef93cff2537900fe1d137b8bc354d7cdc315a6f 100644
--- a/include/tadah/mlip/dataset_readers/castep_md_reader.h
+++ b/include/tadah/mlip/dataset_readers/castep_md_reader.h
@@ -67,6 +67,7 @@ public:
* @brief Prints a summary of the parsed .md data.
*/
virtual void print_summary() const override;
+ virtual std::string get_summary() const override;
/**
* @brief Checks if a string ends with a given suffix.
@@ -107,8 +108,9 @@ protected:
double T = 0; /**< Temperature in atomic units (Hartree/k_B) */
bool stress_tensor_bool = false; /**< Indicates presence of a stress tensor */
- virtual std::string get_first_label(std::string &);
- virtual std::string get_label(std::string &);
+private:
+ virtual std::string get_first_label(std::string &) override;
+ virtual std::string get_label(std::string &) override;
};
diff --git a/include/tadah/mlip/dataset_readers/dataset_reader.h b/include/tadah/mlip/dataset_readers/dataset_reader.h
index ccf4030e89778a5493fa237a092e12eaf51ef388..a83ab7e012fdfd8d4a1ef77edad4ad0b6d9ae529 100644
--- a/include/tadah/mlip/dataset_readers/dataset_reader.h
+++ b/include/tadah/mlip/dataset_readers/dataset_reader.h
@@ -41,7 +41,7 @@ public:
virtual void parse_data() = 0;
/**
- * @brief Prints or returns a summary of the data.
+ * @brief Prints a summary of the data.
*
* This pure virtual function must be implemented by derived classes
* to provide a summary of the dataset.
@@ -50,6 +50,16 @@ public:
*/
virtual void print_summary() const = 0;
+ /**
+ * @brief Returns a summary of the data.
+ *
+ * This pure virtual function must be implemented by derived classes
+ * to provide a summary of the dataset.
+ *
+ * @param stdb Reference to a StructureDB object for data summary.
+ */
+ virtual std::string get_summary() const = 0;
+
/**
* @brief Constructor initializing the reference.
*
@@ -69,5 +79,8 @@ public:
protected:
StructureDB& stdb; /**< Reference to store parsed data. */
std::string filename; /**< Filename for data reading. */
+private:
+ virtual std::string get_first_label(std::string &);
+ virtual std::string get_label(std::string &);
};
#endif // DATASET_READER_H
diff --git a/include/tadah/mlip/dataset_readers/dataset_reader_selector.h b/include/tadah/mlip/dataset_readers/dataset_reader_selector.h
new file mode 100644
index 0000000000000000000000000000000000000000..9c4808b416a9469d2b562883faa815a9f0b499bb
--- /dev/null
+++ b/include/tadah/mlip/dataset_readers/dataset_reader_selector.h
@@ -0,0 +1,34 @@
+#ifndef DATASET_READER_SELECTOR_H
+#define DATASET_READER_SELECTOR_H
+
+#include <tadah/mlip/structure_db.h>
+#include <tadah/mlip/dataset_readers/dataset_reader.h>
+#include <string>
+#include <memory>
+
+/**
+ * @class DatasetReaderSelector
+ * @brief Selects the appropriate DatasetReader based on file type.
+ */
+class DatasetReaderSelector {
+public:
+ /**
+ * @brief Factory method to create specific DatasetReader objects.
+ *
+ * @param type The type of the dataset reader to create.
+ * @param db Reference to a StructureDB object to store parsed data.
+ * @return A unique pointer to a DatasetReader object.
+ */
+ static std::unique_ptr<DatasetReader> get_reader(const std::string& type, StructureDB& db);
+
+ /**
+ * @brief Determines the file type based on its content.
+ *
+ * @param filepath File path to check the content.
+ * @return A string representing the detected file type.
+ */
+ static std::string determine_file_type_by_content(const std::string& filepath);
+
+};
+
+#endif // DATASET_READER_SELECTOR_H
diff --git a/include/tadah/mlip/dataset_readers/vasp_outcar_reader.h b/include/tadah/mlip/dataset_readers/vasp_outcar_reader.h
index 81b4e6f772b3aed8e5cccc8764b35474f2e123c7..b5bc0644fd5e30e7faef4d08d62499f4ffe0e8c6 100644
--- a/include/tadah/mlip/dataset_readers/vasp_outcar_reader.h
+++ b/include/tadah/mlip/dataset_readers/vasp_outcar_reader.h
@@ -68,10 +68,12 @@ public:
*
* @param stdb Reference to a StructureDB object for data summary.
*/
- void print_summary() const override;
+ virtual void print_summary() const override;
+ virtual std::string get_summary() const override;
private:
std::string raw_data_; // Stores raw file data
+ double s_conv = 6.241509074e-4; // kbar -> eV/A^3
};
#endif // VASP_OUTCAR_READER_H
diff --git a/include/tadah/mlip/dataset_readers/vasp_vasprun_reader.h b/include/tadah/mlip/dataset_readers/vasp_vasprun_reader.h
index 589d8d3995a5e9e0a63c45abb6d705a0deba278c..b43e279f822909b7a0660d0c5d1274824f863384 100644
--- a/include/tadah/mlip/dataset_readers/vasp_vasprun_reader.h
+++ b/include/tadah/mlip/dataset_readers/vasp_vasprun_reader.h
@@ -84,7 +84,8 @@ public:
*
* Uses the parsed data stored in the StructureDB to provide a summary.
*/
- void print_summary() const override;
+ virtual void print_summary() const override;
+ virtual std::string get_summary() const override;
protected:
/**
@@ -159,6 +160,7 @@ protected:
private:
Structure _s; ///< Internal structure representation.
bool stress_tensor_bool = false; ///< Flag indicating stress tensor presence.
+ double s_conv = 6.241509074e-4; // kbar -> eV/A^3
};
#endif // VASP_VASPRUN_READER_H
diff --git a/include/tadah/mlip/descriptors_calc.hpp b/include/tadah/mlip/descriptors_calc.hpp
index 74b4b91b5b922d12ae501d2ff0b9de27d9fdf884..7cf86c1a321cdc794a57d2d1ef2067b070595509 100644
--- a/include/tadah/mlip/descriptors_calc.hpp
+++ b/include/tadah/mlip/descriptors_calc.hpp
@@ -443,7 +443,9 @@ template <typename D2, typename D3, typename DM, typename C2, typename C3, typen
StDescriptorsDB DescriptorsCalc<D2,D3,DM,C2,C3,CM>::calc(const StructureDB &stdb) {
StDescriptorsDB st_desc_db(stdb, config);
-#pragma omp parallel for
+#ifdef _OPENMP
+ #pragma omp parallel for
+#endif
for(size_t i=0; i<stdb.size(); ++i)
if (config.get<bool>("DIMER",0))
calc_dimer(stdb(i),st_desc_db(i));
diff --git a/include/tadah/mlip/design_matrix/design_matrix.h b/include/tadah/mlip/design_matrix/design_matrix.h
index 3f87b5fec3bb6b1188e33da264b93ab0af37c2d2..0289b7a61a3c6ccd522d3bd38419509924968b84 100644
--- a/include/tadah/mlip/design_matrix/design_matrix.h
+++ b/include/tadah/mlip/design_matrix/design_matrix.h
@@ -11,15 +11,15 @@
class DesignMatrixBase {
- public:
- static int phi_rows_num(Config &c, int nstruct_tot, int natoms_tot) {
- bool force = c.get<bool>("FORCE");
- bool stress = c.get<bool>("STRESS");
- int rows = nstruct_tot;
- if (stress) rows += 6*nstruct_tot;
- if (force) rows += 3*natoms_tot;
- return rows;
- }
+public:
+ static int phi_rows_num(Config &c, int nstruct_tot, int natoms_tot) {
+ bool force = c.get<bool>("FORCE");
+ bool stress = c.get<bool>("STRESS");
+ int rows = nstruct_tot;
+ if (stress) rows += 6*nstruct_tot;
+ if (force) rows += 3*natoms_tot;
+ return rows;
+ }
};
@@ -65,19 +65,19 @@ class DesignMatrixBase {
template <typename F>
class DesignMatrix : public DesignMatrixBase {
- public:
+public:
- F f;
- phi_type Phi;
- t_type T;
- t_type Tlabels; // 0-Energy, 1-Force, 2-Stress // TODO should be array of int not double
- bool scale=true; // Control escale,fscale,sscale
+ F f;
+ phi_type Phi;
+ t_type T;
+ t_type Tlabels; // 0-Energy, 1-Force, 2-Stress // TODO should be array of int not double
+ bool scale=true; // Control escale,fscale,sscale
- double e_std_dev=1;
- double f_std_dev=1;
- double s_std_dev[6] = {1,1,1,1,1,1};
+ double e_std_dev=1;
+ double f_std_dev=1;
+ double s_std_dev[6] = {1,1,1,1,1,1};
- /** \brief This constructor fully initialise this object
+ /** \brief This constructor fully initialise this object
*
* This class is used to build a Design Matrix.
*
@@ -89,15 +89,15 @@ class DesignMatrix : public DesignMatrixBase {
*
* \endcode
*/
- DesignMatrix(F &f, Config &c):
- f(f),
- config(c),
- force(config.get<bool>("FORCE")),
- stress(config.get<bool>("STRESS")),
- verbose(config.get<int>("VERBOSE")),
- eweightglob(config.get<double>("EWEIGHT")),
- fweightglob(config.get<double>("FWEIGHT")),
- sweightglob(config.get<double>("SWEIGHT"))
+ DesignMatrix(F &f, Config &c):
+ f(f),
+ config(c),
+ force(config.get<bool>("FORCE")),
+ stress(config.get<bool>("STRESS")),
+ verbose(config.get<int>("VERBOSE")),
+ eweightglob(config.get<double>("EWEIGHT")),
+ fweightglob(config.get<double>("FWEIGHT")),
+ sweightglob(config.get<double>("SWEIGHT"))
{
if (config.exist("ESTDEV"))
e_std_dev = config.get<double>("ESTDEV");
@@ -108,215 +108,219 @@ class DesignMatrix : public DesignMatrixBase {
}
- /** \brief Build design matrix from already calculated StDescriptorsDB
+ /** \brief Build design matrix from already calculated StDescriptorsDB
*
* Here we simply build matrix from already calculated descriptors.
* The vector of targets **T** is build from StructureDB.
* D2, D3 and DM calculators are not used.
*/
- void build(StDescriptorsDB &st_desc_db, const StructureDB &stdb) {
- resize(stdb);
- compute_stdevs(stdb);
- fill_T(stdb);
- std::vector<size_t> rows(stdb.size());
- size_t row=0;
- for (size_t s=0; s<stdb.size(); ++s) {
- rows[s] = row;
- row++;
- if (force) {
- for (size_t a=0; a<stdb(s).natoms(); ++a) {
- row+=3;
- }
- }
- if (stress) {
- row+=6;
+ void build(StDescriptorsDB &st_desc_db, const StructureDB &stdb) {
+ resize(stdb);
+ compute_stdevs(stdb);
+ fill_T(stdb);
+ std::vector<size_t> rows(stdb.size());
+ size_t row=0;
+ for (size_t s=0; s<stdb.size(); ++s) {
+ rows[s] = row;
+ row++;
+ if (force) {
+ for (size_t a=0; a<stdb(s).natoms(); ++a) {
+ row+=3;
}
}
- // loop over all structures and build
-#pragma omp parallel for
- for (size_t s=0; s<stdb.size(); ++s) {
- build(rows[s], stdb(s),st_desc_db(s));
+ if (stress) {
+ row+=6;
}
- };
-
- /** \brief Calculate descriptors and build design matrix. */
- template <typename DC>
- void build(const StructureDB &stdb, Normaliser &norm,
- DC &dc) {
- //DescriptorsCalc<D2,D3,DM,C2,C3,CM> dc(config);
- resize(stdb); // call after dc set DSIZE key
- compute_stdevs(stdb);
- fill_T(stdb);
- // for opm we need to find first rows for each structure
-
-
- std::vector<size_t> rows(stdb.size());
- size_t row=0;
- for (size_t s=0; s<stdb.size(); ++s) {
- rows[s] = row;
- row++;
- if (force) {
- for (size_t a=0; a<stdb(s).natoms(); ++a) {
- row+=3;
- }
- }
- if (stress) {
- row+=6;
- }
+ }
+ // loop over all structures and build
+#ifdef _OPENMP
+ #pragma omp parallel for
+#endif
+ for (size_t s=0; s<stdb.size(); ++s) {
+ build(rows[s], stdb(s),st_desc_db(s));
+ }
+ };
+
+ /** \brief Calculate descriptors and build design matrix. */
+ template <typename DC>
+ void build(const StructureDB &stdb, Normaliser &norm,
+ DC &dc) {
+ //DescriptorsCalc<D2,D3,DM,C2,C3,CM> dc(config);
+ resize(stdb); // call after dc set DSIZE key
+ compute_stdevs(stdb);
+ fill_T(stdb);
+ // for opm we need to find first rows for each structure
+
+
+ std::vector<size_t> rows(stdb.size());
+ size_t row=0;
+ for (size_t s=0; s<stdb.size(); ++s) {
+ rows[s] = row;
+ row++;
+ if (force) {
+ for (size_t a=0; a<stdb(s).natoms(); ++a) {
+ row+=3;
}
-#pragma omp parallel for
- for (size_t s=0; s<stdb.size(); ++s) {
- StDescriptors st_d = dc.calc(stdb(s));
+ }
+ if (stress) {
+ row+=6;
+ }
+ }
+#ifdef _OPENMP
+ #pragma omp parallel for
+#endif
+ for (size_t s=0; s<stdb.size(); ++s) {
+ StDescriptors st_d = dc.calc(stdb(s));
- if(config.get<bool>("NORM"))
- norm.normalise(st_d);
+ if(config.get<bool>("NORM"))
+ norm.normalise(st_d);
- build(rows[s], stdb(s), st_d);
- }
+ build(rows[s], stdb(s), st_d);
+ }
- }
- void build(size_t &row, const Structure &st, const StDescriptors &st_d) {
+ }
+ void build(size_t &row, const Structure &st, const StDescriptors &st_d) {
+
+ double escale = 1;
+ if (scale) escale = st.eweight*eweightglob/st.natoms();
+ f.calc_phi_energy_row(Phi,row,escale,st,st_d);
+ if (force) {
+ double fscale = 1;
+ if (scale) fscale = st.fweight*fweightglob/st.natoms()/3.0;///f_std_dev;
+ f.calc_phi_force_rows(Phi,row,fscale,st,st_d);
+ }
+ if (stress) {
+ double sscale_arr[6] {1,1,1,1,1,1};
+ if (scale)
+ for(size_t xy=0;xy<6;++xy)
+ sscale_arr[xy] = st.sweight*sweightglob/6.0;///s_std_dev[xy];
+ f.calc_phi_stress_rows(Phi,row,sscale_arr,st,st_d);
+ }
+ }
+ void fill_T(const StructureDB &stdb, size_t start=0) {
+ size_t j=start;
+ for (size_t s=0; s<stdb.size(); ++s) {
double escale = 1;
- if (scale) escale = st.eweight*eweightglob/st.natoms();
- f.calc_phi_energy_row(Phi,row,escale,st,st_d);
+ if (scale) escale = stdb(s).eweight*eweightglob/stdb(s).natoms();///e_std_dev;
+ Tlabels(j) = 0;
+ T(j++) = stdb(s).energy*escale;
+
if (force) {
double fscale = 1;
- if (scale) fscale = st.fweight*fweightglob/st.natoms()/3.0;///f_std_dev;
- f.calc_phi_force_rows(Phi,row,fscale,st,st_d);
+ if (scale) fscale = stdb(s).fweight*fweightglob/stdb(s).natoms()/3.0;///e_std_dev/f_std_dev;
+ for (const Atom &a : stdb(s).atoms) {
+ Tlabels(j) = 1;
+ T(j++) = a.force(0)*fscale;
+ Tlabels(j) = 1;
+ T(j++) = a.force(1)*fscale;
+ Tlabels(j) = 1;
+ T(j++) = a.force(2)*fscale;
+ }
}
if (stress) {
double sscale_arr[6] {1,1,1,1,1,1};
if (scale)
for(size_t xy=0;xy<6;++xy)
- sscale_arr[xy] = st.sweight*sweightglob/6.0;///s_std_dev[xy];
- f.calc_phi_stress_rows(Phi,row,sscale_arr,st,st_d);
- }
- }
- void fill_T(const StructureDB &stdb, size_t start=0) {
- size_t j=start;
- for (size_t s=0; s<stdb.size(); ++s) {
-
- double escale = 1;
- if (scale) escale = stdb(s).eweight*eweightglob/stdb(s).natoms();///e_std_dev;
- Tlabels(j) = 0;
- T(j++) = stdb(s).energy*escale;
-
- if (force) {
- double fscale = 1;
- if (scale) fscale = stdb(s).fweight*fweightglob/stdb(s).natoms()/3.0;///e_std_dev/f_std_dev;
- for (const Atom &a : stdb(s).atoms) {
- Tlabels(j) = 1;
- T(j++) = a.force(0)*fscale;
- Tlabels(j) = 1;
- T(j++) = a.force(1)*fscale;
- Tlabels(j) = 1;
- T(j++) = a.force(2)*fscale;
- }
- }
- if (stress) {
- double sscale_arr[6] {1,1,1,1,1,1};
- if (scale)
- for(size_t xy=0;xy<6;++xy)
- sscale_arr[xy] = stdb(s).sweight*sweightglob/6.0;///e_std_dev/s_std_dev[xy];
- size_t xy=0;
- for (size_t x=0; x<3; ++x) {
- for (size_t y=x; y<3; ++y) {
- Tlabels(j) = 2;
- T(j++)=stdb(s).stress(x,y)*sscale_arr[xy++];
- }
+ sscale_arr[xy] = stdb(s).sweight*sweightglob/6.0;///e_std_dev/s_std_dev[xy];
+ size_t xy=0;
+ for (size_t x=0; x<3; ++x) {
+ for (size_t y=x; y<3; ++y) {
+ Tlabels(j) = 2;
+ T(j++)=stdb(s).stress(x,y)*sscale_arr[xy++];
}
}
}
}
+ }
- private:
- Config &config;
- size_t rows=0;
- size_t cols=0;
- bool force;
- bool stress;
- int verbose;
- double eweightglob;
- double fweightglob;
- double sweightglob;
-
- // resize Phi and T and set all elements to zero
- void resize(const StructureDB &stdb) {
- rows=0;
- cols = f.get_phi_cols(config);
-
- for (size_t s=0; s<stdb.size(); ++s) {
- rows++;
- if (stress) rows+=6;
- if (force) rows+=stdb(s).natoms()*3;
- }
+private:
+ Config &config;
+ size_t rows=0;
+ size_t cols=0;
+ bool force;
+ bool stress;
+ int verbose;
+ double eweightglob;
+ double fweightglob;
+ double sweightglob;
+
+ // resize Phi and T and set all elements to zero
+ void resize(const StructureDB &stdb) {
+ rows=0;
+ cols = f.get_phi_cols(config);
+
+ for (size_t s=0; s<stdb.size(); ++s) {
+ rows++;
+ if (stress) rows+=6;
+ if (force) rows+=stdb(s).natoms()*3;
+ }
- T.resize(rows);
- Tlabels.resize(rows);
- Phi.resize(rows,cols);
+ T.resize(rows);
+ Tlabels.resize(rows);
+ Phi.resize(rows,cols);
- if (verbose) {
- std::cout << "Phi rows: "<< Phi.rows() << std::endl;
- std::cout << "Phi cols: "<< Phi.cols() << std::endl;
- }
+ if (verbose) {
+ std::cout << "Phi rows: "<< Phi.rows() << std::endl;
+ std::cout << "Phi cols: "<< Phi.cols() << std::endl;
+ }
- T.set_zero();
- Phi.set_zero();
+ T.set_zero();
+ Phi.set_zero();
- }
+ }
- void compute_stdevs(const StructureDB &stdb) {
- t_type evec(stdb.size());
- Matrix svec(stdb.size(),6);
- size_t num_forces=0;
- for (size_t s=0; s<stdb.size(); ++s) {
- evec(s) = stdb(s).energy/stdb(s).natoms();
- if (stress) {
- size_t j=0;
- for (size_t x=0; x<3; ++x) {
- for (size_t y=x; y<3; ++y) {
- svec(s,j++)=stdb(s).stress(x,y);
- }
+ void compute_stdevs(const StructureDB &stdb) {
+ t_type evec(stdb.size());
+ Matrix svec(stdb.size(),6);
+ size_t num_forces=0;
+ for (size_t s=0; s<stdb.size(); ++s) {
+ evec(s) = stdb(s).energy/stdb(s).natoms();
+ if (stress) {
+ size_t j=0;
+ for (size_t x=0; x<3; ++x) {
+ for (size_t y=x; y<3; ++y) {
+ svec(s,j++)=stdb(s).stress(x,y);
}
}
- num_forces +=3*stdb(s).natoms();
}
+ num_forces +=3*stdb(s).natoms();
+ }
- //e_std_dev = std::sqrt((evec - evec.mean()).square().sum()/(evec.size()-1));
- e_std_dev = evec.std_dev(evec.mean(), evec.size()-1);
- if (verbose) std::cout << "Energy standard deviation (eV/atom): " << e_std_dev << std::endl;
+ //e_std_dev = std::sqrt((evec - evec.mean()).square().sum()/(evec.size()-1));
+ e_std_dev = evec.std_dev(evec.mean(), evec.size()-1);
+ if (verbose) std::cout << "Energy standard deviation (eV/atom): " << e_std_dev << std::endl;
- if (stress) {
- for (size_t j=0; j<6; ++j) {
- s_std_dev[j] = svec.col(j).std_dev(svec.col(j).mean(), svec.col(j).size()-1);
- if (verbose) std::cout << "Stress standard deviation (eV): " << s_std_dev[j] << std::endl;
- }
+ if (stress) {
+ for (size_t j=0; j<6; ++j) {
+ s_std_dev[j] = svec.col(j).std_dev(svec.col(j).mean(), svec.col(j).size()-1);
+ if (verbose) std::cout << "Stress standard deviation (eV): " << s_std_dev[j] << std::endl;
}
+ }
- if (force) {
- size_t j=0;
- t_type fvec(num_forces);
- for (size_t s=0; s<stdb.size(); ++s) {
- for (const Atom &a : stdb(s).atoms) {
- fvec(j++) = a.force(0);
- fvec(j++) = a.force(1);
- fvec(j++) = a.force(2);
- }
+ if (force) {
+ size_t j=0;
+ t_type fvec(num_forces);
+ for (size_t s=0; s<stdb.size(); ++s) {
+ for (const Atom &a : stdb(s).atoms) {
+ fvec(j++) = a.force(0);
+ fvec(j++) = a.force(1);
+ fvec(j++) = a.force(2);
}
- //fvec /= e_std_dev;
- //svec /= e_std_dev;
- // e_std_dev has units of energy
- // f_std_dev has units of inverse distance
- f_std_dev = fvec.std_dev(fvec.mean(),fvec.size()-1);
- if (verbose) std::cout << "Force standard deviation (1/A): " << f_std_dev << std::endl;
}
-
- config.add("ESTDEV",e_std_dev);
- config.add("FSTDEV",f_std_dev);
- for (size_t j=0; j<6; ++j)
- config.add("SSTDEV",s_std_dev[j]);
+ //fvec /= e_std_dev;
+ //svec /= e_std_dev;
+ // e_std_dev has units of energy
+ // f_std_dev has units of inverse distance
+ f_std_dev = fvec.std_dev(fvec.mean(),fvec.size()-1);
+ if (verbose) std::cout << "Force standard deviation (1/A): " << f_std_dev << std::endl;
}
+
+ config.add("ESTDEV",e_std_dev);
+ config.add("FSTDEV",f_std_dev);
+ for (size_t j=0; j<6; ++j)
+ config.add("SSTDEV",s_std_dev[j]);
+ }
};
#endif
diff --git a/include/tadah/mlip/models/m_blr.h b/include/tadah/mlip/models/m_blr.h
index eafc784ea1734ddbc6028c99637067fcdfc39b1f..82ebbffa15b34b1fb2d404a98dada21d796f5b89 100644
--- a/include/tadah/mlip/models/m_blr.h
+++ b/include/tadah/mlip/models/m_blr.h
@@ -71,9 +71,9 @@ template
<class BF=DM_Function_Base&>
class M_BLR: public M_Tadah_Base, public M_BLR_Train<BF> {
- public:
+public:
- /** This constructor will preapare this object for either training
+ /** This constructor will preapare this object for either training
* or prediction (if potential is provides as a Config)
*
* Usage example:
@@ -84,16 +84,16 @@ class M_BLR: public M_Tadah_Base, public M_BLR_Train<BF> {
* \endcode
*
*/
- using M_BLR_Train<BF>::config;
- using M_BLR_Train<BF>::bf;
- M_BLR(Config &c):
- M_BLR_Train<BF>(c),
- desmat(M_BLR_Train<BF>::bf,c)
+ using M_BLR_Train<BF>::config;
+ using M_BLR_Train<BF>::bf;
+ M_BLR(Config &c):
+ M_BLR_Train<BF>(c),
+ desmat(M_BLR_Train<BF>::bf,c)
{
norm = Normaliser(c);
}
- /** This constructor will preapare this object for either training
+ /** This constructor will preapare this object for either training
* or prediction (if potential is provides as a Config)
*
* Usage example:
@@ -105,260 +105,260 @@ class M_BLR: public M_Tadah_Base, public M_BLR_Train<BF> {
* \endcode
*
*/
- M_BLR(BF &bf, Config &c):
- M_BLR_Train<BF>(bf,c),
- desmat(bf,c)
+ M_BLR(BF &bf, Config &c):
+ M_BLR_Train<BF>(bf,c),
+ desmat(bf,c)
{
norm = Normaliser(c);
}
- double epredict(const aed_type2 &aed) const{
- return bf.epredict(weights,aed);
- };
+ double epredict(const aed_type2 &aed) const{
+ return bf.epredict(weights,aed);
+ };
- double fpredict(const fd_type &fdij, const aed_type2 &aedi, const size_t k) const{
- return bf.fpredict(weights,fdij,aedi,k);
- }
-
- force_type fpredict(const fd_type &fdij, const aed_type2 &aedi) const{
- return bf.fpredict(weights,fdij,aedi);
- }
+ double fpredict(const fd_type &fdij, const aed_type2 &aedi, const size_t k) const{
+ return bf.fpredict(weights,fdij,aedi,k);
+ }
- void train(StDescriptorsDB &st_desc_db, const StructureDB &stdb) {
+ force_type fpredict(const fd_type &fdij, const aed_type2 &aedi) const{
+ return bf.fpredict(weights,fdij,aedi);
+ }
- if(config.template get<bool>("NORM"))
- norm = Normaliser(config,st_desc_db);
+ void train(StDescriptorsDB &st_desc_db, const StructureDB &stdb) {
- desmat.build(st_desc_db,stdb);
- train(desmat);
- }
+ if(config.template get<bool>("NORM"))
+ norm = Normaliser(config,st_desc_db);
- void train(StructureDB &stdb, DC_Base &dc) {
+ desmat.build(st_desc_db,stdb);
+ train(desmat);
+ }
- if(config.template get<bool>("NORM")) {
+ void train(StructureDB &stdb, DC_Base &dc) {
- std::string force=config.template get<std::string>("FORCE");
- std::string stress=config.template get<std::string>("STRESS");
+ if(config.template get<bool>("NORM")) {
- config.remove("FORCE");
- config.remove("STRESS");
- config.add("FORCE", "false");
- config.add("STRESS", "false");
+ std::string force=config.template get<std::string>("FORCE");
+ std::string stress=config.template get<std::string>("STRESS");
- StDescriptorsDB st_desc_db_temp = dc.calc(stdb);
+ config.remove("FORCE");
+ config.remove("STRESS");
+ config.add("FORCE", "false");
+ config.add("STRESS", "false");
- if(config.template get<bool>("NORM")) {
- norm = Normaliser(config);
- norm.learn(st_desc_db_temp);
- // norm.normalise(st_desc_db_temp);
- }
+ StDescriptorsDB st_desc_db_temp = dc.calc(stdb);
- config.remove("FORCE");
- config.remove("STRESS");
- config.add("FORCE", force);
- config.add("STRESS", stress);
+ if(config.template get<bool>("NORM")) {
+ norm = Normaliser(config);
+ norm.learn(st_desc_db_temp);
+ // norm.normalise(st_desc_db_temp);
}
- desmat.build(stdb,norm,dc);
- train(desmat);
+ config.remove("FORCE");
+ config.remove("STRESS");
+ config.add("FORCE", force);
+ config.add("STRESS", stress);
}
- Structure predict(const Config &c, StDescriptors &std, const Structure &st) {
- if(config.template get<bool>("NORM") && !std.normalised && bf.get_label()!="BF_Linear")
- norm.normalise(std);
- return M_Tadah_Base::predict(c,std,st);
- }
+ desmat.build(stdb,norm,dc);
+ train(desmat);
+ }
- StructureDB predict(Config &c, const StructureDB &stdb, DC_Base &dc) {
- return M_Tadah_Base::predict(c,stdb,dc);
+ Structure predict(const Config &c, StDescriptors &std, const Structure &st) {
+ if(config.template get<bool>("NORM") && !std.normalised && bf.get_label()!="BF_Linear")
+ norm.normalise(std);
+ return M_Tadah_Base::predict(c,std,st);
+ }
+
+ StructureDB predict(Config &c, const StructureDB &stdb, DC_Base &dc) {
+ return M_Tadah_Base::predict(c,stdb,dc);
+ }
+
+ Config get_param_file() {
+ Config c = config;
+ //c.remove("ALPHA");
+ //c.remove("BETA");
+ c.remove("DBFILE");
+ c.remove("FORCE");
+ c.remove("STRESS");
+ c.remove("VERBOSE");
+ c.add("VERBOSE", 0);
+
+ c.clear_internal_keys();
+ c.remove("MODEL");
+ c.add("MODEL", label);
+ c.add("MODEL", bf.get_label());
+
+ for (size_t i=0;i<weights.size();++i) {
+ c.add("WEIGHTS", weights(i));
}
- Config get_param_file() {
- Config c = config;
- //c.remove("ALPHA");
- //c.remove("BETA");
- c.remove("DBFILE");
- c.remove("FORCE");
- c.remove("STRESS");
- c.remove("VERBOSE");
- c.add("VERBOSE", 0);
-
- c.clear_internal_keys();
- c.remove("MODEL");
- c.add("MODEL", label);
- c.add("MODEL", bf.get_label());
-
- for (size_t i=0;i<weights.size();++i) {
- c.add("WEIGHTS", weights(i));
+ if(config.template get<bool>("NORM")) {
+ for (size_t i=0;i<norm.mean.size();++i) {
+ c.add("NMEAN", norm.mean[i]);
}
-
- if(config.template get<bool>("NORM")) {
- for (size_t i=0;i<norm.mean.size();++i) {
- c.add("NMEAN", norm.mean[i]);
- }
- for (size_t i=0;i<norm.std_dev.size();++i) {
- c.add("NSTDEV", norm.std_dev[i]);
- }
+ for (size_t i=0;i<norm.std_dev.size();++i) {
+ c.add("NSTDEV", norm.std_dev[i]);
}
- return c;
}
- StructureDB predict(Config config_pred, StructureDB &stdb, DC_Base &dc,
- aed_type2 &predicted_error) {
-
- LinearRegressor::read_sigma(config_pred,Sigma);
- DesignMatrix<BF> dm(bf,config_pred);
- dm.scale=false; // do not scale energy, forces and stresses
- dm.build(stdb,norm,dc);
-
- predicted_error = T_MDMT_diag(dm.Phi, Sigma);
- double pmean = sqrt(predicted_error.mean());
-
- // compute energy, forces and stresses
- aed_type2 Tpred = T_dgemv(dm.Phi, weights);
-
- // Construct StructureDB object with predicted values
- StructureDB stdb_;
- stdb_.structures.resize(stdb.size());
- size_t i=0;
- for (size_t s=0; s<stdb.size(); ++s) {
- stdb_(s) = Structure(stdb(s));
-
- predicted_error(i) = (sqrt(predicted_error(i))-pmean)/stdb(s).natoms();
- stdb_(s).energy = Tpred(i++);
- if (config_pred.get<bool>("FORCE")) {
- for (size_t a=0; a<stdb(s).natoms(); ++a) {
- for (size_t k=0; k<3; ++k) {
- stdb_(s).atoms[a].force[k] = Tpred(i++);
- predicted_error(i) = (sqrt(predicted_error(i))-pmean);
- }
+ return c;
+ }
+ StructureDB predict(Config config_pred, StructureDB &stdb, DC_Base &dc,
+ aed_type2 &predicted_error) {
+
+ LinearRegressor::read_sigma(config_pred,Sigma);
+ DesignMatrix<BF> dm(bf,config_pred);
+ dm.scale=false; // do not scale energy, forces and stresses
+ dm.build(stdb,norm,dc);
+
+ predicted_error = T_MDMT_diag(dm.Phi, Sigma);
+ double pmean = sqrt(predicted_error.mean());
+
+ // compute energy, forces and stresses
+ aed_type2 Tpred = T_dgemv(dm.Phi, weights);
+
+ // Construct StructureDB object with predicted values
+ StructureDB stdb_;
+ stdb_.structures.resize(stdb.size());
+ size_t i=0;
+ for (size_t s=0; s<stdb.size(); ++s) {
+ stdb_(s) = Structure(stdb(s));
+
+ predicted_error(i) = (sqrt(predicted_error(i))-pmean)/stdb(s).natoms();
+ stdb_(s).energy = Tpred(i++);
+ if (config_pred.get<bool>("FORCE")) {
+ for (size_t a=0; a<stdb(s).natoms(); ++a) {
+ for (size_t k=0; k<3; ++k) {
+ stdb_(s).atoms[a].force[k] = Tpred(i++);
+ predicted_error(i) = (sqrt(predicted_error(i))-pmean);
}
}
- if (config_pred.get<bool>("STRESS")) {
- for (size_t x=0; x<3; ++x) {
- for (size_t y=x; y<3; ++y) {
- stdb_(s).stress(x,y) = Tpred(i++);
- predicted_error(i) = (sqrt(predicted_error(i))-pmean);
- if (x!=y)
- stdb_(s).stress(y,x) = stdb_(s).stress(x,y);
- }
+ }
+ if (config_pred.get<bool>("STRESS")) {
+ for (size_t x=0; x<3; ++x) {
+ for (size_t y=x; y<3; ++y) {
+ stdb_(s).stress(x,y) = Tpred(i++);
+ predicted_error(i) = (sqrt(predicted_error(i))-pmean);
+ if (x!=y)
+ stdb_(s).stress(y,x) = stdb_(s).stress(x,y);
}
}
}
- return stdb_;
}
- StructureDB predict(StructureDB &stdb) {
- if(!trained) throw std::runtime_error("This object is not trained!\n\
- Hint: check different predict() methods.");
-
- phi_type &Phi = desmat.Phi;
- //std::cout << Phi.row(0) << std::endl;
-
- // compute energy, forces and stresses
- aed_type2 Tpred = T_dgemv(Phi, weights);
-
- double eweightglob=config.template get<double>("EWEIGHT");
- double fweightglob=config.template get<double>("FWEIGHT");
- double sweightglob=config.template get<double>("SWEIGHT");
-
- // Construct StructureDB object with predicted values
- StructureDB stdb_;
- stdb_.structures.resize(stdb.size());
- size_t s=0;
- size_t i=0;
- while (i<Phi.rows()) {
-
- stdb_(s).energy = Tpred(i++)*stdb(s).natoms()/eweightglob/stdb(s).eweight;
- if (config.template get<bool>("FORCE")) {
- stdb_(s).atoms.resize(stdb(s).natoms());
- for (size_t a=0; a<stdb(s).natoms(); ++a) {
- for (size_t k=0; k<3; ++k) {
- stdb_(s).atoms[a].force[k] = Tpred(i++)/fweightglob/stdb(s).fweight;
- }
+ return stdb_;
+ }
+ StructureDB predict(StructureDB &stdb) {
+ if(!trained) throw std::runtime_error("This object is not trained!\n\
+Hint: check different predict() methods.");
+
+ phi_type &Phi = desmat.Phi;
+ //std::cout << Phi.row(0) << std::endl;
+
+ // compute energy, forces and stresses
+ aed_type2 Tpred = T_dgemv(Phi, weights);
+
+ double eweightglob=config.template get<double>("EWEIGHT");
+ double fweightglob=config.template get<double>("FWEIGHT");
+ double sweightglob=config.template get<double>("SWEIGHT");
+
+ // Construct StructureDB object with predicted values
+ StructureDB stdb_;
+ stdb_.structures.resize(stdb.size());
+ size_t s=0;
+ size_t i=0;
+ while (i<Phi.rows()) {
+
+ stdb_(s).energy = Tpred(i++)*stdb(s).natoms()/eweightglob/stdb(s).eweight;
+ if (config.template get<bool>("FORCE")) {
+ stdb_(s).atoms.resize(stdb(s).natoms());
+ for (size_t a=0; a<stdb(s).natoms(); ++a) {
+ for (size_t k=0; k<3; ++k) {
+ stdb_(s).atoms[a].force[k] = Tpred(i++)/fweightglob/stdb(s).fweight;
}
}
- if (config.template get<bool>("STRESS")) {
- for (size_t x=0; x<3; ++x) {
- for (size_t y=x; y<3; ++y) {
- stdb_(s).stress(x,y) = Tpred(i++)/sweightglob/stdb(s).sweight;
- if (x!=y)
- stdb_(s).stress(y,x) = stdb_(s).stress(x,y);
- }
+ }
+ if (config.template get<bool>("STRESS")) {
+ for (size_t x=0; x<3; ++x) {
+ for (size_t y=x; y<3; ++y) {
+ stdb_(s).stress(x,y) = Tpred(i++)/sweightglob/stdb(s).sweight;
+ if (x!=y)
+ stdb_(s).stress(y,x) = stdb_(s).stress(x,y);
}
}
- s++;
}
- return stdb_;
+ s++;
}
+ return stdb_;
+ }
- private:
- std::string label="M_BLR";
- DesignMatrix<BF> desmat;
+private:
+ std::string label="M_BLR";
+ DesignMatrix<BF> desmat;
- // normalise weights such that when predict is called
- // we can supply it with a non-normalised descriptor
- t_type convert_to_nweights(const t_type &weights) const {
- if(bf.get_label()!="BF_Linear") {
- throw std::runtime_error("Cannot convert weights to nweights for\n\
- non linear basis function\n");
- }
- t_type nw(weights.rows());
- nw(0) = weights(0);
- for (size_t i=1; i<weights.size(); ++i) {
+ // normalise weights such that when predict is called
+ // we can supply it with a non-normalised descriptor
+ t_type convert_to_nweights(const t_type &weights) const {
+ if(bf.get_label()!="BF_Linear") {
+ throw std::runtime_error("Cannot convert weights to nweights for\n\
+non linear basis function\n");
+ }
+ t_type nw(weights.rows());
+ nw(0) = weights(0);
+ for (size_t i=1; i<weights.size(); ++i) {
- if (norm.std_dev[i] > std::numeric_limits<double>::min())
- nw(i) = weights(i) / norm.std_dev[i];
- else
- nw(i) = weights(i);
+ if (norm.std_dev[i] > std::numeric_limits<double>::min())
+ nw(i) = weights(i) / norm.std_dev[i];
+ else
+ nw(i) = weights(i);
- nw(0) -= norm.mean[i]*nw(i);
+ nw(0) -= norm.mean[i]*nw(i);
- }
- return nw;
}
- // The opposite of convert_to_nweights()
- t_type convert_to_weights(const t_type &nw) const {
- if(bf.get_label()!="BF_Linear") {
- throw std::runtime_error("Cannot convert nweights to weights for\n\
- non linear basis function\n");
- }
- // convert normalised weights back to "normal"
- t_type w(nw.rows());
- w(0) = nw(0);
- for (size_t i=1; i<nw.size(); ++i) {
- if (norm.std_dev[i] > std::numeric_limits<double>::min())
- w(i) = nw(i) * norm.std_dev[i];
- else
- w(i) = nw(i);
-
- w(0) += nw(i)*norm.mean[i];
- }
- return w;
+ return nw;
+ }
+ // The opposite of convert_to_nweights()
+ t_type convert_to_weights(const t_type &nw) const {
+ if(bf.get_label()!="BF_Linear") {
+ throw std::runtime_error("Cannot convert nweights to weights for\n\
+non linear basis function\n");
}
+ // convert normalised weights back to "normal"
+ t_type w(nw.rows());
+ w(0) = nw(0);
+ for (size_t i=1; i<nw.size(); ++i) {
+ if (norm.std_dev[i] > std::numeric_limits<double>::min())
+ w(i) = nw(i) * norm.std_dev[i];
+ else
+ w(i) = nw(i);
+
+ w(0) += nw(i)*norm.mean[i];
+ }
+ return w;
+ }
- template <typename D>
- void train(D &desmat) {
- // TODO
- // the train method destroys the Phi matrix
- // In consequence, we cannot use it for quick prediction
- // The simple solution, for now, is to make a copy of the Phi matrix
- //phi_type &Phi = desmat.Phi;
- phi_type Phi = desmat.Phi;
- t_type T = desmat.T;
- //t_type &T = desmat.T;
- M_BLR_Train<BF>::train(Phi,T);
-
- if (config.template get<bool>("NORM") &&
- bf.get_label()=="BF_Linear") {
- weights = convert_to_nweights(weights);
- }
- }
+ template <typename D>
+ void train(D &desmat) {
+ // TODO
+ // the train method destroys the Phi matrix
+ // In consequence, we cannot use it for quick prediction
+ // The simple solution, for now, is to make a copy of the Phi matrix
+ //phi_type &Phi = desmat.Phi;
+ phi_type Phi = desmat.Phi;
+ t_type T = desmat.T;
+ //t_type &T = desmat.T;
+ M_BLR_Train<BF>::train(Phi,T);
+
+ if (config.template get<bool>("NORM") &&
+ bf.get_label()=="BF_Linear") {
+ weights = convert_to_nweights(weights);
+ }
+ }
- // Do we want to confuse user with those and make them public?
- // Either way they must be stated as below to silence clang warning
- using M_BLR_Train<BF>::predict;
- using M_BLR_Train<BF>::train;
- using M_BLR_Train<BF>::trained;
- using M_BLR_Train<BF>::weights;
- using M_BLR_Train<BF>::Sigma;
+ // Do we want to confuse user with those and make them public?
+ // Either way they must be stated as below to silence clang warning
+ using M_BLR_Train<BF>::predict;
+ using M_BLR_Train<BF>::train;
+ using M_BLR_Train<BF>::trained;
+ using M_BLR_Train<BF>::weights;
+ using M_BLR_Train<BF>::Sigma;
};
#endif
diff --git a/include/tadah/mlip/models/m_krr.h b/include/tadah/mlip/models/m_krr.h
index 9062779b400a239743eb54f244205176b392d46f..6e79ae3363f5079b1be9c7cb9a2a7c68a002541a 100644
--- a/include/tadah/mlip/models/m_krr.h
+++ b/include/tadah/mlip/models/m_krr.h
@@ -49,12 +49,12 @@ template
<class K=DM_Function_Base&>
class M_KRR: public M_Tadah_Base,
public M_KRR_Train<K>
- //public M_KRR_Predict<K>
+//public M_KRR_Predict<K>
{
- public:
+public:
- /** This constructor will preapare this object for either training
+ /** This constructor will preapare this object for either training
* or prediction (if potential is provides as a Config)
*
* Usage example:
@@ -65,15 +65,15 @@ class M_KRR: public M_Tadah_Base,
* \endcode
*
*/
- M_KRR(Config &c):
- M_KRR_Train<K>(c),
- basis(c),
- desmat(kernel,c)
+ M_KRR(Config &c):
+ M_KRR_Train<K>(c),
+ basis(c),
+ desmat(kernel,c)
{
norm = Normaliser(c);
}
- /** This constructor will preapare this object for either training
+ /** This constructor will preapare this object for either training
* or prediction (if potential is provides as a Config)
*
* Usage example:
@@ -85,330 +85,330 @@ class M_KRR: public M_Tadah_Base,
* \endcode
*
*/
- M_KRR(K &kernel, Config &c):
- M_KRR_Train<K>(kernel,c),
- basis(c),
- desmat(kernel,c)
+ M_KRR(K &kernel, Config &c):
+ M_KRR_Train<K>(kernel,c),
+ basis(c),
+ desmat(kernel,c)
{
norm = Normaliser(c);
}
- double epredict(const aed_type2 &aed) const {
- return kernel.epredict(weights,aed);
- };
+ double epredict(const aed_type2 &aed) const {
+ return kernel.epredict(weights,aed);
+ };
- double fpredict(const fd_type &fdij, const aed_type2 &aedi, const size_t k) const {
- return kernel.fpredict(weights,fdij,aedi,k);
- }
+ double fpredict(const fd_type &fdij, const aed_type2 &aedi, const size_t k) const {
+ return kernel.fpredict(weights,fdij,aedi,k);
+ }
- force_type fpredict(const fd_type &fdij, const aed_type2 &aedi) const {
- return kernel.fpredict(weights,fdij,aedi);
- }
+ force_type fpredict(const fd_type &fdij, const aed_type2 &aedi) const {
+ return kernel.fpredict(weights,fdij,aedi);
+ }
- void train(StDescriptorsDB &st_desc_db, const StructureDB &stdb) {
+ void train(StDescriptorsDB &st_desc_db, const StructureDB &stdb) {
- if(config.template get<bool>("NORM"))
- norm = Normaliser(config,st_desc_db);
+ if(config.template get<bool>("NORM"))
+ norm = Normaliser(config,st_desc_db);
- desmat.build(st_desc_db,stdb);
- train(desmat);
- }
+ desmat.build(st_desc_db,stdb);
+ train(desmat);
+ }
- void train(StructureDB &stdb, DC_Base &dc) {
- int modelN;
- try {
- modelN=config.template get<int>("MODEL",2);
- }
- catch(std::runtime_error &e) {
- // use default model
- modelN=1;
- config.add("MODEL", modelN);
- }
- if (modelN==1)
- train1(stdb,dc);
- else if (modelN==2)
- train2(stdb,dc);
- else
- throw
- std::runtime_error(
- "This KRR implementation does exist: "\
- + std::to_string(modelN)+"\n");
+ void train(StructureDB &stdb, DC_Base &dc) {
+ int modelN;
+ try {
+ modelN=config.template get<int>("MODEL",2);
}
- void train1(StructureDB &stdb, DC_Base &dc) {
- // KRR implementation using EKM
- if(config.template get<bool>("NORM") || kernel.get_label()!="Kern_Linear") {
- // either build basis or prep normaliser
- std::string force=config.template get<std::string>("FORCE");
- std::string stress=config.template get<std::string>("STRESS");
-
- config.remove("FORCE");
- config.remove("STRESS");
- config.add("FORCE", "false");
- config.add("STRESS", "false");
-
- StDescriptorsDB st_desc_db_temp = dc.calc(stdb);
-
- if(config.template get<bool>("NORM")) {
- norm = Normaliser(config);
- norm.learn(st_desc_db_temp);
- norm.normalise(st_desc_db_temp);
- }
-
- config.remove("FORCE");
- config.remove("STRESS");
- config.add("FORCE", force);
- config.add("STRESS", stress);
-
- if (kernel.get_label()!="Kern_Linear") {
- basis.build_random_basis(config.template get<size_t>("SBASIS"),st_desc_db_temp);
- desmat.f.set_basis(basis.b);
- kernel.set_basis(basis.b);
- // to configure ekm, we need basis vectors
- ekm.configure(basis.b);
- }
- }
- desmat.build(stdb,norm,dc);
- train(desmat);
+ catch(std::runtime_error &e) {
+ // use default model
+ modelN=1;
+ config.add("MODEL", modelN);
}
-
- void train2(StructureDB &stdb, DC_Base &dc) {
-
- // NEW (BASIC) IMPLEMENTATION OF KRR //
+ if (modelN==1)
+ train1(stdb,dc);
+ else if (modelN==2)
+ train2(stdb,dc);
+ else
+ throw
+ std::runtime_error(
+ "This KRR implementation does exist: "\
+ + std::to_string(modelN)+"\n");
+ }
+ void train1(StructureDB &stdb, DC_Base &dc) {
+ // KRR implementation using EKM
+ if(config.template get<bool>("NORM") || kernel.get_label()!="Kern_Linear") {
+ // either build basis or prep normaliser
std::string force=config.template get<std::string>("FORCE");
std::string stress=config.template get<std::string>("STRESS");
+
config.remove("FORCE");
config.remove("STRESS");
config.add("FORCE", "false");
config.add("STRESS", "false");
+
StDescriptorsDB st_desc_db_temp = dc.calc(stdb);
+
if(config.template get<bool>("NORM")) {
norm = Normaliser(config);
norm.learn(st_desc_db_temp);
norm.normalise(st_desc_db_temp);
}
+
config.remove("FORCE");
config.remove("STRESS");
config.add("FORCE", force);
config.add("STRESS", stress);
- basis.prep_basis_for_krr(st_desc_db_temp,stdb);
- kernel.set_basis(basis.b);
- M_KRR_Train<K>::train2(basis.b, basis.T);
+
+ if (kernel.get_label()!="Kern_Linear") {
+ basis.build_random_basis(config.template get<size_t>("SBASIS"),st_desc_db_temp);
+ desmat.f.set_basis(basis.b);
+ kernel.set_basis(basis.b);
+ // to configure ekm, we need basis vectors
+ ekm.configure(basis.b);
+ }
}
+ desmat.build(stdb,norm,dc);
+ train(desmat);
+ }
- Structure predict(const Config &c, StDescriptors &std, const Structure &st) {
- if(config.template get<bool>("NORM") && !std.normalised && kernel.get_label()!="Kern_Linear")
- norm.normalise(std);
- return M_Tadah_Base::predict(c,std,st);
+ void train2(StructureDB &stdb, DC_Base &dc) {
+
+ // NEW (BASIC) IMPLEMENTATION OF KRR //
+ std::string force=config.template get<std::string>("FORCE");
+ std::string stress=config.template get<std::string>("STRESS");
+ config.remove("FORCE");
+ config.remove("STRESS");
+ config.add("FORCE", "false");
+ config.add("STRESS", "false");
+ StDescriptorsDB st_desc_db_temp = dc.calc(stdb);
+ if(config.template get<bool>("NORM")) {
+ norm = Normaliser(config);
+ norm.learn(st_desc_db_temp);
+ norm.normalise(st_desc_db_temp);
}
+ config.remove("FORCE");
+ config.remove("STRESS");
+ config.add("FORCE", force);
+ config.add("STRESS", stress);
+ basis.prep_basis_for_krr(st_desc_db_temp,stdb);
+ kernel.set_basis(basis.b);
+ M_KRR_Train<K>::train2(basis.b, basis.T);
+ }
+
+ Structure predict(const Config &c, StDescriptors &std, const Structure &st) {
+ if(config.template get<bool>("NORM") && !std.normalised && kernel.get_label()!="Kern_Linear")
+ norm.normalise(std);
+ return M_Tadah_Base::predict(c,std,st);
+ }
+
+ StructureDB predict(Config &c, const StructureDB &stdb, DC_Base &dc) {
+ return M_Tadah_Base::predict(c,stdb,dc);
+ }
- StructureDB predict(Config &c, const StructureDB &stdb, DC_Base &dc) {
- return M_Tadah_Base::predict(c,stdb,dc);
+ Config get_param_file() {
+ Config c = config;
+ c.remove("ALPHA");
+ c.remove("BETA");
+ c.remove("DBFILE");
+ c.remove("FORCE");
+ c.remove("STRESS");
+ c.remove("VERBOSE");
+ c.add("VERBOSE", 0);
+
+ c.clear_internal_keys();
+ c.remove("MODEL");
+ c.add("MODEL", label);
+ c.add("MODEL", kernel.get_label());
+ int modelN=config.template get<int>("MODEL",2);
+ c.add("MODEL", modelN);
+
+ for (size_t i=0;i<weights.size();++i) {
+ c.add("WEIGHTS", weights(i));
}
- Config get_param_file() {
- Config c = config;
- c.remove("ALPHA");
- c.remove("BETA");
- c.remove("DBFILE");
- c.remove("FORCE");
- c.remove("STRESS");
- c.remove("VERBOSE");
- c.add("VERBOSE", 0);
-
- c.clear_internal_keys();
- c.remove("MODEL");
- c.add("MODEL", label);
- c.add("MODEL", kernel.get_label());
- int modelN=config.template get<int>("MODEL",2);
- c.add("MODEL", modelN);
-
- for (size_t i=0;i<weights.size();++i) {
- c.add("WEIGHTS", weights(i));
+ if(config.template get<bool>("NORM")) {
+ for (size_t i=0;i<norm.mean.size();++i) {
+ c.add("NMEAN", norm.mean[i]);
}
-
- if(config.template get<bool>("NORM")) {
- for (size_t i=0;i<norm.mean.size();++i) {
- c.add("NMEAN", norm.mean[i]);
- }
- for (size_t i=0;i<norm.std_dev.size();++i) {
- c.add("NSTDEV", norm.std_dev[i]);
- }
+ for (size_t i=0;i<norm.std_dev.size();++i) {
+ c.add("NSTDEV", norm.std_dev[i]);
}
- if (kernel.get_label()!="Kern_Linear") {
- // dump basis to the config file file
- // make sure keys are not accidently assigned
- if (c.exist("SBASIS"))
- c.remove("SBASIS");
- if (c.exist("BASIS"))
- c.remove("BASIS");
- c.add("SBASIS", basis.b.cols());
- for (size_t i=0;i<basis.b.cols();++i) {
- for (size_t j=0;j<basis.b.rows();++j) {
- c.add("BASIS", basis.b(j,i));
- }
+ }
+ if (kernel.get_label()!="Kern_Linear") {
+ // dump basis to the config file file
+ // make sure keys are not accidently assigned
+ if (c.exist("SBASIS"))
+ c.remove("SBASIS");
+ if (c.exist("BASIS"))
+ c.remove("BASIS");
+ c.add("SBASIS", basis.b.cols());
+ for (size_t i=0;i<basis.b.cols();++i) {
+ for (size_t j=0;j<basis.b.rows();++j) {
+ c.add("BASIS", basis.b(j,i));
}
}
- return c;
}
- StructureDB predict(Config config_pred, StructureDB &stdb, DC_Base &dc,
- aed_type2 &predicted_error) {
-
- LinearRegressor::read_sigma(config_pred,Sigma);
- DesignMatrix<K> dm(kernel,config_pred);
- dm.scale=false; // do not scale energy, forces and stresses
- dm.build(stdb,norm,dc);
-
- // compute error
- predicted_error = T_MDMT_diag(dm.Phi, Sigma);
- double pmean = sqrt(predicted_error.mean());
-
- // compute energy, forces and stresses
- aed_type2 Tpred = T_dgemv(dm.Phi, weights);
-
- // Construct StructureDB object with predicted values
- StructureDB stdb_;
- stdb_.structures.resize(stdb.size());
- size_t i=0;
- for (size_t s=0; s<stdb.size(); ++s) {
- stdb_(s) = Structure(stdb(s));
-
- stdb_(s).energy = Tpred(i++);
- predicted_error(i) = (sqrt(predicted_error(i))-pmean)/stdb(s).natoms();
- if (config_pred.get<bool>("FORCE")) {
- for (size_t a=0; a<stdb(s).natoms(); ++a) {
- for (size_t k=0; k<3; ++k) {
- stdb_(s).atoms[a].force[k] = Tpred(i++);
- predicted_error(i) = (sqrt(predicted_error(i))-pmean);
- }
+ return c;
+ }
+ StructureDB predict(Config config_pred, StructureDB &stdb, DC_Base &dc,
+ aed_type2 &predicted_error) {
+
+ LinearRegressor::read_sigma(config_pred,Sigma);
+ DesignMatrix<K> dm(kernel,config_pred);
+ dm.scale=false; // do not scale energy, forces and stresses
+ dm.build(stdb,norm,dc);
+
+ // compute error
+ predicted_error = T_MDMT_diag(dm.Phi, Sigma);
+ double pmean = sqrt(predicted_error.mean());
+
+ // compute energy, forces and stresses
+ aed_type2 Tpred = T_dgemv(dm.Phi, weights);
+
+ // Construct StructureDB object with predicted values
+ StructureDB stdb_;
+ stdb_.structures.resize(stdb.size());
+ size_t i=0;
+ for (size_t s=0; s<stdb.size(); ++s) {
+ stdb_(s) = Structure(stdb(s));
+
+ stdb_(s).energy = Tpred(i++);
+ predicted_error(i) = (sqrt(predicted_error(i))-pmean)/stdb(s).natoms();
+ if (config_pred.get<bool>("FORCE")) {
+ for (size_t a=0; a<stdb(s).natoms(); ++a) {
+ for (size_t k=0; k<3; ++k) {
+ stdb_(s).atoms[a].force[k] = Tpred(i++);
+ predicted_error(i) = (sqrt(predicted_error(i))-pmean);
}
}
- if (config_pred.get<bool>("STRESS")) {
- for (size_t x=0; x<3; ++x) {
- for (size_t y=x; y<3; ++y) {
- predicted_error(i) = (sqrt(predicted_error(i))-pmean);
- stdb_(s).stress(x,y) = Tpred(i++);
- if (x!=y)
- stdb_(s).stress(y,x) = stdb_(s).stress(x,y);
- }
+ }
+ if (config_pred.get<bool>("STRESS")) {
+ for (size_t x=0; x<3; ++x) {
+ for (size_t y=x; y<3; ++y) {
+ predicted_error(i) = (sqrt(predicted_error(i))-pmean);
+ stdb_(s).stress(x,y) = Tpred(i++);
+ if (x!=y)
+ stdb_(s).stress(y,x) = stdb_(s).stress(x,y);
}
}
}
- return stdb_;
}
- StructureDB predict(StructureDB &stdb) {
- if(!trained) throw std::runtime_error("This object is not trained!\n\
- Hint: check different predict() methods.");
-
- phi_type &Phi = desmat.Phi;
-
- // compute energy, forces and stresses
- aed_type2 Tpred = T_dgemv(Phi, weights);
-
- double eweightglob=config.template get<double>("EWEIGHT");
- double fweightglob=config.template get<double>("FWEIGHT");
- double sweightglob=config.template get<double>("SWEIGHT");
-
- // Construct StructureDB object with predicted values
- StructureDB stdb_;
- stdb_.structures.resize(stdb.size());
- size_t s=0;
- size_t i=0;
- while (i<Phi.rows()) {
-
- stdb_(s).energy = Tpred(i++)*stdb(s).natoms()/eweightglob/stdb(s).eweight;
- if (config.template get<bool>("FORCE")) {
- stdb_(s).atoms.resize(stdb(s).natoms());
- for (size_t a=0; a<stdb(s).natoms(); ++a) {
- for (size_t k=0; k<3; ++k) {
- stdb_(s).atoms[a].force[k] = Tpred(i++)/fweightglob/stdb(s).fweight;
- }
+ return stdb_;
+ }
+ StructureDB predict(StructureDB &stdb) {
+ if(!trained) throw std::runtime_error("This object is not trained!\n\
+Hint: check different predict() methods.");
+
+ phi_type &Phi = desmat.Phi;
+
+ // compute energy, forces and stresses
+ aed_type2 Tpred = T_dgemv(Phi, weights);
+
+ double eweightglob=config.template get<double>("EWEIGHT");
+ double fweightglob=config.template get<double>("FWEIGHT");
+ double sweightglob=config.template get<double>("SWEIGHT");
+
+ // Construct StructureDB object with predicted values
+ StructureDB stdb_;
+ stdb_.structures.resize(stdb.size());
+ size_t s=0;
+ size_t i=0;
+ while (i<Phi.rows()) {
+
+ stdb_(s).energy = Tpred(i++)*stdb(s).natoms()/eweightglob/stdb(s).eweight;
+ if (config.template get<bool>("FORCE")) {
+ stdb_(s).atoms.resize(stdb(s).natoms());
+ for (size_t a=0; a<stdb(s).natoms(); ++a) {
+ for (size_t k=0; k<3; ++k) {
+ stdb_(s).atoms[a].force[k] = Tpred(i++)/fweightglob/stdb(s).fweight;
}
}
- if (config.template get<bool>("STRESS")) {
- for (size_t x=0; x<3; ++x) {
- for (size_t y=x; y<3; ++y) {
- stdb_(s).stress(x,y) = Tpred(i++)/sweightglob/stdb(s).sweight;
- if (x!=y)
- stdb_(s).stress(y,x) = stdb_(s).stress(x,y);
- }
+ }
+ if (config.template get<bool>("STRESS")) {
+ for (size_t x=0; x<3; ++x) {
+ for (size_t y=x; y<3; ++y) {
+ stdb_(s).stress(x,y) = Tpred(i++)/sweightglob/stdb(s).sweight;
+ if (x!=y)
+ stdb_(s).stress(y,x) = stdb_(s).stress(x,y);
}
}
- s++;
}
- return stdb_;
+ s++;
}
+ return stdb_;
+ }
- private:
- std::string label="M_KRR";
- Basis<K> basis;
- DesignMatrix<K> desmat;
+private:
+ std::string label="M_KRR";
+ Basis<K> basis;
+ DesignMatrix<K> desmat;
- t_type convert_to_nweights(const t_type &weights) const {
- if(kernel.get_label()!="Kern_Linear") {
- throw std::runtime_error("Cannot convert weights to nweights for\n\
- non linear kernel\n");
- }
- t_type kw(weights.rows());
- if(config.template get<bool>("NORM") && kernel.get_label()=="Kern_Linear") {
- // normalise weights such that when predict is called
- // we can supply it with a non-normalised descriptor
- kw.resize(weights.rows());
- kw(0) = weights(0);
- for (size_t i=1; i<weights.size(); ++i) {
+ t_type convert_to_nweights(const t_type &weights) const {
+ if(kernel.get_label()!="Kern_Linear") {
+ throw std::runtime_error("Cannot convert weights to nweights for\n\
+non linear kernel\n");
+ }
+ t_type kw(weights.rows());
+ if(config.template get<bool>("NORM") && kernel.get_label()=="Kern_Linear") {
+ // normalise weights such that when predict is called
+ // we can supply it with a non-normalised descriptor
+ kw.resize(weights.rows());
+ kw(0) = weights(0);
+ for (size_t i=1; i<weights.size(); ++i) {
- if (norm.std_dev[i] > std::numeric_limits<double>::min())
- kw(i) = weights(i) / norm.std_dev[i];
- else
- kw(i) = weights(i);
+ if (norm.std_dev[i] > std::numeric_limits<double>::min())
+ kw(i) = weights(i) / norm.std_dev[i];
+ else
+ kw(i) = weights(i);
- kw(0) -= norm.mean[i]*kw(i);
+ kw(0) -= norm.mean[i]*kw(i);
- }
}
- return kw;
}
- // The opposite of convert_to_nweights()
- t_type convert_to_weights(const t_type &kw) const {
- if(kernel.get_label()!="Kern_Linear") {
- throw std::runtime_error("Cannot convert nweights to weights for\n\
- non linear kernel\n");
- }
- // convert normalised weights back to "normal"
- t_type w(kw.rows());
- w(0) = kw(0);
- for (size_t i=1; i<kw.size(); ++i) {
- if (norm.std_dev[i] > std::numeric_limits<double>::min())
- w(i) = kw(i) * norm.std_dev[i];
- else
- w(i) = kw(i);
+ return kw;
+ }
+ // The opposite of convert_to_nweights()
+ t_type convert_to_weights(const t_type &kw) const {
+ if(kernel.get_label()!="Kern_Linear") {
+ throw std::runtime_error("Cannot convert nweights to weights for\n\
+non linear kernel\n");
+ }
+ // convert normalised weights back to "normal"
+ t_type w(kw.rows());
+ w(0) = kw(0);
+ for (size_t i=1; i<kw.size(); ++i) {
+ if (norm.std_dev[i] > std::numeric_limits<double>::min())
+ w(i) = kw(i) * norm.std_dev[i];
+ else
+ w(i) = kw(i);
- w(0) += kw(i)*norm.mean[i];
- }
- return w;
+ w(0) += kw(i)*norm.mean[i];
}
+ return w;
+ }
- template <typename D>
- void train(D &desmat) {
- // TODO see comments in M_BLR
- phi_type Phi = desmat.Phi;
- t_type T = desmat.T;
- M_KRR_Train<K>::train(Phi,T);
+ template <typename D>
+ void train(D &desmat) {
+ // TODO see comments in M_BLR
+ phi_type Phi = desmat.Phi;
+ t_type T = desmat.T;
+ M_KRR_Train<K>::train(Phi,T);
- if (config.template get<bool>("NORM") &&
- kernel.get_label()=="Kern_Linear") {
- weights = convert_to_nweights(weights);
- }
- }
+ if (config.template get<bool>("NORM") &&
+ kernel.get_label()=="Kern_Linear") {
+ weights = convert_to_nweights(weights);
+ }
+ }
- // Do we want to confuse user with those and make them public?
- // Either way they must be stated as below to silence clang warning
- using M_KRR_Train<K>::predict;
- using M_KRR_Train<K>::train;
- using M_KRR_Train<K>::trained;
- using M_KRR_Train<K>::weights;
- using M_KRR_Train<K>::Sigma;
- using M_KRR_Train<K>::config;
- using M_KRR_Train<K>::kernel;
- using M_KRR_Train<K>::ekm;
+ // Do we want to confuse user with those and make them public?
+ // Either way they must be stated as below to silence clang warning
+ using M_KRR_Train<K>::predict;
+ using M_KRR_Train<K>::train;
+ using M_KRR_Train<K>::trained;
+ using M_KRR_Train<K>::weights;
+ using M_KRR_Train<K>::Sigma;
+ using M_KRR_Train<K>::config;
+ using M_KRR_Train<K>::kernel;
+ using M_KRR_Train<K>::ekm;
};
#endif
diff --git a/include/tadah/mlip/structure.h b/include/tadah/mlip/structure.h
index e9171f6c472c0fd12a984e921e0751937802fa96..1fa835b4a0b852dc47bfc5d2f01e619f167091d7 100644
--- a/include/tadah/mlip/structure.h
+++ b/include/tadah/mlip/structure.h
@@ -109,8 +109,6 @@ struct Structure {
*/
double sweight=1.0;
- /** List of chemical elements in this structure. */
- std::set<Element> unique_elements;
/** @return a reference to the i-th Atom.
*
@@ -271,9 +269,19 @@ struct Structure {
std::vector<Atom>::const_iterator begin() const;
std::vector<Atom>::const_iterator end() const;
+ /** Method to dump class content to a file */
+ void dump_to_file(std::ostream &file, size_t prec=12) const;
+
+ /** Method to dump class content to a file */
+ void dump_to_file(const std::string& filepath, size_t prec=12) const;
+
+ /** List of chemical elements in this structure. */
+ std::set<Element> get_unique_elements() const;
+
private:
const static size_t w=15; // controls output width
const static size_t p=6; // controls output precision
+
};
#endif
diff --git a/include/tadah/mlip/structure_db.h b/include/tadah/mlip/structure_db.h
index 74697d6edb2dc255ab051141ea135e12337348b6..8354890fe31eb3c269ad1f89c04f739a14baf4dc 100644
--- a/include/tadah/mlip/structure_db.h
+++ b/include/tadah/mlip/structure_db.h
@@ -1,6 +1,7 @@
#ifndef STRUCTURE_DB_h
#define STRUCTURE_DB_h
+#include "tadah/core/utils.h"
#include <tadah/core/element.h>
#include <tadah/core/config.h>
#include <tadah/mlip/structure.h>
@@ -39,31 +40,31 @@
*
*/
struct StructureDB {
- std::vector<Structure> structures;
+ std::vector<Structure> structures;
- /** Create an empty StructureDB object. */
- StructureDB();
+ /** Create an empty StructureDB object. */
+ StructureDB();
- /** Create this object and load structures
+ /** Create this object and load structures
* listed in the config file
*
* \note
* Required Config key: \ref DBFILE
*/
- StructureDB(Config &config);
+ StructureDB(Config &config);
- /** Add structures listed in the config file
+ /** Add structures listed in the config file
*
* \note
* Required Config key: \ref DBFILE
*
*/
- void add(Config &config);
+ void add(Config &config);
- /** Add all structures from a file */
- void add(const std::string fn);
+ /** Add all structures from a file */
+ void add(const std::string fn);
- /** Add N structures from a file begining from first index.
+ /** Add N structures from a file begining from first index.
*
* Indexing starts from zero, i.e.
* first=0 corresponds to the first structure in the file.
@@ -73,24 +74,27 @@ struct StructureDB {
*
* Return the number of loaded structures.
*/
- int add(const std::string fn, int first, int N);
+ int add(const std::string fn, size_t first, int N);
- /** Add a single Structure object to this container */
- void add(const Structure &s);
+ /** Add a single Structure object to this container */
+ void add(const Structure &s);
- /** remove i-th Structure object from this container */
- void remove(size_t i);
+ /** Add all structure from other Structure object to this container */
+ void add(const StructureDB &stdb);
- /** \return number of structures held by this object */
- size_t size() const;
+ /** remove i-th Structure object from this container */
+ void remove(size_t i);
- /** \return number of structures in the n-th DBFILE
+ /** \return number of structures held by this object */
+ size_t size() const;
+
+ /** \return number of structures in the n-th DBFILE
*
* n={0,...,number of DBFILEs-1}
*/
- size_t size(size_t n) const;
+ size_t size(size_t n) const;
- /** \return reference to the s-th structure
+ /** \return reference to the s-th structure
*
* Usage example:
*
@@ -98,10 +102,10 @@ struct StructureDB {
* # and bind it to Structure st.
* Structure &st = st(1);
*/
- Structure& operator()(size_t s);
- const Structure& operator()(size_t s) const;
+ Structure& operator()(size_t s);
+ const Structure& operator()(size_t s) const;
- /** \return reference to the a-th atom in the s-th structure
+ /** \return reference to the a-th atom in the s-th structure
*
* Usage example:
*
@@ -109,58 +113,62 @@ struct StructureDB {
* # held by this object and bind it to the atom object.
* Atom &atom = st(2,4);
*/
- Atom& operator()(size_t s, size_t a);
+ Atom& operator()(size_t s, size_t a);
- /** Print this object summary to the stream */
- friend std::ostream& operator<<(std::ostream& os, const StructureDB& stdb)
- {
- os << "# of structures : " << std::left << stdb.structures.size() << std::endl;
- return os;
- }
+ /** Print this object summary to the stream */
+ friend std::ostream& operator<<(std::ostream& os, const StructureDB& stdb)
+ {
+ os << stdb.summary();
+ return os;
+ }
+ std::string summary() const;
- /** Store indices for each dataset.
+ /** Store indices for each dataset.
*
* e.g. if 3 datasets of sizes 11,13,15
* dbidx=={0,11,24,39}
*/
- std::vector<size_t> dbidx;
+ std::vector<size_t> dbidx;
- /** Calculate total number of atoms stored by this object. */
- size_t calc_natoms() const;
+ /** Calculate total number of atoms stored by this object. */
+ size_t calc_natoms() const;
- /** Calculate total number of atoms in the n-th DBFILE.
+ /** Calculate total number of atoms in the n-th DBFILE.
*
* n={0,...,number of DBFILEs-1}
*/
- size_t calc_natoms(size_t n) const;
+ size_t calc_natoms(size_t n) const;
+
+ /** Return unique elements for all Structures. */
+ std::set<Element> get_unique_elements() const;
- /** Return unique elements for all Structures. */
- std::set<Element> get_unique_elements() const;
+ /** Find unique elements in provided Config file */
+ static std::set<Element> find_unique_elements(const Config &c);
- /** Find unique elements in provided Config file */
- static std::set<Element> find_unique_elements(const Config &c);
+ /** Find unique elements in provided file */
+ static std::set<Element> find_unique_elements(const std::string &fn);
- /** Find unique elements in provided file */
- static std::set<Element> find_unique_elements(const std::string &fn);
+ /** Count number of structures and atoms in all datasets from the Config file. */
+ static std::pair<int,int> count(const Config &c);
- /** Count number of structures and atoms in all datasets from the Config file. */
- static std::pair<int,int> count(const Config &c);
+ /** Count number of structures and atoms in a single dataset. */
+ static std::pair<int,int> count(const std::string fn);
- /** Count number of structures and atoms in a single dataset. */
- static std::pair<int,int> count(const std::string fn);
+ void clear_nn();
- void clear_nn();
+ /** Check consistency of the ATOMS key. */
+ static void check_atoms_key(Config &config, std::set<Element> &unique_elements);
- /** Check consistency of the ATOMS key. */
- static void check_atoms_key(Config &config, std::set<Element> &unique_elements);
+ /** Check consistency of the WATOMS key. Add if missing*/
+ static void check_watoms_key(Config &config, std::set<Element> &unique_elements);
- /** Check consistency of the WATOMS key. Add if missing*/
- static void check_watoms_key(Config &config, std::set<Element> &unique_elements);
+ // Methods to enable range-based for loop
+ std::vector<Structure>::iterator begin();
+ std::vector<Structure>::iterator end();
+ std::vector<Structure>::const_iterator begin() const;
+ std::vector<Structure>::const_iterator end() const;
- // Methods to enable range-based for loop
- std::vector<Structure>::iterator begin();
- std::vector<Structure>::iterator end();
- std::vector<Structure>::const_iterator begin() const;
- std::vector<Structure>::const_iterator end() const;
+ /** Method to dump class content to a file */
+ void dump_to_file(const std::string& filepath, size_t prec=12) const;
};
#endif
diff --git a/src/castep_castep_reader.cpp b/src/castep_castep_reader.cpp
index ad07f944a28896b23c3604e9d8c57f016a332a7c..89fed3a698fe276636ae9f808a7e8207adda284d 100644
--- a/src/castep_castep_reader.cpp
+++ b/src/castep_castep_reader.cpp
@@ -11,7 +11,6 @@ CastepCastepReader::CastepCastepReader(StructureDB& db) : DatasetReader(db) {}
CastepCastepReader::CastepCastepReader(StructureDB& db, const std::string& filename)
: DatasetReader(db, filename) {
read_data(filename);
- parse_data();
}
void CastepCastepReader::read_data(const std::string& filename) {
@@ -36,24 +35,52 @@ void CastepCastepReader::parse_data() {
bool stress_tensor_bool = false;
bool constant_volume = false;
bool complete_structure = false;
+ bool md_run = false;
+ bool go_run = false;
+ bool restart = false;
+ int scf_idx = 0;
Structure s;
std::string label;
+ size_t counter=0;
while (std::getline(stream, line)) {
- if (line.find("Unit Cell") != std::string::npos) {
+
+ if (line.find("type of calculation") != std::string::npos) {
+ stress_tensor_bool=false;
+ constant_volume=false;
+ md_run = false;
+ go_run = false;
+ restart=false;
+ if (line.find(": geometry optimization") != std::string::npos) {
+ go_run = true;
+ }
+ if (line.find(": molecular dynamics") != std::string::npos) {
+ md_run = true;
+ }
+ }
+ else if (line.find("Restarting MD") != std::string::npos) {
+ restart=true;
+ }
+ else if (line.find("Unit Cell") != std::string::npos) {
if (!std::getline(stream, line) || !std::getline(stream, line)) {
+ std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
std::cerr << "Warning: Unexpected end of data when reading atom information" << std::endl;
}
+ counter++;
+ counter++;
s = Structure();
for (int i = 0; i < 3; ++i) {
if (!std::getline(stream, line)) {
+ std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
std::cerr << "Warning: Unexpected end of data when reading lattice vectors at row " << i << std::endl;
break;
}
+ counter++;
std::istringstream iss(line);
if (!(iss >> s.cell(0,i) >> s.cell(1,i) >> s.cell(2,i))) {
+ std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
std::cerr << "Warning: Unexpected end of data when reading lattice vectors at row " << i << std::endl;
break;
}
@@ -72,16 +99,16 @@ void CastepCastepReader::parse_data() {
// Process the line to reach the 8th element
while (iss >> temp) {
if (++count == 7 && !(iss >> natoms)) {
+ std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
std::cerr << "Error: Failed to read number of atoms from line: " << line << std::endl;
}
}
// Check if the line was too short
if (count < 7) {
+ std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
std::cerr << "Error: Line is too short to extract total number of ions in a cell. Line: " << line << std::endl;
}
- stress_tensor_bool=false;
- constant_volume=false;
}
else if (line.find("so fixing cell parameters") != std::string::npos) {
@@ -98,25 +125,36 @@ void CastepCastepReader::parse_data() {
label = "CASTEP MD, const. volume: " + oss.str() + ", step: " + step;
}
+
else if (constant_volume && line.find("Cell Contents") != std::string::npos) {
- s = Structure();
- s.cell = stdb.structures.back().cell; // copy last cell as it is not repeated in castep for const. volume
+ if (restart) {
+ s.atoms.clear();
+ } else {
+ s = Structure();
+ s.cell = stdb.structures.back().cell; // copy last cell as it is not repeated in castep for const. volume
+ }
}
else if (line.find("Fractional coordinates of atoms") != std::string::npos) {
if (!std::getline(stream, line) || !std::getline(stream, line)) {
+ std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
std::cerr << "Warning: Unexpected end of data when reading atom information" << std::endl;
}
+ counter++;
+ counter++;
for (size_t i = 0; i < natoms; ++i) {
if (!std::getline(stream, line)) {
+ std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
std::cerr << "Warning: Unexpected end of data when reading atomic coordinates at row " << i << std::endl;
break;
}
+ counter++;
std::istringstream iss(line);
std::string type, tmp;
double px,py,pz;
if (!(iss >> tmp >> type >> tmp >> px >> py >> pz)) {
+ std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
std::cerr << "Warning: Unexpected end of data when reading atomic coordiantes at row " << i << std::endl;
break;
}
@@ -126,18 +164,26 @@ void CastepCastepReader::parse_data() {
}
else if (line.find("Cartesian components (eV/A)") != std::string::npos) {
+ if (s.natoms()!=natoms) continue;
if (!std::getline(stream, line) || !std::getline(stream, line) || !std::getline(stream, line)) {
+ std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
std::cerr << "Warning: Unexpected end of data when reading atom forces" << std::endl;
}
+ counter++;
+ counter++;
+ counter++;
for (size_t i = 0; i < natoms; ++i) {
if (!std::getline(stream, line)) {
+ std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
std::cerr << "Warning: Unexpected end of data when reading atom forces: " << line << std::endl;
break;
}
+ counter++;
std::istringstream iss(line);
std::string tmp;
double fx,fy,fz;
if (!(iss >> tmp >> tmp >> tmp >> fx >> fy >> fz)) {
+ std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
std::cerr << "Warning: Unexpected end of data when reading atom forces: " << line << std::endl;
} else {
s.atoms[i].force = Vec3d(fx,fy,fz);
@@ -147,16 +193,23 @@ void CastepCastepReader::parse_data() {
else if (line.find("Cartesian components (GPa)") != std::string::npos) {
if (!std::getline(stream, line) || !std::getline(stream, line) || !std::getline(stream, line)) {
+ std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
std::cerr << "Warning: Unexpected end of data when reading stress tensor" << std::endl;
}
+ counter++;
+ counter++;
+ counter++;
for (size_t i = 0; i < 3; ++i) {
if (!std::getline(stream, line)) {
+ std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
std::cerr << "Warning: Unexpected end of data when reading stress tensor: " << line << std::endl;
break;
}
+ counter++;
std::istringstream iss(line);
std::string tmp;
if (!(iss >> tmp >> tmp >> s.stress(i,0) >> s.stress(i,1) >> s.stress(i,2))) {
+ std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
std::cerr << "Warning: Unexpected end of data when reading atom forces: " << line << std::endl;
}
}
@@ -170,8 +223,14 @@ void CastepCastepReader::parse_data() {
std::istringstream iss(line);
std::string tmp;
if (!(iss >> tmp >> tmp >> tmp >> tmp >> tmp >> s.energy)) {
+ std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
std::cerr << "Warning: Unexpected end of data when reading total energy" << std::endl;
}
+ // scf only loop
+ if (!md_run && !go_run) {
+ s.label = "SCF run: " + std::to_string(scf_idx++);
+ complete_structure = true;
+ }
}
else if (line.find("enthalpy=") != std::string::npos) {
@@ -190,6 +249,7 @@ void CastepCastepReader::parse_data() {
std::istringstream iss(line);
std::string tmp;
if (!(iss >> tmp >> tmp >> tmp >> s.energy)) {
+ std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
std::cerr << "Warning: Unexpected end of data when reading total energy" << std::endl;
}
@@ -207,12 +267,15 @@ void CastepCastepReader::parse_data() {
stdb.add(s);
complete_structure = false;
}
-
+ counter++;
}
}
void CastepCastepReader::print_summary() const {
- std::cout << stdb;
+ std::cout << get_summary();
}
+std::string CastepCastepReader::get_summary() const {
+ return stdb.summary();
+}
diff --git a/src/castep_md_reader.cpp b/src/castep_md_reader.cpp
index 43809c1383b441354b9e2d10f4f75b556518ca8b..a592172754bda721a102bac7326d85a9c1763d35 100644
--- a/src/castep_md_reader.cpp
+++ b/src/castep_md_reader.cpp
@@ -7,7 +7,6 @@ CastepMDReader::CastepMDReader(StructureDB& db)
CastepMDReader::CastepMDReader(StructureDB& db, const std::string& filename)
: DatasetReader(db, filename) {
read_data(filename);
- parse_data();
}
void CastepMDReader::read_data(const std::string& filename) {
@@ -62,7 +61,16 @@ std::string CastepMDReader::get_first_label(std::string &time) {
+ std::to_string(std::stod(time)*t_conv) + " ps";
}
std::string CastepMDReader::get_label(std::string &time) {
- return "Time: " + std::to_string(std::stod(time)*t_conv) + " ps";
+ try {
+ return "Time: " + std::to_string(std::stod(time)*t_conv) + " ps";
+ } catch (const std::invalid_argument& e) {
+ std::cerr << "Warning: " << filename << std::endl;
+ std::cerr << "Invalid argument: unable to convert to double: " << time << std::endl;
+ } catch (const std::out_of_range& e) {
+ std::cerr << "Warning: " << filename << std::endl;
+ std::cerr << "Out of range: string represents a value too large: " << time << std::endl;
+ }
+ return "Time: FAIL" ;
}
void CastepMDReader::parse_data() {
@@ -80,41 +88,72 @@ void CastepMDReader::parse_data() {
while (std::getline(stream, line)) {
std::istringstream iss(line);
if (ends_with(line,"<-- E")) {
- s.label = get_first_label(time);
iss >> s.energy;
s.energy *= e_conv;
break;
}
iss >> time;
}
+ bool error=false;
+ //bool T_flag=false;
+ bool E_flag=false;
+ int H_flag=0;
+ int S_flag=0;
+ bool R_flag=false;
+ bool F_flag=false;
+ bool complete_structure=false;
while (std::getline(stream, line)) {
if (ends_with(line,"<-- T")) {
+ if (/* T_flag || */ complete_structure) {
+ error=true;
+ continue;
+ }
std::istringstream iss(line);
iss >> T;
+ //T_flag=true;
}
else if (ends_with(line,"<-- E")) {
+ if (/* T_flag || */ E_flag || complete_structure) {
+ error=true;
+ continue;
+ }
std::istringstream iss(line);
iss >> s.energy;
s.energy *= e_conv;
+ E_flag=true;
}
else if (ends_with(line,"<-- h")) {
// the current matrix of cell vectors
+ if (/* !T_flag || */ !E_flag || H_flag==3 || complete_structure) {
+ error=true;
+ continue;
+ }
std::istringstream iss(line);
if (!(iss >> s.cell(0,cell_idx) >> s.cell(1,cell_idx) >> s.cell(2,cell_idx)))
std::cerr << "Warning: Unexpected end of data when reading lattice vectors at row " << cell_idx << std::endl;
cell_idx++;
+ H_flag++;
}
else if (ends_with(line,"<-- S")) {
// The full pressure tensor (including kinetic contributions)
+ if (/* !T_flag || */ !E_flag || H_flag!=3 || S_flag==3 || complete_structure) {
+ error=true;
+ continue;
+ }
std::istringstream iss(line);
if (!(iss >> s.stress(0,stress_idx) >> s.stress(1,stress_idx) >> s.stress(2,stress_idx)))
std::cerr << "Warning: Unexpected end of data when reading stress tensor at row " << stress_idx << std::endl;
stress_idx++;
stress_tensor_bool = true;
+ S_flag++;
}
else if (ends_with(line,"<-- R")) {
+ if (/* !T_flag || */ !E_flag || H_flag!=3 || F_flag || complete_structure) {
+ error=true;
+ continue;
+ }
// First the position vectors of all ions are printed with the label <-- R.
std::string element;
int temp;
@@ -123,8 +162,13 @@ void CastepMDReader::parse_data() {
if (!(iss >> element >> temp >> px >> py >> pz))
std::cerr << "Warning: Unexpected end of data when reading atomic positions:\n" << line << std::endl;
s.add_atom(Atom(Element(element),px*d_conv,py*d_conv,pz*d_conv,0,0,0));
+ R_flag=true;
}
else if (ends_with(line,"<-- F")) {
+ if (/* !T_flag || */ !E_flag || H_flag!=3 || !R_flag || force_idx==s.natoms() || complete_structure) {
+ error=true;
+ continue;
+ }
std::string element;
int temp;
double fx, fy, fz;
@@ -135,15 +179,28 @@ void CastepMDReader::parse_data() {
s.atoms[force_idx].force[1]=fy*f_conv;
s.atoms[force_idx].force[2]=fz*f_conv;
force_idx++;
+ F_flag=true;
+ if (force_idx==s.natoms()) complete_structure=true;
}
else if (is_blank_line(line)) {
- postproc_structure(s);
+ if (!error && complete_structure)
+ postproc_structure(s);
+
+ error=false;
+ //T_flag=false;
+ E_flag=false;
+ H_flag=0;
+ S_flag=0;
+ R_flag=false;
+ F_flag=false;
+ complete_structure=false;
+
if (std::getline(stream, line)) {
std::string time;
std::istringstream iss(line);
iss >> time;
- s.label = get_label(time);
+ s.label = !stdb.size() ? get_first_label(time) : get_label(time);
}
cell_idx=0;
@@ -154,11 +211,15 @@ void CastepMDReader::parse_data() {
}
// in case there is no blank line at the end we have to add last strcuture here
- if (s.natoms()) {
+ if (s.natoms() && !error && complete_structure) {
postproc_structure(s);
}
}
void CastepMDReader::print_summary() const {
- std::cout << stdb;
+ std::cout << get_summary();
+}
+
+std::string CastepMDReader::get_summary() const {
+ return stdb.summary();
}
diff --git a/src/dataset_reader.cpp b/src/dataset_reader.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..048bbd6b1481a5f76ec8306541b701b6dd259a68
--- /dev/null
+++ b/src/dataset_reader.cpp
@@ -0,0 +1,4 @@
+#include <tadah/mlip/dataset_readers/dataset_reader.h>
+
+std::string DatasetReader::get_first_label(std::string &) { return std::string(); }
+std::string DatasetReader::get_label(std::string &) { return std::string(); }
diff --git a/src/dataset_reader_selector.cpp b/src/dataset_reader_selector.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..bdc6d2004520d482132c70e7627dd562d7cef1ee
--- /dev/null
+++ b/src/dataset_reader_selector.cpp
@@ -0,0 +1,62 @@
+#include <tadah/mlip/dataset_readers/dataset_reader_selector.h>
+#include <tadah/mlip/dataset_readers/castep_castep_reader.h>
+#include <tadah/mlip/dataset_readers/castep_md_reader.h>
+#include <tadah/mlip/dataset_readers/castep_geom_reader.h>
+#include <tadah/mlip/dataset_readers/vasp_outcar_reader.h>
+#include <tadah/mlip/dataset_readers/vasp_vasprun_reader.h>
+
+#include <fstream>
+#include <iostream>
+
+// Factory method implementation
+std::unique_ptr<DatasetReader> DatasetReaderSelector::get_reader(const std::string& filepath, StructureDB& db) {
+
+ std::string type = determine_file_type_by_content(filepath);
+
+ if (type == "CASTEP.CASTEP") {
+ return std::make_unique<CastepCastepReader>(db,filepath);
+ } else if (type == "CASTEP.MD") {
+ return std::make_unique<CastepMDReader>(db,filepath);
+ } else if (type == "CASTEP.GEOM") {
+ return std::make_unique<CastepGeomReader>(db,filepath);
+ } else if (type == "VASP.VASPRUN") {
+ return std::make_unique<VaspVasprunReader>(db,filepath);
+ } else if (type == "VASP.OUTCAR") {
+ return std::make_unique<VaspOutcarReader>(db,filepath);
+ } else {
+ std::cerr << "Unknown type! Returning nullptr." << std::endl;
+ return nullptr;
+ }
+
+}
+
+// Function to determine the file type based on content
+std::string DatasetReaderSelector::determine_file_type_by_content(const std::string& filepath) {
+ std::ifstream file(filepath);
+ if (!file.is_open()) {
+ std::cerr << "Could not open file: " << filepath << std::endl;
+ return "Unknown file type";
+ }
+
+ std::string line;
+ while (std::getline(file, line)) {
+
+ if (line.find("vasp") != std::string::npos) {
+ if (line.find("incar:") != std::string::npos || line.find("outcar") != std::string::npos) {
+ return "VASP.OUTCAR";
+ } else if (line.find("<modeling>") != std::string::npos || line.find("<calculation>") != std::string::npos) {
+ return "VASP.VASPRUN";
+ }
+ }
+ else if (line.find("<-- c") != std::string::npos) {
+ return "CASTEP.GEOM";
+ } else if (line.find("<-- E") != std::string::npos) {
+ // <-- E is also in .geom but .geom has <-- c before <-- E
+ return "CASTEP.MD";
+ } else if (line.find("Unit Cell") != std::string::npos) {
+ return "CASTEP.CASTEP";
+ }
+ }
+
+ return "Unknown file type";
+}
diff --git a/src/dm_bf_linear.cpp b/src/dm_bf_linear.cpp
index f04f66e4921900f8ec3dea20e5c5adae8bc3fd1d..ab467e8c4ba7eb31f43ab3cdc26ec860061b312a 100644
--- a/src/dm_bf_linear.cpp
+++ b/src/dm_bf_linear.cpp
@@ -44,6 +44,7 @@ void DM_BF_Linear::calc_phi_force_rows(phi_type &Phi, size_t &row,
void DM_BF_Linear::calc_phi_stress_rows(phi_type &Phi, size_t &row,
const double fac[6], const Structure &st, const StDescriptors &st_d)
{
+ double V_inv = 1/st.get_volume();
for (size_t i=0; i<st.natoms(); ++i) {
const Vec3d &ri = st(i).position;
for (size_t jj=0; jj<st_d.fd[i].size(); ++jj) {
@@ -56,7 +57,7 @@ void DM_BF_Linear::calc_phi_stress_rows(phi_type &Phi, size_t &row,
for (size_t x=0; x<3; ++x) {
for (size_t y=x; y<3; ++y) {
for (size_t d=0; d<fdij.rows(); ++d) {
- Phi(row+mn,d) += (fdij(d,y)-fdji(d,y))*0.5*fac[mn]*(ri(x)-rj(x));
+ Phi(row+mn,d) += V_inv*(fdij(d,y)-fdji(d,y))*0.5*fac[mn]*(ri(x)-rj(x));
}
mn++;
}
diff --git a/src/dm_bf_polynomial2.cpp b/src/dm_bf_polynomial2.cpp
index 51c3f561ce32df7c67017f379ec9f76a5eb3f123..6638fdb19ce46998b511e14e90b8b0b0f2f51c0f 100644
--- a/src/dm_bf_polynomial2.cpp
+++ b/src/dm_bf_polynomial2.cpp
@@ -64,6 +64,7 @@ void DM_BF_Polynomial2::calc_phi_stress_rows(phi_type &Phi,
const Structure &st,
const StDescriptors &st_d)
{
+ double V_inv = 1/st.get_volume();
for (size_t a=0; a<st.natoms(); ++a) {
const Vec3d &ri = st(a).position;
const aed_type2& aedi = st_d.get_aed(a);
@@ -80,7 +81,7 @@ void DM_BF_Polynomial2::calc_phi_stress_rows(phi_type &Phi,
size_t b=0;
for (size_t i=0; i<fdij.rows(); ++i) {
for (size_t ii=i; ii<fdij.rows(); ++ii) {
- Phi(row+mn,b) += 0.5*fac[mn]*(ri(x)-rj(x))
+ Phi(row+mn,b) += V_inv*0.5*fac[mn]*(ri(x)-rj(x))
*(fdij(i,y)*aedi(ii) + fdij(ii,y)*aedi(i)
- fdji(i,y)*aedj(ii) - fdji(ii,y)*aedj(i));
b++;
diff --git a/src/dm_kern_base.cpp b/src/dm_kern_base.cpp
index 92d62af48cb6227225fd049ada42970b2bfed683..ecf679c39ad18a36219dc36aa0aa3de34cb80c95 100644
--- a/src/dm_kern_base.cpp
+++ b/src/dm_kern_base.cpp
@@ -3,64 +3,65 @@
DM_Kern_Base::~DM_Kern_Base() {}
size_t DM_Kern_Base::get_phi_cols(const Config &)
{
- return basis.cols();
+ return basis.cols();
}
void DM_Kern_Base::calc_phi_energy_row(phi_type &Phi, size_t &row, const double fac,
- const Structure &, const StDescriptors &st_d)
+ const Structure &, const StDescriptors &st_d)
{
- for (size_t a=0; a<st_d.naed();++a) {
- for (size_t b=0; b<basis.cols(); ++b) {
- Phi(row,b) += (*this)(basis.col(b),st_d.get_aed(a))*fac;
- }
+ for (size_t a=0; a<st_d.naed();++a) {
+ for (size_t b=0; b<basis.cols(); ++b) {
+ Phi(row,b) += (*this)(basis.col(b),st_d.get_aed(a))*fac;
}
- row++;
- //Phi.row(row++) *= fac;
+ }
+ row++;
+ //Phi.row(row++) *= fac;
}
void DM_Kern_Base::calc_phi_force_rows(phi_type &Phi, size_t &row, const double fac,
- const Structure &st, const StDescriptors &st_d) {
- for (size_t i=0; i<st.natoms(); ++i) {
- const aed_type2& aedi = st_d.get_aed(i);
- for (size_t jj=0; jj<st_d.fd[i].size(); ++jj) {
- size_t j=st.near_neigh_idx[i][jj];
- size_t ii = st.get_nn_iindex(i,j,jj);
- const fd_type &fdji = st_d.fd[j][ii];
- const fd_type &fdij = st_d.fd[i][jj];
- const aed_type2& aedj = st_d.get_aed(j);
- for (size_t b=0; b<basis.cols(); ++b) {
- for (size_t k=0; k<3; ++k) {
- Phi(row+k,b) -= fac*((*this).prime(basis.col(b), aedi,fdij(k)) -
- (*this).prime(basis.col(b),aedj,fdji(k)));
- }
- }
+ const Structure &st, const StDescriptors &st_d) {
+ for (size_t i=0; i<st.natoms(); ++i) {
+ const aed_type2& aedi = st_d.get_aed(i);
+ for (size_t jj=0; jj<st_d.fd[i].size(); ++jj) {
+ size_t j=st.near_neigh_idx[i][jj];
+ size_t ii = st.get_nn_iindex(i,j,jj);
+ const fd_type &fdji = st_d.fd[j][ii];
+ const fd_type &fdij = st_d.fd[i][jj];
+ const aed_type2& aedj = st_d.get_aed(j);
+ for (size_t b=0; b<basis.cols(); ++b) {
+ for (size_t k=0; k<3; ++k) {
+ Phi(row+k,b) -= fac*((*this).prime(basis.col(b), aedi,fdij(k)) -
+ (*this).prime(basis.col(b),aedj,fdji(k)));
}
- row+=3;
+ }
}
+ row+=3;
+ }
}
void DM_Kern_Base::calc_phi_stress_rows(phi_type &Phi, size_t &row, const double fac[6],
- const Structure &st, const StDescriptors &st_d)
+ const Structure &st, const StDescriptors &st_d)
{
- for (size_t i=0; i<st.natoms(); ++i) {
- const Vec3d &ri = st(i).position;
- const aed_type2& aedi = st_d.get_aed(i);
- for (size_t jj=0; jj<st_d.fd[i].size(); ++jj) {
- size_t j=st.near_neigh_idx[i][jj];
- size_t ii = st.get_nn_iindex(i,j,jj);
- const fd_type &fdji = st_d.fd[j][ii];
- const fd_type &fdij = st_d.fd[i][jj];
- const aed_type2& aedj = st_d.get_aed(j);
- const Vec3d &rj = st.nn_pos(i,jj);
- size_t mn=0;
- for (size_t x=0; x<3; ++x) {
- for (size_t y=x; y<3; ++y) {
- for (size_t b=0; b<basis.cols(); ++b) {
- Phi(row+mn,b) += 0.5*fac[mn]*(ri(x)-rj(x))*
- ((*this).prime(basis.col(b),aedi,fdij(y)) -
- (*this).prime(basis.col(b),aedj,fdji(y)));
- }
- mn++;
- }
- }
+ double V_inv = 1/st.get_volume();
+ for (size_t i=0; i<st.natoms(); ++i) {
+ const Vec3d &ri = st(i).position;
+ const aed_type2& aedi = st_d.get_aed(i);
+ for (size_t jj=0; jj<st_d.fd[i].size(); ++jj) {
+ size_t j=st.near_neigh_idx[i][jj];
+ size_t ii = st.get_nn_iindex(i,j,jj);
+ const fd_type &fdji = st_d.fd[j][ii];
+ const fd_type &fdij = st_d.fd[i][jj];
+ const aed_type2& aedj = st_d.get_aed(j);
+ const Vec3d &rj = st.nn_pos(i,jj);
+ size_t mn=0;
+ for (size_t x=0; x<3; ++x) {
+ for (size_t y=x; y<3; ++y) {
+ for (size_t b=0; b<basis.cols(); ++b) {
+ Phi(row+mn,b) += V_inv*0.5*fac[mn]*(ri(x)-rj(x))*
+ ((*this).prime(basis.col(b),aedi,fdij(y)) -
+ (*this).prime(basis.col(b),aedj,fdji(y)));
+ }
+ mn++;
}
+ }
}
- row+=6;
+ }
+ row+=6;
}
diff --git a/src/dm_kern_linear.cpp b/src/dm_kern_linear.cpp
index c04a361d072d474389ef8b0bcbdee9cc25340ba2..90f97a7eda24374a7bad06a72f926a97c67370fe 100644
--- a/src/dm_kern_linear.cpp
+++ b/src/dm_kern_linear.cpp
@@ -8,61 +8,62 @@ DM_Kern_Linear::DM_Kern_Linear (const Config &c): Kern_Linear(c)
{}
size_t DM_Kern_Linear::get_phi_cols(const Config &config)
{
- size_t cols = config.get<size_t>("DSIZE");
- return cols;
+ size_t cols = config.get<size_t>("DSIZE");
+ return cols;
}
void DM_Kern_Linear::calc_phi_energy_row(phi_type &Phi, size_t &row,
- const double fac, const Structure &, const StDescriptors &st_d)
+ const double fac, const Structure &, const StDescriptors &st_d)
{
- for (size_t a=0; a<st_d.naed();++a) {
- const aed_type2 &aed = st_d.get_aed(a); // TODO
- for (size_t j=0; j<aed.size(); ++j) {
- Phi(row,j)+=aed[j]*fac;
- }
+ for (size_t a=0; a<st_d.naed();++a) {
+ const aed_type2 &aed = st_d.get_aed(a); // TODO
+ for (size_t j=0; j<aed.size(); ++j) {
+ Phi(row,j)+=aed[j]*fac;
}
- row++;
+ }
+ row++;
}
void DM_Kern_Linear::calc_phi_force_rows(phi_type &Phi, size_t &row,
- const double fac, const Structure &st, const StDescriptors &st_d)
+ const double fac, const Structure &st, const StDescriptors &st_d)
{
- for (size_t a=0; a<st.natoms(); ++a) {
- for (size_t jj=0; jj<st_d.fd[a].size(); ++jj) {
- const size_t j=st.near_neigh_idx[a][jj];
- const size_t aa = st.get_nn_iindex(a,j,jj);
- for (size_t k=0; k<3; ++k) {
- aed_type2 temp = (st_d.fd[a][jj](k)-
- st_d.fd[j][aa](k))*fac;
- for (size_t d=0; d<temp.size(); ++d) {
- Phi(row+k,d) -= temp[d];
- }
- }
+ for (size_t a=0; a<st.natoms(); ++a) {
+ for (size_t jj=0; jj<st_d.fd[a].size(); ++jj) {
+ const size_t j=st.near_neigh_idx[a][jj];
+ const size_t aa = st.get_nn_iindex(a,j,jj);
+ for (size_t k=0; k<3; ++k) {
+ aed_type2 temp = (st_d.fd[a][jj](k)-
+ st_d.fd[j][aa](k))*fac;
+ for (size_t d=0; d<temp.size(); ++d) {
+ Phi(row+k,d) -= temp[d];
}
- row+=3;
+ }
}
+ row+=3;
+ }
}
void DM_Kern_Linear::calc_phi_stress_rows(phi_type &Phi, size_t &row,
- const double fac[6], const Structure &st, const StDescriptors &st_d)
+ const double fac[6], const Structure &st, const StDescriptors &st_d)
{
- for (size_t i=0; i<st.natoms(); ++i) {
- const Vec3d &ri = st(i).position;
- for (size_t jj=0; jj<st_d.fd[i].size(); ++jj) {
- const size_t j=st.near_neigh_idx[i][jj];
- const size_t ii = st.get_nn_iindex(i,j,jj);
- const fd_type &fdij = st_d.fd[i][jj];
- const fd_type &fdji = st_d.fd[j][ii];
- const Vec3d &rj = st.nn_pos(i,jj);
- size_t mn=0;
- for (size_t x=0; x<3; ++x) {
- for (size_t y=x; y<3; ++y) {
- aed_type2 temp = (fdij(y)-fdji(y))*0.5*fac[mn]*(ri(x)-rj(x));
- for (size_t d=0; d<temp.size(); ++d) {
- Phi(row+mn,d) += temp[d];
- }
- mn++;
- }
- }
+ double V_inv = 1/st.get_volume();
+ for (size_t i=0; i<st.natoms(); ++i) {
+ const Vec3d &ri = st(i).position;
+ for (size_t jj=0; jj<st_d.fd[i].size(); ++jj) {
+ const size_t j=st.near_neigh_idx[i][jj];
+ const size_t ii = st.get_nn_iindex(i,j,jj);
+ const fd_type &fdij = st_d.fd[i][jj];
+ const fd_type &fdji = st_d.fd[j][ii];
+ const Vec3d &rj = st.nn_pos(i,jj);
+ size_t mn=0;
+ for (size_t x=0; x<3; ++x) {
+ for (size_t y=x; y<3; ++y) {
+ aed_type2 temp = V_inv*(fdij(y)-fdji(y))*0.5*fac[mn]*(ri(x)-rj(x));
+ for (size_t d=0; d<temp.size(); ++d) {
+ Phi(row+mn,d) += temp[d];
+ }
+ mn++;
}
+ }
}
- row += 6;
+ }
+ row += 6;
}
diff --git a/src/dm_kern_lq.cpp b/src/dm_kern_lq.cpp
index 0333db06a7ce4a9c9113e4b484bc1dc007d43db4..3c14dfaad5465facd3ef725b13d7a323fd29f7b0 100644
--- a/src/dm_kern_lq.cpp
+++ b/src/dm_kern_lq.cpp
@@ -4,8 +4,8 @@
//CONFIG::Registry<DM_Function_Base,Config&>::Register<DM_Kern_LQ> DM_Kern_LQ_2( "Kern_LQ" );
DM_Kern_LQ::DM_Kern_LQ():
- Kern_LQ()
+ Kern_LQ()
{}
DM_Kern_LQ::DM_Kern_LQ(const Config &c):
- Kern_LQ(c)
+ Kern_LQ(c)
{}
diff --git a/src/dm_kern_polynomial.cpp b/src/dm_kern_polynomial.cpp
index b5fccbd4ab82ae3c397a002abcdadddeacb582c8..b60e9d913d808a63f48a6bb76cbb2547888b3500 100644
--- a/src/dm_kern_polynomial.cpp
+++ b/src/dm_kern_polynomial.cpp
@@ -4,8 +4,8 @@
//CONFIG::Registry<DM_Function_Base,Config&>::Register<DM_Kern_Polynomial> DM_Kern_Polynomial_2( "Kern_Polynomial" );
DM_Kern_Polynomial::DM_Kern_Polynomial():
- Kern_Polynomial()
+ Kern_Polynomial()
{}
DM_Kern_Polynomial::DM_Kern_Polynomial(const Config &c):
- Kern_Polynomial(c)
+ Kern_Polynomial(c)
{}
diff --git a/src/dm_kern_quadratic.cpp b/src/dm_kern_quadratic.cpp
index 402c7771f57933a289a08802eddc6de1ad79ddfb..83a71981b1312f04f7c713d21f1e4ac546402d08 100644
--- a/src/dm_kern_quadratic.cpp
+++ b/src/dm_kern_quadratic.cpp
@@ -4,8 +4,8 @@
//CONFIG::Registry<DM_Function_Base,Config&>::Register<DM_Kern_Quadratic> DM_Kern_Quadratic_2( "Kern_Quadratic" );
DM_Kern_Quadratic::DM_Kern_Quadratic():
- Kern_Quadratic()
+ Kern_Quadratic()
{}
DM_Kern_Quadratic::DM_Kern_Quadratic(const Config &c):
- Kern_Quadratic(c)
+ Kern_Quadratic(c)
{}
diff --git a/src/dm_kern_rbf.cpp b/src/dm_kern_rbf.cpp
index 7ff05ef7af2d432ef6a82e33d1118c1d1ae31374..1870190d591d2c0df7b88acadbcd00f9b5839326 100644
--- a/src/dm_kern_rbf.cpp
+++ b/src/dm_kern_rbf.cpp
@@ -4,8 +4,8 @@
//CONFIG::Registry<DM_Function_Base,Config&>::Register<DM_Kern_RBF> DM_Kern_RBF_2( "Kern_RBF" );
DM_Kern_RBF::DM_Kern_RBF():
- Kern_RBF()
+ Kern_RBF()
{}
DM_Kern_RBF::DM_Kern_RBF(const Config &c):
- Kern_RBF(c)
+ Kern_RBF(c)
{}
diff --git a/src/dm_kern_sigmoid.cpp b/src/dm_kern_sigmoid.cpp
index d1fb598553daa2c9fb695f2da49c3393e246ed6e..2da37c905a1be2f801beafd7ed9bbcbd83f99295 100644
--- a/src/dm_kern_sigmoid.cpp
+++ b/src/dm_kern_sigmoid.cpp
@@ -4,8 +4,8 @@
//CONFIG::Registry<DM_Function_Base,Config&>::Register<DM_Kern_Sigmoid> DM_Kern_Sigmoid_2( "Kern_Sigmoid" );
DM_Kern_Sigmoid::DM_Kern_Sigmoid():
- Kern_Sigmoid()
+ Kern_Sigmoid()
{}
DM_Kern_Sigmoid::DM_Kern_Sigmoid(const Config &c):
- Kern_Sigmoid(c)
+ Kern_Sigmoid(c)
{}
diff --git a/src/m_tadah_base.cpp b/src/m_tadah_base.cpp
index 11cac065b7dff94a3c0eb954d44c95b9c88ab74c..66a70b0747838608dceb6505fbefeb4caa328e37 100644
--- a/src/m_tadah_base.cpp
+++ b/src/m_tadah_base.cpp
@@ -63,7 +63,9 @@ predict(const Config &c, StDescriptorsDB &st_desc_db, const StructureDB &stdb)
{
StructureDB stdb_;
stdb_.structures.resize(stdb.size());
+#ifdef _OPENMP
#pragma omp parallel for
+#endif
for (size_t i=0; i<stdb.size(); ++i) {
stdb_(i) = predict(c,st_desc_db(i), stdb(i));
}
@@ -75,7 +77,9 @@ predict(Config &c, const StructureDB &stdb, DC_Base &dc)
{
StructureDB stdb_;
stdb_.structures.resize(stdb.size());
+#ifdef _OPENMP
#pragma omp parallel for
+#endif
for (size_t i=0; i<stdb.size(); ++i) {
StDescriptors st_d = dc.calc(stdb(i));
stdb_(i) = predict(c,st_d, stdb(i));
@@ -105,6 +109,7 @@ void M_Tadah_Base::
spredict(const size_t a, stress_type &s,
const StDescriptors &std, const Structure &st)
{
+ double V_inv = 1/st.get_volume();
const Vec3d &ri = st.atoms[a].position;
const aed_type2 &aedi = std.get_aed(a);
for (size_t jj=0; jj<st.nn_size(a); ++jj) {
@@ -122,7 +127,7 @@ spredict(const size_t a, stress_type &s,
// resutling from the pairwise i-j interaction.
for (size_t x=0; x<3; ++x) {
for (size_t y=x; y<3; ++y) {
- s(x,y) -= 0.5*(ri[x]-rj[x])*(fij[y]-fji[y]);
+ s(x,y) -= V_inv*0.5*(ri[x]-rj[x])*(fij[y]-fji[y]);
}
}
}
diff --git a/src/nn_finder.cpp b/src/nn_finder.cpp
index 9c41cb4d4fbe4713447c104111ecbf7fc5e8bfdf..c2840d9cd04d2265724e183075f772b6d8f2819c 100644
--- a/src/nn_finder.cpp
+++ b/src/nn_finder.cpp
@@ -72,7 +72,9 @@ void NNFinder::calc(Structure &st) {
}
}
void NNFinder::calc(StructureDB &stdb) {
+#ifdef _OPENMP
#pragma omp parallel for
+#endif
for (size_t s=0; s<stdb.size(); ++s) {
calc(stdb(s));
}
diff --git a/src/structure.cpp b/src/structure.cpp
index 4c923ac9966a283dcca399b05f5ba3a1e363e98d..4aa06757172e37fc6e5ac39e66845846f5d99222 100644
--- a/src/structure.cpp
+++ b/src/structure.cpp
@@ -87,7 +87,6 @@ int Structure::read(std::ifstream &ifs) {
std::istringstream tmp(line);
tmp >> symbol >> px >> py >> pz >> fx >> fy >> fz;
Element e = PeriodicTable::find_by_symbol(symbol);
- unique_elements.insert(e);
atoms.push_back(Atom(e,px,py,pz,fx,fy,fz));
//Atom &a = atoms.back();
@@ -241,3 +240,57 @@ std::vector<Atom>::const_iterator Structure::begin() const {
std::vector<Atom>::const_iterator Structure::end() const {
return atoms.cend();
}
+void Structure::dump_to_file(std::ostream& file, size_t prec) const {
+ const int n = 5;
+ file << label << std::endl;
+ file << std::fixed << std::setprecision(prec);
+ file << eweight << " " << fweight << " " << sweight << std::endl;
+ file << energy << std::endl;
+
+ file
+ << std::setw(prec+n) << cell(0,0) << " "
+ << std::setw(prec+n) << cell(0,1) << " "
+ << std::setw(prec+n) << cell(0,2) << " " << std::endl
+ << std::setw(prec+n) << cell(1,0) << " "
+ << std::setw(prec+n) << cell(1,1) << " "
+ << std::setw(prec+n) << cell(1,2) << " " << std::endl
+ << std::setw(prec+n) << cell(2,0) << " "
+ << std::setw(prec+n) << cell(2,1) << " "
+ << std::setw(prec+n) << cell(2,2) << " " << std::endl;
+
+ file
+ << std::setw(prec+n) << stress(0,0) << " "
+ << std::setw(prec+n) << stress(0,1) << " "
+ << std::setw(prec+n) << stress(0,2) << " " << std::endl
+ << std::setw(prec+n) << stress(1,0) << " "
+ << std::setw(prec+n) << stress(1,1) << " "
+ << std::setw(prec+n) << stress(1,2) << " " << std::endl
+ << std::setw(prec+n) << stress(2,0) << " "
+ << std::setw(prec+n) << stress(2,1) << " "
+ << std::setw(prec+n) << stress(2,2) << " " << std::endl;
+
+ for (const auto& a : atoms) {
+ file << std::setw(2) << a.symbol << " "
+ << std::setw(prec+n) << a.position[0] << " "
+ << std::setw(prec+n) << a.position[1] << " "
+ << std::setw(prec+n) << a.position[2] << " "
+ << std::setw(prec+n) << a.force[0] << " "
+ << std::setw(prec+n) << a.force[1] << " "
+ << std::setw(prec+n) << a.force[2] << std::endl;
+ }
+ file << std::endl;
+}
+void Structure::dump_to_file(const std::string& filepath, size_t prec) const {
+ std::ofstream file(filepath, std::ios::app); // Open in append mode
+ if (!file.is_open()) {
+ std::cerr << "Error: Could not open file for writing: " << filepath << std::endl;
+ return;
+ }
+ dump_to_file(file,prec);
+ file.close();
+}
+std::set<Element> Structure::get_unique_elements() const{
+ std::set<Element> unique_elements;
+ for (const auto& a:atoms) unique_elements.insert(a);
+ return unique_elements;
+}
diff --git a/src/structure_db.cpp b/src/structure_db.cpp
index 08caaffbb156c3b4967c53675ab1515c3822fbf0..384e0a7a563514c4188f76f2f9a762a9b28ff572 100644
--- a/src/structure_db.cpp
+++ b/src/structure_db.cpp
@@ -1,3 +1,4 @@
+#include "tadah/core/element.h"
#include <tadah/mlip/structure_db.h>
#include <tadah/core/periodic_table.h>
#include <cstdio>
@@ -27,7 +28,7 @@ void StructureDB::add(const std::string fn) {
}
ifs.close();
}
-int StructureDB::add(const std::string fn, int first, int N) {
+int StructureDB::add(const std::string fn, size_t first, int N) {
std::ifstream ifs(fn);
if (!ifs.is_open()) {
throw std::runtime_error("DBFILE does not exist: "+fn);
@@ -57,6 +58,9 @@ int StructureDB::add(const std::string fn, int first, int N) {
void StructureDB::add(const Structure &s) {
structures.push_back(s);
}
+void StructureDB::add(const StructureDB &stdb) {
+ for (const auto &s: stdb) add(s);
+}
void StructureDB::remove(size_t i) {
structures.erase(structures.begin()+i);
@@ -105,8 +109,10 @@ size_t StructureDB::calc_natoms(size_t n) const {
}
std::set<Element> StructureDB::get_unique_elements() const {
std::set<Element> s;
- for (const auto & st: structures) s.insert(
- st.unique_elements.begin(),st.unique_elements.end());
+ for (const auto & st: structures) {
+ std::set<Element> u = st.get_unique_elements();
+ s.insert(u.cbegin(),u.cend());
+ }
return s;
}
std::set<Element> StructureDB::find_unique_elements(const std::string &fn) {
@@ -248,3 +254,26 @@ std::vector<Structure>::const_iterator StructureDB::begin() const {
std::vector<Structure>::const_iterator StructureDB::end() const {
return structures.cend();
}
+void StructureDB::dump_to_file(const std::string& filepath, size_t prec) const {
+ std::ofstream file(filepath, std::ios::app); // Open in append mode
+ if (!file.is_open()) {
+ std::cerr << "Error: Could not open file for writing: " << filepath << std::endl;
+ return;
+ }
+ for (const auto &s : structures) {
+ s.dump_to_file(file,prec);
+ }
+ file.close();
+}
+
+std::string StructureDB::summary() const {
+ std::string str = "# of structures : " + to_string(structures.size());
+
+ str += " | # of atoms : " + to_string(calc_natoms());
+
+ str += " | Elements : ";
+ std::set<Element> ue = get_unique_elements();
+ for (const auto &e: ue) str+= e.symbol + " ";
+ str+="\n";
+ return str;
+}
diff --git a/src/vasp_outcar_reader.cpp b/src/vasp_outcar_reader.cpp
index 2f3f53a8c133f0dea4c72f23f6a76c1ce846a118..d5fccef6162056f6137a513447d1b122a0452d15 100644
--- a/src/vasp_outcar_reader.cpp
+++ b/src/vasp_outcar_reader.cpp
@@ -12,7 +12,6 @@ VaspOutcarReader::VaspOutcarReader(StructureDB& db) : DatasetReader(db) {}
VaspOutcarReader::VaspOutcarReader(StructureDB& db, const std::string& filename)
: DatasetReader(db, filename) {
read_data(filename);
- parse_data();
}
void VaspOutcarReader::read_data(const std::string& filename) {
@@ -110,6 +109,7 @@ void VaspOutcarReader::parse_data() {
s.stress(0,1) = s.stress(1,0) = row[3]; // xy
s.stress(1,2) = s.stress(2,1) = row[4]; // yz
s.stress(0,2) = s.stress(2,0) = row[5]; // zx
+ s.stress *= s_conv;
}
}
@@ -183,5 +183,9 @@ void VaspOutcarReader::parse_data() {
}
void VaspOutcarReader::print_summary() const {
- std::cout << stdb;
+ std::cout << get_summary();
+}
+
+std::string VaspOutcarReader::get_summary() const {
+ return stdb.summary();
}
diff --git a/src/vasp_vasprun_reader.cpp b/src/vasp_vasprun_reader.cpp
index cf72d1d27d9704c85d9efbe0765ef079963bcc5d..cc8e6620f9f2970a1a00eae8418991c35cbdf667 100644
--- a/src/vasp_vasprun_reader.cpp
+++ b/src/vasp_vasprun_reader.cpp
@@ -6,7 +6,6 @@ VaspVasprunReader::VaspVasprunReader(StructureDB& stdb)
VaspVasprunReader::VaspVasprunReader(StructureDB& stdb, const std::string& filename)
: DatasetReader(stdb, filename), stdb(stdb) {
read_data(filename);
- parse_data();
}
VaspVasprunReader::~VaspVasprunReader() {
@@ -141,6 +140,7 @@ void VaspVasprunReader::extract_stress_tensor(rx::xml_node<> *calculation_node)
_s.stress(r, 0) = x;
_s.stress(r, 1) = y;
_s.stress(r, 2) = z;
+ _s.stress *= s_conv;
} else {
std::cerr << "Error parsing stress tensor components." << std::endl;
}
@@ -230,6 +230,9 @@ void VaspVasprunReader::extract_forces(rx::xml_node<> *calculation_node) {
}
void VaspVasprunReader::print_summary() const {
- std::cout << stdb;
+ std::cout << get_summary();
}
+std::string VaspVasprunReader::get_summary() const {
+ return stdb.summary();
+}
diff --git a/tests/test_atom.cpp b/tests/test_atom.cpp
index 359a8bf4affbe413975b52449968f7b889c94922..fb60b03fa03c14229235eb93a8950fb5ef8dabdb 100644
--- a/tests/test_atom.cpp
+++ b/tests/test_atom.cpp
@@ -1,4 +1,5 @@
#include "catch2/catch.hpp"
+#include "tadah/core/periodic_table.h"
#include <tadah/mlip/atom.h>
#include <string>
@@ -15,6 +16,10 @@ Vec3d pos2(-1.0,-2.0,-3.0);
Vec3d force2(-4.0,-5.0,-6.0);
Element element2(symbol2,Z2);
+TEST_CASE("Testing Atom PeriodicTable Initialization") {
+ PeriodicTable::initialize();
+}
+
TEST_CASE( "Testing Atom class constructor", "[atom]" ) {
@@ -24,22 +29,19 @@ TEST_CASE( "Testing Atom class constructor", "[atom]" ) {
REQUIRE( pos1 == a.position );
REQUIRE( force1 == a.force );
- REQUIRE( symbol1[0] == a.symbol[0] );
- REQUIRE( symbol1[1] == a.symbol[1] );
+ REQUIRE( symbol1 == a.symbol );
REQUIRE( Z1 == a.Z );
// Trivial case 2/2
Atom b;
b.position = pos1;
b.force = force1;
- b.symbol[0] = symbol1[0];
- b.symbol[1] = symbol1[1];
+ b.symbol = symbol1;
b.Z = Z1;
REQUIRE( pos1 == b.position );
REQUIRE( force1 == b.force );
- REQUIRE( symbol1[0] == b.symbol[0] );
- REQUIRE( symbol1[1] == b.symbol[1] );
+ REQUIRE( symbol1 == b.symbol );
REQUIRE( Z1 == b.Z );
REQUIRE( a == b );
diff --git a/tests/test_dataset_readers.cpp b/tests/test_dataset_readers.cpp
index 5c1fc06f8b83bffda1e1a484f8d0253b46a24f3d..430bd3d55f7b4497ffadcdcdb1bcbd94aa71c209 100644
--- a/tests/test_dataset_readers.cpp
+++ b/tests/test_dataset_readers.cpp
@@ -21,6 +21,9 @@ std::vector<std::string> get_all_files(const std::string& directory) {
}
return filenames;
}
+TEST_CASE("Dataset Readers PeriodicTable Initialization") {
+ PeriodicTable::initialize();
+}
TEST_CASE("Dataset Readers process datasets in directories", "[DatasetReaders]") {
diff --git a/tests/test_structure.cpp b/tests/test_structure.cpp
index 1a0292c725f931e458256a6f5717bd6b58ead8a5..055f39a11503c12b1dfd3066d3b0e293abc0769d 100644
--- a/tests/test_structure.cpp
+++ b/tests/test_structure.cpp
@@ -1,6 +1,6 @@
#include <string>
-#include <filesystem>
#include "catch2/catch.hpp"
+#include "tadah/core/element.h"
#include <tadah/mlip/atom.h>
#include <tadah/mlip/structure.h>
@@ -8,6 +8,9 @@
double fac = 1602.1766208;
+TEST_CASE("Testing Structure PeriodicTable Initialization") {
+ PeriodicTable::initialize();
+}
TEST_CASE( "Testing Structure class volume", "[structure_volume]" ) {
//using vec=Eigen::Vector3d;
@@ -54,7 +57,6 @@ TEST_CASE( "Testing Structure virial pressure calculations", "[structure_virial_
}
TEST_CASE( "Testing Structure read and write", "[structure_read_write]" ) {
- PeriodicTable::initialize();
Structure st;
st.read("tests_data/structure_1.dat");
@@ -82,7 +84,6 @@ TEST_CASE( "Testing Structure read and write", "[structure_read_write]" ) {
}
TEST_CASE( "Testing Structure compare", "[structure_compare]" ) {
- PeriodicTable::initialize();
Structure st;
st.read("tests_data/structure_1.dat");
std::string tempfile = std::tmpnam(nullptr);
@@ -114,9 +115,13 @@ TEST_CASE( "Testing Structure compare", "[structure_compare]" ) {
std::remove(tempfile.c_str());
}
TEST_CASE( "Testing Structure copy", "[structure_copy]" ) {
- PeriodicTable::initialize();
Structure st;
st.read("tests_data/structure_1.dat");
Structure st2=st;
REQUIRE(st==st2);
}
+TEST_CASE("Testing Structure Unique Element") {
+ Structure st;
+ st.add_atom(Atom(Element("Ta"),0,0,0,0,0,0));
+ REQUIRE(st.get_unique_elements().size()==1);
+}
diff --git a/tests/tests_data/valid_castep_castep/Gd0.castep b/tests/tests_data/valid_castep_castep/Gd0.castep
new file mode 100755
index 0000000000000000000000000000000000000000..c6177a5b0f2351428947c259ec67fae93055e8d7
--- /dev/null
+++ b/tests/tests_data/valid_castep_castep/Gd0.castep
@@ -0,0 +1,5860 @@
+ +-------------------------------------------------+
+ | |
+ | CCC AA SSS TTTTT EEEEE PPPP |
+ | C A A S T E P P |
+ | C AAAA SS T EEE PPPP |
+ | C A A S T E P |
+ | CCC A A SSS T EEEEE P |
+ | |
+ +-------------------------------------------------+
+ | |
+ | Welcome to Academic Release CASTEP version 18.1 |
+ | Ab Initio Total Energy Program |
+ | |
+ | Authors: |
+ | M. Segall, M. Probert, C. Pickard, P. Hasnip, |
+ | S. Clark, K. Refson, J. R. Yates, M. Payne |
+ | |
+ | Contributors: |
+ | P. Lindan, P. Haynes, J. White, V. Milman, |
+ | N. Govind, M. Gibson, P. Tulip, V. Cocula, |
+ | B. Montanari, D. Quigley, M. Glover, |
+ | L. Bernasconi, A. Perlov, M. Plummer, |
+ | E. McNellis, J. Meyer, J. Gale, D. Jochym |
+ | J. Aarons, B. Walker, R. Gillen, D. Jones |
+ | T. Green, I. J. Bush, C. J. Armstrong, |
+ | E. J. Higgins, E. L. Brown, M. S. McFly, |
+ | J. Wilkins, B-C. Shih, P. J. P. Byrne |
+ | |
+ | Copyright (c) 2000 - 2017 |
+ | |
+ | Distributed under the terms of an |
+ | Agreement between the United Kingdom |
+ | Car-Parrinello (UKCP) Consortium, |
+ | Daresbury Laboratory and Accelrys, Inc. |
+ | |
+ | Please cite |
+ | |
+ | "First principles methods using CASTEP" |
+ | |
+ | Zeitschrift fuer Kristallographie |
+ | 220(5-6) pp. 567-570 (2005) |
+ | |
+ | S. J. Clark, M. D. Segall, C. J. Pickard, |
+ | P. J. Hasnip, M. J. Probert, K. Refson, |
+ | M. C. Payne |
+ | |
+ | in all publications arising from |
+ | your use of CASTEP |
+ | |
+ +-------------------------------------------------+
+
+
+ Compiled for linux_x86_64_gfortran4.8 on Thu, 19 Jul 2018 15:42:32 +0100
+ from code version 70483bd0ad64+ Sun, 10 Dec 2017 12:18:29 +0000
+ Compiler: GNU Fortran 4.8.5; Optimisation: fast
+ MATHLIBS: Intel MKL(2018.0.0) (LAPACK version 3.7.0)
+ FFT Lib : mkl
+ Fundamental constants values: CODATA 2014
+
+ Run started: Fri, 23 Jul 2021 22:08:58 +0100
+ Info: number of up-spin electrons is equal to the
+ number of down-spins and spin_polarized=true
+ - consider setting spin_polarized=false.
+
+ Atomic calculation performed for Gd:
+ 1s2 2s2 2p6 3s2 3p6 3d10 4s2 4p6 4d10 4f7 5s2 5p6 5d1 6s2
+
+ Converged in 116 iterations to an ae energy of -306496.732 eV
+
+ ============================================================
+ | Pseudopotential Report - Date of generation 23-07-2021 |
+ ------------------------------------------------------------
+ | Element: Gd Ionic charge: 18.00 Level of theory: LDA |
+ | Atomic Solver: Koelling-Harmon |
+ | |
+ | Reference Electronic Structure |
+ | Orbital Occupation Energy |
+ | 5s 2.000 -1.832 |
+ | 5p 6.000 -1.005 |
+ | 4f 7.000 -0.327 |
+ | 6s 2.000 -0.157 |
+ | 5d 1.000 -0.099 |
+ | |
+ | Pseudopotential Definition |
+ | Beta l e Rc scheme norm |
+ | 1 0 -1.832 2.098 qc 0 |
+ | 2 0 -0.157 2.098 qc 0 |
+ | 3 0 0.250 2.098 qc 0 |
+ | 4 1 -1.005 2.098 qc 0 |
+ | 5 1 0.250 2.098 qc 0 |
+ | 6 3 -0.327 2.098 qc 0 |
+ | 7 3 0.250 2.098 qc 0 |
+ | loc 2 -0.099 2.098 qc 1 |
+ | |
+ | Augmentation charge Rinner = 1.466 |
+ | Partial core correction Rc = 1.466 |
+ ------------------------------------------------------------
+ | "2|2.1|10|12|13|50U:60:51:52L:43(qc=6)" |
+ ------------------------------------------------------------
+ | Author: Chris J. Pickard, Cambridge University |
+ ============================================================
+
+ Pseudo atomic calculation performed for Gd 4f7 5s2 5p6 5d1 6s2
+
+ Converged in 36 iterations to a total energy of -3032.2161 eV
+
+ Calculation parallelised over 16 processes.
+ Data is distributed by G-vector(4-way) and k-point(4-way)
+
+ ************************************ Title ************************************
+
+
+ ***************************** General Parameters ******************************
+
+ output verbosity : normal (1)
+ write checkpoint data to : Gd0.check
+ type of calculation : band structure
+ stress calculation : off
+ density difference calculation : off
+ electron localisation func (ELF) calculation : off
+ Hirshfeld analysis : off
+ unlimited duration calculation
+ timing information : on
+ memory usage estimate : on
+ write extra output files : on
+ write final potential to formatted file : off
+ write final density to formatted file : off
+ write BibTeX reference list : on
+ write OTFG pseudopotential files : on
+ write electrostatic potential file : on
+ write bands file : on
+ checkpoint writing : both castep_bin and check files
+
+ output length unit : A
+ output mass unit : amu
+ output time unit : ps
+ output charge unit : e
+ output spin unit : hbar/2
+ output energy unit : eV
+ output force unit : eV/A
+ output velocity unit : A/ps
+ output pressure unit : GPa
+ output inv_length unit : 1/A
+ output frequency unit : cm-1
+ output force constant unit : eV/A**2
+ output volume unit : A**3
+ output IR intensity unit : (D/A)**2/amu
+ output dipole unit : D
+ output efield unit : eV/A/e
+ output entropy unit : J/mol/K
+
+ wavefunctions paging : none
+ random number generator seed : randomised (220859301)
+ data distribution : optimal for this architecture
+ optimization strategy : maximize speed(+++)
+
+ *********************** Exchange-Correlation Parameters ***********************
+
+ using functional : Local Density Approximation
+ relativistic treatment : Koelling-Harmon
+ DFT+D: Semi-empirical dispersion correction : off
+
+ ************************* Pseudopotential Parameters **************************
+
+ pseudopotential representation : reciprocal space
+ <beta|phi> representation : reciprocal space
+ spin-orbit coupling : off
+
+ **************************** Basis Set Parameters *****************************
+
+ plane wave basis set cut-off : 425.0000 eV
+ size of standard grid : 1.7500
+ size of fine gmax : 18.4829 1/A
+ finite basis set correction : none
+
+ **************************** Electronic Parameters ****************************
+
+ number of electrons : 18.00
+ net charge of system : 0.000
+ net spin of system : 0.000
+ number of up spins : 9.000
+ number of down spins : 9.000
+ treating system as spin-polarized
+ number of bands : 29
+
+ ********************* Electronic Minimization Parameters **********************
+
+ Method: Treating system as metallic with density mixing treatment of electrons,
+ and number of SD steps : 1
+ and number of CG steps : 4
+
+ total energy / atom convergence tol. : 0.5000E-06 eV
+ eigen-energy convergence tolerance : 0.1724E-07 eV
+ max force / atom convergence tol. : ignored
+ convergence tolerance window : 3 cycles
+ max. number of SCF cycles : 100
+ number of fixed-spin iterations : 10
+ smearing scheme : Gaussian
+ smearing width : 0.2000 eV
+ Fermi energy convergence tolerance : 0.2721E-13 eV
+ periodic dipole correction : NONE
+
+ ************************** Density Mixing Parameters **************************
+
+ density-mixing scheme : Broyden
+ max. length of mixing history : 20
+ charge density mixing amplitude : 0.8000
+ spin density mixing amplitude : 2.000
+ cut-off energy for mixing : 425.0 eV
+
+ *********************** Population Analysis Parameters ************************
+
+ Population analysis with cutoff : 3.000 A
+ Population analysis output : summary and pdos components
+
+ ************************** Band Structure Parameters **************************
+
+ max. number of iterations : 60
+ max. CG steps in BS calc : 25
+ number of bands / k-point : 56
+ band convergence tolerance : 0.1000E-05 eV
+ write orbitals file : on
+
+ *******************************************************************************
+
+
+ -------------------------------
+ Unit Cell
+ -------------------------------
+ Real Lattice(A) Reciprocal Lattice(1/A)
+ 0.0000000 2.6200000 2.6200000 -1.199081165 1.199081165 1.199081165
+ 2.6200000 0.0000000 2.6200000 1.199081165 -1.199081165 1.199081165
+ 2.6200000 2.6200000 0.0000000 1.199081165 1.199081165 -1.199081165
+
+ Lattice parameters(A) Cell Angles
+ a = 3.705240 alpha = 60.000000
+ b = 3.705240 beta = 60.000000
+ c = 3.705240 gamma = 60.000000
+
+ Current cell volume = 35.969456 A**3
+ density = 4.371765 AMU/A**3
+ = 7.259486 g/cm^3
+
+ -------------------------------
+ Cell Contents
+ -------------------------------
+ Total number of ions in cell = 1
+ Total number of species in cell = 1
+ Max number of any one species = 1
+
+ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+ x Element Atom Fractional coordinates of atoms x
+ x Number u v w x
+ x----------------------------------------------------------x
+ x Gd 1 0.000000 0.000000 0.000000 x
+ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+
+
+ No user defined ionic velocities
+
+ -------------------------------
+ Details of Species
+ -------------------------------
+
+ Mass of species in AMU
+ Gd 157.2500000
+
+ Electric Quadrupole Moment (Barn)
+ Gd 1.3500000 Isotope157
+
+
+ Quantisation axis: 1.00000 -1.00000 1.00000
+
+ Units for Hubbard U values are eV
+ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+ | Element Atom Hubbard U values by orbital type |
+ | Number s p d f |
+ |------------------------------------------------------------------|
+ |Gd 1 0.00000 0.00000 0.00000 6.70000 |
+ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+
+
+ Files used for pseudopotentials:
+ Gd 2|2.1|10|12|13|50U:60:51:52L:43(qc=6)
+
+ -------------------------------
+ k-Points For BZ Sampling
+ -------------------------------
+ Number of kpoints used = 468
+
+ -------------------------------
+ Symmetry and Constraints
+ -------------------------------
+
+ Maximum deviation from symmetry = 0.470004E-15 ANG
+ Magnetic structure symmetry:
+ User supplied or default Hubbard U data has reduced the symmetry of the system
+
+ Number of symmetry operations = 16
+ Number of ionic constraints = 3
+ Point group of crystal = 15: D4h, 4/mmm, 4/m 2/m 2/m
+ Space group of crystal = 225: Fm-3m, -F 4 2 3
+
+ Set iprint > 1 for details on symmetry rotations/translations
+
+ Centre of mass is constrained
+ Set iprint > 1 for details of linear ionic constraints
+
+ Number of cell constraints= 5
+ Cell constraints are: 1 1 1 0 0 0
+
+ External pressure/stress (GPa)
+ 0.00000 0.00000 0.00000
+ 0.00000 0.00000
+ 0.00000
+
++---------------- MEMORY AND SCRATCH DISK ESTIMATES PER PROCESS --------------+
+| Memory Disk |
+| Baseline code, static data and system overhead 412.0 MB 0.0 MB |
+| BLAS internal memory storage 0.0 MB 0.0 MB |
+| Model and support data 61.3 MB 0.0 MB |
+| Electronic energy minimisation requirements 46.4 MB 0.0 MB |
+| Force calculation requirements 0.8 MB 0.0 MB |
+| ----------------------------- |
+| Approx. total storage required per process 519.8 MB 0.0 MB |
+| |
+| Requirements will fluctuate during execution and may exceed these estimates |
++-----------------------------------------------------------------------------+
+Calculating total energy with cut-off of 425.000 eV.
+
+ Pseudo atomic calculation performed for Gd 4f7 5s2 5p6 5d1 6s2
+
+ Converged in 36 iterations to a total energy of -3032.2161 eV
+
+------------------------------------------------------------------------ <-- SCF
+SCF loop Energy Fermi Energy gain Timer <-- SCF
+ energy per atom (sec) <-- SCF
+------------------------------------------------------------------------ <-- SCF
+Initial -2.89965509E+003 0.00000000E+000 23.29 <-- SCF
+ 1 -2.98520074E+003 5.92001968E+000 8.55456534E+001 31.55 <-- SCF
+ 2 -3.03447725E+003 3.86911470E+000 4.92765152E+001 36.97 <-- SCF
+ 3 -3.03681060E+003 3.63238351E+000 2.33334698E+000 43.81 <-- SCF
+ 4 -3.08547151E+003 1.11125785E+001 4.86609050E+001 50.50 <-- SCF
+ 5 -3.08550199E+003 1.11064276E+001 3.04836941E-002 56.76 <-- SCF
+ 6 -3.02275477E+003 6.81693038E+000 -6.27472234E+001 63.20 <-- SCF
+ 7 -3.02299014E+003 6.77095701E+000 2.35372118E-001 70.44 <-- SCF
+ 8 -3.04218983E+003 1.36123180E-001 1.91996938E+001 77.78 <-- SCF
+ 9 -3.04226024E+003 1.32481040E-001 7.04039618E-002 83.82 <-- SCF
+ 10 -3.04346335E+003 -3.60111841E-002 1.20311029E+000 90.86 <-- SCF
+ 11 -3.18377830E+003 1.23926479E+001 1.40314957E+002 97.55 <-- SCF
+ 12 -3.18388218E+003 1.23786135E+001 1.03873732E-001 103.56 <-- SCF
+ 13 -3.04005602E+003 9.81148656E+000 -1.43826153E+002 110.06 <-- SCF
+ 14 -3.04060896E+003 9.64709145E+000 5.52934090E-001 116.82 <-- SCF
+ 15 -3.21926684E+003 -2.66698179E+001 1.78657886E+002 126.49 <-- SCF
+ 16 -3.21995318E+003 -2.66884642E+001 6.86339316E-001 132.70 <-- SCF
+ 17 -3.06822919E+003 -1.00743714E+001 -1.51723994E+002 139.43 <-- SCF
+ 18 -3.06839525E+003 -1.00807260E+001 1.66060994E-001 146.17 <-- SCF
+ 19 -3.03568611E+003 6.91936508E+000 -3.27091430E+001 152.51 <-- SCF
+ 20 -3.03577872E+003 6.91141545E+000 9.26104454E-002 160.06 <-- SCF
+ 21 -3.03377995E+003 3.72897532E+000 -1.99877019E+000 166.53 <-- SCF
+ 22 -3.03551763E+003 4.26115079E+000 1.73767987E+000 172.99 <-- SCF
+ 23 -3.03667303E+003 5.67930673E+000 1.15539756E+000 180.65 <-- SCF
+ 24 -3.03773904E+003 5.77488976E+000 1.06601260E+000 187.04 <-- SCF
+ 25 -3.03530269E+003 5.55347087E+000 -2.43634714E+000 194.27 <-- SCF
+ 26 -3.05032776E+003 -9.70548183E-001 1.50250654E+001 201.68 <-- SCF
+ 27 -3.05033208E+003 -9.70678755E-001 4.32051862E-003 208.85 <-- SCF
+ 28 -3.04539413E+003 -1.45391667E-001 -4.93794546E+000 215.82 <-- SCF
+ 29 -3.04539557E+003 -1.45497023E-001 1.44054842E-003 222.81 <-- SCF
+ 30 -3.13452484E+003 1.30254108E+001 8.91292691E+001 229.42 <-- SCF
+ 31 -3.13460994E+003 1.30110021E+001 8.50980851E-002 235.51 <-- SCF
+ 32 -3.06845909E+003 1.14127813E+001 -6.61508513E+001 241.91 <-- SCF
+ 33 -3.06850908E+003 1.14098622E+001 4.99932106E-002 248.67 <-- SCF
+ 34 -3.20411507E+003 -2.77108829E+001 1.35605986E+002 256.46 <-- SCF
+ 35 -3.20803541E+003 -2.77582286E+001 3.92034643E+000 263.96 <-- SCF
+ 36 -3.20804627E+003 -2.77582828E+001 1.08581388E-002 269.81 <-- SCF
+ 37 -3.12705607E+003 -3.12322670E+001 -8.09902058E+001 276.78 <-- SCF
+ 38 -3.12726508E+003 -3.12325885E+001 2.09016565E-001 283.24 <-- SCF
+ 39 -2.80683975E+003 1.00683380E+001 -3.20425334E+002 289.43 <-- SCF
+ 40 -2.80981984E+003 1.00332056E+001 2.98008829E+000 296.42 <-- SCF
+ 41 -2.80983673E+003 1.00330337E+001 1.68957548E-002 302.66 <-- SCF
+ 42 -3.04675051E+003 3.05979985E+000 2.36913775E+002 309.19 <-- SCF
+ 43 -3.04770013E+003 3.04477995E+000 9.49622910E-001 316.24 <-- SCF
+ 44 -3.04319238E+003 6.32951414E+000 -4.50775184E+000 322.94 <-- SCF
+ 45 -3.04321010E+003 6.32922112E+000 1.77232477E-002 329.70 <-- SCF
+ 46 -3.04943311E+003 5.58467038E+000 6.22300834E+000 336.05 <-- SCF
+ 47 -3.04945005E+003 5.58445434E+000 1.69348793E-002 343.45 <-- SCF
+ 48 -3.05455023E+003 5.39146007E+000 5.10018256E+000 349.77 <-- SCF
+ 49 -3.05456243E+003 5.39108103E+000 1.22027647E-002 357.67 <-- SCF
+ 50 -3.05493417E+003 5.26679242E+000 3.71738203E-001 364.01 <-- SCF
+ 51 -3.05525737E+003 4.90318130E+000 3.23200386E-001 370.46 <-- SCF
+ 52 -3.05506850E+003 4.95046824E+000 -1.88868372E-001 376.87 <-- SCF
+ 53 -3.05509778E+003 4.93855394E+000 2.92747541E-002 383.16 <-- SCF
+ 54 -3.05515680E+003 4.98485842E+000 5.90291045E-002 389.88 <-- SCF
+ 55 -3.05516098E+003 4.95329078E+000 4.17686172E-003 396.12 <-- SCF
+ 56 -3.05516001E+003 4.95987680E+000 -9.74111769E-004 403.37 <-- SCF
+ 57 -3.05515903E+003 4.97052811E+000 -9.74714884E-004 410.40 <-- SCF
+ 58 -3.05515905E+003 4.97104973E+000 1.55635104E-005 417.73 <-- SCF
+ 59 -3.05515907E+003 4.97088718E+000 2.60727692E-005 423.86 <-- SCF
+ 60 -3.05515908E+003 4.97087885E+000 1.64496093E-006 427.91 <-- SCF
+ 61 -3.05515908E+003 4.97088929E+000 5.32972948E-008 431.93 <-- SCF
+ 62 -3.05515908E+003 4.97090488E+000 1.03062499E-008 435.90 <-- SCF
+------------------------------------------------------------------------ <-- SCF
+
+Integrated Spin Density = -7.72332 hbar/2
+Integrated |Spin Density| = 7.72332 hbar/2
+
+
+ Hubbard U occupation numbers
+ ----------------------------
+Species Ion l spin occupancies
+==================================================================
+ Gd 1 3 up: 0.00 0.00 0.00 0.00 0.00 0.00 0.00
+ dn: 1.00 1.00 1.00 1.00 1.00 1.00 1.00
+==================================================================
+
+Final energy, E = -3055.124910556 eV
+Final free energy (E-TS) = -3055.159075896 eV
+(energies not corrected for finite basis set)
+
+NB est. 0K energy (E-0.5TS) = -3055.141993226 eV
+
+
+Writing analysis data to Gd0.castep_bin
+
+Writing model to Gd0.check
+
++---------------- MEMORY AND SCRATCH DISK ESTIMATES PER PROCESS --------------+
+| Memory Disk |
+| Baseline code, static data and system overhead 412.0 MB 0.0 MB |
+| BLAS internal memory storage 0.0 MB 0.0 MB |
+| Model and support data 38.3 MB 0.0 MB |
+| Band structure calculation requirements 12.2 MB 0.0 MB |
+| Force calculation requirements 0.8 MB 0.0 MB |
+| ----------------------------- |
+| Approx. total storage required per process 462.5 MB 0.0 MB |
+| |
+| Requirements will fluctuate during execution and may exceed these estimates |
++-----------------------------------------------------------------------------+
+ =====================================================================
+ + Fermi energy for spin up electrons is: 4.97090 eV +
+ + Fermi energy for spin down electrons is: 4.97090 eV +
+ + +
+ + B A N D S T R U C T U R E C A L C U L A T I O N +
+ + (General k-point calculation - complex wavefunctions) +
+ + +
+ + Calculation re-parallelised over 16 processes. +
+ + Data distributed by G-vector(4-way), k-point(4-way) +
+ + +
+
+ Pseudo atomic calculation performed for Gd 4f7 5s2 5p6 5d1 6s2
+
+ Converged in 36 iterations to a total energy of -3032.2161 eV
+
+ + ================================================================= +
+ + +
+ + Band Structure Calculation: Progress report on root process +
+ + +
+ + There are 44 BS k-points. Root process contains 11 of them. +
+ + +
+ + Spin= 1 of 2, K-point= 1 of 11 completed, Time: 0.83s. +
+ + Spin= 1 of 2, K-point= 2 of 11 completed, Time: 0.87s. +
+ + Spin= 1 of 2, K-point= 3 of 11 completed, Time: 0.88s. +
+ + Spin= 1 of 2, K-point= 4 of 11 completed, Time: 0.82s. +
+ + Spin= 1 of 2, K-point= 5 of 11 completed, Time: 0.82s. +
+ + Spin= 1 of 2, K-point= 6 of 11 completed, Time: 0.83s. +
+ + Spin= 1 of 2, K-point= 7 of 11 completed, Time: 0.83s. +
+ + Spin= 1 of 2, K-point= 8 of 11 completed, Time: 0.84s. +
+ + Spin= 1 of 2, K-point= 9 of 11 completed, Time: 0.85s. +
+ + Spin= 1 of 2, K-point= 10 of 11 completed, Time: 0.85s. +
+ + Spin= 1 of 2, K-point= 11 of 11 completed, Time: 0.86s. +
+ + Spin= 2 of 2, K-point= 1 of 11 completed, Time: 0.84s. +
+ + Spin= 2 of 2, K-point= 2 of 11 completed, Time: 0.86s. +
+ + Spin= 2 of 2, K-point= 3 of 11 completed, Time: 0.88s. +
+ + Spin= 2 of 2, K-point= 4 of 11 completed, Time: 0.84s. +
+ + Spin= 2 of 2, K-point= 5 of 11 completed, Time: 0.87s. +
+ + Spin= 2 of 2, K-point= 6 of 11 completed, Time: 0.91s. +
+ + Spin= 2 of 2, K-point= 7 of 11 completed, Time: 0.90s. +
+ + Spin= 2 of 2, K-point= 8 of 11 completed, Time: 0.89s. +
+ + Spin= 2 of 2, K-point= 9 of 11 completed, Time: 0.90s. +
+ + Spin= 2 of 2, K-point= 10 of 11 completed, Time: 0.89s. +
+ + Spin= 2 of 2, K-point= 11 of 11 completed, Time: 0.86s. +
+ + Finished BS calculation on root process (waiting for others). +
+ + +
+ + ================================================================= +
+ + Electronic energies +
+ + ------------------- +
+ + +
+ + Band number Energy in eV +
+ + ================================================================= +
+ + +
+ + ----------------------------------------------------------------- +
+ + Spin=1 kpt= 1 ( 0.500000 0.250000 0.750000) kpt-group= 1 +
+ + ----------------------------------------------------------------- +
+ + +
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+ + 2 -15.675150 +
+ + 3 -15.675127 +
+ + 4 -15.491406 +
+ + 5 4.646509 +
+ + 6 5.744927 +
+ + 7 5.744930 +
+ + 8 7.771775 +
+ + 9 11.451284 +
+ + 10 11.451325 +
+ + 11 11.464830 +
+ + 12 11.838905 +
+ + 13 11.975861 +
+ + 14 11.976025 +
+ + 15 11.976082 +
+ + 16 12.012922 +
+ + 17 13.221744 +
+ + 18 13.583317 +
+ + 19 13.583344 +
+ + 20 16.423704 +
+ + 21 21.923485 +
+ + 22 21.923487 +
+ + 23 22.058452 +
+ + 24 26.139975 +
+ + 25 26.350079 +
+ + 26 26.606292 +
+ + 27 26.606304 +
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+ + 29 33.506718 +
+ + 30 33.506723 +
+ + 31 33.543138 +
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+ + 52 56.807616 +
+ + 53 59.304086 +
+ + 54 59.304095 +
+ + 55 59.912768 +
+ + 56 63.944189 +
+ + ----------------------------------------------------------------- +
+ + Spin=1 kpt= 2 ( 0.500000 0.361111 0.638889) kpt-group= 1 +
+ + ----------------------------------------------------------------- +
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+ + 53 60.634973 +
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+ + 55 61.944860 +
+ + 56 62.588523 +
+ + ----------------------------------------------------------------- +
+ + Spin=1 kpt= 3 ( 0.500000 0.472222 0.527778) kpt-group= 1 +
+ + ----------------------------------------------------------------- +
+ + +
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+ + 52 58.929312 +
+ + 53 58.975595 +
+ + 54 60.274465 +
+ + 55 60.829303 +
+ + 56 62.215372 +
+ + ----------------------------------------------------------------- +
+ + Spin=1 kpt= 4 ( 0.363636 0.363636 0.363636) kpt-group= 1 +
+ + ----------------------------------------------------------------- +
+ + +
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+ + 53 58.829869 +
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+ + 55 62.856355 +
+ + 56 63.560807 +
+ + ----------------------------------------------------------------- +
+ + Spin=1 kpt= 5 ( 0.181818 0.181818 0.181818) kpt-group= 1 +
+ + ----------------------------------------------------------------- +
+ + +
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+ + 52 56.212049 +
+ + 53 57.138467 +
+ + 54 57.557465 +
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+ + Spin=1 kpt= 6 ( 0.000000 0.000000 0.000000) kpt-group= 1 +
+ + ----------------------------------------------------------------- +
+ + +
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+ + ----------------------------------------------------------------- +
+ + Spin=1 kpt= 7 ( 0.166667 0.000000 0.166667) kpt-group= 1 +
+ + ----------------------------------------------------------------- +
+ + +
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+ + ----------------------------------------------------------------- +
+ + Spin=1 kpt= 8 ( 0.333333 0.000000 0.333333) kpt-group= 1 +
+ + ----------------------------------------------------------------- +
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+ + ----------------------------------------------------------------- +
+ + Spin=1 kpt= 9 ( 0.500000 0.000000 0.500000) kpt-group= 1 +
+ + ----------------------------------------------------------------- +
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+ + 27 27.431822 +
+ + 28 30.246232 +
+ + 29 31.392366 +
+ + 30 31.392373 +
+ + 31 34.825130 +
+ + 32 34.825131 +
+ + 33 35.984498 +
+ + 34 37.762934 +
+ + 35 38.522108 +
+ + 36 41.596497 +
+ + 37 41.596497 +
+ + 38 41.601170 +
+ + 39 43.830843 +
+ + 40 43.830847 +
+ + 41 45.034732 +
+ + 42 47.575120 +
+ + 43 47.575123 +
+ + 44 47.745834 +
+ + 45 48.614621 +
+ + 46 49.253667 +
+ + 47 49.783775 +
+ + 48 52.203717 +
+ + 49 52.203717 +
+ + 50 52.807275 +
+ + 51 54.592938 +
+ + 52 58.137770 +
+ + 53 58.137771 +
+ + 54 58.412775 +
+ + 55 59.083579 +
+ + 56 59.235713 +
+ + ----------------------------------------------------------------- +
+ + Spin=2 kpt= 8 ( 0.458333 0.000000 0.458333) kpt-group= 4 +
+ + ----------------------------------------------------------------- +
+ + +
+ + 1 -40.751760 +
+ + 2 -18.271076 +
+ + 3 -17.975428 +
+ + 4 -17.975415 +
+ + 5 -4.959319 +
+ + 6 -4.923150 +
+ + 7 -4.923100 +
+ + 8 -4.916230 +
+ + 9 -4.892335 +
+ + 10 -4.892261 +
+ + 11 -4.881396 +
+ + 12 2.818387 +
+ + 13 3.588672 +
+ + 14 6.771829 +
+ + 15 9.511377 +
+ + 16 9.745457 +
+ + 17 9.745457 +
+ + 18 12.638760 +
+ + 19 12.638762 +
+ + 20 13.121480 +
+ + 21 18.284347 +
+ + 22 21.237127 +
+ + 23 22.399692 +
+ + 24 25.474519 +
+ + 25 25.474521 +
+ + 26 25.591255 +
+ + 27 27.871270 +
+ + 28 28.271741 +
+ + 29 28.271743 +
+ + 30 32.277371 +
+ + 31 32.554980 +
+ + 32 32.554987 +
+ + 33 33.822843 +
+ + 34 38.391008 +
+ + 35 39.289786 +
+ + 36 40.772607 +
+ + 37 40.772607 +
+ + 38 42.358898 +
+ + 39 43.150994 +
+ + 40 43.870849 +
+ + 41 45.198121 +
+ + 42 45.198126 +
+ + 43 47.769165 +
+ + 44 48.429158 +
+ + 45 50.605495 +
+ + 46 50.605496 +
+ + 47 50.884578 +
+ + 48 50.884578 +
+ + 49 51.302601 +
+ + 50 54.214224 +
+ + 51 55.605588 +
+ + 52 57.849822 +
+ + 53 57.849826 +
+ + 54 60.298649 +
+ + 55 60.727199 +
+ + 56 64.177145 +
+ + ----------------------------------------------------------------- +
+ + Spin=2 kpt= 9 ( 0.500000 0.125000 0.625000) kpt-group= 4 +
+ + ----------------------------------------------------------------- +
+ + +
+ + 1 -40.751187 +
+ + 2 -18.235476 +
+ + 3 -18.023381 +
+ + 4 -17.980781 +
+ + 5 -4.952104 +
+ + 6 -4.939347 +
+ + 7 -4.934283 +
+ + 8 -4.912184 +
+ + 9 -4.898552 +
+ + 10 -4.894685 +
+ + 11 -4.884503 +
+ + 12 3.241417 +
+ + 13 3.884168 +
+ + 14 6.073195 +
+ + 15 8.214926 +
+ + 16 9.966001 +
+ + 17 10.830943 +
+ + 18 11.619828 +
+ + 19 12.357738 +
+ + 20 14.497212 +
+ + 21 19.285276 +
+ + 22 20.826591 +
+ + 23 21.626723 +
+ + 24 24.319087 +
+ + 25 25.987271 +
+ + 26 26.529706 +
+ + 27 26.839228 +
+ + 28 30.015859 +
+ + 29 30.142489 +
+ + 30 30.159328 +
+ + 31 30.525099 +
+ + 32 35.464737 +
+ + 33 36.257695 +
+ + 34 36.547194 +
+ + 35 37.142738 +
+ + 36 37.609725 +
+ + 37 41.256363 +
+ + 38 41.914365 +
+ + 39 42.990590 +
+ + 40 43.667330 +
+ + 41 45.319471 +
+ + 42 46.206774 +
+ + 43 46.679629 +
+ + 44 48.440851 +
+ + 45 49.627063 +
+ + 46 51.594658 +
+ + 47 51.894837 +
+ + 48 52.028263 +
+ + 49 54.323058 +
+ + 50 56.804553 +
+ + 51 56.934157 +
+ + 52 58.334126 +
+ + 53 58.533396 +
+ + 54 60.966543 +
+ + 55 61.184337 +
+ + 56 61.418613 +
+ + ----------------------------------------------------------------- +
+ + Spin=2 kpt= 10 ( 0.475000 0.275000 0.750000) kpt-group= 4 +
+ + ----------------------------------------------------------------- +
+ + +
+ + 1 -40.751665 +
+ + 2 -18.151986 +
+ + 3 -18.109728 +
+ + 4 -17.978820 +
+ + 5 -4.942362 +
+ + 6 -4.939230 +
+ + 7 -4.926119 +
+ + 8 -4.905691 +
+ + 9 -4.904160 +
+ + 10 -4.894982 +
+ + 11 -4.886456 +
+ + 12 3.841489 +
+ + 13 4.550094 +
+ + 14 5.034065 +
+ + 15 7.008730 +
+ + 16 9.893566 +
+ + 17 11.296256 +
+ + 18 11.874190 +
+ + 19 12.339792 +
+ + 20 15.024398 +
+ + 21 20.088764 +
+ + 22 20.654717 +
+ + 23 21.404014 +
+ + 24 24.533227 +
+ + 25 24.873447 +
+ + 26 25.713627 +
+ + 27 26.040825 +
+ + 28 31.087607 +
+ + 29 31.702291 +
+ + 30 32.373898 +
+ + 31 32.723596 +
+ + 32 32.886560 +
+ + 33 34.587853 +
+ + 34 34.759256 +
+ + 35 37.018837 +
+ + 36 38.619226 +
+ + 37 40.221052 +
+ + 38 41.084471 +
+ + 39 41.966491 +
+ + 40 44.038782 +
+ + 41 44.132672 +
+ + 42 45.587444 +
+ + 43 48.358003 +
+ + 44 48.640143 +
+ + 45 52.027504 +
+ + 46 52.027571 +
+ + 47 54.146651 +
+ + 48 54.442214 +
+ + 49 54.780900 +
+ + 50 55.991076 +
+ + 51 56.356994 +
+ + 52 57.219751 +
+ + 53 57.923417 +
+ + 54 58.280674 +
+ + 55 59.415325 +
+ + 56 62.047639 +
+ + ----------------------------------------------------------------- +
+ + Spin=2 kpt= 11 ( 0.375000 0.375000 0.750000) kpt-group= 4 +
+ + ----------------------------------------------------------------- +
+ + +
+ + 1 -40.752526 +
+ + 2 -18.194395 +
+ + 3 -18.090403 +
+ + 4 -17.938437 +
+ + 5 -4.951669 +
+ + 6 -4.943773 +
+ + 7 -4.916169 +
+ + 8 -4.913839 +
+ + 9 -4.913448 +
+ + 10 -4.886237 +
+ + 11 -4.884246 +
+ + 12 3.551748 +
+ + 13 4.059645 +
+ + 14 5.682649 +
+ + 15 7.942736 +
+ + 16 9.276351 +
+ + 17 9.941364 +
+ + 18 12.041648 +
+ + 19 13.840893 +
+ + 20 15.064315 +
+ + 21 18.235020 +
+ + 22 21.791190 +
+ + 23 21.836784 +
+ + 24 21.929859 +
+ + 25 27.414411 +
+ + 26 27.581317 +
+ + 27 27.804858 +
+ + 28 28.655009 +
+ + 29 29.997583 +
+ + 30 30.791633 +
+ + 31 32.026341 +
+ + 32 32.842045 +
+ + 33 34.555766 +
+ + 34 35.570893 +
+ + 35 39.001025 +
+ + 36 39.757045 +
+ + 37 40.955651 +
+ + 38 41.260678 +
+ + 39 43.265450 +
+ + 40 43.331295 +
+ + 41 44.446977 +
+ + 42 45.054750 +
+ + 43 46.351843 +
+ + 44 48.991931 +
+ + 45 49.757220 +
+ + 46 51.716374 +
+ + 47 51.928976 +
+ + 48 53.047105 +
+ + 49 54.636833 +
+ + 50 57.751309 +
+ + 51 58.083900 +
+ + 52 59.312153 +
+ + 53 60.076093 +
+ + 54 60.760223 +
+ + 55 61.301766 +
+ + 56 61.660072 +
+ =====================================================================
+
+Writing model to Gd0.orbitals
+ + Calculation re-parallelised over 16 processes. +
+ + Data distributed by G-vector(4-way), k-point(4-way) +
+
+ Pseudo atomic calculation performed for Gd 4f7 5s2 5p6 5d1 6s2
+
+ Converged in 36 iterations to a total energy of -3032.2161 eV
+
+
+ ******************** Symmetrised Forces ********************
+ * *
+ * Cartesian components (eV/A) *
+ * -------------------------------------------------------- *
+ * x y z *
+ * *
+ * Gd 1 0.00000 0.00000 0.00000 *
+ * *
+ ************************************************************
+
+ Pseudo atomic calculation performed for Gd 4f7 5s2 5p6 5d1 6s2
+
+ Converged in 36 iterations to a total energy of -3032.2161 eV
+
+Charge spilling parameter for spin component 1 = 0.06%
+Charge spilling parameter for spin component 2 = 0.05%
+
+ Orbital Populations
+ ---------------------------------------------------------------
+ Ion Atom Orbital Up Down Spin
+ ---------------------------------------------------------------
+ Gd 1 S 1.018 0.994 0.024
+ Gd 1 Px 1.019 0.997 0.022
+ Gd 1 Py 1.020 0.997 0.023
+ Gd 1 Pz 1.020 0.997 0.023
+ Gd 1 Fxxx 0.000 1.000 -1.000
+ Gd 1 Fyyy 0.000 1.000 -1.000
+ Gd 1 Fzzz 0.000 1.000 -1.000
+ Gd 1 Fxyz 0.000 1.000 -1.000
+ Gd 1 Fz(xx-yy) 0.000 1.000 -1.000
+ Gd 1 Fy(zz-xx) 0.000 1.000 -1.000
+ Gd 1 Fx(yy-zz) 0.000 1.000 -1.000
+ Gd 1 S 0.266 0.299 -0.033
+ Gd 1 Dzz 0.133 0.213 -0.080
+ Gd 1 Dzy 0.121 0.282 -0.162
+ Gd 1 Dzx 0.123 0.272 -0.149
+ Gd 1 Dxx-yy 0.143 0.224 -0.081
+ Gd 1 Dxy 0.124 0.261 -0.136
+ Gd 1 Px 0.052 0.110 -0.058
+ Gd 1 Py 0.050 0.109 -0.058
+ Gd 1 Pz 0.049 0.107 -0.058
+ ---------------------------------------------------------------
+ Total: 5.138 12.862 -7.723
+ ---------------------------------------------------------------
+
+ Atomic Populations (Mulliken)
+ -----------------------------
+Species Ion Spin s p d f Total Charge(e) Spin(hbar/2)
+=========================================================================================
+ Gd 1 up: 1.28 3.21 0.64 0.00 5.14 0.00 -7.72
+ 1 dn: 1.29 3.32 1.25 7.00 12.86
+=========================================================================================
+
+ Bond Population Spin Length (A)
+================================================================================
+================================================================================
+
+
+Writing analysis data to Gd0.castep_bin
+
+Writing model to Gd0.check
+
+ A BibTeX formatted list of references used in this run has been written to
+ Gd0.bib
+
+Initialisation time = 18.92 s
+Calculation time = 447.53 s
+Finalisation time = 5.50 s
+Total time = 471.94 s
+Peak Memory Use = 860972 kB
+
+Overall parallel efficiency rating: Poor (46%)
+
+Data was distributed by:-
+G-vector (4-way); efficiency rating: Poor (48%)
+k-point (4-way); efficiency rating: Excellent (92%)
+
+Parallel notes:
+1) Calculation only took 466.5 s, so efficiency estimates may be inaccurate.
diff --git a/tests/tests_data/valid_castep_castep/combined.castep b/tests/tests_data/valid_castep_castep/combined.castep
index a9e9c6ba46889f00ada106a48840c61779d737a2..5e29d0e15ebe687abb5333017352656115b4c3fd 100644
--- a/tests/tests_data/valid_castep_castep/combined.castep
+++ b/tests/tests_data/valid_castep_castep/combined.castep
@@ -5542,3 +5542,844 @@ Final energy = -2397.023600256 eV
--------------------------------------------------------------------------------
... finished MD iteration 3
+ +-------------------------------------------------+
+ | |
+ | CCC AA SSS TTTTT EEEEE PPPP |
+ | C A A S T E P P |
+ | C AAAA SS T EEE PPPP |
+ | C A A S T E P |
+ | CCC A A SSS T EEEEE P |
+ | |
+ +-------------------------------------------------+
+ | |
+ | Welcome to Academic Release CASTEP version 18.1 |
+ | Ab Initio Total Energy Program |
+ | |
+ | Authors: |
+ | M. Segall, M. Probert, C. Pickard, P. Hasnip, |
+ | S. Clark, K. Refson, J. R. Yates, M. Payne |
+ | |
+ | Contributors: |
+ | P. Lindan, P. Haynes, J. White, V. Milman, |
+ | N. Govind, M. Gibson, P. Tulip, V. Cocula, |
+ | B. Montanari, D. Quigley, M. Glover, |
+ | L. Bernasconi, A. Perlov, M. Plummer, |
+ | E. McNellis, J. Meyer, J. Gale, D. Jochym |
+ | J. Aarons, B. Walker, R. Gillen, D. Jones |
+ | T. Green, I. J. Bush, C. J. Armstrong, |
+ | E. J. Higgins, E. L. Brown, M. S. McFly, |
+ | J. Wilkins, B-C. Shih, P. J. P. Byrne |
+ | |
+ | Copyright (c) 2000 - 2017 |
+ | |
+ | Distributed under the terms of an |
+ | Agreement between the United Kingdom |
+ | Car-Parrinello (UKCP) Consortium, |
+ | Daresbury Laboratory and Accelrys, Inc. |
+ | |
+ | Please cite |
+ | |
+ | "First principles methods using CASTEP" |
+ | |
+ | Zeitschrift fuer Kristallographie |
+ | 220(5-6) pp. 567-570 (2005) |
+ | |
+ | S. J. Clark, M. D. Segall, C. J. Pickard, |
+ | P. J. Hasnip, M. J. Probert, K. Refson, |
+ | M. C. Payne |
+ | |
+ | in all publications arising from |
+ | your use of CASTEP |
+ | |
+ +-------------------------------------------------+
+
+
+ Compiled for linux_x86_64_gfortran4.8 on Thu, 19 Jul 2018 15:42:32 +0100
+ from code version 70483bd0ad64+ Sun, 10 Dec 2017 12:18:29 +0000
+ Compiler: GNU Fortran 4.8.5; Optimisation: fast
+ MATHLIBS: Intel MKL(2018.0.0) (LAPACK version 3.7.0)
+ FFT Lib : mkl
+ Fundamental constants values: CODATA 2014
+
+ Run started: Fri, 23 Jul 2021 22:08:58 +0100
+ Info: number of up-spin electrons is equal to the
+ number of down-spins and spin_polarized=true
+ - consider setting spin_polarized=false.
+
+ Atomic calculation performed for Gd:
+ 1s2 2s2 2p6 3s2 3p6 3d10 4s2 4p6 4d10 4f7 5s2 5p6 5d1 6s2
+
+ Converged in 116 iterations to an ae energy of -306496.732 eV
+
+ ============================================================
+ | Pseudopotential Report - Date of generation 23-07-2021 |
+ ------------------------------------------------------------
+ | Element: Gd Ionic charge: 18.00 Level of theory: LDA |
+ | Atomic Solver: Koelling-Harmon |
+ | |
+ | Reference Electronic Structure |
+ | Orbital Occupation Energy |
+ | 5s 2.000 -1.832 |
+ | 5p 6.000 -1.005 |
+ | 4f 7.000 -0.327 |
+ | 6s 2.000 -0.157 |
+ | 5d 1.000 -0.099 |
+ | |
+ | Pseudopotential Definition |
+ | Beta l e Rc scheme norm |
+ | 1 0 -1.832 2.098 qc 0 |
+ | 2 0 -0.157 2.098 qc 0 |
+ | 3 0 0.250 2.098 qc 0 |
+ | 4 1 -1.005 2.098 qc 0 |
+ | 5 1 0.250 2.098 qc 0 |
+ | 6 3 -0.327 2.098 qc 0 |
+ | 7 3 0.250 2.098 qc 0 |
+ | loc 2 -0.099 2.098 qc 1 |
+ | |
+ | Augmentation charge Rinner = 1.466 |
+ | Partial core correction Rc = 1.466 |
+ ------------------------------------------------------------
+ | "2|2.1|10|12|13|50U:60:51:52L:43(qc=6)" |
+ ------------------------------------------------------------
+ | Author: Chris J. Pickard, Cambridge University |
+ ============================================================
+
+ Pseudo atomic calculation performed for Gd 4f7 5s2 5p6 5d1 6s2
+
+ Converged in 36 iterations to a total energy of -3032.2161 eV
+
+ Calculation parallelised over 16 processes.
+ Data is distributed by G-vector(4-way) and k-point(4-way)
+
+ ************************************ Title ************************************
+
+
+ ***************************** General Parameters ******************************
+
+ output verbosity : normal (1)
+ write checkpoint data to : Gd0.check
+ type of calculation : band structure
+ stress calculation : off
+ density difference calculation : off
+ electron localisation func (ELF) calculation : off
+ Hirshfeld analysis : off
+ unlimited duration calculation
+ timing information : on
+ memory usage estimate : on
+ write extra output files : on
+ write final potential to formatted file : off
+ write final density to formatted file : off
+ write BibTeX reference list : on
+ write OTFG pseudopotential files : on
+ write electrostatic potential file : on
+ write bands file : on
+ checkpoint writing : both castep_bin and check files
+
+ output length unit : A
+ output mass unit : amu
+ output time unit : ps
+ output charge unit : e
+ output spin unit : hbar/2
+ output energy unit : eV
+ output force unit : eV/A
+ output velocity unit : A/ps
+ output pressure unit : GPa
+ output inv_length unit : 1/A
+ output frequency unit : cm-1
+ output force constant unit : eV/A**2
+ output volume unit : A**3
+ output IR intensity unit : (D/A)**2/amu
+ output dipole unit : D
+ output efield unit : eV/A/e
+ output entropy unit : J/mol/K
+
+ wavefunctions paging : none
+ random number generator seed : randomised (220859301)
+ data distribution : optimal for this architecture
+ optimization strategy : maximize speed(+++)
+
+ *********************** Exchange-Correlation Parameters ***********************
+
+ using functional : Local Density Approximation
+ relativistic treatment : Koelling-Harmon
+ DFT+D: Semi-empirical dispersion correction : off
+
+ ************************* Pseudopotential Parameters **************************
+
+ pseudopotential representation : reciprocal space
+ <beta|phi> representation : reciprocal space
+ spin-orbit coupling : off
+
+ **************************** Basis Set Parameters *****************************
+
+ plane wave basis set cut-off : 425.0000 eV
+ size of standard grid : 1.7500
+ size of fine gmax : 18.4829 1/A
+ finite basis set correction : none
+
+ **************************** Electronic Parameters ****************************
+
+ number of electrons : 18.00
+ net charge of system : 0.000
+ net spin of system : 0.000
+ number of up spins : 9.000
+ number of down spins : 9.000
+ treating system as spin-polarized
+ number of bands : 29
+
+ ********************* Electronic Minimization Parameters **********************
+
+ Method: Treating system as metallic with density mixing treatment of electrons,
+ and number of SD steps : 1
+ and number of CG steps : 4
+
+ total energy / atom convergence tol. : 0.5000E-06 eV
+ eigen-energy convergence tolerance : 0.1724E-07 eV
+ max force / atom convergence tol. : ignored
+ convergence tolerance window : 3 cycles
+ max. number of SCF cycles : 100
+ number of fixed-spin iterations : 10
+ smearing scheme : Gaussian
+ smearing width : 0.2000 eV
+ Fermi energy convergence tolerance : 0.2721E-13 eV
+ periodic dipole correction : NONE
+
+ ************************** Density Mixing Parameters **************************
+
+ density-mixing scheme : Broyden
+ max. length of mixing history : 20
+ charge density mixing amplitude : 0.8000
+ spin density mixing amplitude : 2.000
+ cut-off energy for mixing : 425.0 eV
+
+ *********************** Population Analysis Parameters ************************
+
+ Population analysis with cutoff : 3.000 A
+ Population analysis output : summary and pdos components
+
+ ************************** Band Structure Parameters **************************
+
+ max. number of iterations : 60
+ max. CG steps in BS calc : 25
+ number of bands / k-point : 56
+ band convergence tolerance : 0.1000E-05 eV
+ write orbitals file : on
+
+ *******************************************************************************
+
+
+ -------------------------------
+ Unit Cell
+ -------------------------------
+ Real Lattice(A) Reciprocal Lattice(1/A)
+ 0.0000000 2.6200000 2.6200000 -1.199081165 1.199081165 1.199081165
+ 2.6200000 0.0000000 2.6200000 1.199081165 -1.199081165 1.199081165
+ 2.6200000 2.6200000 0.0000000 1.199081165 1.199081165 -1.199081165
+
+ Lattice parameters(A) Cell Angles
+ a = 3.705240 alpha = 60.000000
+ b = 3.705240 beta = 60.000000
+ c = 3.705240 gamma = 60.000000
+
+ Current cell volume = 35.969456 A**3
+ density = 4.371765 AMU/A**3
+ = 7.259486 g/cm^3
+
+ -------------------------------
+ Cell Contents
+ -------------------------------
+ Total number of ions in cell = 1
+ Total number of species in cell = 1
+ Max number of any one species = 1
+
+ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+ x Element Atom Fractional coordinates of atoms x
+ x Number u v w x
+ x----------------------------------------------------------x
+ x Gd 1 0.000000 0.000000 0.000000 x
+ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+
+
+ No user defined ionic velocities
+
+ -------------------------------
+ Details of Species
+ -------------------------------
+
+ Mass of species in AMU
+ Gd 157.2500000
+
+ Electric Quadrupole Moment (Barn)
+ Gd 1.3500000 Isotope157
+
+
+ Quantisation axis: 1.00000 -1.00000 1.00000
+
+ Units for Hubbard U values are eV
+ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+ | Element Atom Hubbard U values by orbital type |
+ | Number s p d f |
+ |------------------------------------------------------------------|
+ |Gd 1 0.00000 0.00000 0.00000 6.70000 |
+ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+
+
+ Files used for pseudopotentials:
+ Gd 2|2.1|10|12|13|50U:60:51:52L:43(qc=6)
+
+ -------------------------------
+ k-Points For BZ Sampling
+ -------------------------------
+ Number of kpoints used = 468
+
+ -------------------------------
+ Symmetry and Constraints
+ -------------------------------
+
+ Maximum deviation from symmetry = 0.470004E-15 ANG
+ Magnetic structure symmetry:
+ User supplied or default Hubbard U data has reduced the symmetry of the system
+
+ Number of symmetry operations = 16
+ Number of ionic constraints = 3
+ Point group of crystal = 15: D4h, 4/mmm, 4/m 2/m 2/m
+ Space group of crystal = 225: Fm-3m, -F 4 2 3
+
+ Set iprint > 1 for details on symmetry rotations/translations
+
+ Centre of mass is constrained
+ Set iprint > 1 for details of linear ionic constraints
+
+ Number of cell constraints= 5
+ Cell constraints are: 1 1 1 0 0 0
+
+ External pressure/stress (GPa)
+ 0.00000 0.00000 0.00000
+ 0.00000 0.00000
+ 0.00000
+
++---------------- MEMORY AND SCRATCH DISK ESTIMATES PER PROCESS --------------+
+| Memory Disk |
+| Baseline code, static data and system overhead 412.0 MB 0.0 MB |
+| BLAS internal memory storage 0.0 MB 0.0 MB |
+| Model and support data 61.3 MB 0.0 MB |
+| Electronic energy minimisation requirements 46.4 MB 0.0 MB |
+| Force calculation requirements 0.8 MB 0.0 MB |
+| ----------------------------- |
+| Approx. total storage required per process 519.8 MB 0.0 MB |
+| |
+| Requirements will fluctuate during execution and may exceed these estimates |
++-----------------------------------------------------------------------------+
+Calculating total energy with cut-off of 425.000 eV.
+
+ Pseudo atomic calculation performed for Gd 4f7 5s2 5p6 5d1 6s2
+
+ Converged in 36 iterations to a total energy of -3032.2161 eV
+
+------------------------------------------------------------------------ <-- SCF
+SCF loop Energy Fermi Energy gain Timer <-- SCF
+ energy per atom (sec) <-- SCF
+------------------------------------------------------------------------ <-- SCF
+Initial -2.89965509E+003 0.00000000E+000 23.29 <-- SCF
+ 1 -2.98520074E+003 5.92001968E+000 8.55456534E+001 31.55 <-- SCF
+ 2 -3.03447725E+003 3.86911470E+000 4.92765152E+001 36.97 <-- SCF
+ 3 -3.03681060E+003 3.63238351E+000 2.33334698E+000 43.81 <-- SCF
+ 4 -3.08547151E+003 1.11125785E+001 4.86609050E+001 50.50 <-- SCF
+ 5 -3.08550199E+003 1.11064276E+001 3.04836941E-002 56.76 <-- SCF
+ 6 -3.02275477E+003 6.81693038E+000 -6.27472234E+001 63.20 <-- SCF
+ 7 -3.02299014E+003 6.77095701E+000 2.35372118E-001 70.44 <-- SCF
+ 8 -3.04218983E+003 1.36123180E-001 1.91996938E+001 77.78 <-- SCF
+ 9 -3.04226024E+003 1.32481040E-001 7.04039618E-002 83.82 <-- SCF
+ 10 -3.04346335E+003 -3.60111841E-002 1.20311029E+000 90.86 <-- SCF
+ 11 -3.18377830E+003 1.23926479E+001 1.40314957E+002 97.55 <-- SCF
+ 12 -3.18388218E+003 1.23786135E+001 1.03873732E-001 103.56 <-- SCF
+ 13 -3.04005602E+003 9.81148656E+000 -1.43826153E+002 110.06 <-- SCF
+ 14 -3.04060896E+003 9.64709145E+000 5.52934090E-001 116.82 <-- SCF
+ 15 -3.21926684E+003 -2.66698179E+001 1.78657886E+002 126.49 <-- SCF
+ 16 -3.21995318E+003 -2.66884642E+001 6.86339316E-001 132.70 <-- SCF
+ 17 -3.06822919E+003 -1.00743714E+001 -1.51723994E+002 139.43 <-- SCF
+ 18 -3.06839525E+003 -1.00807260E+001 1.66060994E-001 146.17 <-- SCF
+ 19 -3.03568611E+003 6.91936508E+000 -3.27091430E+001 152.51 <-- SCF
+ 20 -3.03577872E+003 6.91141545E+000 9.26104454E-002 160.06 <-- SCF
+ 21 -3.03377995E+003 3.72897532E+000 -1.99877019E+000 166.53 <-- SCF
+ 22 -3.03551763E+003 4.26115079E+000 1.73767987E+000 172.99 <-- SCF
+ 23 -3.03667303E+003 5.67930673E+000 1.15539756E+000 180.65 <-- SCF
+ 24 -3.03773904E+003 5.77488976E+000 1.06601260E+000 187.04 <-- SCF
+ 25 -3.03530269E+003 5.55347087E+000 -2.43634714E+000 194.27 <-- SCF
+ 26 -3.05032776E+003 -9.70548183E-001 1.50250654E+001 201.68 <-- SCF
+ 27 -3.05033208E+003 -9.70678755E-001 4.32051862E-003 208.85 <-- SCF
+ 28 -3.04539413E+003 -1.45391667E-001 -4.93794546E+000 215.82 <-- SCF
+ 29 -3.04539557E+003 -1.45497023E-001 1.44054842E-003 222.81 <-- SCF
+ 30 -3.13452484E+003 1.30254108E+001 8.91292691E+001 229.42 <-- SCF
+ 31 -3.13460994E+003 1.30110021E+001 8.50980851E-002 235.51 <-- SCF
+ 32 -3.06845909E+003 1.14127813E+001 -6.61508513E+001 241.91 <-- SCF
+ 33 -3.06850908E+003 1.14098622E+001 4.99932106E-002 248.67 <-- SCF
+ 34 -3.20411507E+003 -2.77108829E+001 1.35605986E+002 256.46 <-- SCF
+ 35 -3.20803541E+003 -2.77582286E+001 3.92034643E+000 263.96 <-- SCF
+ 36 -3.20804627E+003 -2.77582828E+001 1.08581388E-002 269.81 <-- SCF
+ 37 -3.12705607E+003 -3.12322670E+001 -8.09902058E+001 276.78 <-- SCF
+ 38 -3.12726508E+003 -3.12325885E+001 2.09016565E-001 283.24 <-- SCF
+ 39 -2.80683975E+003 1.00683380E+001 -3.20425334E+002 289.43 <-- SCF
+ 40 -2.80981984E+003 1.00332056E+001 2.98008829E+000 296.42 <-- SCF
+ 41 -2.80983673E+003 1.00330337E+001 1.68957548E-002 302.66 <-- SCF
+ 42 -3.04675051E+003 3.05979985E+000 2.36913775E+002 309.19 <-- SCF
+ 43 -3.04770013E+003 3.04477995E+000 9.49622910E-001 316.24 <-- SCF
+ 44 -3.04319238E+003 6.32951414E+000 -4.50775184E+000 322.94 <-- SCF
+ 45 -3.04321010E+003 6.32922112E+000 1.77232477E-002 329.70 <-- SCF
+ 46 -3.04943311E+003 5.58467038E+000 6.22300834E+000 336.05 <-- SCF
+ 47 -3.04945005E+003 5.58445434E+000 1.69348793E-002 343.45 <-- SCF
+ 48 -3.05455023E+003 5.39146007E+000 5.10018256E+000 349.77 <-- SCF
+ 49 -3.05456243E+003 5.39108103E+000 1.22027647E-002 357.67 <-- SCF
+ 50 -3.05493417E+003 5.26679242E+000 3.71738203E-001 364.01 <-- SCF
+ 51 -3.05525737E+003 4.90318130E+000 3.23200386E-001 370.46 <-- SCF
+ 52 -3.05506850E+003 4.95046824E+000 -1.88868372E-001 376.87 <-- SCF
+ 53 -3.05509778E+003 4.93855394E+000 2.92747541E-002 383.16 <-- SCF
+ 54 -3.05515680E+003 4.98485842E+000 5.90291045E-002 389.88 <-- SCF
+ 55 -3.05516098E+003 4.95329078E+000 4.17686172E-003 396.12 <-- SCF
+ 56 -3.05516001E+003 4.95987680E+000 -9.74111769E-004 403.37 <-- SCF
+ 57 -3.05515903E+003 4.97052811E+000 -9.74714884E-004 410.40 <-- SCF
+ 58 -3.05515905E+003 4.97104973E+000 1.55635104E-005 417.73 <-- SCF
+ 59 -3.05515907E+003 4.97088718E+000 2.60727692E-005 423.86 <-- SCF
+ 60 -3.05515908E+003 4.97087885E+000 1.64496093E-006 427.91 <-- SCF
+ 61 -3.05515908E+003 4.97088929E+000 5.32972948E-008 431.93 <-- SCF
+ 62 -3.05515908E+003 4.97090488E+000 1.03062499E-008 435.90 <-- SCF
+------------------------------------------------------------------------ <-- SCF
+
+Integrated Spin Density = -7.72332 hbar/2
+Integrated |Spin Density| = 7.72332 hbar/2
+
+
+ Hubbard U occupation numbers
+ ----------------------------
+Species Ion l spin occupancies
+==================================================================
+ Gd 1 3 up: 0.00 0.00 0.00 0.00 0.00 0.00 0.00
+ dn: 1.00 1.00 1.00 1.00 1.00 1.00 1.00
+==================================================================
+
+Final energy, E = -3055.124910556 eV
+Final free energy (E-TS) = -3055.159075896 eV
+(energies not corrected for finite basis set)
+
+NB est. 0K energy (E-0.5TS) = -3055.141993226 eV
+
+ +-------------------------------------------------+
+ | |
+ | CCC AA SSS TTTTT EEEEE PPPP |
+ | C A A S T E P P |
+ | C AAAA SS T EEE PPPP |
+ | C A A S T E P |
+ | CCC A A SSS T EEEEE P |
+ | |
+ +-------------------------------------------------+
+ | |
+ | Welcome to Academic Release CASTEP version 18.1 |
+ | Ab Initio Total Energy Program |
+ | |
+ | Authors: |
+ | M. Segall, M. Probert, C. Pickard, P. Hasnip, |
+ | S. Clark, K. Refson, J. R. Yates, M. Payne |
+ | |
+ | Contributors: |
+ | P. Lindan, P. Haynes, J. White, V. Milman, |
+ | N. Govind, M. Gibson, P. Tulip, V. Cocula, |
+ | B. Montanari, D. Quigley, M. Glover, |
+ | L. Bernasconi, A. Perlov, M. Plummer, |
+ | E. McNellis, J. Meyer, J. Gale, D. Jochym |
+ | J. Aarons, B. Walker, R. Gillen, D. Jones |
+ | T. Green, I. J. Bush, C. J. Armstrong, |
+ | E. J. Higgins, E. L. Brown, M. S. McFly, |
+ | J. Wilkins, B-C. Shih, P. J. P. Byrne |
+ | |
+ | Copyright (c) 2000 - 2017 |
+ | |
+ | Distributed under the terms of an |
+ | Agreement between the United Kingdom |
+ | Car-Parrinello (UKCP) Consortium, |
+ | Daresbury Laboratory and Accelrys, Inc. |
+ | |
+ | Please cite |
+ | |
+ | "First principles methods using CASTEP" |
+ | |
+ | Zeitschrift fuer Kristallographie |
+ | 220(5-6) pp. 567-570 (2005) |
+ | |
+ | S. J. Clark, M. D. Segall, C. J. Pickard, |
+ | P. J. Hasnip, M. J. Probert, K. Refson, |
+ | M. C. Payne |
+ | |
+ | in all publications arising from |
+ | your use of CASTEP |
+ | |
+ +-------------------------------------------------+
+
+
+ Compiled for linux_x86_64_gfortran4.8 on Thu, 19 Jul 2018 15:42:32 +0100
+ from code version 70483bd0ad64+ Sun, 10 Dec 2017 12:18:29 +0000
+ Compiler: GNU Fortran 4.8.5; Optimisation: fast
+ MATHLIBS: Intel MKL(2018.0.0) (LAPACK version 3.7.0)
+ FFT Lib : mkl
+ Fundamental constants values: CODATA 2014
+
+ Run started: Fri, 23 Jul 2021 22:08:58 +0100
+ Info: number of up-spin electrons is equal to the
+ number of down-spins and spin_polarized=true
+ - consider setting spin_polarized=false.
+
+ Atomic calculation performed for Gd:
+ 1s2 2s2 2p6 3s2 3p6 3d10 4s2 4p6 4d10 4f7 5s2 5p6 5d1 6s2
+
+ Converged in 116 iterations to an ae energy of -306496.732 eV
+
+ ============================================================
+ | Pseudopotential Report - Date of generation 23-07-2021 |
+ ------------------------------------------------------------
+ | Element: Gd Ionic charge: 18.00 Level of theory: LDA |
+ | Atomic Solver: Koelling-Harmon |
+ | |
+ | Reference Electronic Structure |
+ | Orbital Occupation Energy |
+ | 5s 2.000 -1.832 |
+ | 5p 6.000 -1.005 |
+ | 4f 7.000 -0.327 |
+ | 6s 2.000 -0.157 |
+ | 5d 1.000 -0.099 |
+ | |
+ | Pseudopotential Definition |
+ | Beta l e Rc scheme norm |
+ | 1 0 -1.832 2.098 qc 0 |
+ | 2 0 -0.157 2.098 qc 0 |
+ | 3 0 0.250 2.098 qc 0 |
+ | 4 1 -1.005 2.098 qc 0 |
+ | 5 1 0.250 2.098 qc 0 |
+ | 6 3 -0.327 2.098 qc 0 |
+ | 7 3 0.250 2.098 qc 0 |
+ | loc 2 -0.099 2.098 qc 1 |
+ | |
+ | Augmentation charge Rinner = 1.466 |
+ | Partial core correction Rc = 1.466 |
+ ------------------------------------------------------------
+ | "2|2.1|10|12|13|50U:60:51:52L:43(qc=6)" |
+ ------------------------------------------------------------
+ | Author: Chris J. Pickard, Cambridge University |
+ ============================================================
+
+ Pseudo atomic calculation performed for Gd 4f7 5s2 5p6 5d1 6s2
+
+ Converged in 36 iterations to a total energy of -3032.2161 eV
+
+ Calculation parallelised over 16 processes.
+ Data is distributed by G-vector(4-way) and k-point(4-way)
+
+ ************************************ Title ************************************
+
+
+ ***************************** General Parameters ******************************
+
+ output verbosity : normal (1)
+ write checkpoint data to : Gd0.check
+ type of calculation : band structure
+ stress calculation : off
+ density difference calculation : off
+ electron localisation func (ELF) calculation : off
+ Hirshfeld analysis : off
+ unlimited duration calculation
+ timing information : on
+ memory usage estimate : on
+ write extra output files : on
+ write final potential to formatted file : off
+ write final density to formatted file : off
+ write BibTeX reference list : on
+ write OTFG pseudopotential files : on
+ write electrostatic potential file : on
+ write bands file : on
+ checkpoint writing : both castep_bin and check files
+
+ output length unit : A
+ output mass unit : amu
+ output time unit : ps
+ output charge unit : e
+ output spin unit : hbar/2
+ output energy unit : eV
+ output force unit : eV/A
+ output velocity unit : A/ps
+ output pressure unit : GPa
+ output inv_length unit : 1/A
+ output frequency unit : cm-1
+ output force constant unit : eV/A**2
+ output volume unit : A**3
+ output IR intensity unit : (D/A)**2/amu
+ output dipole unit : D
+ output efield unit : eV/A/e
+ output entropy unit : J/mol/K
+
+ wavefunctions paging : none
+ random number generator seed : randomised (220859301)
+ data distribution : optimal for this architecture
+ optimization strategy : maximize speed(+++)
+
+ *********************** Exchange-Correlation Parameters ***********************
+
+ using functional : Local Density Approximation
+ relativistic treatment : Koelling-Harmon
+ DFT+D: Semi-empirical dispersion correction : off
+
+ ************************* Pseudopotential Parameters **************************
+
+ pseudopotential representation : reciprocal space
+ <beta|phi> representation : reciprocal space
+ spin-orbit coupling : off
+
+ **************************** Basis Set Parameters *****************************
+
+ plane wave basis set cut-off : 425.0000 eV
+ size of standard grid : 1.7500
+ size of fine gmax : 18.4829 1/A
+ finite basis set correction : none
+
+ **************************** Electronic Parameters ****************************
+
+ number of electrons : 18.00
+ net charge of system : 0.000
+ net spin of system : 0.000
+ number of up spins : 9.000
+ number of down spins : 9.000
+ treating system as spin-polarized
+ number of bands : 29
+
+ ********************* Electronic Minimization Parameters **********************
+
+ Method: Treating system as metallic with density mixing treatment of electrons,
+ and number of SD steps : 1
+ and number of CG steps : 4
+
+ total energy / atom convergence tol. : 0.5000E-06 eV
+ eigen-energy convergence tolerance : 0.1724E-07 eV
+ max force / atom convergence tol. : ignored
+ convergence tolerance window : 3 cycles
+ max. number of SCF cycles : 100
+ number of fixed-spin iterations : 10
+ smearing scheme : Gaussian
+ smearing width : 0.2000 eV
+ Fermi energy convergence tolerance : 0.2721E-13 eV
+ periodic dipole correction : NONE
+
+ ************************** Density Mixing Parameters **************************
+
+ density-mixing scheme : Broyden
+ max. length of mixing history : 20
+ charge density mixing amplitude : 0.8000
+ spin density mixing amplitude : 2.000
+ cut-off energy for mixing : 425.0 eV
+
+ *********************** Population Analysis Parameters ************************
+
+ Population analysis with cutoff : 3.000 A
+ Population analysis output : summary and pdos components
+
+ ************************** Band Structure Parameters **************************
+
+ max. number of iterations : 60
+ max. CG steps in BS calc : 25
+ number of bands / k-point : 56
+ band convergence tolerance : 0.1000E-05 eV
+ write orbitals file : on
+
+ *******************************************************************************
+
+
+ -------------------------------
+ Unit Cell
+ -------------------------------
+ Real Lattice(A) Reciprocal Lattice(1/A)
+ 0.0000000 2.6200000 2.6200000 -1.199081165 1.199081165 1.199081165
+ 2.6200000 0.0000000 2.6200000 1.199081165 -1.199081165 1.199081165
+ 2.6200000 2.6200000 0.0000000 1.199081165 1.199081165 -1.199081165
+
+ Lattice parameters(A) Cell Angles
+ a = 3.705240 alpha = 60.000000
+ b = 3.705240 beta = 60.000000
+ c = 3.705240 gamma = 60.000000
+
+ Current cell volume = 35.969456 A**3
+ density = 4.371765 AMU/A**3
+ = 7.259486 g/cm^3
+
+ -------------------------------
+ Cell Contents
+ -------------------------------
+ Total number of ions in cell = 1
+ Total number of species in cell = 1
+ Max number of any one species = 1
+
+ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+ x Element Atom Fractional coordinates of atoms x
+ x Number u v w x
+ x----------------------------------------------------------x
+ x Gd 1 0.000000 0.000000 0.000000 x
+ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+
+
+ No user defined ionic velocities
+
+ -------------------------------
+ Details of Species
+ -------------------------------
+
+ Mass of species in AMU
+ Gd 157.2500000
+
+ Electric Quadrupole Moment (Barn)
+ Gd 1.3500000 Isotope157
+
+
+ Quantisation axis: 1.00000 -1.00000 1.00000
+
+ Units for Hubbard U values are eV
+ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+ | Element Atom Hubbard U values by orbital type |
+ | Number s p d f |
+ |------------------------------------------------------------------|
+ |Gd 1 0.00000 0.00000 0.00000 6.70000 |
+ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+
+
+ Files used for pseudopotentials:
+ Gd 2|2.1|10|12|13|50U:60:51:52L:43(qc=6)
+
+ -------------------------------
+ k-Points For BZ Sampling
+ -------------------------------
+ Number of kpoints used = 468
+
+ -------------------------------
+ Symmetry and Constraints
+ -------------------------------
+
+ Maximum deviation from symmetry = 0.470004E-15 ANG
+ Magnetic structure symmetry:
+ User supplied or default Hubbard U data has reduced the symmetry of the system
+
+ Number of symmetry operations = 16
+ Number of ionic constraints = 3
+ Point group of crystal = 15: D4h, 4/mmm, 4/m 2/m 2/m
+ Space group of crystal = 225: Fm-3m, -F 4 2 3
+
+ Set iprint > 1 for details on symmetry rotations/translations
+
+ Centre of mass is constrained
+ Set iprint > 1 for details of linear ionic constraints
+
+ Number of cell constraints= 5
+ Cell constraints are: 1 1 1 0 0 0
+
+ External pressure/stress (GPa)
+ 0.00000 0.00000 0.00000
+ 0.00000 0.00000
+ 0.00000
+
++---------------- MEMORY AND SCRATCH DISK ESTIMATES PER PROCESS --------------+
+| Memory Disk |
+| Baseline code, static data and system overhead 412.0 MB 0.0 MB |
+| BLAS internal memory storage 0.0 MB 0.0 MB |
+| Model and support data 61.3 MB 0.0 MB |
+| Electronic energy minimisation requirements 46.4 MB 0.0 MB |
+| Force calculation requirements 0.8 MB 0.0 MB |
+| ----------------------------- |
+| Approx. total storage required per process 519.8 MB 0.0 MB |
+| |
+| Requirements will fluctuate during execution and may exceed these estimates |
++-----------------------------------------------------------------------------+
+Calculating total energy with cut-off of 425.000 eV.
+
+ Pseudo atomic calculation performed for Gd 4f7 5s2 5p6 5d1 6s2
+
+ Converged in 36 iterations to a total energy of -3032.2161 eV
+
+------------------------------------------------------------------------ <-- SCF
+SCF loop Energy Fermi Energy gain Timer <-- SCF
+ energy per atom (sec) <-- SCF
+------------------------------------------------------------------------ <-- SCF
+Initial -2.89965509E+003 0.00000000E+000 23.29 <-- SCF
+ 1 -2.98520074E+003 5.92001968E+000 8.55456534E+001 31.55 <-- SCF
+ 2 -3.03447725E+003 3.86911470E+000 4.92765152E+001 36.97 <-- SCF
+ 3 -3.03681060E+003 3.63238351E+000 2.33334698E+000 43.81 <-- SCF
+ 4 -3.08547151E+003 1.11125785E+001 4.86609050E+001 50.50 <-- SCF
+ 5 -3.08550199E+003 1.11064276E+001 3.04836941E-002 56.76 <-- SCF
+ 6 -3.02275477E+003 6.81693038E+000 -6.27472234E+001 63.20 <-- SCF
+ 7 -3.02299014E+003 6.77095701E+000 2.35372118E-001 70.44 <-- SCF
+ 8 -3.04218983E+003 1.36123180E-001 1.91996938E+001 77.78 <-- SCF
+ 9 -3.04226024E+003 1.32481040E-001 7.04039618E-002 83.82 <-- SCF
+ 10 -3.04346335E+003 -3.60111841E-002 1.20311029E+000 90.86 <-- SCF
+ 11 -3.18377830E+003 1.23926479E+001 1.40314957E+002 97.55 <-- SCF
+ 12 -3.18388218E+003 1.23786135E+001 1.03873732E-001 103.56 <-- SCF
+ 13 -3.04005602E+003 9.81148656E+000 -1.43826153E+002 110.06 <-- SCF
+ 14 -3.04060896E+003 9.64709145E+000 5.52934090E-001 116.82 <-- SCF
+ 15 -3.21926684E+003 -2.66698179E+001 1.78657886E+002 126.49 <-- SCF
+ 16 -3.21995318E+003 -2.66884642E+001 6.86339316E-001 132.70 <-- SCF
+ 17 -3.06822919E+003 -1.00743714E+001 -1.51723994E+002 139.43 <-- SCF
+ 18 -3.06839525E+003 -1.00807260E+001 1.66060994E-001 146.17 <-- SCF
+ 19 -3.03568611E+003 6.91936508E+000 -3.27091430E+001 152.51 <-- SCF
+ 20 -3.03577872E+003 6.91141545E+000 9.26104454E-002 160.06 <-- SCF
+ 21 -3.03377995E+003 3.72897532E+000 -1.99877019E+000 166.53 <-- SCF
+ 22 -3.03551763E+003 4.26115079E+000 1.73767987E+000 172.99 <-- SCF
+ 23 -3.03667303E+003 5.67930673E+000 1.15539756E+000 180.65 <-- SCF
+ 24 -3.03773904E+003 5.77488976E+000 1.06601260E+000 187.04 <-- SCF
+ 25 -3.03530269E+003 5.55347087E+000 -2.43634714E+000 194.27 <-- SCF
+ 26 -3.05032776E+003 -9.70548183E-001 1.50250654E+001 201.68 <-- SCF
+ 27 -3.05033208E+003 -9.70678755E-001 4.32051862E-003 208.85 <-- SCF
+ 28 -3.04539413E+003 -1.45391667E-001 -4.93794546E+000 215.82 <-- SCF
+ 29 -3.04539557E+003 -1.45497023E-001 1.44054842E-003 222.81 <-- SCF
+ 30 -3.13452484E+003 1.30254108E+001 8.91292691E+001 229.42 <-- SCF
+ 31 -3.13460994E+003 1.30110021E+001 8.50980851E-002 235.51 <-- SCF
+ 32 -3.06845909E+003 1.14127813E+001 -6.61508513E+001 241.91 <-- SCF
+ 33 -3.06850908E+003 1.14098622E+001 4.99932106E-002 248.67 <-- SCF
+ 34 -3.20411507E+003 -2.77108829E+001 1.35605986E+002 256.46 <-- SCF
+ 35 -3.20803541E+003 -2.77582286E+001 3.92034643E+000 263.96 <-- SCF
+ 36 -3.20804627E+003 -2.77582828E+001 1.08581388E-002 269.81 <-- SCF
+ 37 -3.12705607E+003 -3.12322670E+001 -8.09902058E+001 276.78 <-- SCF
+ 38 -3.12726508E+003 -3.12325885E+001 2.09016565E-001 283.24 <-- SCF
+ 39 -2.80683975E+003 1.00683380E+001 -3.20425334E+002 289.43 <-- SCF
+ 40 -2.80981984E+003 1.00332056E+001 2.98008829E+000 296.42 <-- SCF
+ 41 -2.80983673E+003 1.00330337E+001 1.68957548E-002 302.66 <-- SCF
+ 42 -3.04675051E+003 3.05979985E+000 2.36913775E+002 309.19 <-- SCF
+ 43 -3.04770013E+003 3.04477995E+000 9.49622910E-001 316.24 <-- SCF
+ 44 -3.04319238E+003 6.32951414E+000 -4.50775184E+000 322.94 <-- SCF
+ 45 -3.04321010E+003 6.32922112E+000 1.77232477E-002 329.70 <-- SCF
+ 46 -3.04943311E+003 5.58467038E+000 6.22300834E+000 336.05 <-- SCF
+ 47 -3.04945005E+003 5.58445434E+000 1.69348793E-002 343.45 <-- SCF
+ 48 -3.05455023E+003 5.39146007E+000 5.10018256E+000 349.77 <-- SCF
+ 49 -3.05456243E+003 5.39108103E+000 1.22027647E-002 357.67 <-- SCF
+ 50 -3.05493417E+003 5.26679242E+000 3.71738203E-001 364.01 <-- SCF
+ 51 -3.05525737E+003 4.90318130E+000 3.23200386E-001 370.46 <-- SCF
+ 52 -3.05506850E+003 4.95046824E+000 -1.88868372E-001 376.87 <-- SCF
+ 53 -3.05509778E+003 4.93855394E+000 2.92747541E-002 383.16 <-- SCF
+ 54 -3.05515680E+003 4.98485842E+000 5.90291045E-002 389.88 <-- SCF
+ 55 -3.05516098E+003 4.95329078E+000 4.17686172E-003 396.12 <-- SCF
+ 56 -3.05516001E+003 4.95987680E+000 -9.74111769E-004 403.37 <-- SCF
+ 57 -3.05515903E+003 4.97052811E+000 -9.74714884E-004 410.40 <-- SCF
+ 58 -3.05515905E+003 4.97104973E+000 1.55635104E-005 417.73 <-- SCF
+ 59 -3.05515907E+003 4.97088718E+000 2.60727692E-005 423.86 <-- SCF
+ 60 -3.05515908E+003 4.97087885E+000 1.64496093E-006 427.91 <-- SCF
+ 61 -3.05515908E+003 4.97088929E+000 5.32972948E-008 431.93 <-- SCF
+ 62 -3.05515908E+003 4.97090488E+000 1.03062499E-008 435.90 <-- SCF
+------------------------------------------------------------------------ <-- SCF
+
+Integrated Spin Density = -7.72332 hbar/2
+Integrated |Spin Density| = 7.72332 hbar/2
+
+
+ Hubbard U occupation numbers
+ ----------------------------
+Species Ion l spin occupancies
+==================================================================
+ Gd 1 3 up: 0.00 0.00 0.00 0.00 0.00 0.00 0.00
+ dn: 1.00 1.00 1.00 1.00 1.00 1.00 1.00
+==================================================================
+
+Final energy, E = -3055.124910556 eV
+Final free energy (E-TS) = -3055.159075896 eV
+(energies not corrected for finite basis set)
+
+NB est. 0K energy (E-0.5TS) = -3055.141993226 eV