diff --git a/include/tadah/mlip/dataset_readers/vasp_outcar_reader.h b/include/tadah/mlip/dataset_readers/vasp_outcar_reader.h
index b5bc0644fd5e30e7faef4d08d62499f4ffe0e8c6..34c861a26cc041f7331a3e2bcbea0211a2150ff8 100644
--- a/include/tadah/mlip/dataset_readers/vasp_outcar_reader.h
+++ b/include/tadah/mlip/dataset_readers/vasp_outcar_reader.h
@@ -73,6 +73,7 @@ public:
private:
std::string raw_data_; // Stores raw file data
+ std::string filename_; // Stores raw file data
double s_conv = 6.241509074e-4; // kbar -> eV/A^3
};
diff --git a/include/tadah/mlip/structure.h b/include/tadah/mlip/structure.h
index 9648e651d066839a2cac3953d789717a4369064f..306ca2c7e87695b5041881c41795e5e066fb48ea 100644
--- a/include/tadah/mlip/structure.h
+++ b/include/tadah/mlip/structure.h
@@ -62,6 +62,12 @@ struct Structure {
/** Container for atoms which belong to this structure */
std::vector<Atom> atoms;
+ /** Temperature of this structure.
+ *
+ * Default is 0.0
+ */
+ double T=0;
+
/**
* Container for nearest neighbour atoms for every atom in the structure.
*/
diff --git a/src/castep_castep_reader.cpp b/src/castep_castep_reader.cpp
index 89fed3a698fe276636ae9f808a7e8207adda284d..b27d0bd7d3869202c10120a3bd861585f0968a6b 100644
--- a/src/castep_castep_reader.cpp
+++ b/src/castep_castep_reader.cpp
@@ -245,13 +245,21 @@ void CastepCastepReader::parse_data() {
}
else if (line.find("Potential Energy:") != std::string::npos) {
- // MD: end of iteration
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;
}
+ }
+ else if (line.find("Temperature:") != std::string::npos) {
+ // MD: end of iteration
+ std::istringstream iss(line);
+ std::string tmp;
+ if (!(iss >> tmp >> tmp >> s.T)) {
+ std::cerr << "Warning, file" << filename << " line: " << counter << std::endl;
+ std::cerr << "Warning: Unexpected end of data when reading temperature" << std::endl;
+ }
if (!label.size())label = "CASTEP MD, const. volume: false, step: 0"; // the last option
s.label = label;
diff --git a/src/castep_md_reader.cpp b/src/castep_md_reader.cpp
index a592172754bda721a102bac7326d85a9c1763d35..d75b260c441f298c11273da9dc44d661e446bad2 100644
--- a/src/castep_md_reader.cpp
+++ b/src/castep_md_reader.cpp
@@ -46,7 +46,7 @@ void CastepMDReader::postproc_structure(Structure &s) {
// finish conversion
s.cell *= d_conv;
s.stress *= s_conv;
- // T /= k_b;
+ s.T = T/k_b;
// add to database
stdb.add(s);
@@ -101,17 +101,18 @@ void CastepMDReader::parse_data() {
int S_flag=0;
bool R_flag=false;
bool F_flag=false;
+ bool T_flag=false;
bool complete_structure=false;
while (std::getline(stream, line)) {
if (ends_with(line,"<-- T")) {
- if (/* T_flag || */ complete_structure) {
+ if (T_flag || complete_structure) {
error=true;
continue;
}
std::istringstream iss(line);
iss >> T;
- //T_flag=true;
+ T_flag=true;
}
else if (ends_with(line,"<-- E")) {
if (/* T_flag || */ E_flag || complete_structure) {
@@ -187,7 +188,7 @@ void CastepMDReader::parse_data() {
postproc_structure(s);
error=false;
- //T_flag=false;
+ T_flag=false;
E_flag=false;
H_flag=0;
S_flag=0;
diff --git a/src/dataset_reader_selector.cpp b/src/dataset_reader_selector.cpp
index bdc6d2004520d482132c70e7627dd562d7cef1ee..ef5d8b1cd6ce3d692796a424c5cb36f4b8a1353c 100644
--- a/src/dataset_reader_selector.cpp
+++ b/src/dataset_reader_selector.cpp
@@ -41,12 +41,11 @@ std::string DatasetReaderSelector::determine_file_type_by_content(const std::str
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";
- }
+ if (line.find("incar:") != std::string::npos || line.find("OUTCAR:") != std::string::npos ||
+ line.find("outcar") != std::string::npos || line.find("POTCAR:") != 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";
diff --git a/src/structure.cpp b/src/structure.cpp
index f5c67485f3266e556818436c1e8b250be8613a37..2d870bbecdacab8f4fd35779ef42c9f6cc111174 100644
--- a/src/structure.cpp
+++ b/src/structure.cpp
@@ -53,8 +53,17 @@ int Structure::read(std::ifstream &ifs) {
stream.clear();
stream.seekg(0, std::ios::beg);
stream >> eweight >> fweight >> sweight;
- // energy
- ifs >> energy;
+ std::getline(ifs,line);
+ std::stringstream stream2(line);
+ // energy and T
+ stream2 >> energy;
+ if(stream2) stream2 >> T;
+ }
+ else if (count == 2) {
+ stream.clear();
+ stream.seekg(0, std::ios::beg);
+ // energy and T
+ stream >> energy >> T;
}
else {
energy = std::stod(line);
@@ -262,7 +271,7 @@ void Structure::dump_to_file(std::ostream& file, size_t prec) const {
file << label << std::endl;
file << std::fixed << std::setprecision(prec);
file << eweight << " " << fweight << " " << sweight << std::endl;
- file << energy << std::endl;
+ file << energy << " " << T << std::endl;
file
<< std::setw(prec+n) << cell(0,0) << " "
diff --git a/src/vasp_outcar_reader.cpp b/src/vasp_outcar_reader.cpp
index d5fccef6162056f6137a513447d1b122a0452d15..d1ead35e7ecb00f1c860d7559574f78e475af0e9 100644
--- a/src/vasp_outcar_reader.cpp
+++ b/src/vasp_outcar_reader.cpp
@@ -10,7 +10,7 @@
VaspOutcarReader::VaspOutcarReader(StructureDB& db) : DatasetReader(db) {}
VaspOutcarReader::VaspOutcarReader(StructureDB& db, const std::string& filename)
-: DatasetReader(db, filename) {
+: DatasetReader(db, filename), filename_(filename) {
read_data(filename);
}
@@ -38,14 +38,21 @@ void VaspOutcarReader::parse_data() {
size_t natoms;;
bool stress_tensor_bool = false;
bool complete_structure = false;
+ bool is_md = false;
Structure s;
+ size_t counter=0;
while (std::getline(stream, line)) {
- if (line.find("VRHFIN") != std::string::npos) {
+ if (line.find("molecular dynamics") != std::string::npos) {
+ is_md = true;
+ s.label += "MD ";
+ }
+ else if (line.find("VRHFIN") != std::string::npos) {
std::string type = line.substr(line.find("=") + 1);
type = type.substr(0, type.find(":"));
atom_types.push_back(type);
+ s.label += filename_ + " ";
}
else if (line.find("NIONS") != std::string::npos) {
@@ -164,8 +171,20 @@ void VaspOutcarReader::parse_data() {
if (!(iss >> tmp >> tmp >> tmp >> s.energy)) {
std::cerr << "Warning: Unexpected end of data when reading total energy" << std::endl;
}
+ else if (!is_md) {
+ complete_structure = true;
+ s.label += "Structure " + std::to_string(++counter);
+ }
+ }
+ else if (line.find("EKIN_LAT=") != std::string::npos) {
+ std::istringstream iss(line);
+ std::string tmp;
+ if (!(iss >> tmp >> tmp >> tmp >> tmp >> tmp >> s.T)) {
+ std::cerr << "Warning: Unexpected end of data when reading temperature" << std::endl;
+ }
else {
complete_structure = true;
+ s.label += "Structure " + std::to_string(++counter);
}
}
diff --git a/src/vasp_vasprun_reader.cpp b/src/vasp_vasprun_reader.cpp
index cc8e6620f9f2970a1a00eae8418991c35cbdf667..c6917d31174be17004b1f9e8be6c6ef6c14a04d6 100644
--- a/src/vasp_vasprun_reader.cpp
+++ b/src/vasp_vasprun_reader.cpp
@@ -25,6 +25,8 @@ void VaspVasprunReader::read_data(const std::string& filename) {
} catch (std::exception &e) {
std::cerr << "Error reading file: " << e.what() << std::endl;
}
+
+ _s.label = filename + " ";
}
void VaspVasprunReader::parse_data() {
@@ -83,6 +85,7 @@ void VaspVasprunReader::extract_atom_types(rx::xml_node<> *root_node) {
}
void VaspVasprunReader::extract_calculations(rx::xml_node<> *root_node) {
+ size_t counter=0;
for (auto calculation_node = root_node->first_node("calculation");
calculation_node; calculation_node = calculation_node->next_sibling("calculation")) {
@@ -102,6 +105,7 @@ void VaspVasprunReader::extract_calculations(rx::xml_node<> *root_node) {
extract_forces(calculation_node);
+ _s.label += "Structure " + std::to_string(++counter);
stdb.add(_s);
_s = Structure(); // reset
}
@@ -140,12 +144,12 @@ 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;
}
r++;
}
+ _s.stress *= s_conv;
break;
}
varray_node = varray_node->next_sibling("varray");