From 9efa31c40e7321198d0777a1bb117b2d68794995 Mon Sep 17 00:00:00 2001
From: mkirsz <s1351949@sms.ed.ac.uk>
Date: Wed, 26 Feb 2025 09:04:48 +0000
Subject: [PATCH] Parser improvements
---
src/castep_castep_reader.cpp | 594 +++++++++++------------------------
1 file changed, 187 insertions(+), 407 deletions(-)
diff --git a/src/castep_castep_reader.cpp b/src/castep_castep_reader.cpp
index b04545e..bc9a055 100644
--- a/src/castep_castep_reader.cpp
+++ b/src/castep_castep_reader.cpp
@@ -36,6 +36,73 @@ void CastepCastepReader::parse_data() {
SinglePoint // SCF or single-point run
};
+ struct Label {
+ Label(const std::string& filename) : filename(filename) {}
+ CalcState calcState = CalcState::Idle;
+ std::string simType = "Unknown";
+ std::string algo = "Unknown";
+ std::string ensemble = "Unknown";
+ int startLine = -1;
+ int stopLine = -1;
+ int positionsStartLine = -1;
+ int positionsStopLine = -1;
+ int forcesStartLine = -1;
+ int forcesStopLine = -1;
+ int stressStartLine = -1;
+ int stressStopLine = -1;
+ int energyLine = -1;
+ double T=-1.0;
+ std::string stress="DNF";
+ bool useStress=false;
+ std::size_t stepNumber=0;
+ std::string filename;
+
+ std::string getStateLabel() {
+ switch (calcState) {
+ case CalcState::Idle: return "Idle";
+ case CalcState::GeometryOptimization: return "GO";
+ case CalcState::MolecularDynamics: return "MD";
+ case CalcState::SinglePoint: return "SPC";
+ }
+ return "Unknown";
+ }
+ std::string getMDLabel() {
+ std::string state = getStateLabel();
+ return "File: " + filename + " Lines: (" + std::to_string(startLine) + " : " + std::to_string(stopLine) + ") "
+ + simType + " " + ensemble + " T: " + std::to_string(T) + " Step: " + std::to_string(stepNumber) + " Stress: " + stress
+ + " Parser State: " + state
+ + " | C: (" + std::to_string(positionsStartLine) + " : " + std::to_string(positionsStopLine)
+ + ") F: (" + std::to_string(forcesStartLine) + " : " + std::to_string(forcesStopLine)
+ + ") S: (" + std::to_string(stressStartLine) + " : " + std::to_string(stressStopLine) + ") + E: " + std::to_string(energyLine);
+ }
+ std::string getGOLabel() {
+ std::string state = getStateLabel();
+ return "File: " + filename + " Lines: (" + std::to_string(startLine) + " : " + std::to_string(stopLine) + ") "
+ + simType + " " + algo + " Step: " + std::to_string(stepNumber) + " stress: " + stress + " Parser State: " + state
+ + " | C: (" + std::to_string(positionsStartLine) + " : " + std::to_string(positionsStopLine)
+ + ") F: (" + std::to_string(forcesStartLine) + " : " + std::to_string(forcesStopLine)
+ + ") S: (" + std::to_string(stressStartLine) + " : " + std::to_string(stressStopLine) + ") + E: " + std::to_string(energyLine);
+ }
+ std::string getSPLabel() {
+ std::string state = getStateLabel();
+ return "File: " + filename + " Lines: (" + std::to_string(startLine) + " : " + std::to_string(stopLine) + ") "
+ + simType + " SPC #: " + std::to_string(stepNumber) + " stress: " + stress + " Parser State: " + state
+ + " | C: (" + std::to_string(positionsStartLine) + " : " + std::to_string(positionsStopLine)
+ + ") F: (" + std::to_string(forcesStartLine) + " : " + std::to_string(forcesStopLine)
+ + ") S: (" + std::to_string(stressStartLine) + " : " + std::to_string(stressStopLine) + ") + E: " + std::to_string(energyLine);
+ }
+ std::string getLabel() {
+ switch (calcState) {
+ case CalcState::Idle: return "Idle";
+ case CalcState::GeometryOptimization: return getGOLabel();
+ case CalcState::MolecularDynamics: return getMDLabel();
+ case CalcState::SinglePoint: return getSPLabel();
+ }
+ return "Unknown";
+ }
+
+ } simLabel(filename);
+
// Current parser state and relevant flags
CalcState current_state = CalcState::Idle;
bool stress_tensor_found = false;
@@ -44,7 +111,6 @@ void CastepCastepReader::parse_data() {
// Local counters and accumulators
size_t natoms = 0; // Number of atoms from the input
- int scf_counter = 0; // Index for SCF runs (tracking distinct single-point steps)
size_t line_counter = 0; // Tracks line number for warnings
bool debug = false; // Local debug toggle
@@ -52,6 +118,17 @@ void CastepCastepReader::parse_data() {
Structure s;
std::vector<Atom> atoms;
+ std::string line;
+ auto jumpNLines = [&](std::istringstream& stream, int n) {
+ for (int i = 0; i < n; ++i) {
+ if (!std::getline(stream, line)) {
+ std::cerr << "Warning: Unexpected end of file while skipping lines" << std::endl;
+ break;
+ }
+ ++line_counter;
+ }
+ };
+
// Internal helper to finalize a structure's data:
// This updates derived data (like stress if absent) and adds to the structure DB.
auto finalize_structure = [&]() {
@@ -69,6 +146,7 @@ void CastepCastepReader::parse_data() {
s.atoms[i].force = atoms[i].force;
s.atoms[i].symbol = atoms[i].symbol;
}
+ s.label = simLabel.getLabel();
stdb.add(s);
};
@@ -81,21 +159,86 @@ void CastepCastepReader::parse_data() {
// Use a string stream to iterate over lines in raw_data_
std::istringstream stream(raw_data_);
- std::string line;
while (std::getline(stream, line)) {
++line_counter;
+ // Detect starting SP calculation (zeroth step)
+ if (line.find("single point energy") != std::string::npos) {
+ reset_flags(CalcState::SinglePoint);
+ if (!std::getline(stream, line)) break;
+ ++line_counter;
+ std::istringstream iss(line);
+ std::string ignore, stress;
+ iss >> ignore >> ignore >> ignore >> stress;
+ simLabel.calcState = CalcState::SinglePoint;
+ simLabel.startLine = line_counter;
+ simLabel.simType = "CASTEP SPC";
+ simLabel.stepNumber = 0;
+ simLabel.stress = stress;
+ simLabel.useStress = stress == "on" ? true : false;
+ if (debug) std::cout << "single point energy" << std::endl;
+ }
+
+ // Detect starting GO calculation (zeroth step)
+ if (line.find("geometry optimization") != std::string::npos) {
+ reset_flags(CalcState::GeometryOptimization);
+ jumpNLines(stream, 1);
+ std::istringstream iss(line);
+ std::string ignore, stress;
+ iss >> ignore >> ignore >> ignore >> stress;
+ simLabel.calcState = CalcState::GeometryOptimization;
+ simLabel.startLine = line_counter;
+ simLabel.simType = "CASTEP GO";
+ simLabel.stepNumber = 0;
+ simLabel.stress = stress;
+ simLabel.useStress = stress == "on" ? true : false;
+ if (debug) std::cout << "geometry optimization" << std::endl;
+ }
+
+ // Detect MD calculation type (zeroth step)
+ if (line.find("molecular dynamics") != std::string::npos) {
+ reset_flags(CalcState::MolecularDynamics);
+ jumpNLines(stream, 1);
+ std::istringstream iss(line);
+ std::string ignore, stress;
+ iss >> ignore >> ignore >> ignore >> stress;
+ simLabel.calcState = CalcState::MolecularDynamics;
+ simLabel.startLine = line_counter;
+ simLabel.simType = "CASTEP MD";
+ simLabel.stepNumber = 0;
+ simLabel.stress = stress;
+ simLabel.useStress = stress == "on" ? true : false;
+ if (debug) std::cout << "molecular dynamics" << std::endl;
+ }
+
+ // Get GO algorithm name at step zero
+ if (line.find("Geometry Optimization Parameters") != std::string::npos) {
+ std::string ignore, algo;
+ jumpNLines(stream, 2);
+ std::istringstream iss(line);
+ iss >> ignore >> ignore >> ignore >> algo;
+ simLabel.algo = algo;
+ if (debug) std::cout << "Geometry Optimization Parameters" << std::endl;
+ }
+
+ // Get MD ensemble name at step zero
+ if (line.find("Molecular Dynamics Parameters") != std::string::npos) {
+ reset_flags(CalcState::MolecularDynamics);
+ jumpNLines(stream, 2);
+ std::istringstream iss(line);
+ std::string ignore, ensemble;
+ iss >> ignore >> ignore >> ensemble;
+ simLabel.ensemble = ensemble;
+ if (debug) std::cout << "Molecular Dynamics Parameters" << std::endl;
+ }
+
// Detect or store the "Unit Cell"
if (line.find("Unit Cell") != std::string::npos) {
// A new cell is encountered. Prepare to read the next three lines of vectors.
// Finalize any incomplete data set if logic demands it, but not strictly necessary here
if (debug) std::cout << "Reading 3 lines of Unit Cell" << std::endl;
- // Skip the next two lines, often blank or headers
- if (!std::getline(stream, line)) break;
- ++line_counter;
- if (!std::getline(stream, line)) break;
- ++line_counter;
+ jumpNLines(stream, 2);
// Read the 3 lattice vectors
for (int i = 0; i < 3; ++i) {
@@ -134,109 +277,45 @@ void CastepCastepReader::parse_data() {
continue;
}
- // Detect starting MD iteration
- if (line.find("Starting MD iteration") != std::string::npos) {
- reset_flags(CalcState::MolecularDynamics);
- std::istringstream iss(line);
- std::string ignore, step;
- iss >> ignore >> ignore >> ignore >> step;
-
- // Remove last step from label
- while (s.label.back() != ' ')
- s.label.pop_back();
-
- s.label += step;
-
- if (debug) std::cout << "Starting MD iteration " << step << std::endl;
- continue;
- }
-
- // Detect starting SP calculation (zeroth step)
- if (line.find("single point energy") != std::string::npos) {
- reset_flags(CalcState::SinglePoint);
- if (!std::getline(stream, line)) break;
- ++line_counter;
- std::istringstream iss(line);
- std::string ignore, stress;
- iss >> ignore >> ignore >> ignore >> stress;
- s.label = "File: " + filename + " | CASTEP single point calculation, stress: " + stress;
- if (stress == "on") {
- is_stress = true;
- }
- else {
- is_stress = false;
- }
- if (debug) std::cout << "single point energy" << std::endl;
- }
-
- // Detect starting GO iteration (zeroth step)
- if (line.find("Geometry Optimization Parameters") != std::string::npos) {
- reset_flags(CalcState::GeometryOptimization);
- std::string ignore, algo;
-
- if (!std::getline(stream, line)) break;
- ++line_counter;
- if (!std::getline(stream, line)) break;
- ++line_counter;
- std::istringstream iss(line);
- iss >> ignore >> ignore >> ignore >> algo;
- s.label = "File: " + filename + " | CASTEP GO, "+algo+ ", step: ";
- if (debug) std::cout << "Geometry Optimization Parameters" << std::endl;
- }
-
- // Detect starting MD simulation (zeroth step)
- if (line.find("Molecular Dynamics Parameters") != std::string::npos) {
- reset_flags(CalcState::MolecularDynamics);
-
- if (!std::getline(stream, line)) break;
- ++line_counter;
- if (!std::getline(stream, line)) break;
- ++line_counter;
- std::istringstream iss(line);
- std::string ignore, ensemble;
- iss >> ignore >> ignore >> ensemble;
- s.label = "File: " + filename + " | CASTEP MD, "+ensemble+" step: " + "0";
- if (debug) std::cout << "Molecular Dynamics Parameters" << std::endl;
- continue;
- }
-
- // Detect starting GO iteration
+ // Detect GO iteration
if (line.find("Starting BFGS iteration") != std::string::npos ||
line.find("Starting LBFGS iteration") != std::string::npos ||
line.find("Starting Delocalized iteration") != std::string::npos ||
line.find("Starting DampedMD iteration") != std::string::npos ||
line.find("Starting TPSD iteration") != std::string::npos) {
reset_flags(CalcState::GeometryOptimization);
- // This line often carries the iteration number
std::istringstream iss(line);
std::string ignore, algo, step_str;
- // The typical format: "Starting MD iteration N ..."
- // Attempt to parse out the iteration number as step_str
iss >> ignore >> algo >> ignore >> step_str;
- // Store it in a label for clarity
- s.label = "File: " + filename + " | CASTEP GO, "+algo+" step: ";
+ simLabel.simType = "CASTEP GO";
+ simLabel.startLine = line_counter;
+ simLabel.algo = algo;
+ simLabel.stepNumber = std::stoi(step_str);
+ simLabel.calcState = CalcState::GeometryOptimization;
if (debug) std::cout << "Starting" +algo+ " iteration " << step_str << std::endl;
- continue;
}
- // if (line.find("finished MD iteration") != std::string::npos) {
- // reset_flags(CalcState::Idle);
- // }
+ // Detect MD iteration
+ if (line.find("Starting MD iteration") != std::string::npos) {
+ reset_flags(CalcState::MolecularDynamics);
+ std::istringstream iss(line);
+ std::string ignore, step;
+ iss >> ignore >> ignore >> ignore >> step;
+ simLabel.simType = "CASTEP MD";
+ simLabel.startLine = line_counter;
+ simLabel.stepNumber = std::stoi(step);
+ simLabel.calcState = CalcState::MolecularDynamics;
+ if (debug) std::cout << "Starting MD iteration " << step << std::endl;
+ continue;
+ }
// Detect fractional coordinates block
if (line.find("Fractional coordinates of atoms") != std::string::npos) {
if (debug) std::cout << "Fractional coordinates of atoms" << std::endl;
- // Typically followed by two header/blank lines
- if (!std::getline(stream, line)) break;
- ++line_counter;
- if (!std::getline(stream, line)) break;
- ++line_counter;
-
- // If constant volume, the code does not always reprint the cell.
- // The logic here re-uses the last known cell if needed.
+ jumpNLines(stream, 2);
atoms.clear(); // Clear old atoms or partial data
-
atoms.reserve(natoms);
+ simLabel.positionsStartLine = line_counter + 1;
for (size_t i = 0; i < natoms; ++i) {
if (!std::getline(stream, line)) {
std::cerr << "Warning: Truncated file reading fractional coords at row " << i
@@ -258,7 +337,7 @@ void CastepCastepReader::parse_data() {
Atom a(Element(species), px, py, pz, 0.0, 0.0, 0.0);
atoms.push_back(a); // keep it fractional for now
}
- continue;
+ simLabel.positionsStopLine = line_counter;
}
// The old cell is reverted and printed before final enthalpy from the current iteration
@@ -278,14 +357,9 @@ void CastepCastepReader::parse_data() {
if (line.find("Cartesian components (eV/A)") != std::string::npos) {
if (debug) std::cout << "Reading forces..." << std::endl;
// Usually there are three lines of header/blank text before actual force lines
- for (int i = 0; i < 3; ++i) {
- if (!std::getline(stream, line)) {
- std::cerr << "Warning: Incomplete forces header block (line: " << line_counter << ")." << std::endl;
- break;
- }
- ++line_counter;
- }
+ jumpNLines(stream, 3);
// Read force for each atom
+ simLabel.forcesStartLine = line_counter+1;
for (size_t i = 0; i < natoms; ++i) {
if (!std::getline(stream, line)) {
std::cerr << "Warning: Truncated file reading forces at row " << i
@@ -297,32 +371,24 @@ void CastepCastepReader::parse_data() {
std::istringstream iss(line);
std::string tmp;
double fx, fy, fz;
- // Format typically: " ??? ??? ??? fx fy fz "
if (!(iss >> tmp >> tmp >> tmp >> fx >> fy >> fz)) {
std::cerr << "Warning: Could not parse atomic forces (line: "
<< line_counter << ")." << std::endl;
break;
}
- // Assign force to the matching atom
if (i < atoms.size()) {
atoms[i].force = Vec3d(fx, fy, fz);
}
}
- continue;
+ simLabel.forcesStopLine = line_counter;
}
// Detect stress block
if (line.find("Cartesian components (GPa)") != std::string::npos) {
if (debug) std::cout << "Reading stress..." << std::endl;
- // Usually there are three lines of header/blank text
- for (int i = 0; i < 3; ++i) {
- if (!std::getline(stream, line)) {
- std::cerr << "Warning: Incomplete stress header block (line: " << line_counter << ")." << std::endl;
- break;
- }
- ++line_counter;
- }
+ jumpNLines(stream, 3);
// A 3x3 matrix is expected
+ simLabel.stressStartLine = line_counter + 1;
for (int row = 0; row < 3; ++row) {
if (!std::getline(stream, line)) {
std::cerr << "Warning: Truncated file reading stress row " << row
@@ -333,7 +399,6 @@ void CastepCastepReader::parse_data() {
std::istringstream iss(line);
std::string ignore;
double v1, v2, v3;
- // Format: " ??? ??? val1 val2 val3 "
if (!(iss >> ignore >> ignore >> v1 >> v2 >> v3)) {
std::cerr << "Warning: Could not parse stress row (line: "
<< line_counter << ")." << std::endl;
@@ -342,13 +407,14 @@ void CastepCastepReader::parse_data() {
s.stress(row, 0) = v1;
s.stress(row, 1) = v2;
s.stress(row, 2) = v3;
+ simLabel.stressStopLine = line_counter;
}
stress_tensor_found = true;
if (current_state == CalcState::SinglePoint) {
- s.label += " SCF run: " + std::to_string(scf_counter++);
+ simLabel.stepNumber++;
if (is_stress) data_block_complete = true;
+ simLabel.stopLine = line_counter;
}
- continue;
}
// Detect final free energy for single-point or last iteration in GO
@@ -366,16 +432,16 @@ void CastepCastepReader::parse_data() {
<< line_counter << ")." << std::endl;
} else {
s.energy = energy;
+ simLabel.energyLine = line_counter;
}
// Single-point detection: if current_state is Idle or SinglePoint, treat it as an SCF run
// but it might also appear mid-GO. The code below sets a label if no other structure data is present.
if (current_state == CalcState::SinglePoint && !is_stress) {
- s.label += " SCF run: " + std::to_string(scf_counter++);
+ simLabel.stepNumber++;
+ simLabel.stopLine = line_counter;
data_block_complete = true;
}
- // Mark that data is complete for this structure
- continue;
}
// Detect the line with "enthalpy=" used in geometry optimization
@@ -388,15 +454,14 @@ void CastepCastepReader::parse_data() {
std::cerr << "Warning: Could not parse final free energy (line: "
<< line_counter << ")." << std::endl;
}
- s.label += step;
+ simLabel.stepNumber = std::stoi(step);
+ simLabel.stopLine = line_counter;
data_block_complete = true;
- continue;
}
// Detect potential energy line used in MD
if (line.find("Potential Energy:") != std::string::npos && current_state == CalcState::MolecularDynamics) {
if (debug) std::cout << "Potential Energy:" << std::endl;
- // Format: "Potential Energy: <value>"
std::istringstream iss(line);
std::string ignore;
double energy;
@@ -416,19 +481,15 @@ void CastepCastepReader::parse_data() {
std::istringstream iss(line);
std::string ignore;
double temperature;
- // Format: "Temperature: <value>"
if (!(iss >> ignore >> ignore >> temperature)) {
std::cerr << "Warning: Could not parse temperature in MD (line: "
<< line_counter << ")." << std::endl;
} else {
s.T = temperature;
}
- // If a label has not been set, create a fallback
- // if (s.label.empty()) {
- // s.label = "CASTEP MD step (no step # found)";
- // }
+ simLabel.T = temperature;
+ simLabel.stopLine = line_counter;
data_block_complete = true;
- continue;
}
// If a completed data set is detected, finalize
@@ -437,289 +498,8 @@ void CastepCastepReader::parse_data() {
reset_flags(CalcState::Idle);
}
} // end while getline
-
- // At file end, if a data block was incomplete but has partial data,
- // it can either be discarded or stored as partial.
- // For safety, only store if data_block_complete was triggered.
- // No action is taken here unless a user-specific policy is desired.
}
-// void CastepCastepReader::parse_data() {
-// std::istringstream stream(raw_data_);
-// std::string line;
-//
-// size_t natoms;;
-// 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;
-//
-// bool debug = false;
-//
-// while (std::getline(stream, line)) {
-//
-// 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) {
-// if (debug) std::cout << "GO run" << std::endl;
-// 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 (debug) std::cout << "Unit Cell" << std::endl;
-// 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;
-// }
-// }
-//
-// if (constant_volume) label.clear();
-// constant_volume = false;
-// if (debug) std::cout << s.cell << std::endl;
-// }
-//
-// else if (line.find("Total number of ions in cell") != std::string::npos) {
-// // this line indicates new type of computation, so we reset flags here
-// std::istringstream iss(line);
-// std::string temp;
-// int count = 0;
-//
-// // 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;
-// }
-// if (debug) std::cout << "Number of atoms: " << natoms << std::endl;
-// }
-//
-// else if (line.find("so fixing cell parameters") != std::string::npos) {
-// if (debug) std::cout << "so fixing cell parameters" << std::endl;
-// constant_volume=true;
-// label = "CASTEP MD, const. volume: true, step: 0";
-// }
-//
-// else if (line.find("Starting MD iteration") != std::string::npos) {
-// if (debug) std::cout << "Starting MD iteration" << std::endl;
-// std::istringstream iss(line);
-// std::string step;
-// iss >> step >> step >> step >> step;
-// std::ostringstream oss;
-// oss << std::boolalpha << constant_volume;
-// label = "CASTEP MD, const. volume: " + oss.str() + ", step: " + step;
-// }
-//
-//
-// else if (constant_volume && line.find("Cell Contents") != std::string::npos) {
-// if (debug) std::cout << "Cell Contents" << std::endl;
-// if (restart) {
-// if (debug) std::cout << "Cell Contents restart" << std::endl;
-// s.atoms.clear();
-// } else {
-// if (debug) std::cout << "Cell Contents no restart" << std::endl;
-// if (debug) std::cout << line << std::endl;
-// 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 (debug) std::cout << "Fractional coordinates of atoms" << std::endl;
-// // Ideally st.natoms() should be zero by now. However for constant volum GO this is not the case.
-// // Therfore we need to clear the atoms vector but we keep the st.cell as it is.
-// s.atoms.clear();
-// 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;
-// }
-// s.add_atom(Atom(Element(type),px,py,pz,0,0,0));
-// s.atoms[i].position = s.cell * s.atoms[i].position; // convert to abs
-// }
-// if (debug) std::cout << "natoms: " << s.natoms() << std::endl;
-// }
-//
-// else if (line.find("Cartesian components (eV/A)") != std::string::npos) {
-// if (debug) std::cout << "Cartesian components (eV/A)" << std::endl;
-// 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);
-// }
-// }
-// }
-//
-// else if (line.find("Cartesian components (GPa)") != std::string::npos) {
-// if (debug) std::cout << "Cartesian components (GPa)" << std::endl;
-// 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;
-// }
-// }
-// stress_tensor_bool = true;
-// }
-// // Potential Energy // MD
-// // Total energy corrected for finite basis set = -2690.182502 eV // GO, first step only
-// // enthalpy= indicates end of iteration for GO
-//
-// else if (line.find("Final free energy (E-TS)") != std::string::npos) {
-// if (debug) std::cout << "Final free energy (E-TS)" << std::endl;
-// 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) {
-// if (debug) std::cout << "enthalpy=" << std::endl;
-// // GO: the last extracted free energy is correct one!
-// std::istringstream iss(line);
-// std::string step;
-// iss >> step >> step >> step >> step; // safe as found enthalpy=
-// std::ostringstream oss;
-// oss << std::boolalpha << constant_volume;
-// s.label = "CASTEP GO, const. volume: " + oss.str() + ", step: " + step;
-// complete_structure = true;
-// }
-//
-// else if (line.find("Potential Energy:") != std::string::npos) {
-// if (debug) std::cout << "Potential Energy:" << std::endl;
-// 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) {
-// if (debug) std::cout << "Temperature:" << std::endl;
-// // 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;
-// complete_structure = true;
-// }
-// if (complete_structure) {
-// if (!stress_tensor_bool) {
-// s.stress.set_zero();
-// }
-// else {
-// s.stress *= p_conv; // GPa -> eV/A^3
-// }
-// stdb.add(s);
-// complete_structure = false;
-// }
-// counter++;
-// }
-//
-// }
-
void CastepCastepReader::print_summary() const {
std::cout << get_summary();
}
--
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