From cecc436292ce7c03ad710d46099790bb38dbcf71 Mon Sep 17 00:00:00 2001
From: Marcin Kirsz <mkirsz@ed.ac.uk>
Date: Fri, 6 Dec 2024 16:18:19 +0000
Subject: [PATCH] Castep/VASP/LAMMPS data writers, including factory
---
.../dataset_readers/dataset_reader_selector.h | 4 +-
.../mlip/dataset_writers/castep_cell_writer.h | 23 ++++++
.../mlip/dataset_writers/dataset_writer.h | 23 ++++++
.../dataset_writers/dataset_writer_selector.h | 15 ++++
.../dataset_writers/lammps_structure_writer.h | 21 +++++
.../mlip/dataset_writers/vasp_poscar_writer.h | 21 +++++
src/castep_cell_writer.cpp | 53 ++++++++++++
src/dataset_writer_selector.cpp | 23 ++++++
src/lammps_structure_writer.cpp | 81 +++++++++++++++++++
src/vasp_poscar_writer.cpp | 79 ++++++++++++++++++
10 files changed, 341 insertions(+), 2 deletions(-)
create mode 100644 include/tadah/mlip/dataset_writers/castep_cell_writer.h
create mode 100644 include/tadah/mlip/dataset_writers/dataset_writer.h
create mode 100644 include/tadah/mlip/dataset_writers/dataset_writer_selector.h
create mode 100644 include/tadah/mlip/dataset_writers/lammps_structure_writer.h
create mode 100644 include/tadah/mlip/dataset_writers/vasp_poscar_writer.h
create mode 100644 src/castep_cell_writer.cpp
create mode 100644 src/dataset_writer_selector.cpp
create mode 100644 src/lammps_structure_writer.cpp
create mode 100644 src/vasp_poscar_writer.cpp
diff --git a/include/tadah/mlip/dataset_readers/dataset_reader_selector.h b/include/tadah/mlip/dataset_readers/dataset_reader_selector.h
index 9c4808b..a09803e 100644
--- a/include/tadah/mlip/dataset_readers/dataset_reader_selector.h
+++ b/include/tadah/mlip/dataset_readers/dataset_reader_selector.h
@@ -15,11 +15,11 @@ public:
/**
* @brief Factory method to create specific DatasetReader objects.
*
- * @param type The type of the dataset reader to create.
+ * @param filepath File path to check the content.
* @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);
+ static std::unique_ptr<DatasetReader> get_reader(const std::string& filepath, StructureDB& db);
/**
* @brief Determines the file type based on its content.
diff --git a/include/tadah/mlip/dataset_writers/castep_cell_writer.h b/include/tadah/mlip/dataset_writers/castep_cell_writer.h
new file mode 100644
index 0000000..90b799c
--- /dev/null
+++ b/include/tadah/mlip/dataset_writers/castep_cell_writer.h
@@ -0,0 +1,23 @@
+#ifndef CASTEP_CELL_WRITER_H
+#define CASTEP_CELL_WRITER_H
+
+#include <tadah/mlip/structure.h>
+#include <tadah/mlip/structure_db.h>
+#include <tadah/mlip/dataset_writers/dataset_writer.h>
+
+#include <iostream>
+#include <fstream>
+#include <sstream>
+#include <vector>
+#include <stdexcept>
+class CastepCellWriter : public DatasetWriter {
+public:
+ CastepCellWriter(StructureDB& db);
+
+ virtual void write_data(const std::string& filename, const size_t i) override;
+
+};
+
+#endif // CASTEP_CELL_WRITER_H
+
+
diff --git a/include/tadah/mlip/dataset_writers/dataset_writer.h b/include/tadah/mlip/dataset_writers/dataset_writer.h
new file mode 100644
index 0000000..91ff858
--- /dev/null
+++ b/include/tadah/mlip/dataset_writers/dataset_writer.h
@@ -0,0 +1,23 @@
+#ifndef DATASET_WRITER_H
+#define DATASET_WRITER_H
+
+#include <tadah/mlip/structure_db.h>
+#include <string>
+#include <vector>
+
+class DatasetWriter {
+ public:
+ virtual ~DatasetWriter() = default;
+
+ virtual void write_data(const std::string& filename, const size_t i) = 0;
+
+ DatasetWriter(StructureDB& db) : stdb(db) {};
+
+ virtual void set_precision(const size_t _p) { p = _p; w = p+6; };
+
+ protected:
+ StructureDB& stdb;
+ double p = 10; // output precision
+ double w = p+6; // column width
+};
+#endif // DATASET_WRITER_H
diff --git a/include/tadah/mlip/dataset_writers/dataset_writer_selector.h b/include/tadah/mlip/dataset_writers/dataset_writer_selector.h
new file mode 100644
index 0000000..7ea4f85
--- /dev/null
+++ b/include/tadah/mlip/dataset_writers/dataset_writer_selector.h
@@ -0,0 +1,15 @@
+#ifndef DATASET_WRITER_SELECTOR_H
+#define DATASET_WRITER_SELECTOR_H
+
+#include <tadah/mlip/structure_db.h>
+#include <tadah/mlip/dataset_writers/dataset_writer.h>
+#include <string>
+#include <memory>
+
+class DatasetWriterSelector {
+ public:
+ static std::unique_ptr<DatasetWriter> get_writer(const std::string& type, StructureDB& db);
+
+};
+
+#endif // DATASET_WRITER_SELECTOR_H
diff --git a/include/tadah/mlip/dataset_writers/lammps_structure_writer.h b/include/tadah/mlip/dataset_writers/lammps_structure_writer.h
new file mode 100644
index 0000000..5ee539a
--- /dev/null
+++ b/include/tadah/mlip/dataset_writers/lammps_structure_writer.h
@@ -0,0 +1,21 @@
+#ifndef LAMMPS_STRUCTURE_WRITER_H
+#define LAMMPS_STRUCTURE_WRITER_H
+
+#include <tadah/mlip/structure.h>
+#include <tadah/mlip/structure_db.h>
+#include <tadah/mlip/dataset_writers/dataset_writer.h>
+
+#include <iostream>
+#include <fstream>
+#include <sstream>
+#include <vector>
+#include <stdexcept>
+class LammpsStructureWriter : public DatasetWriter {
+public:
+ LammpsStructureWriter(StructureDB& db);
+
+ virtual void write_data(const std::string& filename, const size_t i) override;
+
+};
+
+#endif // LAMMPS_STRUCTURE_WRITER_H
diff --git a/include/tadah/mlip/dataset_writers/vasp_poscar_writer.h b/include/tadah/mlip/dataset_writers/vasp_poscar_writer.h
new file mode 100644
index 0000000..abd58b8
--- /dev/null
+++ b/include/tadah/mlip/dataset_writers/vasp_poscar_writer.h
@@ -0,0 +1,21 @@
+#ifndef VASP_POSCAR_WRITER_H
+#define VASP_POSCAR_WRITER_H
+
+#include <tadah/mlip/structure.h>
+#include <tadah/mlip/structure_db.h>
+#include <tadah/mlip/dataset_writers/dataset_writer.h>
+
+#include <iostream>
+#include <fstream>
+#include <sstream>
+#include <vector>
+#include <stdexcept>
+class VaspPoscarWriter : public DatasetWriter {
+public:
+ VaspPoscarWriter(StructureDB& db);
+
+ virtual void write_data(const std::string& filename, const size_t i) override;
+
+};
+
+#endif // VASP_POSCAR_WRITER_H
diff --git a/src/castep_cell_writer.cpp b/src/castep_cell_writer.cpp
new file mode 100644
index 0000000..144da27
--- /dev/null
+++ b/src/castep_cell_writer.cpp
@@ -0,0 +1,53 @@
+#include <tadah/mlip/structure.h>
+#include <tadah/mlip/structure_db.h>
+#include <tadah/mlip/dataset_writers/castep_cell_writer.h>
+
+CastepCellWriter::CastepCellWriter(StructureDB& db) : DatasetWriter(db) {}
+
+void CastepCellWriter::write_data(const std::string& filename, const size_t i) {
+
+ if (i >= stdb.size()) {
+ throw std::out_of_range("Index i is out of range.");
+ }
+
+ std::ofstream file(filename);
+ if (!file.is_open()) {
+ throw std::runtime_error("Could not open the file: " + filename);
+ }
+
+ const Structure &st = stdb(i);
+
+ // write label
+ file << "# " << st.label << std::endl;
+
+ // write cell
+ file << "%BLOCK LATTICE_CART" << std::endl;
+ file << "ANG" << std::endl;
+ for (int i=0; i<3; ++i) {
+ file << std::right << std::fixed << std::setw(w)
+ << std::setprecision(p) << st.cell(i,0);
+ file << std::right << std::fixed << std::setw(w)
+ << std::setprecision(p) << st.cell(i,1);
+ file << std::right << std::fixed << std::setw(w)
+ << std::setprecision(p) << st.cell(i,2);
+ file << std::endl;
+ }
+ file << "%ENDBLOCK LATTICE_CART" << std::endl;
+
+ file << std::endl;
+
+ file << "%BLOCK POSITIONS_ABS" << std::endl;
+ for (const auto &atom : st) {
+ file << std::right << std::fixed << std::setw(w)
+ << atom.symbol;
+ file << std::right << std::fixed << std::setw(w)
+ << std::setprecision(p) << atom.position(0);
+ file << std::right << std::fixed << std::setw(w)
+ << std::setprecision(p) << atom.position(1);
+ file << std::right << std::fixed << std::setw(w)
+ << std::setprecision(p) << atom.position(2);
+ file << std::endl;
+ }
+ file << "%ENDBLOCK POSITIONS_ABS " << std::endl;
+ file.close();
+}
diff --git a/src/dataset_writer_selector.cpp b/src/dataset_writer_selector.cpp
new file mode 100644
index 0000000..0be08eb
--- /dev/null
+++ b/src/dataset_writer_selector.cpp
@@ -0,0 +1,23 @@
+#include <tadah/mlip/dataset_writers/dataset_writer_selector.h>
+#include <tadah/mlip/dataset_writers/castep_cell_writer.h>
+#include <tadah/mlip/dataset_writers/vasp_poscar_writer.h>
+#include <tadah/mlip/dataset_writers/lammps_structure_writer.h>
+
+#include <fstream>
+#include <iostream>
+
+// Factory method implementation
+std::unique_ptr<DatasetWriter> DatasetWriterSelector::get_writer(const std::string& type, StructureDB& db) {
+
+ if (type == "CASTEP") {
+ return std::make_unique<CastepCellWriter>(db);
+ } else if (type == "VASP") {
+ return std::make_unique<VaspPoscarWriter>(db);
+ } else if (type == "LAMMPS") {
+ return std::make_unique<LammpsStructureWriter>(db);
+ } else {
+ std::cerr << "Unknown type! Returning nullptr." << std::endl;
+ return nullptr;
+ }
+
+}
diff --git a/src/lammps_structure_writer.cpp b/src/lammps_structure_writer.cpp
new file mode 100644
index 0000000..0c37059
--- /dev/null
+++ b/src/lammps_structure_writer.cpp
@@ -0,0 +1,81 @@
+#include <tadah/mlip/structure.h>
+#include <tadah/mlip/structure_db.h>
+#include <tadah/mlip/dataset_writers/lammps_structure_writer.h>
+
+LammpsStructureWriter::LammpsStructureWriter(StructureDB& db) : DatasetWriter(db) {}
+
+void LammpsStructureWriter::write_data(const std::string& filename, const size_t i) {
+
+ if (i >= stdb.size()) {
+ throw std::out_of_range("Index i is out of range.");
+ }
+
+ std::ofstream file(filename);
+ if (!file.is_open()) {
+ throw std::runtime_error("Could not open the file: " + filename);
+ }
+
+ const Structure &st = stdb(i);
+
+ // compute number of atoms for a given element
+ const auto &elements = st.get_unique_elements();
+ std::map<std::string, size_t> nelements;
+ std::map<std::string, size_t> type;
+ // Initialize the count for each element
+ for (const auto& element : elements) {
+ nelements[element.symbol] = 0;
+ }
+ // then count...
+ size_t t=0;
+ for (const auto &atom : st) {
+ nelements[atom.symbol]++;
+ if (type.find(atom.symbol) == type.end()) {
+ type[atom.symbol] = ++t;
+ }
+ }
+
+ // BEGIN OF LAMMPS HEADER
+ file << st.label << std::endl;
+ file << std::endl;
+ file << st.natoms() << " atoms" << std::endl;
+ file << nelements.size() << " atom types" << std::endl;
+ file << std::endl;
+
+ // General triclinic box format
+ std::vector<std::string> abcvec = {"avec", "bvec", "cvec"};
+ for (int i=0; i<3; ++i) {
+ file << std::right << std::fixed << std::setw(w)
+ << std::setprecision(p) << st.cell(i,0);
+ file << std::right << std::fixed << std::setw(w)
+ << std::setprecision(p) << st.cell(i,1);
+ file << std::right << std::fixed << std::setw(w)
+ << std::setprecision(p) << st.cell(i,2)
+ << " " << abcvec[i];
+ file << std::endl;
+ }
+ file << " 0.0 0.0 0.0 abc origin" << std::endl;
+ // END LAMMPS HEADER
+
+ // BEGIN LAMMPS BODY
+ file << std::endl;
+ file << "Atoms # atomic" << std::endl;
+ file << std::endl;
+ // atomic: atom-ID [int, 1-Natoms] atom-type [int, 1-Ntype] x y z
+
+ size_t idx=1;
+ for (const auto &atom : st) {
+ file << std::right << std::fixed << std::setw(w) << idx;
+ file << std::right << std::fixed << std::setw(w) << type[atom.symbol];
+ file << std::right << std::fixed << std::setw(w)
+ << std::setprecision(p) << atom.position(0);
+ file << std::right << std::fixed << std::setw(w)
+ << std::setprecision(p) << atom.position(1);
+ file << std::right << std::fixed << std::setw(w)
+ << std::setprecision(p) << atom.position(2);
+ file << std::endl;
+ idx++;
+ }
+ // END LAMMPS BODY
+
+ file.close();
+}
diff --git a/src/vasp_poscar_writer.cpp b/src/vasp_poscar_writer.cpp
new file mode 100644
index 0000000..3314418
--- /dev/null
+++ b/src/vasp_poscar_writer.cpp
@@ -0,0 +1,79 @@
+#include <tadah/mlip/structure.h>
+#include <tadah/mlip/structure_db.h>
+#include <tadah/mlip/dataset_writers/vasp_poscar_writer.h>
+
+#include <fstream>
+
+VaspPoscarWriter::VaspPoscarWriter(StructureDB& db) : DatasetWriter(db) {}
+
+void VaspPoscarWriter::write_data(const std::string& filename, const size_t i) {
+
+ if (i >= stdb.size()) {
+ throw std::out_of_range("Index i is out of range.");
+ }
+
+ std::ofstream file(filename);
+ if (!file.is_open()) {
+ throw std::runtime_error("Could not open the file: " + filename);
+ }
+
+ const Structure &st = stdb(i);
+
+ // write scaling factor
+ file << st.label << std::endl;
+ file << "1.0" << std::endl;
+
+ // write cell
+ for (int i=0; i<3; ++i) {
+ file << std::right << std::fixed << std::setw(w)
+ << std::setprecision(p) << st.cell(i,0);
+ file << std::right << std::fixed << std::setw(w)
+ << std::setprecision(p) << st.cell(i,1);
+ file << std::right << std::fixed << std::setw(w)
+ << std::setprecision(p) << st.cell(i,2);
+ file << std::endl;
+ }
+
+
+ // compute number of atoms for a given element
+ const auto &elements = st.get_unique_elements();
+ std::map<std::string, size_t> nelements;
+ // Initialize the count for each element
+ for (const auto& element : elements) {
+ nelements[element.symbol] = 0;
+ }
+ // then count...
+ for (const auto &atom : st) {
+ nelements[atom.symbol]++;
+ }
+
+ // write elements
+ for (const auto& pair: nelements) {
+ file << pair.first << " ";
+ }
+ file << std::endl;
+
+ // write number of every elements
+ for (const auto& pair: nelements) {
+ file << pair.second << " ";
+ }
+ file << std::endl;
+
+ file << "Cartesian" << std::endl;
+
+ for (const auto& pair: nelements) {
+ for (const auto &atom : st) {
+ if (pair.first == atom.symbol) {
+ file << std::right << std::fixed << std::setw(w)
+ << std::setprecision(p) << atom.position(0);
+ file << std::right << std::fixed << std::setw(w)
+ << std::setprecision(p) << atom.position(1);
+ file << std::right << std::fixed << std::setw(w)
+ << std::setprecision(p) << atom.position(2);
+ file << std::endl;
+ }
+ }
+ }
+
+ file.close();
+}
--
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