Overload important functions for compatibility (#37)

marvinfriede · web-flow · commit 55ffafbe47fd · 2024-09-28T22:54:19.000-05:00
diff --git a/.vscode/c_cpp_properties.json b/.vscode/c_cpp_properties.json
@@ -0,0 +1,18 @@
+{
+    "configurations": [
+        {
+            "name": "Linux",
+            "includePath": [
+                "${workspaceFolder}/**",
+                "/opt/software/openblas/**",
+                "/opt/software/lapack/**"
+            ],
+            "defines": [],
+            "compilerPath": "/usr/bin/gcc",
+            "cStandard": "c17",
+            "cppStandard": "gnu++17",
+            "intelliSenseMode": "linux-gcc-x64"
+        }
+    ],
+    "version": 4
+}
diff --git a/README.md b/README.md
@@ -6,8 +6,6 @@
 This project is a port of the [`dftd4`](https://github.com/dftd4/dftd4) project
 to C++ and provides the D4(EEQ)-ATM method.
 
-**NOTE:** This branch contains some adaptations for compatibility with the ORCA Quantum Chemistry program. This inludes some renaming of variables and functions, and, most notably, the handling of ghost atoms.
-
 ## Building This Project
 
 This project is build with `meson`, to setup and perform a build run:
diff --git a/app/main.cpp b/app/main.cpp
@@ -163,15 +163,6 @@ int main(int argc, char **argv) {
   dftd4::TCutoff cutoff;
   dftd4::TD4Model d4;
 
-  // masking (nothing excluded)
-  dftd4::TVector<int> realIdx;
-  realIdx.NewVec(mol.NAtoms);
-  int nat = 0;
-  for (int i = 0; i != mol.NAtoms; i++) {
-    realIdx(i) = nat;
-    nat++;
-  }
-
   // analytical gradient
   double *d4grad;
   if (lgrad) {
@@ -183,9 +174,7 @@ int main(int argc, char **argv) {
     d4grad = nullptr;
   }
 
-  info = dftd4::get_dispersion(
-    mol, realIdx, charge, d4, par, cutoff, energy, d4grad
-  );
+  info = dftd4::get_dispersion(mol, charge, d4, par, cutoff, energy, d4grad);
   if (info != EXIT_SUCCESS) return info;
 
   // Print results
diff --git a/include/dftd_dispersion.h b/include/dftd_dispersion.h
@@ -27,6 +27,17 @@
 
 namespace dftd4 {
 
+/**
+ * @brief Container for DFT-D4 damping parameters.
+ *
+ * @param s6 C6 damping parameter. Usually 1.
+ * @param s8 C8 damping parameter.
+ * @param s10 C10 damping parameter. Always 0 currently.
+ * @param s9 ATM (three-body) damping parameter. Usually 1.
+ * @param a1 Becke-Johnson damping parameter.
+ * @param a2 Becke-Johnson damping parameter.
+ * @param alp ATM (three-body) damping parameter. Usually 16.
+ */
 class dparam {
   public:
     double s6;
@@ -42,7 +53,32 @@ class dparam {
  * @brief Wrapper to handle the evaluation of dispersion energy and derivatives.
  *
  * @param mol Molecular geometry.
- * @param realIdx List for real atoms excluding ghost/non atoms
+ * @param charge Molecular charge.
+ * @param par DFT-D4 parameters.
+ * @param d4 Base D4 dispersion model.
+ * @param cutoff Real-space cutoffs for CN and dispersion.
+ * @param energy Dispersion energy (inout).
+ * @param GRAD Dispersion gradient (inout).
+ * @return Exit status.
+ */
+extern int get_dispersion(
+  const TMolecule &mol,
+  int charge,
+  const TD4Model &d4,
+  const dparam &par,
+  TCutoff cutoff,
+  double &energy,
+  double *GRAD
+);
+
+/**
+ * @brief Wrapper to handle the evaluation of dispersion energy and derivatives.
+ *
+ * This function calculates the dispersion energy and gradients for the given
+ * molecular geometry, considering only the atoms specified in `realIdx`.
+ *
+ * @param mol Molecular geometry.
+ * @param realIdx List for real atoms excluding ghost/non atoms.
  * @param charge Molecular charge.
  * @param par DFT-D4 parameters.
  * @param d4 Base D4 dispersion model.
diff --git a/include/dftd_eeq.h b/include/dftd_eeq.h
@@ -27,6 +27,44 @@
 
 namespace dftd4 {
 
+/**
+ * Get the EEQ charges for a given molecule.
+ *
+ * @param mol     The molecule object
+ * @param dist    The distance matrix
+ * @param charge  The total charge of the molecule
+ * @param cutoff  The cutoff for the EEQ coordination number
+ * @param q       The EEQ charges
+ * @param dqdr    The derivative of the EEQ charges
+ * @param lgrad   Flag for the gradient
+ *
+ * @return 0 if successful, 1 otherwise
+ */
+extern int get_charges(
+  const TMolecule &mol,
+  const TMatrix<double> &dist,
+  int charge,
+  double cutoff,
+  TVector<double> &q,
+  TMatrix<double> &dqdr,
+  bool lgrad
+);
+
+/**
+ * Get the EEQ charges for a given molecule for the atoms specified by the
+ * indices in `realIdx`.
+ *
+ * @param mol     The molecule object
+ * @param realIdx The real atom indices (for excluding dummy atoms)
+ * @param dist    The distance matrix
+ * @param charge  The total charge of the molecule
+ * @param cutoff  The cutoff for the EEQ coordination number
+ * @param q       The EEQ charges
+ * @param dqdr    The derivative of the EEQ charges
+ * @param lgrad   Flag for the gradient
+ *
+ * @return 0 if successful, 1 otherwise
+ */
 extern int get_charges(
   const TMolecule &mol,
   const TIVector &realIdx,
diff --git a/include/dftd_ncoord.h b/include/dftd_ncoord.h
@@ -32,7 +32,7 @@ namespace dftd4 {
  * Calculate all distance pairs and store in matrix.
  *
  * @param mol Molecule object.
- * @param realIdx List for real atoms excluding ghost/non atoms
+ * @param realIdx List for real atoms excluding ghost/non atoms.
  * @param dist Distance matrix (inout).
  * @return Exit status.
  */
@@ -42,11 +42,23 @@ extern int calc_distances(
   TMatrix<double> &dist
 );
 
+/**
+ * Initialize real indices to all atoms in the molecule.
+ *
+ * @param nat Number of atoms in the molecule.
+ * @param realIdx Vector to store the real indices.
+ * @return void
+ */
+void initializeRealIdx(int nat, TVector<int> &realIdx);
+
+///////////////////////////////////////////////////////////////////////////////
+///////////////////////////////////////////////////////////////////////////////
+
 /**
  * Wrapper for error function coordination number.
  *
  * @param mol Molecule object.
- * @param realIdx List for real atoms excluding ghost/non atoms
+ * @param realIdx List for real atoms excluding ghost/non atoms.
  * @param dist Distance matrix.
  * @param cn Vector of coordination numbers.
  * @param cutoff Real-space cutoff (default: @see {dftd_cutoff.h}).
@@ -64,11 +76,31 @@ extern int get_ncoord_erf(
   bool lgrad = false
 );
 
+/**
+ * Wrapper for error function coordination number.
+ *
+ * @param mol Molecule object.
+ * @param dist Distance matrix.
+ * @param cn Vector of coordination numbers.
+ * @param cutoff Real-space cutoff (default: @see {dftd_cutoff.h}).
+ * @param dcndr Derivative of coordination number.
+ * @param lgrad Flag for gradient computation.
+ * @return Exit status.
+ */
+extern int get_ncoord_erf(
+  const TMolecule &mol,
+  const TMatrix<double> &dist,
+  double cutoff,
+  TVector<double> &cn,
+  TMatrix<double> &dcndr,
+  bool lgrad = false
+);
+
 /**
  * Calculate error function coordination number.
  *
  * @param mol Molecule object.
- * @param realIdx List for real atoms excluding ghost/non atoms
+ * @param realIdx List for real atoms excluding ghost/non atoms.
  * @param dist Distance matrix.
  * @param cutoff Real-space cutoff (default: @see {dftd_cutoff.h}).
  * @param cn Vector of coordination numbers.
@@ -87,7 +119,7 @@ extern int ncoord_erf(
  * w.r.t. nuclear coordinates.
  *
  * @param mol Molecule object.
- * @param realIdx List for real atoms excluding ghost/non atoms
+ * @param realIdx List for real atoms excluding ghost/non atoms.
  * @param dist Distance matrix.
  * @param cutoff Real-space cutoff (default: @see {dftd_cutoff.h}).
  * @param cn Vector of coordination numbers.
@@ -103,11 +135,14 @@ extern int dncoord_erf(
   TMatrix<double> &dcndr
 );
 
+///////////////////////////////////////////////////////////////////////////////
+///////////////////////////////////////////////////////////////////////////////
+
 /**
  * Wrapper for error function coordination number for DFT-D4.
  *
  * @param mol Molecule object.
- * @param realIdx List for real atoms excluding ghost/non atoms
+ * @param realIdx List for real atoms excluding ghost/non atoms.
  * @param dist Distance matrix.
  * @param cutoff Real-space cutoff (default: @see {dftd_cutoff.h}).
  * @param cn Vector of coordination numbers.
@@ -123,11 +158,29 @@ extern int get_ncoord_d4(
   bool lgrad = false
 );
 
+/**
+ * Wrapper for error function coordination number for DFT-D4.
+ *
+ * @param mol Molecule object.
+ * @param dist Distance matrix.
+ * @param cutoff Real-space cutoff (default: @see {dftd_cutoff.h}).
+ * @param cn Vector of coordination numbers.
+ * @return Exit status.
+ */
+extern int get_ncoord_d4(
+  const TMolecule &mol,
+  const TMatrix<double> &dist,
+  double cutoff,
+  TVector<double> &cn,
+  TMatrix<double> &dcndr,
+  bool lgrad = false
+);
+
 /**
  * Calculate covalent coordination number for DFT-D4.
  *
  * @param mol Molecule object.
- * @param realIdx List for real atoms excluding ghost/non atoms
+ * @param realIdx List for real atoms excluding ghost/non atoms.
  * @param dist Distance matrix.
  * @param cutoff Real-space cutoff (default: @see {dftd_cutoff.h}).
  * @param cn Vector of coordination numbers.
@@ -146,7 +199,7 @@ extern int ncoord_d4(
  * w.r.t. nuclear coordinates
  *
  * @param mol Molecule object.
- * @param realIdx List for real atoms excluding ghost/non atoms
+ * @param realIdx List for real atoms excluding ghost/non atoms.
  * @param dist Distance matrix.
  * @param cutoff Real-space cutoff (default: @see {dftd_cutoff.h}).
  * @param cn Vector of coordination numbers.
@@ -162,6 +215,9 @@ extern int dncoord_d4(
   TMatrix<double> &dcndr
 );
 
+///////////////////////////////////////////////////////////////////////////////
+///////////////////////////////////////////////////////////////////////////////
+
 /**
  * Error function counting function for coordination number contributions.
  *
diff --git a/scripts/README.md b/scripts/README.md
@@ -1,3 +1,4 @@
 # Scripts
 
 Scripts for creating the ORCA source files. This mainly concatenates the corresponding files and adds headers and footers. Execute within the `scripts` directory.
+This is only useful for ORCA developers.
diff --git a/src/dftd_dispersion.cpp b/src/dftd_dispersion.cpp
@@ -34,6 +34,21 @@
 
 namespace dftd4 {
 
+int get_dispersion(
+  const TMolecule &mol,
+  const int charge,
+  const TD4Model &d4,
+  const dparam &par,
+  const TCutoff cutoff,
+  double &energy,
+  double *GRAD
+) {
+  TVector<int> realIdx;
+  initializeRealIdx(mol.NAtoms, realIdx);
+
+  return get_dispersion(mol, realIdx, charge, d4, par, cutoff, energy, GRAD);
+}
+
 int get_dispersion(
   const TMolecule &mol,
   const TIVector &realIdx,
diff --git a/src/dftd_eeq.cpp b/src/dftd_eeq.cpp
@@ -129,6 +129,21 @@ static const double pi = 3.1415926535897932384626433832795029;
 static const double sqrtpi = std::sqrt(pi);
 static const double sqrt2pi = std::sqrt(2.0 / pi);
 
+int get_charges(
+  const TMolecule &mol,
+  const TMatrix<double> &dist,
+  const int charge,
+  const double cutoff,
+  TVector<double> &q,
+  TMatrix<double> &dqdr,
+  bool lgrad
+) {
+  TIVector realIdx;
+  initializeRealIdx(mol.NAtoms, realIdx);
+
+  return get_charges(mol, realIdx, dist, charge, cutoff, q, dqdr, lgrad);
+};
+
 int get_charges(
   const TMolecule &mol,
   const TIVector &realIdx,
diff --git a/src/dftd_ncoord.cpp b/src/dftd_ncoord.cpp

Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,4 @@`
`1`	`1`	`# Scripts`
`2`	`2`
`3`	`3`	Scripts for creating the ORCA source files. This mainly concatenates the corresponding files and adds headers and footers. Execute within the `scripts` directory.
	`4`	`+This is only useful for ORCA developers.`