Merge ORCA branch

Author: marvinfriede

.gitignore

@@ -35,3 +35,8 @@
 /build*/
 /install*/
 /_*/
+
+# project-specific
+/scripts/old/*
+/scripts/*.h
+/scripts/*.cpp

.vscode/settings.json

@@ -0,0 +1,10 @@
+{
+  "files.associations": {
+    "cassert": "cpp",
+    "cmath": "cpp",
+    "complex": "cpp",
+    "functional": "cpp",
+    "iostream": "cpp",
+    "new": "cpp"
+  }
+}

README.md

@@ -1,11 +1,13 @@
-# C++ Port of DFT-D4
+# C++ Port of DFT-D4 (for ORCA)
 
 [![License](https://img.shields.io/github/license/dftd4/cpp-d4)](https://github.com/dftd4/cpp-d4/blob/master/COPYING)
 [![Latest Version](https://img.shields.io/github/v/release/dftd4/cpp-d4)](https://github.com/dftd4/cpp-d4/releases/latest)
 
 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:

app/main.cpp

@@ -163,6 +163,15 @@ 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) {
@@ -174,7 +183,9 @@ int main(int argc, char **argv) {
     d4grad = nullptr;
   }
 
-  info = dftd4::get_dispersion(mol, charge, d4, par, cutoff, energy, d4grad);
+  info = dftd4::get_dispersion(
+    mol, realIdx, charge, d4, par, cutoff, energy, d4grad
+  );
   if (info != EXIT_SUCCESS) return info;
 
   // Print results
@@ -196,6 +207,7 @@ int main(int argc, char **argv) {
   }
 
   mol.FreeMemory();
+  delete[] d4grad;
 
   return EXIT_SUCCESS;
 }

app/readxyz.cpp

@@ -56,11 +56,11 @@ void read_xyzfile(const std::string &name, dftd4::TMolecule &mol) {
       printf("Error: Input file could not be read.");
       exit(EXIT_FAILURE);
     }
-    mol.xyz(i, 0) = x * aatoau;
-    mol.xyz(i, 1) = y * aatoau;
-    mol.xyz(i, 2) = z * aatoau;
+    mol.CC(i, 0) = x * aatoau;
+    mol.CC(i, 1) = y * aatoau;
+    mol.CC(i, 2) = z * aatoau;
     at = element(sym);
-    mol.at(i) = at;
+    mol.ATNO(i) = at;
   }
 
   geo.close();

include/damping/dftd_atm.h

@@ -29,6 +29,7 @@ namespace dftd4 {
 
 extern int get_atm_dispersion(
   const TMolecule &mol,
+  const TIVector &realIdx,
   const TMatrix<double> &dist,
   double cutoff,
   double s9,
@@ -47,6 +48,7 @@ extern int get_atm_dispersion(
 
 extern int get_atm_dispersion_energy(
   const TMolecule &mol,
+  const TIVector &realIdx,
   const TMatrix<double> &dist,
   double cutoff,
   double s9,
@@ -59,6 +61,7 @@ extern int get_atm_dispersion_energy(
 
 extern int get_atm_dispersion_derivs(
   const TMolecule &mol,
+  const TIVector &realIdx,
   const TMatrix<double> &dist,
   double cutoff,
   double s9,

include/damping/dftd_rational.h

@@ -31,6 +31,7 @@ extern inline double fdmprdr_bj(int n, double r, double c);
 
 extern int get_dispersion2(
   const TMolecule &mol,
+  const TIVector &realIdx,
   const TMatrix<double> &dist,
   double cutoff,
   const dparam &par,
@@ -46,6 +47,7 @@ extern int get_dispersion2(
 
 extern int get_dispersion3(
   const TMolecule &mol,
+  const TIVector &realIdx,
   const TMatrix<double> &dist,
   double cutoff,
   const dparam &par,
@@ -63,6 +65,7 @@ extern int get_dispersion3(
 
 extern int get_dispersion2_energy(
   const TMolecule &mol,
+  const TIVector &realIdx,
   const TMatrix<double> &dist,
   double cutoff,
   const dparam &par,
@@ -72,6 +75,7 @@ extern int get_dispersion2_energy(
 
 extern int get_dispersion2_derivs(
   const TMolecule &mol,
+  const TIVector &realIdx,
   const TMatrix<double> &dist,
   double cutoff,
   const dparam &par,

include/dftd_dispersion.h

@@ -42,6 +42,7 @@ 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.
@@ -52,6 +53,7 @@ class dparam {
  */
 extern int get_dispersion(
   const TMolecule &mol,
+  const TIVector &realIdx,
   int charge,
   const TD4Model &d4,
   const dparam &par,

include/dftd_eeq.h

@@ -29,6 +29,7 @@ namespace dftd4 {
 
 extern int get_charges(
   const TMolecule &mol,
+  const TIVector &realIdx,
   const TMatrix<double> &dist,
   int charge,
   double cutoff,
@@ -39,6 +40,7 @@ extern int get_charges(
 
 extern int get_vrhs(
   const TMolecule &mol,
+  const TIVector &realIdx,
   const int &charge,
   const TVector<double> &cn,
   TVector<double> &Xvec,
@@ -48,12 +50,14 @@ extern int get_vrhs(
 
 extern int get_amat_0d(
   const TMolecule &mol,
+  const TIVector &realIdx,
   const TMatrix<double> &dist,
   TMatrix<double> &Amat
 );
 
 extern int get_damat_0d(
   const TMolecule &mol,
+  const TIVector &realIdx,
   const TMatrix<double> &dist,
   const TVector<double> &q,
   const TMatrix<double> &Amat,
@@ -63,6 +67,7 @@ extern int get_damat_0d(
 
 extern int eeq_chrgeq(
   const TMolecule &mol,
+  const TIVector &realIdx,
   const TMatrix<double> &dist,
   const int &charge,
   const TVector<double> &cn,

include/dftd_geometry.h

@@ -25,22 +25,22 @@ namespace dftd4 {
 class TMolecule {
   public:
     int NAtoms;
-    TMatrix<double> xyz; // Cartesian Coordinates: (NAtoms x 3)-matrix
-    TVector<int> at;     // atomic numbers
+    TMatrix<double> CC; // Cartesian Coordinates: (NAtoms x 3)-matrix
+    TVector<int> ATNO;  // atomic numbers
 
     TMolecule() { NAtoms = 0; }
     ~TMolecule() { FreeMemory(); }
 
     void GetMemory(int NumAt_) {
       FreeMemory();
       NAtoms = NumAt_;
-      xyz.New(NAtoms, 3);
-      at.New(NAtoms);
+      CC.New(NAtoms, 3);
+      ATNO.New(NAtoms);
     }
 
-    void FreeMemory() {
-      xyz.Delete();
-      at.Delete();
+    void FreeMemory(void) {
+      CC.Delete();
+      ATNO.Delete();
     }
 };