Add handling of ghost atoms

marvinfriede · Apr 28, 2023 · 76dd2be · 76dd2be
1 parent 3ec87b8
commit 76dd2be
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Showing 29 changed files with 1,357 additions and 769 deletions.
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -0,0 +1,9 @@
+{
+  "files.associations": {
+    "functional": "cpp",
+    "cmath": "cpp",
+    "complex": "cpp",
+    "iostream": "cpp",
+    "new": "cpp"
+  }
+}
diff --git a/include/damping/atm.h b/include/damping/atm.h
@@ -29,6 +29,7 @@ namespace dftd4 {
 
 extern int get_atm_dispersion(
   const TMolecule &mol,
+  const TIVector &realIdx,
   const TMatrix<double> &dist,
   const double cutoff,
   const 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,
   const double cutoff,
   const 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,
   const double cutoff,
   const double s9,

diff --git a/include/damping/rational.h b/include/damping/rational.h
@@ -31,6 +31,7 @@ extern inline double fdmprdr_bj(const int n, const double r, const double c);
 
 extern int get_dispersion2(
   const TMolecule &mol,
+  const TIVector &realIdx,
   const TMatrix<double> &dist,
   const 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,
   const 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,
   const 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,
   const double cutoff,
   const dparam &par,

diff --git a/include/dftd_dispersion.h b/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,
   const int charge,
   const TD4Model &d4,
   const dparam &par,

diff --git a/include/dftd_eeq.h b/include/dftd_eeq.h
@@ -29,6 +29,7 @@ namespace dftd4 {
 
 extern int get_charges(
   const TMolecule &mol,
+  const TIVector &realIdx,
   const TMatrix<double> &dist,
   const int charge,
   const 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,

diff --git a/include/dftd_geometry.h b/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(void) {
-    xyz.Delete();
-    at.Delete();
+    CC.Delete();
+    ATNO.Delete();
   }
 };