refactor: Add back function parameters lost during rebase

Author: giacomofiorin

src/colvarcomp_coordnums.cpp

@@ -232,11 +232,13 @@ void inline colvar::coordnum::main_loop()
          compute_pair_coordnum<flags | ef_use_internal_pbc>(inv_r0_vec, inv_r0sq_vec, en, ed,
                                                             x1, y1, z1, x2, y2, z2,
                                                             gx1, gy1, gz1, gx2, gy2, gz2,
-                                                            tolerance, tolerance_l2_max) :
+                                                            tolerance, tolerance_l2_max,
+                                                            cvmodule) :
          compute_pair_coordnum<flags>(inv_r0_vec, inv_r0sq_vec, en, ed,
                                       x1, y1, z1, x2, y2, z2,
                                       gx1, gy1, gz1, gx2, gy2, gz2,
-                                      tolerance, tolerance_l2_max) ) :
+                                      tolerance, tolerance_l2_max,
+                                      cvmodule) ) :
         0.0;
 
       if ((flags & ef_use_pairlist) && (flags & ef_rebuild_pairlist)) {
@@ -444,7 +446,8 @@ void colvar::h_bond::calc_value()
                                                         atom_groups[0]->grad_x(1),
                                                         atom_groups[0]->grad_y(1),
                                                         atom_groups[0]->grad_z(1),
-                                                        0.0, 1.0e20);
+                                                        0.0, 1.0e20,
+                                                        cvmodule);
   // Skip the gradient
 }
 
@@ -475,7 +478,8 @@ void colvar::h_bond::calc_gradients()
                                          atom_groups[0]->grad_x(1),
                                          atom_groups[0]->grad_y(1),
                                          atom_groups[0]->grad_z(1),
-                                         0.0, 1.0e20);
+                                         0.0, 1.0e20,
+                                         cvmodule);
 }
 
 
@@ -517,11 +521,13 @@ template <int flags> inline void colvar::selfcoordnum::selfcoordnum_sequential_l
          compute_pair_coordnum<flags | ef_use_internal_pbc>(inv_r0_vec, inv_r0sq_vec, en, ed,
                                                             x1, y1, z1, x2, y2, z2,
                                                             gx1, gy1, gz1, gx2, gy2, gz2,
-                                                            tolerance, tolerance_l2_max) :
+                                                            tolerance, tolerance_l2_max,
+                                                            cvmodule) :
          compute_pair_coordnum<flags>(inv_r0_vec, inv_r0sq_vec, en, ed,
                                       x1, y1, z1, x2, y2, z2,
                                       gx1, gy1, gz1, gx2, gy2, gz2,
-                                      tolerance, tolerance_l2_max) ) :
+                                      tolerance, tolerance_l2_max,
+                                      cvmodule) ) :
         0.0;
 
       if ((flags & ef_use_pairlist) && (flags & ef_rebuild_pairlist)) {

src/colvarcomp_coordnums.h

@@ -55,7 +55,8 @@ class colvar::coordnum : public colvar::cvc {
                                          const cvm::real a2x, const cvm::real a2y, const cvm::real a2z,
                                          cvm::real &g1x, cvm::real &g1y, cvm::real &g1z,
                                          cvm::real &g2x, cvm::real &g2y, cvm::real &g2z,
-                                         cvm::real pairlist_tol, cvm::real pairlist_tol_l2_max);
+                                         cvm::real pairlist_tol, cvm::real pairlist_tol_l2_max,
+                                         colvarmodule *cvmodule);
 
   /// Workhorse function
   template <bool use_group1_com, bool use_group2_com, int flags> int compute_coordnum();
@@ -245,13 +246,14 @@ inline cvm::real colvar::coordnum::compute_pair_coordnum(cvm::rvector const &inv
                                                          cvm::real& g2y,
                                                          cvm::real& g2z,
                                                          cvm::real pairlist_tol,
-                                                         cvm::real pairlist_tol_l2_max)
+                                                         cvm::real pairlist_tol_l2_max,
+                                                         colvarmodule *cvmodule_in)
 {
   const cvm::atom_pos pos1{a1x, a1y, a1z};
   const cvm::atom_pos pos2{a2x, a2y, a2z};
   cvm::rvector const diff = (flags & ef_use_internal_pbc)
-                                ? cvm::main()->proxy->position_distance_internal(pos1, pos2)
-                                : cvm::main()->proxy->position_distance(pos1, pos2);
+                                ? cvmodule_in->proxy->position_distance_internal(pos1, pos2)
+                                : cvmodule_in->proxy->position_distance(pos1, pos2);
 
   cvm::rvector const scal_diff(diff.x * inv_r0_vec.x,
                                diff.y * inv_r0_vec.y,