Pass restraint data structures to bonded functions

This adds explicitly the t_disresdata and t_oriresdata structures to all
bonded force calculation calls, instead of passing them as members of
the t_fcdata structure. This is an unfortunate but necessary step in
order to be able to separate bondedtable_t from the two restraint
data structures. The splitting of t_fcdata into separate table data and
restraint data structures is needed to simplify the initialization of
the forcerec.

diff --git a/src/gromacs/gmxana/gmx_disre.cpp b/src/gromacs/gmxana/gmx_disre.cpp
index 8b8eade002dcbbcf615e0f5b4b431b4dc3afd676..bd3feef0437da3b4e6bc022e0a2d719e3de37e83 100644 (file)
--- a/src/gromacs/gmxana/gmx_disre.cpp
+++ b/src/gromacs/gmxana/gmx_disre.cpp
@@ -4,7 +4,7 @@
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
  * Copyright (c) 2013,2014,2015,2016,2017 The GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -205,10 +205,6 @@ static void check_viol(FILE*                          log,
         }
     }
 
-    // Set up t_fcdata, only needed for calling ta_disres()
-    t_fcdata fcd;
-    fcd.disres = disresdata;
-
     // Get offset for label index
     label_old = forceparams[forceatoms[0]].disres.label;
     for (i = 0; (i < disres.size());)
@@ -241,7 +237,7 @@ static void check_viol(FILE*                          log,
         dr[clust_id].aver_6[ndr] += disresdata->Rt_6[label];
 
         snew(fshift, SHIFTS);
-        ta_disres(n, &forceatoms[i], forceparams.data(), x, f, fshift, pbc, lam, &dvdl, nullptr, &fcd, nullptr);
+        ta_disres(n, &forceatoms[i], forceparams.data(), x, f, fshift, pbc, lam, &dvdl, nullptr, nullptr, disresdata, nullptr, nullptr);
         sfree(fshift);
         viol = disresdata->sumviol;
 

diff --git a/src/gromacs/listed_forces/bonded.cpp b/src/gromacs/listed_forces/bonded.cpp
index d5b939696bfc0dc604ea4608a023418dee532400..80ae6741de74293f3cb7182c6fb26d68ce658ca6 100644 (file)
--- a/src/gromacs/listed_forces/bonded.cpp
+++ b/src/gromacs/listed_forces/bonded.cpp
@@ -4,7 +4,7 @@
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
  * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -102,6 +102,8 @@ using BondedFunction = real (*)(int              nbonds,
                                 real*            dvdlambda,
                                 const t_mdatoms* md,
                                 t_fcdata*        fcd,
+                                t_disresdata*    disresdata,
+                                t_oriresdata*    oriresdata,
                                 int*             ddgatindex);
 
 /*! \brief Mysterious CMAP coefficient matrix */
@@ -256,6 +258,8 @@ real morse_bonds(int             nbonds,
                  real*           dvdlambda,
                  const t_mdatoms gmx_unused* md,
                  t_fcdata gmx_unused* fcd,
+                 t_disresdata gmx_unused* disresdata,
+                 t_oriresdata gmx_unused* oriresdata,
                  int gmx_unused* global_atom_index)
 {
     const real one = 1.0;
@@ -324,6 +328,8 @@ real cubic_bonds(int             nbonds,
                  real gmx_unused* dvdlambda,
                  const t_mdatoms gmx_unused* md,
                  t_fcdata gmx_unused* fcd,
+                 t_disresdata gmx_unused* disresdata,
+                 t_oriresdata gmx_unused* oriresdata,
                  int gmx_unused* global_atom_index)
 {
     const real three = 3.0;
@@ -379,7 +385,9 @@ real FENE_bonds(int             nbonds,
                 real gmx_unused* dvdlambda,
                 const t_mdatoms gmx_unused* md,
                 t_fcdata gmx_unused* fcd,
-                int*                 global_atom_index)
+                t_disresdata gmx_unused* disresdata,
+                t_oriresdata gmx_unused* oriresdata,
+                int*                     global_atom_index)
 {
     const real half = 0.5;
     const real one  = 1.0;
@@ -468,6 +476,8 @@ bonds(int             nbonds,
       real*           dvdlambda,
       const t_mdatoms gmx_unused* md,
       t_fcdata gmx_unused* fcd,
+      t_disresdata gmx_unused* disresdata,
+      t_oriresdata gmx_unused* oriresdata,
       int gmx_unused* global_atom_index)
 {
     int  i, ki, ai, aj, type;
@@ -528,6 +538,8 @@ bonds(int             nbonds,
       real gmx_unused* dvdlambda,
       const t_mdatoms gmx_unused* md,
       t_fcdata gmx_unused* fcd,
+      t_disresdata gmx_unused* disresdata,
+      t_oriresdata gmx_unused* oriresdata,
       int gmx_unused* global_atom_index)
 {
     constexpr int                            nfa1 = 3;
@@ -618,6 +630,8 @@ real restraint_bonds(int             nbonds,
                      real*           dvdlambda,
                      const t_mdatoms gmx_unused* md,
                      t_fcdata gmx_unused* fcd,
+                     t_disresdata gmx_unused* disresdata,
+                     t_oriresdata gmx_unused* oriresdata,
                      int gmx_unused* global_atom_index)
 {
     int  i, ki, ai, aj, type;
@@ -706,6 +720,8 @@ real polarize(int              nbonds,
               real*            dvdlambda,
               const t_mdatoms* md,
               t_fcdata gmx_unused* fcd,
+              t_disresdata gmx_unused* disresdata,
+              t_oriresdata gmx_unused* oriresdata,
               int gmx_unused* global_atom_index)
 {
     int  i, ki, ai, aj, type;
@@ -751,6 +767,8 @@ real anharm_polarize(int              nbonds,
                      real*            dvdlambda,
                      const t_mdatoms* md,
                      t_fcdata gmx_unused* fcd,
+                     t_disresdata gmx_unused* disresdata,
+                     t_oriresdata gmx_unused* oriresdata,
                      int gmx_unused* global_atom_index)
 {
     int  i, ki, ai, aj, type;
@@ -805,6 +823,8 @@ real water_pol(int             nbonds,
                real gmx_unused* dvdlambda,
                const t_mdatoms gmx_unused* md,
                t_fcdata gmx_unused* fcd,
+               t_disresdata gmx_unused* disresdata,
+               t_oriresdata gmx_unused* oriresdata,
                int gmx_unused* global_atom_index)
 {
     /* This routine implements anisotropic polarizibility for water, through
@@ -948,6 +968,8 @@ real thole_pol(int             nbonds,
                real gmx_unused* dvdlambda,
                const t_mdatoms* md,
                t_fcdata gmx_unused* fcd,
+               t_disresdata gmx_unused* disresdata,
+               t_oriresdata gmx_unused* oriresdata,
                int gmx_unused* global_atom_index)
 {
     /* Interaction between two pairs of particles with opposite charge */
@@ -999,6 +1021,8 @@ angles(int             nbonds,
        real*           dvdlambda,
        const t_mdatoms gmx_unused* md,
        t_fcdata gmx_unused* fcd,
+       t_disresdata gmx_unused* disresdata,
+       t_oriresdata gmx_unused* oriresdata,
        int gmx_unused* global_atom_index)
 {
     int  i, ai, aj, ak, t1, t2, type;
@@ -1091,6 +1115,8 @@ angles(int             nbonds,
        real gmx_unused* dvdlambda,
        const t_mdatoms gmx_unused* md,
        t_fcdata gmx_unused* fcd,
+       t_disresdata gmx_unused* disresdata,
+       t_oriresdata gmx_unused* oriresdata,
        int gmx_unused* global_atom_index)
 {
     const int                                nfa1 = 4;
@@ -1249,6 +1275,8 @@ real linear_angles(int             nbonds,
                    real*           dvdlambda,
                    const t_mdatoms gmx_unused* md,
                    t_fcdata gmx_unused* fcd,
+                   t_disresdata gmx_unused* disresdata,
+                   t_oriresdata gmx_unused* oriresdata,
                    int gmx_unused* global_atom_index)
 {
     int  i, m, ai, aj, ak, t1, t2, type;
@@ -1319,6 +1347,8 @@ urey_bradley(int             nbonds,
              real*           dvdlambda,
              const t_mdatoms gmx_unused* md,
              t_fcdata gmx_unused* fcd,
+             t_disresdata gmx_unused* disresdata,
+             t_oriresdata gmx_unused* oriresdata,
              int gmx_unused* global_atom_index)
 {
     int  i, m, ai, aj, ak, t1, t2, type, ki;
@@ -1429,6 +1459,8 @@ urey_bradley(int             nbonds,
              real gmx_unused* dvdlambda,
              const t_mdatoms gmx_unused* md,
              t_fcdata gmx_unused* fcd,
+             t_disresdata gmx_unused* disresdata,
+             t_oriresdata gmx_unused* oriresdata,
              int gmx_unused* global_atom_index)
 {
     constexpr int                            nfa1 = 4;
@@ -1571,6 +1603,8 @@ real quartic_angles(int             nbonds,
                     real gmx_unused* dvdlambda,
                     const t_mdatoms gmx_unused* md,
                     t_fcdata gmx_unused* fcd,
+                    t_disresdata gmx_unused* disresdata,
+                    t_oriresdata gmx_unused* oriresdata,
                     int gmx_unused* global_atom_index)
 {
     int  i, j, ai, aj, ak, t1, t2, type;
@@ -1936,6 +1970,8 @@ pdihs(int             nbonds,
       real*           dvdlambda,
       const t_mdatoms gmx_unused* md,
       t_fcdata gmx_unused* fcd,
+      t_disresdata gmx_unused* disresdata,
+      t_oriresdata gmx_unused* oriresdata,
       int gmx_unused* global_atom_index)
 {
     int  t1, t2, t3;
@@ -1997,6 +2033,8 @@ pdihs(int             nbonds,
       real gmx_unused* dvdlambda,
       const t_mdatoms gmx_unused* md,
       t_fcdata gmx_unused* fcd,
+      t_disresdata gmx_unused* disresdata,
+      t_oriresdata gmx_unused* oriresdata,
       int gmx_unused* global_atom_index)
 {
     const int                                nfa1 = 5;
@@ -2111,6 +2149,8 @@ rbdihs(int             nbonds,
        real gmx_unused* dvdlambda,
        const t_mdatoms gmx_unused* md,
        t_fcdata gmx_unused* fcd,
+       t_disresdata gmx_unused* disresdata,
+       t_oriresdata gmx_unused* oriresdata,
        int gmx_unused* global_atom_index)
 {
     const int                                nfa1 = 5;
@@ -2237,6 +2277,8 @@ real idihs(int             nbonds,
            real*           dvdlambda,
            const t_mdatoms gmx_unused* md,
            t_fcdata gmx_unused* fcd,
+           t_disresdata gmx_unused* disresdata,
+           t_oriresdata gmx_unused* oriresdata,
            int gmx_unused* global_atom_index)
 {
     int  i, type, ai, aj, ak, al;
@@ -2403,6 +2445,8 @@ real angres(int             nbonds,
             real*           dvdlambda,
             const t_mdatoms gmx_unused* md,
             t_fcdata gmx_unused* fcd,
+            t_disresdata gmx_unused* disresdata,
+            t_oriresdata gmx_unused* oriresdata,
             int gmx_unused* global_atom_index)
 {
     return low_angres<flavor>(nbonds, forceatoms, forceparams, x, f, fshift, pbc, lambda, dvdlambda, FALSE);
@@ -2420,6 +2464,8 @@ real angresz(int             nbonds,
              real*           dvdlambda,
              const t_mdatoms gmx_unused* md,
              t_fcdata gmx_unused* fcd,
+             t_disresdata gmx_unused* disresdata,
+             t_oriresdata gmx_unused* oriresdata,
              int gmx_unused* global_atom_index)
 {
     return low_angres<flavor>(nbonds, forceatoms, forceparams, x, f, fshift, pbc, lambda, dvdlambda, TRUE);
@@ -2437,6 +2483,8 @@ real dihres(int             nbonds,
             real*           dvdlambda,
             const t_mdatoms gmx_unused* md,
             t_fcdata gmx_unused* fcd,
+            t_disresdata gmx_unused* disresdata,
+            t_oriresdata gmx_unused* oriresdata,
             int gmx_unused* global_atom_index)
 {
     real vtot = 0;
@@ -2530,6 +2578,8 @@ real unimplemented(int gmx_unused nbonds,
                    real gmx_unused* dvdlambda,
                    const t_mdatoms gmx_unused* md,
                    t_fcdata gmx_unused* fcd,
+                   t_disresdata gmx_unused* disresdata,
+                   t_oriresdata gmx_unused* oriresdata,
                    int gmx_unused* global_atom_index)
 {
     gmx_impl("*** you are using a not implemented function");
@@ -2547,6 +2597,8 @@ real restrangles(int             nbonds,
                  real gmx_unused* dvdlambda,
                  const t_mdatoms gmx_unused* md,
                  t_fcdata gmx_unused* fcd,
+                 t_disresdata gmx_unused* disresdata,
+                 t_oriresdata gmx_unused* oriresdata,
                  int gmx_unused* global_atom_index)
 {
     int    i, d, ai, aj, ak, type, m;
@@ -2649,6 +2701,8 @@ real restrdihs(int             nbonds,
                real gmx_unused* dvlambda,
                const t_mdatoms gmx_unused* md,
                t_fcdata gmx_unused* fcd,
+               t_disresdata gmx_unused* disresdata,
+               t_oriresdata gmx_unused* oriresdata,
                int gmx_unused* global_atom_index)
 {
     int  i, d, type, ai, aj, ak, al;
@@ -2771,6 +2825,8 @@ real cbtdihs(int             nbonds,
              real gmx_unused* dvdlambda,
              const t_mdatoms gmx_unused* md,
              t_fcdata gmx_unused* fcd,
+             t_disresdata gmx_unused* disresdata,
+             t_oriresdata gmx_unused* oriresdata,
              int gmx_unused* global_atom_index)
 {
     int  type, ai, aj, ak, al, i, d;
@@ -2886,6 +2942,8 @@ rbdihs(int             nbonds,
        real*           dvdlambda,
        const t_mdatoms gmx_unused* md,
        t_fcdata gmx_unused* fcd,
+       t_disresdata gmx_unused* disresdata,
+       t_oriresdata gmx_unused* oriresdata,
        int gmx_unused* global_atom_index)
 {
     const real c0 = 0.0, c1 = 1.0, c2 = 2.0, c3 = 3.0, c4 = 4.0, c5 = 5.0;
@@ -3036,6 +3094,8 @@ real cmap_dihs(int                 nbonds,
                real gmx_unused* dvdlambda,
                const t_mdatoms gmx_unused* md,
                t_fcdata gmx_unused* fcd,
+               t_disresdata gmx_unused* disresdata,
+               t_oriresdata gmx_unused* oriresdata,
                int gmx_unused* global_atom_index)
 {
     int i, n;
@@ -3440,6 +3500,8 @@ real g96bonds(int             nbonds,
               real*           dvdlambda,
               const t_mdatoms gmx_unused* md,
               t_fcdata gmx_unused* fcd,
+              t_disresdata gmx_unused* disresdata,
+              t_oriresdata gmx_unused* oriresdata,
               int gmx_unused* global_atom_index)
 {
     int  i, ki, ai, aj, type;
@@ -3497,6 +3559,8 @@ real g96angles(int             nbonds,
                real*           dvdlambda,
                const t_mdatoms gmx_unused* md,
                t_fcdata gmx_unused* fcd,
+               t_disresdata gmx_unused* disresdata,
+               t_oriresdata gmx_unused* oriresdata,
                int gmx_unused* global_atom_index)
 {
     int  i, ai, aj, ak, type, m, t1, t2;
@@ -3564,6 +3628,8 @@ real cross_bond_bond(int             nbonds,
                      real gmx_unused* dvdlambda,
                      const t_mdatoms gmx_unused* md,
                      t_fcdata gmx_unused* fcd,
+                     t_disresdata gmx_unused* disresdata,
+                     t_oriresdata gmx_unused* oriresdata,
                      int gmx_unused* global_atom_index)
 {
     /* Potential from Lawrence and Skimmer, Chem. Phys. Lett. 372 (2003)
@@ -3636,6 +3702,8 @@ real cross_bond_angle(int             nbonds,
                       real gmx_unused* dvdlambda,
                       const t_mdatoms gmx_unused* md,
                       t_fcdata gmx_unused* fcd,
+                      t_disresdata gmx_unused* disresdata,
+                      t_oriresdata gmx_unused* oriresdata,
                       int gmx_unused* global_atom_index)
 {
     /* Potential from Lawrence and Skimmer, Chem. Phys. Lett. 372 (2003)
@@ -3772,6 +3840,8 @@ real tab_bonds(int             nbonds,
                real*           dvdlambda,
                const t_mdatoms gmx_unused* md,
                t_fcdata*                   fcd,
+               t_disresdata gmx_unused* disresdata,
+               t_oriresdata gmx_unused* oriresdata,
                int gmx_unused* global_atom_index)
 {
     int  i, ki, ai, aj, type, table;
@@ -3827,6 +3897,8 @@ real tab_angles(int             nbonds,
                 real*           dvdlambda,
                 const t_mdatoms gmx_unused* md,
                 t_fcdata*                   fcd,
+                t_disresdata gmx_unused* disresdata,
+                t_oriresdata gmx_unused* oriresdata,
                 int gmx_unused* global_atom_index)
 {
     int  i, ai, aj, ak, t1, t2, type, table;
@@ -3907,6 +3979,8 @@ real tab_dihs(int             nbonds,
               real*           dvdlambda,
               const t_mdatoms gmx_unused* md,
               t_fcdata*                   fcd,
+              t_disresdata gmx_unused* disresdata,
+              t_oriresdata gmx_unused* oriresdata,
               int gmx_unused* global_atom_index)
 {
     int  i, type, ai, aj, ak, al, table;
@@ -4083,13 +4157,15 @@ real calculateSimpleBond(const int           ftype,
                          real*               dvdlambda,
                          const t_mdatoms*    md,
                          t_fcdata*           fcd,
+                         t_disresdata*       disresdata,
+                         t_oriresdata*       oriresdata,
                          int gmx_unused*          global_atom_index,
                          const BondedKernelFlavor bondedKernelFlavor)
 {
     const BondedInteractions& bonded = c_bondedInteractionFunctionsPerFlavor[bondedKernelFlavor][ftype];
 
     real v = bonded.function(
-            numForceatoms, forceatoms, forceparams, x, f, fshift, pbc, lambda, dvdlambda, md, fcd, global_atom_index);
+            numForceatoms, forceatoms, forceparams, x, f, fshift, pbc, lambda, dvdlambda, md, fcd, disresdata, oriresdata, global_atom_index);
 
     return v;
 }

diff --git a/src/gromacs/listed_forces/bonded.h b/src/gromacs/listed_forces/bonded.h
index beb95b55289bc9d108008e7985c4b7ff42ac406a..d3c006145e1070282bc78e585f6961391eed46e5 100644 (file)
--- a/src/gromacs/listed_forces/bonded.h
+++ b/src/gromacs/listed_forces/bonded.h
@@ -4,7 +4,7 @@
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
  * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -59,6 +59,8 @@ struct t_fcdata;
 struct t_mdatom;
 struct t_nrnb;
 struct t_pbc;
+struct t_disresdata;
+struct t_oriresdata;
 
 namespace gmx
 {
@@ -127,6 +129,8 @@ real cmap_dihs(int                 nbonds,
                real gmx_unused* dvdlambda,
                const t_mdatoms gmx_unused* md,
                t_fcdata gmx_unused* fcd,
+               t_disresdata gmx_unused* disresdata,
+               t_oriresdata gmx_unused* oriresdata,
                int gmx_unused* global_atom_index);
 
 /*! \brief For selecting which flavor of bonded kernel is used for simple bonded types */
@@ -180,6 +184,8 @@ real calculateSimpleBond(int                 ftype,
                          real*               dvdlambda,
                          const t_mdatoms*    md,
                          t_fcdata*           fcd,
+                         t_disresdata*       disresdata,
+                         t_oriresdata*       oriresdata,
                          int gmx_unused*    global_atom_index,
                          BondedKernelFlavor bondedKernelFlavor);
 

diff --git a/src/gromacs/listed_forces/disre.cpp b/src/gromacs/listed_forces/disre.cpp
index d08261a7a88142203a4c82a6feaef902436618c0..1095ab94df32935603332f5d10889c3de1daa114 100644 (file)
--- a/src/gromacs/listed_forces/disre.cpp
+++ b/src/gromacs/listed_forces/disre.cpp
@@ -415,48 +415,48 @@ void calc_disres_R_6(const t_commrec*      cr,
     dd->sumviol = 0;
 }
 
-real ta_disres(int             nfa,
-               const t_iatom   forceatoms[],
-               const t_iparams ip[],
-               const rvec      x[],
-               rvec4           f[],
-               rvec            fshift[],
-               const t_pbc*    pbc,
+real ta_disres(int              nfa,
+               const t_iatom*   forceatoms,
+               const t_iparams* ip,
+               const rvec*      x,
+               rvec4*           f,
+               rvec*            fshift,
+               const t_pbc*     pbc,
                real gmx_unused lambda,
                real gmx_unused* dvdlambda,
                const t_mdatoms gmx_unused* md,
-               t_fcdata*                   fcd,
+               t_fcdata gmx_unused* fcd,
+               t_disresdata*        disresdata,
+               t_oriresdata gmx_unused* oriresdata,
                int gmx_unused* global_atom_index)
 {
     const real seven_three = 7.0 / 3.0;
 
-    rvec          dx;
-    real          weight_rt_1;
-    real          smooth_fc, Rt, Rtav, rt2, *Rtl_6, *Rt_6, *Rtav_6;
-    real          k0, f_scal = 0, fmax_scal, fk_scal, fij;
-    real          tav_viol, instant_viol, mixed_viol, violtot, vtot;
-    real          tav_viol_Rtav7, instant_viol_Rtav7;
-    real          up1, up2, low;
-    gmx_bool      bConservative, bMixed, bViolation;
-    t_disresdata* dd;
-    int           dr_weighting;
-    gmx_bool      dr_bMixed;
-
-    dd           = fcd->disres;
-    dr_weighting = dd->dr_weighting;
-    dr_bMixed    = dd->dr_bMixed;
-    Rtl_6        = dd->Rtl_6;
-    Rt_6         = dd->Rt_6;
-    Rtav_6       = dd->Rtav_6;
+    rvec     dx;
+    real     weight_rt_1;
+    real     smooth_fc, Rt, Rtav, rt2, *Rtl_6, *Rt_6, *Rtav_6;
+    real     k0, f_scal = 0, fmax_scal, fk_scal, fij;
+    real     tav_viol, instant_viol, mixed_viol, violtot, vtot;
+    real     tav_viol_Rtav7, instant_viol_Rtav7;
+    real     up1, up2, low;
+    gmx_bool bConservative, bMixed, bViolation;
+    int      dr_weighting;
+    gmx_bool dr_bMixed;
+
+    dr_weighting = disresdata->dr_weighting;
+    dr_bMixed    = disresdata->dr_bMixed;
+    Rtl_6        = disresdata->Rtl_6;
+    Rt_6         = disresdata->Rt_6;
+    Rtav_6       = disresdata->Rtav_6;
 
     tav_viol = instant_viol = mixed_viol = tav_viol_Rtav7 = instant_viol_Rtav7 = 0;
 
-    smooth_fc = dd->dr_fc;
-    if (dd->dr_tau != 0)
+    smooth_fc = disresdata->dr_fc;
+    if (disresdata->dr_tau != 0)
     {
         /* scaling factor to smoothly turn on the restraint forces *
          * when using time averaging                               */
-        smooth_fc *= (1.0 - dd->exp_min_t_tau);
+        smooth_fc *= (1.0 - disresdata->exp_min_t_tau);
     }
 
     violtot = 0;
@@ -464,7 +464,7 @@ real ta_disres(int             nfa,
 
     /* 'loop' over all atom pairs (pair_nr=fa/3) involved in restraints, *
      * the total number of atoms pairs is nfa/3                          */
-    int faOffset = static_cast<int>(forceatoms - dd->forceatomsStart);
+    int faOffset = static_cast<int>(forceatoms - disresdata->forceatomsStart);
     for (int fa = 0; fa < nfa; fa += 3)
     {
         int type  = forceatoms[fa];
@@ -474,7 +474,7 @@ real ta_disres(int             nfa,
         low       = ip[type].disres.low;
         k0        = smooth_fc * ip[type].disres.kfac;
 
-        int res = type - dd->type_min;
+        int res = type - disresdata->type_min;
 
         /* save some flops when there is only one pair */
         if (ip[type].disres.type != 2)
@@ -605,12 +605,14 @@ real ta_disres(int             nfa,
             {
                 if (!dr_bMixed)
                 {
-                    weight_rt_1 *= std::pow(dd->rm3tav[pair], seven_three);
+                    weight_rt_1 *= std::pow(disresdata->rm3tav[pair], seven_three);
                 }
                 else
                 {
-                    weight_rt_1 *= tav_viol_Rtav7 * std::pow(dd->rm3tav[pair], seven_three)
-                                   + instant_viol_Rtav7 / (dd->rt[pair] * gmx::power6(dd->rt[pair]));
+                    weight_rt_1 *=
+                            tav_viol_Rtav7 * std::pow(disresdata->rm3tav[pair], seven_three)
+                            + instant_viol_Rtav7
+                                      / (disresdata->rt[pair] * gmx::power6(disresdata->rt[pair]));
                 }
             }
 
@@ -632,7 +634,7 @@ real ta_disres(int             nfa,
     }
 
 #pragma omp atomic
-    dd->sumviol += violtot;
+    disresdata->sumviol += violtot;
 
     /* Return energy */
     return vtot;

diff --git a/src/gromacs/listed_forces/disre.h b/src/gromacs/listed_forces/disre.h
index cbe81d778f5c71a8a0961feb02f95de8051d86bd..756cce341c207800fa99a80f7abf9badb25670cb 100644 (file)
--- a/src/gromacs/listed_forces/disre.h
+++ b/src/gromacs/listed_forces/disre.h
@@ -56,6 +56,7 @@ struct gmx_multisim_t;
 class history_t;
 struct t_commrec;
 struct t_disresdata;
+struct t_oriresdata;
 struct t_fcdata;
 struct t_inputrec;
 struct t_pbc;
@@ -107,17 +108,19 @@ void calc_disres_R_6(const t_commrec*      cr,
 
 //! Calculates the distance restraint forces, return the potential.
 real ta_disres(int              nfa,
-               const t_iatom    forceatoms[],
-               const t_iparams  ip[],
-               const rvec       x[],
-               rvec4            f[],
-               rvec             fshift[],
+               const t_iatom*   forceatoms,
+               const t_iparams* ip,
+               const rvec*      x,
+               rvec4*           f,
+               rvec*            fshift,
                const t_pbc*     pbc,
                real             lambda,
                real*            dvdlambda,
                const t_mdatoms* md,
-               t_fcdata*        fcdata,
-               int*             global_atom_index);
+               t_fcdata gmx_unused* fcd,
+               t_disresdata*        disresdata,
+               t_oriresdata gmx_unused* oriresdata,
+               int*                     global_atom_index);
 
 //! Copies the new time averages that have been calculated in calc_disres_R_6.
 void update_disres_history(const t_disresdata& disresdata, history_t* hist);

diff --git a/src/gromacs/listed_forces/listed_forces.cpp b/src/gromacs/listed_forces/listed_forces.cpp
index d855b2e09611ddde3ecfd2e7c76915e5f62a20fe..10e54fb419a2e07a43fd4aa8d8d40de8da1cf976 100644 (file)
--- a/src/gromacs/listed_forces/listed_forces.cpp
+++ b/src/gromacs/listed_forces/listed_forces.cpp
@@ -470,6 +470,8 @@ real calc_one_bond(int                           thread,
                           &(dvdl[efptFTYPE]),
                           md,
                           fcd,
+                          nullptr,
+                          nullptr,
                           global_atom_index);
         }
         else
@@ -486,6 +488,8 @@ real calc_one_bond(int                           thread,
                                     &(dvdl[efptFTYPE]),
                                     md,
                                     fcd,
+                                    fcd->disres,
+                                    fcd->orires,
                                     global_atom_index,
                                     flavor);
         }

diff --git a/src/gromacs/listed_forces/listed_forces.h b/src/gromacs/listed_forces/listed_forces.h
index 4bed406827c1f7780c7332191d8f50cb27e15f48..d82a293b61ce5c84ae523b116be81fff440cdc05 100644 (file)
--- a/src/gromacs/listed_forces/listed_forces.h
+++ b/src/gromacs/listed_forces/listed_forces.h
@@ -94,6 +94,8 @@ struct t_lambda;
 struct t_mdatoms;
 struct t_nrnb;
 class t_state;
+struct t_disresdata;
+struct t_oriresdata;
 
 namespace gmx
 {
@@ -117,6 +119,8 @@ using BondedFunction = real (*)(int              nbonds,
                                 real*            dvdlambda,
                                 const t_mdatoms* md,
                                 t_fcdata*        fcd,
+                                t_disresdata*    disresdata,
+                                t_oriresdata*    oriresdata,
                                 int*             ddgatindex);
 
 //! Getter for finding a callable CPU function to compute an \c ftype interaction.

diff --git a/src/gromacs/listed_forces/orires.cpp b/src/gromacs/listed_forces/orires.cpp
index 47e3eb37144b663d113234d749991e5ff9e02923..ff9a7b5cec8375855afb1464652693c75c4d5c30 100644 (file)
--- a/src/gromacs/listed_forces/orires.cpp
+++ b/src/gromacs/listed_forces/orires.cpp
@@ -658,28 +658,28 @@ real orires(int             nfa,
             real gmx_unused lambda,
             real gmx_unused* dvdlambda,
             const t_mdatoms gmx_unused* md,
-            t_fcdata*                   fcd,
+            t_fcdata gmx_unused* fcd,
+            t_disresdata gmx_unused* disresdata,
+            t_oriresdata*            oriresdata,
             int gmx_unused* global_atom_index)
 {
-    int                 ex, power, ki = CENTRAL;
-    real                r2, invr, invr2, fc, smooth_fc, dev, devins, pfac;
-    rvec                r, Sr, fij;
-    real                vtot;
-    const t_oriresdata* od;
-    gmx_bool            bTAV;
+    int      ex, power, ki = CENTRAL;
+    real     r2, invr, invr2, fc, smooth_fc, dev, devins, pfac;
+    rvec     r, Sr, fij;
+    real     vtot;
+    gmx_bool bTAV;
 
     vtot = 0;
-    od   = fcd->orires;
 
-    if (od->fc != 0)
+    if (oriresdata->fc != 0)
     {
-        bTAV = (od->edt != 0);
+        bTAV = (oriresdata->edt != 0);
 
-        smooth_fc = od->fc;
+        smooth_fc = oriresdata->fc;
         if (bTAV)
         {
             /* Smoothly switch on the restraining when time averaging is used */
-            smooth_fc *= (1.0 - od->exp_min_t_tau);
+            smooth_fc *= (1.0 - oriresdata->exp_min_t_tau);
         }
 
         for (int fa = 0; fa < nfa; fa += 3)
@@ -687,7 +687,7 @@ real orires(int             nfa,
             const int type           = forceatoms[fa];
             const int ai             = forceatoms[fa + 1];
             const int aj             = forceatoms[fa + 2];
-            const int restraintIndex = type - od->typeMin;
+            const int restraintIndex = type - oriresdata->typeMin;
             if (pbc)
             {
                 ki = pbc_dx_aiuc(pbc, x[ai], x[aj], r);
@@ -702,7 +702,7 @@ real orires(int             nfa,
             ex    = ip[type].orires.ex;
             power = ip[type].orires.power;
             fc    = smooth_fc * ip[type].orires.kfac;
-            dev   = od->otav[restraintIndex] - ip[type].orires.obs;
+            dev   = oriresdata->otav[restraintIndex] - ip[type].orires.obs;
 
             /* NOTE:
              * there is no real potential when time averaging is applied
@@ -712,7 +712,7 @@ real orires(int             nfa,
             if (bTAV)
             {
                 /* Calculate the force as the sqrt of tav times instantaneous */
-                devins = od->oins[restraintIndex] - ip[type].orires.obs;
+                devins = oriresdata->oins[restraintIndex] - ip[type].orires.obs;
                 if (dev * devins <= 0)
                 {
                     dev = 0;
@@ -732,7 +732,7 @@ real orires(int             nfa,
             {
                 pfac *= invr;
             }
-            mvmul(od->S[ex], r, Sr);
+            mvmul(oriresdata->S[ex], r, Sr);
             for (int i = 0; i < DIM; i++)
             {
                 fij[i] = -pfac * dev * (4 * Sr[i] - 2 * (2 + power) * invr2 * iprod(Sr, r) * r[i]);

diff --git a/src/gromacs/listed_forces/orires.h b/src/gromacs/listed_forces/orires.h
index 0ad20a07af2fe112c18d71fa2bd3ae46e2d9c960..7c269b02174db8960938e81e46d013d99dd8e64c 100644 (file)
--- a/src/gromacs/listed_forces/orires.h
+++ b/src/gromacs/listed_forces/orires.h
@@ -56,6 +56,8 @@ struct t_inputrec;
 struct t_pbc;
 struct t_commrec;
 struct t_oriresdata;
+struct t_disresdata;
+struct t_fcdata;
 class t_state;
 
 namespace gmx
@@ -119,6 +121,8 @@ real orires(int              nfa,
             real*            dvdlambda,
             const t_mdatoms* md,
             t_fcdata*        fcd,
+            t_disresdata*    disresdata,
+            t_oriresdata*    oriresdata,
             int*             global_atom_index);
 
 //! Copies the new time averages that have been calculated in calc_orires_dev.

diff --git a/src/gromacs/listed_forces/tests/bonded.cpp b/src/gromacs/listed_forces/tests/bonded.cpp
index 554213953ed9acfd76e24c2d204742aa997accb3..2564a77f3c659629c157b50f21a3629a37aed5a0 100644 (file)
--- a/src/gromacs/listed_forces/tests/bonded.cpp
+++ b/src/gromacs/listed_forces/tests/bonded.cpp
@@ -606,6 +606,8 @@ protected:
                                                 &output.dvdlambda,
                                                 &mdatoms,
                                                 /* struct t_fcdata * */ nullptr,
+                                                nullptr,
+                                                nullptr,
                                                 ddgatindex.data(),
                                                 flavor);
             // Internal consistency test of both test input