ArrayRef in pme

diff --git a/src/gromacs/domdec/mdsetup.cpp b/src/gromacs/domdec/mdsetup.cpp
index 0baae937e79f05204e5e1410c47b64e49f3b78a1..b899038106f10cfd1e47de1d422ad9af7269237f 100644 (file)
--- a/src/gromacs/domdec/mdsetup.cpp
+++ b/src/gromacs/domdec/mdsetup.cpp
@@ -143,7 +143,10 @@ void mdAlgorithmsSetupAtomData(const t_commrec*     cr,
          * For PME-only ranks, gmx_pmeonly() has its own call to gmx_pme_reinit_atoms().
          */
         const int numPmeAtoms = numHomeAtoms - fr->n_tpi;
-        gmx_pme_reinit_atoms(fr->pmedata, numPmeAtoms, mdatoms->chargeA, mdatoms->chargeB);
+        gmx_pme_reinit_atoms(fr->pmedata,
+                             numPmeAtoms,
+                             gmx::arrayRefFromArray(mdatoms->chargeA, mdatoms->nr),
+                             gmx::arrayRefFromArray(mdatoms->chargeB, mdatoms->nr));
     }
 
     if (constr)

diff --git a/src/gromacs/ewald/pme.cpp b/src/gromacs/ewald/pme.cpp
index 5f9ffb42d964eb589e4669839abaa4cca967f35a..c9272e056a552b2db9652de2630e2116d3d08a59 100644 (file)
--- a/src/gromacs/ewald/pme.cpp
+++ b/src/gromacs/ewald/pme.cpp
@@ -989,7 +989,10 @@ void gmx_pme_reinit(struct gmx_pme_t** pmedata,
          */
         if (!pme_src->gpu && pme_src->nnodes == 1)
         {
-            gmx_pme_reinit_atoms(*pmedata, pme_src->atc[0].numAtoms(), nullptr, nullptr);
+            gmx_pme_reinit_atoms(*pmedata,
+                                 pme_src->atc[0].numAtoms(),
+                                 {},
+                                 {});
         }
         // TODO this is mostly passing around current values
     }
@@ -1000,7 +1003,7 @@ void gmx_pme_reinit(struct gmx_pme_t** pmedata,
     /* We would like to reuse the fft grids, but that's harder */
 }
 
-void gmx_pme_calc_energy(gmx_pme_t* pme, gmx::ArrayRef<const gmx::RVec> x, gmx::ArrayRef<const real> q, real* V)
+real gmx_pme_calc_energy(gmx_pme_t* pme, gmx::ArrayRef<const gmx::RVec> x, gmx::ArrayRef<const real> q)
 {
     pmegrids_t* grid;
 
@@ -1028,7 +1031,7 @@ void gmx_pme_calc_energy(gmx_pme_t* pme, gmx::ArrayRef<const gmx::RVec> x, gmx::
     /* Only calculate the spline coefficients, don't actually spread */
     spread_on_grid(pme, atc, nullptr, TRUE, FALSE, pme->fftgrid[PME_GRID_QA], FALSE, PME_GRID_QA);
 
-    *V = gather_energy_bsplines(pme, grid->grid.grid, atc);
+    return gather_energy_bsplines(pme, grid->grid.grid, atc);
 }
 
 /*! \brief Calculate initial Lorentz-Berthelot coefficients for LJ-PME */
@@ -1778,13 +1781,16 @@ void gmx_pme_destroy(gmx_pme_t* pme)
     delete pme;
 }
 
-void gmx_pme_reinit_atoms(gmx_pme_t* pme, const int numAtoms, const real* chargesA, const real* chargesB)
+void gmx_pme_reinit_atoms(gmx_pme_t*                pme,
+                          const int                 numAtoms,
+                          gmx::ArrayRef<const real> chargesA,
+                          gmx::ArrayRef<const real> chargesB)
 {
     if (pme->gpu != nullptr)
     {
-        GMX_ASSERT(!(pme->bFEP_q && chargesB == nullptr),
+        GMX_ASSERT(!(pme->bFEP_q && !chargesB.empty()),
                    "B state charges must be specified if running Coulomb FEP on the GPU");
-        pme_gpu_reinit_atoms(pme->gpu, numAtoms, chargesA, pme->bFEP_q ? chargesB : nullptr);
+        pme_gpu_reinit_atoms(pme->gpu, numAtoms, chargesA.data(), pme->bFEP_q ? chargesB.data() : nullptr);
     }
     else
     {

diff --git a/src/gromacs/ewald/pme.h b/src/gromacs/ewald/pme.h
index 9ff1b108f219598f831da4ac806ee76cab0c353e..1e32caf265bbd2feb25a20c31d93bcd884248d53 100644 (file)
--- a/src/gromacs/ewald/pme.h
+++ b/src/gromacs/ewald/pme.h
@@ -233,7 +233,7 @@ int gmx_pme_do(struct gmx_pme_t*              pme,
  * pme struct. Currently does not work in parallel or with free
  * energy.
  */
-void gmx_pme_calc_energy(gmx_pme_t* pme, gmx::ArrayRef<const gmx::RVec> x, gmx::ArrayRef<const real> q, real* V);
+real gmx_pme_calc_energy(gmx_pme_t* pme, gmx::ArrayRef<const gmx::RVec> x, gmx::ArrayRef<const real> q);
 
 /*! \brief
  * This function updates the local atom data on GPU after DD (charges, coordinates, etc.).
@@ -247,7 +247,10 @@ void gmx_pme_calc_energy(gmx_pme_t* pme, gmx::ArrayRef<const gmx::RVec> x, gmx::
  * \param[in]     chargesB   The pointer to the array of particle charges in state B. Only used if
  * charges are perturbed and can otherwise be nullptr.
  */
-void gmx_pme_reinit_atoms(gmx_pme_t* pme, int numAtoms, const real* chargesA, const real* chargesB);
+void gmx_pme_reinit_atoms(gmx_pme_t*                pme,
+                          int                       numAtoms,
+                          gmx::ArrayRef<const real> chargesA,
+                          gmx::ArrayRef<const real> chargesB);
 
 /* A block of PME GPU functions */
 

diff --git a/src/gromacs/ewald/pme_only.cpp b/src/gromacs/ewald/pme_only.cpp
index 64f685ab44a61090250d34e98340f0fed5428669..82d6574866a5223cc74b44a31ae53313c805c671 100644 (file)
--- a/src/gromacs/ewald/pme_only.cpp
+++ b/src/gromacs/ewald/pme_only.cpp
@@ -426,7 +426,7 @@ static int gmx_pme_recv_coeffs_coords(struct gmx_pme_t*            pme,
         {
             if (atomSetChanged)
             {
-                gmx_pme_reinit_atoms(pme, nat, pme_pp->chargeA.data(), pme_pp->chargeB.data());
+                gmx_pme_reinit_atoms(pme, nat, pme_pp->chargeA, pme_pp->chargeB);
                 if (useGpuForPme)
                 {
                     stateGpu->reinit(nat, nat);

diff --git a/src/gromacs/ewald/tests/pmetestcommon.cpp b/src/gromacs/ewald/tests/pmetestcommon.cpp
index d2267521654df420850453c695c22c255ed1a12e..c8e8530ee7924c87d24f9f30ec77a479f1190c83 100644 (file)
--- a/src/gromacs/ewald/tests/pmetestcommon.cpp
+++ b/src/gromacs/ewald/tests/pmetestcommon.cpp
@@ -199,7 +199,7 @@ void pmeInitAtoms(gmx_pme_t*               pme,
             atc              = &(pme->atc[0]);
             atc->x           = coordinates;
             atc->coefficient = charges;
-            gmx_pme_reinit_atoms(pme, atomCount, charges.data(), nullptr);
+            gmx_pme_reinit_atoms(pme, atomCount, charges, {});
             /* With decomposition there would be more boilerplate atc code here, e.g. do_redist_pos_coeffs */
             break;
 
@@ -208,7 +208,7 @@ void pmeInitAtoms(gmx_pme_t*               pme,
             atc = &(pme->atc[0]);
             // We need to set atc->n for passing the size in the tests
             atc->setNumAtoms(atomCount);
-            gmx_pme_reinit_atoms(pme, atomCount, charges.data(), nullptr);
+            gmx_pme_reinit_atoms(pme, atomCount, charges, {});
 
             stateGpu->reinit(atomCount, atomCount);
             stateGpu->copyCoordinatesToGpu(arrayRefFromArray(coordinates.data(), coordinates.size()),

diff --git a/src/gromacs/mdlib/force.cpp b/src/gromacs/mdlib/force.cpp
index ad08c862fb026093653ad7fe820fb36de2ff75a6..bfb1ca7b1d969ef004edb8f369e25fe25710eb33 100644 (file)
--- a/src/gromacs/mdlib/force.cpp
+++ b/src/gromacs/mdlib/force.cpp
@@ -257,11 +257,10 @@ void calculateLongRangeNonbondeds(t_forcerec*                    fr,
                     /* Determine the PME grid energy of the test molecule
                      * with the PME grid potential of the other charges.
                      */
-                    gmx_pme_calc_energy(
+                    Vlr_q = gmx_pme_calc_energy(
                             fr->pmedata,
                             coordinates.subArray(md->homenr - fr->n_tpi, fr->n_tpi),
-                            gmx::arrayRefFromArray(md->chargeA + md->homenr - fr->n_tpi, fr->n_tpi),
-                            &Vlr_q);
+                            gmx::arrayRefFromArray(md->chargeA + md->homenr - fr->n_tpi, fr->n_tpi));
                 }
             }
         }

diff --git a/src/gromacs/mdrun/tpi.cpp b/src/gromacs/mdrun/tpi.cpp
index 687908ebe5195fa2587dde30af1905ada73a5dfa..3b83b4b89e70edc1364454c0b6d79450bee4987f 100644 (file)
--- a/src/gromacs/mdrun/tpi.cpp
+++ b/src/gromacs/mdrun/tpi.cpp
@@ -322,7 +322,7 @@ void LegacySimulator::do_tpi()
 
     if (EEL_PME(fr->ic->eeltype))
     {
-        gmx_pme_reinit_atoms(fr->pmedata, a_tp0, nullptr, nullptr);
+        gmx_pme_reinit_atoms(fr->pmedata, a_tp0, {}, {});
     }
 
     /* With reacion-field we have distance dependent potentials