From: Kevin Boyd <kevin.boyd@uconn.edu>
Date: Tue, 18 Dec 2018 02:37:58 +0000 (-0500)
Subject: Use std::vector for trotter_seq
X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=7ac2bfbefb285574c1c7a1f41587b94061e7dce6;p=alexxy%2Fgromacs.git

Use std::vector for trotter_seq

Fixes an mdrun leak as well

Change-Id: Ib4c708839cc617353b9b038496f10e1b623e4db7
---

diff --git a/src/gromacs/mdlib/coupling.cpp b/src/gromacs/mdlib/coupling.cpp
index 5927ace633..71b7746cc2 100644
--- a/src/gromacs/mdlib/coupling.cpp
+++ b/src/gromacs/mdlib/coupling.cpp
@@ -855,7 +855,8 @@ void nosehoover_tcoupl(const t_grpopts *opts, const gmx_ekindata_t *ekind, real
 void trotter_update(const t_inputrec *ir, int64_t step, gmx_ekindata_t *ekind,
                     const gmx_enerdata_t *enerd, t_state *state,
                     const tensor vir, const t_mdatoms *md,
-                    const t_extmass *MassQ, const int * const *trotter_seqlist, int trotter_seqno)
+                    const t_extmass *MassQ, gmx::ArrayRef < std::vector < int>> trotter_seqlist,
+                    int trotter_seqno)
 {
 
     int              n, i, d, ngtc, gc = 0, t;
@@ -864,7 +865,6 @@ void trotter_update(const t_inputrec *ir, int64_t step, gmx_ekindata_t *ekind,
     int64_t          step_eff;
     real             dt;
     double          *scalefac, dtc;
-    const int       *trotter_seq;
     rvec             sumv = {0, 0, 0};
     gmx_bool         bCouple;
 
@@ -883,7 +883,7 @@ void trotter_update(const t_inputrec *ir, int64_t step, gmx_ekindata_t *ekind,
     bCouple = (ir->nsttcouple == 1 ||
                do_per_step(step_eff+ir->nsttcouple, ir->nsttcouple));
 
-    trotter_seq = trotter_seqlist[trotter_seqno];
+    const gmx::ArrayRef<const int> trotter_seq = trotter_seqlist[trotter_seqno];
 
     if ((trotter_seq[0] == etrtSKIPALL) || (!bCouple))
     {
@@ -1068,12 +1068,12 @@ extern void init_npt_masses(const t_inputrec *ir, t_state *state, t_extmass *Mas
     }
 }
 
-int **init_npt_vars(const t_inputrec *ir, t_state *state, t_extmass *MassQ, gmx_bool bTrotter)
+std::array < std::vector < int>, ettTSEQMAX> init_npt_vars(const t_inputrec *ir, t_state *state,
+                                                           t_extmass *MassQ, gmx_bool bTrotter)
 {
     int              i, j, nnhpres, nh;
     const t_grpopts *opts;
     real             bmass, qmass, reft, kT;
-    int            **trotter_seq;
 
     opts    = &(ir->opts); /* just for ease of referencing */
     nnhpres = state->nnhpres;
@@ -1087,14 +1087,10 @@ int **init_npt_vars(const t_inputrec *ir, t_state *state, t_extmass *MassQ, gmx_
     init_npt_masses(ir, state, MassQ, TRUE);
 
     /* first, initialize clear all the trotter calls */
-    snew(trotter_seq, ettTSEQMAX);
+    std::array < std::vector < int>, ettTSEQMAX> trotter_seq;
     for (i = 0; i < ettTSEQMAX; i++)
     {
-        snew(trotter_seq[i], NTROTTERPARTS);
-        for (j = 0; j < NTROTTERPARTS; j++)
-        {
-            trotter_seq[i][j] = etrtNONE;
-        }
+        trotter_seq[i].resize(NTROTTERPARTS, etrtNONE);
         trotter_seq[i][0] = etrtSKIPALL;
     }
 
diff --git a/src/gromacs/mdlib/update.h b/src/gromacs/mdlib/update.h
index 2179203520..be81265bea 100644
--- a/src/gromacs/mdlib/update.h
+++ b/src/gromacs/mdlib/update.h
@@ -39,6 +39,7 @@
 
 #include "gromacs/math/paddedvector.h"
 #include "gromacs/math/vectypes.h"
+#include "gromacs/mdtypes/md_enums.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/basedefinitions.h"
@@ -226,10 +227,12 @@ void nosehoover_tcoupl(const t_grpopts *opts, const gmx_ekindata_t *ekind, real
                        double xi[], double vxi[], const t_extmass *MassQ);
 
 void trotter_update(const t_inputrec *ir, int64_t step, gmx_ekindata_t *ekind,
-                    const gmx_enerdata_t *enerd, t_state *state, const tensor vir, const t_mdatoms *md,
-                    const t_extmass *MassQ, const int * const *trotter_seqlist, int trotter_seqno);
+                    const gmx_enerdata_t *enerd, t_state *state, const tensor vir,
+                    const t_mdatoms *md, const t_extmass *MassQ,
+                    gmx::ArrayRef < std::vector < int>> trotter_seqlist, int trotter_seqno);
 
-int **init_npt_vars(const t_inputrec *ir, t_state *state, t_extmass *Mass, gmx_bool bTrotter);
+std::array < std::vector < int>, ettTSEQMAX> init_npt_vars(const t_inputrec *ir, t_state *state,
+                                                           t_extmass *Mass, gmx_bool bTrotter);
 
 real NPT_energy(const t_inputrec *ir, const t_state *state, const t_extmass *MassQ);
 /* computes all the pressure/tempertature control energy terms to get a conserved energy */
diff --git a/src/gromacs/mdrun/md.cpp b/src/gromacs/mdrun/md.cpp
index 47b773477b..050eb74284 100644
--- a/src/gromacs/mdrun/md.cpp
+++ b/src/gromacs/mdrun/md.cpp
@@ -192,7 +192,6 @@ void gmx::Integrator::do_md()
     real                    saved_conserved_quantity = 0;
     real                    last_ekin                = 0;
     t_extmass               MassQ;
-    int                   **trotter_seq;
     char                    sbuf[STEPSTRSIZE], sbuf2[STEPSTRSIZE];
 
     /* PME load balancing data for GPU kernels */
@@ -535,7 +534,7 @@ void gmx::Integrator::do_md()
 
     /* need to make an initiation call to get the Trotter variables set, as well as other constants for non-trotter
        temperature control */
-    trotter_seq = init_npt_vars(ir, state, &MassQ, bTrotter);
+    auto trotter_seq = init_npt_vars(ir, state, &MassQ, bTrotter);
 
     if (MASTER(cr))
     {