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Merge release-5-0 into master
[alexxy/gromacs.git] / src / gromacs / mdlib / minimize.c
diff --git a/src/gromacs/mdlib/minimize.c b/src/gromacs/mdlib/minimize.c
index 35e2e1b2b4ac51b191602beacf752b23d224925c..5255d544d146f0fa3cea26efe922ef5f8665a302 100644 (file)
--- a/src/gromacs/mdlib/minimize.c
+++ b/src/gromacs/mdlib/minimize.c
@@ -34,43 +34,40 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "config.h"
 
 #include <math.h>
 #include <string.h>
 #include <time.h>
 
-#include "network.h"
-#include "nrnb.h"
-#include "force.h"
-#include "macros.h"
-#include "names.h"
-#include "txtdump.h"
-#include "typedefs.h"
-#include "update.h"
-#include "constr.h"
-#include "tgroup.h"
-#include "mdebin.h"
-#include "vsite.h"
-#include "force.h"
-#include "mdrun.h"
-#include "md_support.h"
-#include "sim_util.h"
-#include "domdec.h"
-#include "mdatoms.h"
-#include "ns.h"
-#include "mtop_util.h"
-#include "pme.h"
-#include "bondf.h"
-#include "gmx_omp_nthreads.h"
-#include "md_logging.h"
-
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/mtxio.h"
 #include "gromacs/fileio/trajectory_writing.h"
 #include "gromacs/imd/imd.h"
+#include "gromacs/legacyheaders/bonded-threading.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/md_logging.h"
+#include "gromacs/legacyheaders/md_support.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/pme.h"
+#include "gromacs/legacyheaders/sim_util.h"
+#include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/update.h"
+#include "gromacs/legacyheaders/vsite.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/linearalgebra/sparsematrix.h"
 #include "gromacs/math/vec.h"
@@ -78,6 +75,7 @@
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
@@ -312,7 +310,8 @@ void init_em(FILE *fplog, const char *title,
              gmx_vsite_t *vsite, gmx_constr_t constr,
              int nfile, const t_filenm fnm[],
              gmx_mdoutf_t *outf, t_mdebin **mdebin,
-             int imdport, unsigned long gmx_unused Flags)
+             int imdport, unsigned long gmx_unused Flags,
+             gmx_wallcycle_t wcycle)
 {
     int  i;
     real dvdl_constr;
@@ -417,7 +416,7 @@ void init_em(FILE *fplog, const char *title,
             /* Constrain the starting coordinates */
             dvdl_constr = 0;
             constrain(PAR(cr) ? NULL : fplog, TRUE, TRUE, constr, &(*top)->idef,
-                      ir, NULL, cr, -1, 0, mdatoms,
+                      ir, NULL, cr, -1, 0, 1.0, mdatoms,
                       ems->s.x, ems->s.x, NULL, fr->bMolPBC, ems->s.box,
                       ems->s.lambda[efptFEP], &dvdl_constr,
                       NULL, NULL, nrnb, econqCoord, FALSE, 0, 0);
@@ -429,7 +428,7 @@ void init_em(FILE *fplog, const char *title,
         *gstat = global_stat_init(ir);
     }
 
-    *outf = init_mdoutf(fplog, nfile, fnm, 0, cr, ir, top_global, NULL);
+    *outf = init_mdoutf(fplog, nfile, fnm, 0, cr, ir, top_global, NULL, wcycle);
 
     snew(*enerd, 1);
     init_enerdata(top_global->groups.grps[egcENER].nr, ir->fepvals->n_lambda,
@@ -551,6 +550,7 @@ static void do_em_step(t_commrec *cr, t_inputrec *ir, t_mdatoms *md,
     int      start, end;
     rvec    *x1, *x2;
     real     dvdl_constr;
+    int      nthreads gmx_unused;
 
     s1 = &ems1->s;
     s2 = &ems2->s;
@@ -588,7 +588,8 @@ static void do_em_step(t_commrec *cr, t_inputrec *ir, t_mdatoms *md,
     x1 = s1->x;
     x2 = s2->x;
 
-#pragma omp parallel num_threads(gmx_omp_nthreads_get(emntUpdate))
+    nthreads = gmx_omp_nthreads_get(emntUpdate);
+#pragma omp parallel num_threads(nthreads)
     {
         int gf, i, m;
 
@@ -650,7 +651,7 @@ static void do_em_step(t_commrec *cr, t_inputrec *ir, t_mdatoms *md,
         wallcycle_start(wcycle, ewcCONSTR);
         dvdl_constr = 0;
         constrain(NULL, TRUE, TRUE, constr, &top->idef,
-                  ir, NULL, cr, count, 0, md,
+                  ir, NULL, cr, count, 0, 1.0, md,
                   s1->x, s2->x, NULL, bMolPBC, s2->box,
                   s2->lambda[efptBONDED], &dvdl_constr,
                   NULL, NULL, nrnb, econqCoord, FALSE, 0, 0);
@@ -772,7 +773,7 @@ static void evaluate_energy(FILE *fplog, t_commrec *cr,
     }
 
     /* Calculate long range corrections to pressure and energy */
-    calc_dispcorr(fplog, inputrec, fr, count, top_global->natoms, ems->s.box, ems->s.lambda[efptVDW],
+    calc_dispcorr(inputrec, fr, top_global->natoms, ems->s.box, ems->s.lambda[efptVDW],
                   pres, force_vir, &prescorr, &enercorr, &dvdlcorr);
     enerd->term[F_DISPCORR] = enercorr;
     enerd->term[F_EPOT]    += enercorr;
@@ -787,14 +788,10 @@ static void evaluate_energy(FILE *fplog, t_commrec *cr,
         wallcycle_start(wcycle, ewcCONSTR);
         dvdl_constr = 0;
         constrain(NULL, FALSE, FALSE, constr, &top->idef,
-                  inputrec, NULL, cr, count, 0, mdatoms,
+                  inputrec, NULL, cr, count, 0, 1.0, mdatoms,
                   ems->s.x, ems->f, ems->f, fr->bMolPBC, ems->s.box,
                   ems->s.lambda[efptBONDED], &dvdl_constr,
                   NULL, &shake_vir, nrnb, econqForceDispl, FALSE, 0, 0);
-        if (fr->bSepDVDL && fplog)
-        {
-            gmx_print_sepdvdl(fplog, "Constraints", t, dvdl_constr);
-        }
         enerd->term[F_DVDL_CONSTR] += dvdl_constr;
         m_add(force_vir, shake_vir, vir);
         wallcycle_stop(wcycle, ewcCONSTR);
@@ -1002,7 +999,7 @@ double do_cg(FILE *fplog, t_commrec *cr,
     init_em(fplog, CG, cr, inputrec,
             state_global, top_global, s_min, &top, &f, &f_global,
             nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat, vsite, constr,
-            nfile, fnm, &outf, &mdebin, imdport, Flags);
+            nfile, fnm, &outf, &mdebin, imdport, Flags, wcycle);
 
     /* Print to log file */
     print_em_start(fplog, cr, walltime_accounting, wcycle, CG);
@@ -1674,7 +1671,7 @@ double do_lbfgs(FILE *fplog, t_commrec *cr,
     init_em(fplog, LBFGS, cr, inputrec,
             state, top_global, &ems, &top, &f, &f_global,
             nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat, vsite, constr,
-            nfile, fnm, &outf, &mdebin, imdport, Flags);
+            nfile, fnm, &outf, &mdebin, imdport, Flags, wcycle);
     /* Do_lbfgs is not completely updated like do_steep and do_cg,
      * so we free some memory again.
      */
@@ -2418,7 +2415,7 @@ double do_steep(FILE *fplog, t_commrec *cr,
     init_em(fplog, SD, cr, inputrec,
             state_global, top_global, s_try, &top, &f, &f_global,
             nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat, vsite, constr,
-            nfile, fnm, &outf, &mdebin, imdport, Flags);
+            nfile, fnm, &outf, &mdebin, imdport, Flags, wcycle);
 
     /* Print to log file  */
     print_em_start(fplog, cr, walltime_accounting, wcycle, SD);
@@ -2670,7 +2667,7 @@ double do_nm(FILE *fplog, t_commrec *cr,
             state_global, top_global, state_work, &top,
             &f, &f_global,
             nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat, vsite, constr,
-            nfile, fnm, &outf, NULL, imdport, Flags);
+            nfile, fnm, &outf, NULL, imdport, Flags, wcycle);
 
     natoms = top_global->natoms;
     snew(fneg, natoms);
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