biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff
? search:
summary | shortlog | log | commit | commitdiff | tree
raw | inline | side by side
Manually sort some includes in src/gromacs
[alexxy/gromacs.git] / src / gromacs / mdlib / sim_util.c
diff --git a/src/gromacs/mdlib/sim_util.c b/src/gromacs/mdlib/sim_util.c
index 0cdb28b88548189f02a40f075e454dfb2a0baa0a..4090760008135c7cce14eacd163c55c11f2108a5 100644 (file)
--- a/src/gromacs/mdlib/sim_util.c
+++ b/src/gromacs/mdlib/sim_util.c
@@ -36,70 +36,68 @@
  */
 #include "gmxpre.h"
 
-#include "config.h"
+#include "gromacs/legacyheaders/sim_util.h"
 
 #include <assert.h>
 #include <math.h>
 #include <stdio.h>
 #include <string.h>
+
+#include "config.h"
+
 #ifdef HAVE_SYS_TIME_H
 #include <sys/time.h>
 #endif
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/legacyheaders/chargegroup.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/sim_util.h"
-#include "gromacs/legacyheaders/update.h"
-#include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/mdatoms.h"
-#include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/bondf.h"
-#include "gromacs/legacyheaders/pme.h"
-#include "gromacs/legacyheaders/disre.h"
-#include "gromacs/legacyheaders/orires.h"
-#include "gromacs/legacyheaders/network.h"
+#include "gromacs/bonded/bonded.h"
+#include "gromacs/essentialdynamics/edsam.h"
+#include "gromacs/gmxlib/nonbonded/nb_free_energy.h"
+#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
+#include "gromacs/imd/imd.h"
 #include "gromacs/legacyheaders/calcmu.h"
+#include "gromacs/legacyheaders/chargegroup.h"
 #include "gromacs/legacyheaders/constr.h"
 #include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/disre.h"
 #include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/genborn.h"
-#include "nbnxn_atomdata.h"
-#include "nbnxn_search.h"
-#include "nbnxn_kernels/nbnxn_kernel_ref.h"
-#include "nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
-#include "nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
-#include "nbnxn_kernels/nbnxn_kernel_gpu_ref.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nonbonded.h"
-#include "../gmxlib/nonbonded/nb_kernel.h"
-#include "../gmxlib/nonbonded/nb_free_energy.h"
-
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/pme.h"
+#include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/update.h"
 #include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/adress.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_atomdata.h"
+#include "gromacs/mdlib/nbnxn_search.h"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.h"
 #include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.h"
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pulling/pull.h"
+#include "gromacs/pulling/pull_rotation.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/gmxmpi.h"
 #include "gromacs/utility/smalloc.h"
-#include "gromacs/essentialdynamics/edsam.h"
-#include "gromacs/pulling/pull.h"
-#include "gromacs/pulling/pull_rotation.h"
-#include "gromacs/imd/imd.h"
-#include "adress.h"
-#include "gromacs/legacyheaders/qmmm.h"
-
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-
-#include "nbnxn_cuda/nbnxn_cuda.h"
-
-#include "nb_verlet.h"
 
 void print_time(FILE                     *out,
                 gmx_walltime_accounting_t walltime_accounting,
@@ -390,7 +388,8 @@ static void pull_potential_wrapper(t_commrec *cr,
                                    t_mdatoms *mdatoms,
                                    gmx_enerdata_t *enerd,
                                    real *lambda,
-                                   double t)
+                                   double t,
+                                   gmx_wallcycle_t wcycle)
 {
     t_pbc  pbc;
     real   dvdl;
@@ -400,12 +399,14 @@ static void pull_potential_wrapper(t_commrec *cr,
      * The virial contribution is calculated directly,
      * which is why we call pull_potential after calc_virial.
      */
+    wallcycle_start(wcycle, ewcPULLPOT);
     set_pbc(&pbc, ir->ePBC, box);
     dvdl                     = 0;
     enerd->term[F_COM_PULL] +=
         pull_potential(ir->ePull, ir->pull, mdatoms, &pbc,
                        cr, t, lambda[efptRESTRAINT], x, f, vir_force, &dvdl);
     enerd->dvdl_lin[efptRESTRAINT] += dvdl;
+    wallcycle_stop(wcycle, ewcPULLPOT);
 }
 
 static void pme_receive_force_ener(t_commrec      *cr,
@@ -1332,7 +1333,7 @@ void do_force_cutsVERLET(FILE *fplog, t_commrec *cr,
     do_force_lowlevel(fr, inputrec, &(top->idef),
                       cr, nrnb, wcycle, mdatoms,
                       x, hist, f, bSepLRF ? fr->f_twin : f, enerd, fcd, top, fr->born,
-                      &(top->atomtypes), bBornRadii, box,
+                      bBornRadii, box,
                       inputrec->fepvals, lambda, graph, &(top->excls), fr->mu_tot,
                       flags, &cycles_pme);
 
@@ -1513,8 +1514,12 @@ void do_force_cutsVERLET(FILE *fplog, t_commrec *cr,
 
     if (inputrec->ePull == epullUMBRELLA || inputrec->ePull == epullCONST_F)
     {
+        /* Since the COM pulling is always done mass-weighted, no forces are
+         * applied to vsites and this call can be done after vsite spreading.
+         */
         pull_potential_wrapper(cr, inputrec, box, x,
-                               f, vir_force, mdatoms, enerd, lambda, t);
+                               f, vir_force, mdatoms, enerd, lambda, t,
+                               wcycle);
     }
 
     /* Add the forces from enforced rotation potentials (if any) */
@@ -1877,7 +1882,7 @@ void do_force_cutsGROUP(FILE *fplog, t_commrec *cr,
     do_force_lowlevel(fr, inputrec, &(top->idef),
                       cr, nrnb, wcycle, mdatoms,
                       x, hist, f, bSepLRF ? fr->f_twin : f, enerd, fcd, top, fr->born,
-                      &(top->atomtypes), bBornRadii, box,
+                      bBornRadii, box,
                       inputrec->fepvals, lambda,
                       graph, &(top->excls), fr->mu_tot,
                       flags,
@@ -1986,7 +1991,8 @@ void do_force_cutsGROUP(FILE *fplog, t_commrec *cr,
     if (inputrec->ePull == epullUMBRELLA || inputrec->ePull == epullCONST_F)
     {
         pull_potential_wrapper(cr, inputrec, box, x,
-                               f, vir_force, mdatoms, enerd, lambda, t);
+                               f, vir_force, mdatoms, enerd, lambda, t,
+                               wcycle);
     }
 
     /* Add the forces from enforced rotation potentials (if any) */
@@ -2804,7 +2810,8 @@ void init_md(FILE *fplog,
              int nfile, const t_filenm fnm[],
              gmx_mdoutf_t *outf, t_mdebin **mdebin,
              tensor force_vir, tensor shake_vir, rvec mu_tot,
-             gmx_bool *bSimAnn, t_vcm **vcm, unsigned long Flags)
+             gmx_bool *bSimAnn, t_vcm **vcm, unsigned long Flags,
+             gmx_wallcycle_t wcycle)
 {
     int  i, j, n;
     real tmpt, mod;
@@ -2860,7 +2867,7 @@ void init_md(FILE *fplog,
 
     if (nfile != -1)
     {
-        *outf = init_mdoutf(fplog, nfile, fnm, Flags, cr, ir, mtop, oenv);
+        *outf = init_mdoutf(fplog, nfile, fnm, Flags, cr, ir, mtop, oenv, wcycle);
 
         *mdebin = init_mdebin((Flags & MD_APPENDFILES) ? NULL : mdoutf_get_fp_ene(*outf),
                               mtop, ir, mdoutf_get_fp_dhdl(*outf));
Local GROMACS mirror with custom stuff