#include <config.h>
#endif
+#include <stdlib.h>
+
#include "typedefs.h"
-#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
-#include "vec.h"
+#include "gromacs/math/vec.h"
#include "vcm.h"
#include "mdebin.h"
#include "nrnb.h"
#include "md_support.h"
#include "md_logging.h"
#include "network.h"
-#include "xvgr.h"
-#include "physics.h"
#include "names.h"
#include "force.h"
#include "disre.h"
#include "qmmm.h"
#include "domdec.h"
#include "domdec_network.h"
-#include "gromacs/gmxlib/topsort.h"
#include "coulomb.h"
#include "constr.h"
#include "shellfc.h"
#include "gromacs/gmxpreprocess/compute_io.h"
#include "checkpoint.h"
-#include "mtop_util.h"
+#include "gromacs/topology/mtop_util.h"
#include "sighandler.h"
#include "txtdump.h"
#include "gromacs/utility/cstringutil.h"
#include "types/iteratedconstraints.h"
#include "nbnxn_cuda_data_mgmt.h"
-#include "gromacs/utility/gmxmpi.h"
#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/mdoutf.h"
#include "gromacs/fileio/trajectory_writing.h"
#include "gromacs/fileio/trnio.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/xtcio.h"
-#include "gromacs/timing/wallcycle.h"
-#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/imd/imd.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pulling/pull.h"
#include "gromacs/swap/swapcoords.h"
-#include "gromacs/imd/imd.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
#ifdef GMX_FAHCORE
#include "corewrap.h"
rvec mu_tot;
t_vcm *vcm;
t_state *bufstate = NULL;
- matrix *scale_tot, pcoupl_mu, M, ebox;
+ matrix pcoupl_mu, M;
gmx_nlheur_t nlh;
t_trxframe rerun_fr;
gmx_repl_ex_t repl_ex = NULL;
gmx_ekindata_t *ekind, *ekind_save;
gmx_shellfc_t shellfc;
int count, nconverged = 0;
- real timestep = 0;
- double tcount = 0;
- gmx_bool bConverged = TRUE, bOK, bSumEkinhOld, bExchanged, bNeedRepartition;
- gmx_bool bAppend;
+ double tcount = 0;
+ gmx_bool bConverged = TRUE, bOK, bSumEkinhOld, bExchanged, bNeedRepartition;
gmx_bool bResetCountersHalfMaxH = FALSE;
gmx_bool bVV, bIterativeCase, bFirstIterate, bTemp, bPres, bTrotter;
gmx_bool bUpdateDoLR;
double cycles;
real saved_conserved_quantity = 0;
real last_ekin = 0;
- int iter_i;
t_extmass MassQ;
int **trotter_seq;
char sbuf[STEPSTRSIZE], sbuf2[STEPSTRSIZE];
/* Check for special mdrun options */
bRerunMD = (Flags & MD_RERUN);
- bAppend = (Flags & MD_APPENDFILES);
if (Flags & MD_RESETCOUNTERSHALFWAY)
{
if (ir->nsteps > 0)
bStateFromTPX = !bStateFromCP;
bInitStep = bFirstStep && (bStateFromTPX || bVV);
bStartingFromCpt = (Flags & MD_STARTFROMCPT) && bInitStep;
- bLastStep = FALSE;
bSumEkinhOld = FALSE;
bExchanged = FALSE;
bNeedRepartition = FALSE;
step = ir->init_step;
step_rel = 0;
- if (ir->nstlist == -1)
- {
- init_nlistheuristics(&nlh, bGStatEveryStep, step);
- }
+ init_nlistheuristics(&nlh, bGStatEveryStep, step);
if (MULTISIM(cr) && (repl_ex_nst <= 0 ))
{