int get_tpr_version(const char *infile)
{
char buf[STRLEN];
- bool bDouble;
+ gmx_bool bDouble;
int precision,fver;
t_fileio *fio;
{
int i,j,nr,mol_id;
int type=0,block=0;
- bool bNEW;
+ gmx_bool bNEW;
nr=0;
snew(tlist->index,at->nr);
int i,j,at,mol,nmol,nmolbox,count;
t_block *mem_a;
real z,zmin,zmax,mem_area;
- bool bNew;
+ gmx_bool bNew;
atom_id *mol_id;
int type=0,block=0;
return mem_p->mem_at.nr;
}
-void init_resize(t_block *ins_at,rvec *r_ins,pos_ins_t *pos_ins,mem_t *mem_p,rvec *r, bool bALLOW_ASYMMETRY)
+void init_resize(t_block *ins_at,rvec *r_ins,pos_ins_t *pos_ins,mem_t *mem_p,rvec *r, gmx_bool bALLOW_ASYMMETRY)
{
int i,j,at,c,outsidesum,gctr=0;
int idxsum=0;
}
int gen_rm_list(rm_t *rm_p,t_block *ins_at,t_block *rest_at,t_pbc *pbc, gmx_mtop_t *mtop,
- rvec *r, rvec *r_ins, mem_t *mem_p, pos_ins_t *pos_ins, real probe_rad, int low_up_rm, bool bALLOW_ASYMMETRY)
+ rvec *r, rvec *r_ins, mem_t *mem_p, pos_ins_t *pos_ins, real probe_rad, int low_up_rm, gmx_bool bALLOW_ASYMMETRY)
{
int i,j,k,l,at,at2,mol_id;
int type=0,block=0;
int nrm,nupper,nlower;
real r_min_rad,z_lip,min_norm;
- bool bRM;
+ gmx_bool bRM;
rvec dr,dr_tmp;
real *dist;
int *order;
rvec *x_tmp,*v_tmp;
atom_id *list,*new_mols;
unsigned char *new_egrp[egcNR];
- bool bRM;
+ gmx_bool bRM;
snew(list,state->natoms);
n=0;
{
int i,j,m;
int type,natom,nmol,at,atom1=0,rm_at=0;
- bool *bRM,bINS;
+ gmx_bool *bRM,bINS;
/*this routine lives dangerously by assuming that all molecules of a given type are in order in the structure*/
/*this routine does not live as dangerously as it seems. There is namely a check in mdrunner_membed to make
*sure that g_membed exits with a warning when there are molecules of the same type not in the
negative or zero. */
enum { eglsNABNSB, eglsCHKPT, eglsSTOPCOND, eglsRESETCOUNTERS, eglsNR };
/* Is the signal in one simulation independent of other simulations? */
-bool gs_simlocal[eglsNR] = { TRUE, FALSE, FALSE, TRUE };
+gmx_bool gs_simlocal[eglsNR] = { TRUE, FALSE, FALSE, TRUE };
typedef struct {
int nstms; /* The frequency for intersimulation communication */
static int multisim_min(const gmx_multisim_t *ms,int nmin,int n)
{
int *buf;
- bool bPos,bEqual;
+ gmx_bool bPos,bEqual;
int s,d;
snew(buf,ms->nsim);
t_nrnb *nrnb, t_vcm *vcm, gmx_wallcycle_t wcycle,
gmx_enerdata_t *enerd,tensor force_vir, tensor shake_vir, tensor total_vir,
tensor pres, rvec mu_tot, gmx_constr_t constr,
- globsig_t *gs,bool bInterSimGS,
+ globsig_t *gs,gmx_bool bInterSimGS,
matrix box, gmx_mtop_t *top_global, real *pcurr,
- int natoms, bool *bSumEkinhOld, int flags)
+ int natoms, gmx_bool *bSumEkinhOld, int flags)
{
int i,gsi;
real gs_buf[eglsNR];
tensor corr_vir,corr_pres;
- bool bEner,bPres,bTemp;
- bool bRerunMD, bStopCM, bGStat, bIterate,
+ gmx_bool bEner,bPres,bTemp;
+ gmx_bool bRerunMD, bStopCM, bGStat, bIterate,
bFirstIterate,bReadEkin,bEkinAveVel,bScaleEkin, bConstrain;
real prescorr,enercorr,dvdlcorr;
- /* translate CGLO flags to booleans */
+ /* translate CGLO flags to gmx_booleans */
bRerunMD = flags & CGLO_RERUNMD;
bStopCM = flags & CGLO_STOPCM;
bGStat = flags & CGLO_GSTAT;
- bReadEkin = flags & CGLO_READEKIN;
- bScaleEkin = flags & CGLO_SCALEEKIN;
+/* FIX ME after 4.5 */
+/* temporary hack because we are using gmx_bool (unsigned char) */
+
+ bReadEkin = (flags & CGLO_READEKIN) != 0;
+ bScaleEkin = (flags & CGLO_SCALEEKIN) != 0;
bEner = flags & CGLO_ENERGY;
bTemp = flags & CGLO_TEMPERATURE;
- bPres = flags & CGLO_PRESSURE;
- bConstrain = flags & CGLO_CONSTRAINT;
- bIterate = flags & CGLO_ITERATE;
- bFirstIterate = flags & CGLO_FIRSTITERATE;
+ bPres = (flags & CGLO_PRESSURE) != 0;
+ bConstrain = (flags & CGLO_CONSTRAINT) != 0;
+ bIterate = (flags & CGLO_ITERATE) != 0;
+ bFirstIterate = (flags & CGLO_FIRSTITERATE) != 0;
/* we calculate a full state kinetic energy either with full-step velocity verlet
or half step where we need the pressure */
{
real f,fprev,x,xprev;
int iter_i;
- bool bIterate;
+ gmx_bool bIterate;
real allrelerr[MAXITERCONST+2];
int num_close; /* number of "close" violations, caused by limited precision. */
} gmx_iterate_t;
/* maximum length of cyclic traps to check, emerging from limited numerical precision */
#define CYCLEMAX 20
-static void gmx_iterate_init(gmx_iterate_t *iterate,bool bIterate)
+static void gmx_iterate_init(gmx_iterate_t *iterate,gmx_bool bIterate)
{
int i;
}
}
-static bool done_iterating(const t_commrec *cr,FILE *fplog, int nsteps, gmx_iterate_t *iterate, bool bFirstIterate, real fom, real *newf)
+static gmx_bool done_iterating(const t_commrec *cr,FILE *fplog, int nsteps, gmx_iterate_t *iterate, gmx_bool bFirstIterate, real fom, real *newf)
{
/* monitor convergence, and use a secant search to propose new
values.
real relerr,err;
char buf[256];
int i;
- bool incycle;
+ gmx_bool incycle;
if (bFirstIterate)
{
}
typedef struct {
- bool bGStatEveryStep;
+ gmx_bool bGStatEveryStep;
gmx_large_int_t step_ns;
gmx_large_int_t step_nscheck;
gmx_large_int_t nns;
}
static void init_nlistheuristics(gmx_nlheur_t *nlh,
- bool bGStatEveryStep,gmx_large_int_t step)
+ gmx_bool bGStatEveryStep,gmx_large_int_t step)
{
nlh->bGStatEveryStep = bGStatEveryStep;
nlh->nns = 0;
}
}
-static void set_nlistheuristics(gmx_nlheur_t *nlh,bool bReset,gmx_large_int_t step)
+static void set_nlistheuristics(gmx_nlheur_t *nlh,gmx_bool bReset,gmx_large_int_t step)
{
int d;
}
double do_md_membed(FILE *fplog,t_commrec *cr,int nfile,const t_filenm fnm[],
- const output_env_t oenv, bool bVerbose,bool bCompact,
+ const output_env_t oenv, gmx_bool bVerbose,gmx_bool bCompact,
int nstglobalcomm,
gmx_vsite_t *vsite,gmx_constr_t constr,
int stepout,t_inputrec *ir,
gmx_large_int_t step,step_rel;
double run_time;
double t,t0,lam0;
- bool bGStatEveryStep,bGStat,bNstEner,bCalcEnerPres;
- bool bNS,bNStList,bSimAnn,bStopCM,bRerunMD,bNotLastFrame=FALSE,
+ gmx_bool bGStatEveryStep,bGStat,bNstEner,bCalcEnerPres;
+ gmx_bool bNS,bNStList,bSimAnn,bStopCM,bRerunMD,bNotLastFrame=FALSE,
bFirstStep,bStateFromTPX,bInitStep,bLastStep,
bBornRadii,bStartingFromCpt;
- bool bDoDHDL=FALSE;
- bool do_ene,do_log,do_verbose,bRerunWarnNoV=TRUE,
+ gmx_bool bDoDHDL=FALSE;
+ gmx_bool do_ene,do_log,do_verbose,bRerunWarnNoV=TRUE,
bForceUpdate=FALSE,bCPT;
int mdof_flags;
- bool bMasterState;
+ gmx_bool bMasterState;
int force_flags,cglo_flags;
tensor force_vir,shake_vir,total_vir,tmp_vir,pres;
int i,m;
t_graph *graph=NULL;
globsig_t gs;
- bool bFFscan;
+ gmx_bool bFFscan;
gmx_groups_t *groups;
gmx_ekindata_t *ekind, *ekind_save;
gmx_shellfc_t shellfc;
int count,nconverged=0;
real timestep=0;
double tcount=0;
- bool bIonize=FALSE;
- bool bTCR=FALSE,bConverged=TRUE,bOK,bSumEkinhOld,bExchanged;
- bool bAppend;
- bool bResetCountersHalfMaxH=FALSE;
- bool bVV,bIterations,bIterate,bFirstIterate,bTemp,bPres,bTrotter;
+ gmx_bool bIonize=FALSE;
+ gmx_bool bTCR=FALSE,bConverged=TRUE,bOK,bSumEkinhOld,bExchanged;
+ gmx_bool bAppend;
+ gmx_bool bResetCountersHalfMaxH=FALSE;
+ gmx_bool bVV,bIterations,bIterate,bFirstIterate,bTemp,bPres,bTrotter;
real temp0,dvdl;
int a0,a1,ii;
rvec *xcopy=NULL,*vcopy=NULL,*cbuf=NULL;
/* Output stuff */
if (MASTER(cr))
{
- bool do_dr,do_or;
+ gmx_bool do_dr,do_or;
if (!(bStartingFromCpt && (EI_VV(ir->eI))))
{
int mdrunner_membed(FILE *fplog,t_commrec *cr,int nfile,const t_filenm fnm[],
- const output_env_t oenv, bool bVerbose,bool bCompact,
+ const output_env_t oenv, gmx_bool bVerbose,gmx_bool bCompact,
int nstglobalcomm,
ivec ddxyz,int dd_node_order,real rdd,real rconstr,
const char *dddlb_opt,real dlb_scale,
unsigned long Flags,
real xy_fac, real xy_max, real z_fac, real z_max,
int it_xy, int it_z, real probe_rad, int low_up_rm,
- int pieces, bool bALLOW_ASYMMETRY, int maxwarn)
+ int pieces, gmx_bool bALLOW_ASYMMETRY, int maxwarn)
{
double nodetime=0,realtime;
t_inputrec *inputrec;
int i,m,nChargePerturbed=-1,status,nalloc;
char *gro;
gmx_wallcycle_t wcycle;
- bool bReadRNG,bReadEkin;
+ gmx_bool bReadRNG,bReadEkin;
int list;
gmx_runtime_t runtime;
int rc;
mem_t *mem_p;
rm_t *rm_p;
gmx_groups_t *groups;
- bool bExcl=FALSE;
+ gmx_bool bExcl=FALSE;
t_atoms atoms;
t_pbc *pbc;
char **piecename=NULL;
#define NFILE asize(fnm)
/* Command line options ! */
- bool bCart = FALSE;
- bool bPPPME = FALSE;
- bool bPartDec = FALSE;
- bool bDDBondCheck = TRUE;
- bool bDDBondComm = TRUE;
- bool bVerbose = FALSE;
- bool bCompact = TRUE;
- bool bSepPot = FALSE;
- bool bRerunVSite = FALSE;
- bool bIonize = FALSE;
- bool bConfout = TRUE;
- bool bReproducible = FALSE;
+ gmx_bool bCart = FALSE;
+ gmx_bool bPPPME = FALSE;
+ gmx_bool bPartDec = FALSE;
+ gmx_bool bDDBondCheck = TRUE;
+ gmx_bool bDDBondComm = TRUE;
+ gmx_bool bVerbose = FALSE;
+ gmx_bool bCompact = TRUE;
+ gmx_bool bSepPot = FALSE;
+ gmx_bool bRerunVSite = FALSE;
+ gmx_bool bIonize = FALSE;
+ gmx_bool bConfout = TRUE;
+ gmx_bool bReproducible = FALSE;
int npme=-1;
int nmultisim=0;
real rdd=0.0,rconstr=0.0,dlb_scale=0.8,pforce=-1;
char *ddcsx=NULL,*ddcsy=NULL,*ddcsz=NULL;
real cpt_period=15.0,max_hours=-1;
- bool bAppendFiles=TRUE,bAddPart=TRUE;
- bool bResetCountersHalfWay=FALSE;
+ gmx_bool bAppendFiles=TRUE,bAddPart=TRUE;
+ gmx_bool bResetCountersHalfWay=FALSE;
output_env_t oenv=NULL;
const char *deviceOptions = "";
int low_up_rm = 0;
int maxwarn=0;
int pieces=1;
- bool bALLOW_ASYMMETRY=FALSE;
+ gmx_bool bALLOW_ASYMMETRY=FALSE;
/* arguments relevant to OPENMM only*/
unsigned long Flags, PCA_Flags;
ivec ddxyz;
int dd_node_order;
- bool HaveCheckpoint;
+ gmx_bool HaveCheckpoint;
FILE *fplog,*fptest;
int sim_part,sim_part_fn;
const char *part_suffix=".part";
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff