void init_md(FILE *fplog,
t_commrec *cr,t_inputrec *ir,real *t,real *t0,
real *lambda,real *lam0,
t_nrnb *nrnb,gmx_mtop_t *mtop,
gmx_stochd_t *sd,
int nfile,t_filenm fnm[],
int *fp_trn,int *fp_xtc,int *fp_ene,char **fn_cpt,
FILE **fp_dgdl,FILE **fp_field,
t_mdebin **mdebin,
tensor force_vir,tensor shake_vir,rvec mu_tot,
bool *bNEMD,bool *bSimAnn,t_vcm **vcm, unsigned long Flags)
{
int i,j,n;
real tmpt,mod;
char filemode[2];
sprintf(filemode, (Flags & MD_APPENDFILES) ? "a" : "w");
/* Initial values */
*t = *t0 = ir->init_t;
if (ir->efep != efepNO) {
*lam0 = ir->init_lambda;
*lambda = *lam0 + ir->init_step*ir->delta_lambda;
}
else {
*lambda = *lam0 = 0.0;
}
*bSimAnn=FALSE;
for(i=0;i<ir->opts.ngtc;i++) {
/* set bSimAnn if any group is being annealed */
if(ir->opts.annealing[i]!=eannNO)
*bSimAnn = TRUE;
}
if (*bSimAnn) {
update_annealing_target_temp(&(ir->opts),ir->init_t);
}
*bNEMD = (ir->opts.ngacc > 1) || (norm(ir->opts.acc[0]) > 0);
if (sd && (ir->eI == eiBD || EI_SD(ir->eI) || ir->etc == etcVRESCALE)) {
*sd = init_stochd(fplog,ir);
}
if (vcm) {
*vcm = init_vcm(fplog,&mtop->groups,ir);
}
if (EI_DYNAMICS(ir->eI) && !(Flags & MD_APPENDFILES)) {
if (ir->etc == etcBERENDSEN) {
please_cite(fplog,"Berendsen84a");
}
if (ir->etc == etcVRESCALE) {
please_cite(fplog,"Bussi2007a");
}
}
init_nrnb(nrnb);
if (nfile != -1)
{
*fp_trn = -1;
*fp_ene = -1;
*fp_xtc = -1;
if (MASTER(cr))
{
*fp_trn = open_trn(ftp2fn(efTRN,nfile,fnm), filemode);
if (ir->nstxtcout > 0)
{
*fp_xtc = open_xtc(ftp2fn(efXTC,nfile,fnm), filemode);
}
*fp_ene = open_enx(ftp2fn(efENX,nfile,fnm), filemode);
*fn_cpt = opt2fn("-cpo",nfile,fnm);
if ((fp_dgdl != NULL) && ir->efep!=efepNO)
{
if(Flags & MD_APPENDFILES)
{
*fp_dgdl= gmx_fio_fopen(opt2fn("-dgdl",nfile,fnm),filemode);
}
else
{
*fp_dgdl = xvgropen(opt2fn("-dgdl",nfile,fnm),
"dG/d\\8l\\4","Time (ps)",
"dG/d\\8l\\4 (kJ mol\\S-1\\N [\\8l\\4]\\S-1\\N)");
}
}
if ((fp_field != NULL) && (ir->ex[XX].n || ir->ex[YY].n ||ir->ex[ZZ].n))
{
if(Flags & MD_APPENDFILES)
{
*fp_field = gmx_fio_fopen(opt2fn("-field",nfile,fnm),filemode);
}
else
{
*fp_field = xvgropen(opt2fn("-field",nfile,fnm),
"Applied electric field","Time (ps)",
"E (V/nm)");
}
}
}
*mdebin = init_mdebin( (Flags & MD_APPENDFILES) ? -1 : *fp_ene,mtop,ir);
}
/* Initiate variables */
clear_mat(force_vir);
clear_mat(shake_vir);
clear_rvec(mu_tot);
debug_gmx();
}
void init_md(t_commrec *cr,t_inputrec *ir,tensor box,real *t,real *t0,
real *lambda,real *lam0,real *SAfactor,
t_nrnb *mynrnb,bool *bTYZ,t_topology *top,
int nfile,t_filenm fnm[],char **traj,
char **xtc_traj,int *fp_ene,
FILE **fp_dgdl,t_mdebin **mdebin,t_groups *grps,
tensor force_vir,tensor pme_vir,
tensor shake_vir,t_mdatoms *mdatoms,rvec mu_tot,
bool *bNEMD,t_vcm **vcm,t_nsborder *nsb)
{
bool bBHAM,b14,bLR,bLJLR;
int i;
/* Initial values */
*t = *t0 = ir->init_t;
if (ir->efep != efepNO) {
*lambda = *lam0 = ir->init_lambda;
}
else {
*lambda = *lam0 = 0.0;
}
if (ir->bSimAnn) {
*SAfactor = 1.0 - *t0/ir->zero_temp_time;
if (*SAfactor < 0)
*SAfactor = 0;
} else
*SAfactor = 1.0;
init_nrnb(mynrnb);
/* Check Environment variables & other booleans */
#ifdef SPEC_CPU
*bTYZ = FALSE;
#else
*bTYZ=getenv("TYZ") != NULL;
#endif
set_pot_bools(ir,top,&bLR,&bLJLR,&bBHAM,&b14);
if (nfile != -1) {
/* Filenames */
*traj = ftp2fn(efTRN,nfile,fnm);
*xtc_traj = ftp2fn(efXTC,nfile,fnm);
#ifndef SPEC_CPU
if (MASTER(cr)) {
*fp_ene = open_enx(ftp2fn(efENX,nfile,fnm),"w");
if ((fp_dgdl != NULL) && ir->efep!=efepNO)
*fp_dgdl =
xvgropen(opt2fn("-dgdl",nfile,fnm),
"dG/d\\8l\\4","Time (ps)",
"dG/d\\8l\\4 (kJ mol\\S-1\\N nm\\S-2\\N \\8l\\4\\S-1\\N)");
} else
#endif
*fp_ene = -1;
*mdebin = init_mdebin(*fp_ene,grps,&(top->atoms),&(top->idef),
bLR,bLJLR,bBHAM,b14,ir->efep!=efepNO,ir->epc,
ir->eDispCorr,(TRICLINIC(ir->compress) || TRICLINIC(box)),
(ir->etc==etcNOSEHOOVER),cr);
}
/* Initiate variables */
clear_mat(force_vir);
clear_mat(pme_vir);
clear_mat(shake_vir);
clear_rvec(mu_tot);
/* Set initial values for invmass etc. */
init_mdatoms(mdatoms,*lambda,TRUE);
*vcm = init_vcm(stdlog,top,cr,mdatoms,START(nsb),HOMENR(nsb),ir->nstcomm);
debug_gmx();
*bNEMD = (ir->opts.ngacc > 1) || (norm(ir->opts.acc[0]) > 0);
if (ir->eI == eiSD)
init_sd_consts(ir->opts.ngtc,ir->opts.tau_t,ir->delta_t);
}