void upd_mdebin(t_mdebin *md,
gmx_bool bDoDHDL,
gmx_bool bSum,
double time,
real tmass,
gmx_enerdata_t *enerd,
t_state *state,
t_lambda *fep,
t_expanded *expand,
matrix box,
tensor svir,
tensor fvir,
tensor vir,
tensor pres,
gmx_ekindata_t *ekind,
rvec mu_tot,
gmx_constr_t constr)
{
int i, j, k, kk, n, gid;
real crmsd[2], tmp6[6];
real bs[NTRICLBOXS], vol, dens, pv, enthalpy;
real eee[egNR];
real ecopy[F_NRE];
double store_dhdl[efptNR];
real store_energy = 0;
real tmp;
/* Do NOT use the box in the state variable, but the separate box provided
* as an argument. This is because we sometimes need to write the box from
* the last timestep to match the trajectory frames.
*/
copy_energy(md, enerd->term, ecopy);
add_ebin(md->ebin, md->ie, md->f_nre, ecopy, bSum);
if (md->nCrmsd)
{
crmsd[0] = constr_rmsd(constr);
add_ebin(md->ebin, md->iconrmsd, md->nCrmsd, crmsd, FALSE);
}
if (md->bDynBox)
{
int nboxs;
if (md->bTricl)
{
bs[0] = box[XX][XX];
bs[1] = box[YY][YY];
bs[2] = box[ZZ][ZZ];
bs[3] = box[YY][XX];
bs[4] = box[ZZ][XX];
bs[5] = box[ZZ][YY];
nboxs = NTRICLBOXS;
}
else
{
bs[0] = box[XX][XX];
bs[1] = box[YY][YY];
bs[2] = box[ZZ][ZZ];
nboxs = NBOXS;
}
vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
dens = (tmass*AMU)/(vol*NANO*NANO*NANO);
add_ebin(md->ebin, md->ib, nboxs, bs, bSum);
add_ebin(md->ebin, md->ivol, 1, &vol, bSum);
add_ebin(md->ebin, md->idens, 1, &dens, bSum);
if (md->bDiagPres)
{
/* This is pV (in kJ/mol). The pressure is the reference pressure,
not the instantaneous pressure */
pv = vol*md->ref_p/PRESFAC;
add_ebin(md->ebin, md->ipv, 1, &pv, bSum);
enthalpy = pv + enerd->term[F_ETOT];
add_ebin(md->ebin, md->ienthalpy, 1, &enthalpy, bSum);
}
}
if (md->bConstrVir)
{
add_ebin(md->ebin, md->isvir, 9, svir[0], bSum);
add_ebin(md->ebin, md->ifvir, 9, fvir[0], bSum);
}
add_ebin(md->ebin, md->ivir, 9, vir[0], bSum);
add_ebin(md->ebin, md->ipres, 9, pres[0], bSum);
tmp = (pres[ZZ][ZZ]-(pres[XX][XX]+pres[YY][YY])*0.5)*box[ZZ][ZZ];
add_ebin(md->ebin, md->isurft, 1, &tmp, bSum);
if (md->epc == epcPARRINELLORAHMAN || md->epc == epcMTTK)
{
tmp6[0] = state->boxv[XX][XX];
tmp6[1] = state->boxv[YY][YY];
tmp6[2] = state->boxv[ZZ][ZZ];
tmp6[3] = state->boxv[YY][XX];
tmp6[4] = state->boxv[ZZ][XX];
tmp6[5] = state->boxv[ZZ][YY];
add_ebin(md->ebin, md->ipc, md->bTricl ? 6 : 3, tmp6, bSum);
}
if (md->bMu)
{
add_ebin(md->ebin, md->imu, 3, mu_tot, bSum);
}
if (ekind && ekind->cosacc.cos_accel != 0)
{
vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
dens = (tmass*AMU)/(vol*NANO*NANO*NANO);
add_ebin(md->ebin, md->ivcos, 1, &(ekind->cosacc.vcos), bSum);
/* 1/viscosity, unit 1/(kg m^-1 s^-1) */
tmp = 1/(ekind->cosacc.cos_accel/(ekind->cosacc.vcos*PICO)
*dens*gmx::square(box[ZZ][ZZ]*NANO/(2*M_PI)));
add_ebin(md->ebin, md->ivisc, 1, &tmp, bSum);
}
if (md->nE > 1)
{
n = 0;
for (i = 0; (i < md->nEg); i++)
{
for (j = i; (j < md->nEg); j++)
{
gid = GID(i, j, md->nEg);
for (k = kk = 0; (k < egNR); k++)
{
if (md->bEInd[k])
{
eee[kk++] = enerd->grpp.ener[k][gid];
}
}
add_ebin(md->ebin, md->igrp[n], md->nEc, eee, bSum);
n++;
}
}
}
if (ekind)
{
for (i = 0; (i < md->nTC); i++)
{
md->tmp_r[i] = ekind->tcstat[i].T;
}
add_ebin(md->ebin, md->itemp, md->nTC, md->tmp_r, bSum);
if (md->etc == etcNOSEHOOVER)
{
/* whether to print Nose-Hoover chains: */
if (md->bPrintNHChains)
{
if (md->bNHC_trotter)
{
for (i = 0; (i < md->nTC); i++)
{
for (j = 0; j < md->nNHC; j++)
{
k = i*md->nNHC+j;
md->tmp_r[2*k] = state->nosehoover_xi[k];
md->tmp_r[2*k+1] = state->nosehoover_vxi[k];
}
}
add_ebin(md->ebin, md->itc, md->mde_n, md->tmp_r, bSum);
if (md->bMTTK)
{
for (i = 0; (i < md->nTCP); i++)
{
for (j = 0; j < md->nNHC; j++)
{
k = i*md->nNHC+j;
md->tmp_r[2*k] = state->nhpres_xi[k];
md->tmp_r[2*k+1] = state->nhpres_vxi[k];
}
}
add_ebin(md->ebin, md->itcb, md->mdeb_n, md->tmp_r, bSum);
}
}
else
{
for (i = 0; (i < md->nTC); i++)
{
md->tmp_r[2*i] = state->nosehoover_xi[i];
md->tmp_r[2*i+1] = state->nosehoover_vxi[i];
}
add_ebin(md->ebin, md->itc, md->mde_n, md->tmp_r, bSum);
}
}
}
else if (md->etc == etcBERENDSEN || md->etc == etcYES ||
md->etc == etcVRESCALE)
{
for (i = 0; (i < md->nTC); i++)
{
md->tmp_r[i] = ekind->tcstat[i].lambda;
}
add_ebin(md->ebin, md->itc, md->nTC, md->tmp_r, bSum);
}
}
if (ekind && md->nU > 1)
{
for (i = 0; (i < md->nU); i++)
{
copy_rvec(ekind->grpstat[i].u, md->tmp_v[i]);
}
add_ebin(md->ebin, md->iu, 3*md->nU, md->tmp_v[0], bSum);
}
ebin_increase_count(md->ebin, bSum);
/* BAR + thermodynamic integration values */
if ((md->fp_dhdl || md->dhc) && bDoDHDL)
{
for (i = 0; i < enerd->n_lambda-1; i++)
{
/* zero for simulated tempering */
md->dE[i] = enerd->enerpart_lambda[i+1]-enerd->enerpart_lambda[0];
if (md->temperatures != NULL)
{
/* MRS: is this right, given the way we have defined the exchange probabilities? */
/* is this even useful to have at all? */
md->dE[i] += (md->temperatures[i]/
md->temperatures[state->fep_state]-1.0)*
enerd->term[F_EKIN];
}
}
if (md->fp_dhdl)
{
fprintf(md->fp_dhdl, "%.4f", time);
/* the current free energy state */
/* print the current state if we are doing expanded ensemble */
if (expand->elmcmove > elmcmoveNO)
{
fprintf(md->fp_dhdl, " %4d", state->fep_state);
}
/* total energy (for if the temperature changes */
if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
{
switch (fep->edHdLPrintEnergy)
{
case edHdLPrintEnergyPOTENTIAL:
store_energy = enerd->term[F_EPOT];
break;
case edHdLPrintEnergyTOTAL:
case edHdLPrintEnergyYES:
default:
store_energy = enerd->term[F_ETOT];
}
fprintf(md->fp_dhdl, " %#.8g", store_energy);
}
if (fep->dhdl_derivatives == edhdlderivativesYES)
{
for (i = 0; i < efptNR; i++)
{
if (fep->separate_dvdl[i])
{
/* assumes F_DVDL is first */
fprintf(md->fp_dhdl, " %#.8g", enerd->term[F_DVDL+i]);
}
}
}
for (i = fep->lambda_start_n; i < fep->lambda_stop_n; i++)
{
fprintf(md->fp_dhdl, " %#.8g", md->dE[i]);
}
if (md->bDynBox &&
md->bDiagPres &&
(md->epc != epcNO) &&
(enerd->n_lambda > 0) &&
(fep->init_lambda < 0))
{
fprintf(md->fp_dhdl, " %#.8g", pv); /* PV term only needed when
there are alternate state
lambda and we're not in
compatibility mode */
}
fprintf(md->fp_dhdl, "\n");
/* and the binary free energy output */
}
if (md->dhc && bDoDHDL)
{
int idhdl = 0;
for (i = 0; i < efptNR; i++)
{
if (fep->separate_dvdl[i])
{
/* assumes F_DVDL is first */
store_dhdl[idhdl] = enerd->term[F_DVDL+i];
idhdl += 1;
}
}
store_energy = enerd->term[F_ETOT];
/* store_dh is dE */
mde_delta_h_coll_add_dh(md->dhc,
(double)state->fep_state,
store_energy,
pv,
store_dhdl,
md->dE + fep->lambda_start_n,
time);
}
}
}
void upd_mdebin(t_mdebin *md, gmx_bool write_dhdl,
gmx_bool bSum,
double time,
real tmass,
gmx_enerdata_t *enerd,
t_state *state,
matrix box,
tensor svir,
tensor fvir,
tensor vir,
tensor pres,
gmx_ekindata_t *ekind,
rvec mu_tot,
gmx_constr_t constr)
{
int i,j,k,kk,m,n,gid;
real crmsd[2],tmp6[6];
real bs[NTRICLBOXS],vol,dens,pv,enthalpy;
real eee[egNR];
real ecopy[F_NRE];
real tmp;
gmx_bool bNoseHoover;
/* Do NOT use the box in the state variable, but the separate box provided
* as an argument. This is because we sometimes need to write the box from
* the last timestep to match the trajectory frames.
*/
copy_energy(md, enerd->term,ecopy);
add_ebin(md->ebin,md->ie,md->f_nre,ecopy,bSum);
if (md->nCrmsd)
{
crmsd[0] = constr_rmsd(constr,FALSE);
if (md->nCrmsd > 1)
{
crmsd[1] = constr_rmsd(constr,TRUE);
}
add_ebin(md->ebin,md->iconrmsd,md->nCrmsd,crmsd,FALSE);
}
if (md->bDynBox)
{
int nboxs;
if(md->bTricl)
{
bs[0] = box[XX][XX];
bs[1] = box[YY][YY];
bs[2] = box[ZZ][ZZ];
bs[3] = box[YY][XX];
bs[4] = box[ZZ][XX];
bs[5] = box[ZZ][YY];
nboxs=NTRICLBOXS;
}
else
{
bs[0] = box[XX][XX];
bs[1] = box[YY][YY];
bs[2] = box[ZZ][ZZ];
nboxs=NBOXS;
}
vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
dens = (tmass*AMU)/(vol*NANO*NANO*NANO);
/* This is pV (in kJ/mol). The pressure is the reference pressure,
not the instantaneous pressure */
pv = 0;
for (i=0;i<DIM;i++)
{
for (j=0;j<DIM;j++)
{
if (i>j)
{
pv += box[i][j]*md->ref_p[i][j]/PRESFAC;
}
else
{
pv += box[j][i]*md->ref_p[j][i]/PRESFAC;
}
}
}
add_ebin(md->ebin,md->ib ,nboxs,bs ,bSum);
add_ebin(md->ebin,md->ivol ,1 ,&vol ,bSum);
add_ebin(md->ebin,md->idens,1 ,&dens,bSum);
add_ebin(md->ebin,md->ipv ,1 ,&pv ,bSum);
enthalpy = pv + enerd->term[F_ETOT];
add_ebin(md->ebin,md->ienthalpy ,1 ,&enthalpy ,bSum);
}
if (md->bConstrVir)
{
add_ebin(md->ebin,md->isvir,9,svir[0],bSum);
add_ebin(md->ebin,md->ifvir,9,fvir[0],bSum);
}
add_ebin(md->ebin,md->ivir,9,vir[0],bSum);
add_ebin(md->ebin,md->ipres,9,pres[0],bSum);
tmp = (pres[ZZ][ZZ]-(pres[XX][XX]+pres[YY][YY])*0.5)*box[ZZ][ZZ];
add_ebin(md->ebin,md->isurft,1,&tmp,bSum);
if (md->epc == epcPARRINELLORAHMAN || md->epc == epcMTTK)
{
tmp6[0] = state->boxv[XX][XX];
tmp6[1] = state->boxv[YY][YY];
tmp6[2] = state->boxv[ZZ][ZZ];
tmp6[3] = state->boxv[YY][XX];
tmp6[4] = state->boxv[ZZ][XX];
tmp6[5] = state->boxv[ZZ][YY];
add_ebin(md->ebin,md->ipc,md->bTricl ? 6 : 3,tmp6,bSum);
}
add_ebin(md->ebin,md->imu,3,mu_tot,bSum);
if (ekind && ekind->cosacc.cos_accel != 0)
{
vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
dens = (tmass*AMU)/(vol*NANO*NANO*NANO);
add_ebin(md->ebin,md->ivcos,1,&(ekind->cosacc.vcos),bSum);
/* 1/viscosity, unit 1/(kg m^-1 s^-1) */
tmp = 1/(ekind->cosacc.cos_accel/(ekind->cosacc.vcos*PICO)
*vol*sqr(box[ZZ][ZZ]*NANO/(2*M_PI)));
add_ebin(md->ebin,md->ivisc,1,&tmp,bSum);
}
if (md->nE > 1)
{
n=0;
for(i=0; (i<md->nEg); i++)
{
for(j=i; (j<md->nEg); j++)
{
gid=GID(i,j,md->nEg);
for(k=kk=0; (k<egNR); k++)
{
if (md->bEInd[k])
{
eee[kk++] = enerd->grpp.ener[k][gid];
}
}
add_ebin(md->ebin,md->igrp[n],md->nEc,eee,bSum);
n++;
}
}
}
if (ekind)
{
for(i=0; (i<md->nTC); i++)
{
md->tmp_r[i] = ekind->tcstat[i].T;
}
add_ebin(md->ebin,md->itemp,md->nTC,md->tmp_r,bSum);
/* whether to print Nose-Hoover chains: */
bNoseHoover = (getenv("GMX_NOSEHOOVER_CHAINS") != NULL);
if (md->etc == etcNOSEHOOVER)
{
if (bNoseHoover)
{
if (md->bNHC_trotter)
{
for(i=0; (i<md->nTC); i++)
{
for (j=0;j<md->nNHC;j++)
{
k = i*md->nNHC+j;
md->tmp_r[2*k] = state->nosehoover_xi[k];
md->tmp_r[2*k+1] = state->nosehoover_vxi[k];
}
}
add_ebin(md->ebin,md->itc,md->mde_n,md->tmp_r,bSum);
if (md->bMTTK) {
for(i=0; (i<md->nTCP); i++)
{
for (j=0;j<md->nNHC;j++)
{
k = i*md->nNHC+j;
md->tmp_r[2*k] = state->nhpres_xi[k];
md->tmp_r[2*k+1] = state->nhpres_vxi[k];
}
}
add_ebin(md->ebin,md->itcb,md->mdeb_n,md->tmp_r,bSum);
}
}
else
{
for(i=0; (i<md->nTC); i++)
{
md->tmp_r[2*i] = state->nosehoover_xi[i];
md->tmp_r[2*i+1] = state->nosehoover_vxi[i];
}
add_ebin(md->ebin,md->itc,md->mde_n,md->tmp_r,bSum);
}
}
}
else if (md->etc == etcBERENDSEN || md->etc == etcYES ||
md->etc == etcVRESCALE)
{
for(i=0; (i<md->nTC); i++)
{
md->tmp_r[i] = ekind->tcstat[i].lambda;
}
add_ebin(md->ebin,md->itc,md->nTC,md->tmp_r,bSum);
}
}
if (ekind && md->nU > 1)
{
for(i=0; (i<md->nU); i++)
{
copy_rvec(ekind->grpstat[i].u,md->tmp_v[i]);
}
add_ebin(md->ebin,md->iu,3*md->nU,md->tmp_v[0],bSum);
}
ebin_increase_count(md->ebin,bSum);
/* BAR + thermodynamic integration values */
if (write_dhdl)
{
if (md->fp_dhdl)
{
fprintf(md->fp_dhdl,"%.4f", time);
if (md->dhdl_derivatives)
{
fprintf(md->fp_dhdl," %g", enerd->term[F_DVDL]+
enerd->term[F_DKDL]+
enerd->term[F_DHDL_CON]);
}
for(i=1; i<enerd->n_lambda; i++)
{
fprintf(md->fp_dhdl," %g",
enerd->enerpart_lambda[i]-enerd->enerpart_lambda[0]);
}
fprintf(md->fp_dhdl,"\n");
}
/* and the binary BAR output */
if (md->dhc)
{
mde_delta_h_coll_add_dh(md->dhc,
enerd->term[F_DVDL]+ enerd->term[F_DKDL]+
enerd->term[F_DHDL_CON],
enerd->enerpart_lambda, time,
state->lambda);
}
}
}
void upd_mdebin(t_mdebin *md,FILE *fp_dgdl,
real tmass,int step,real time,
real ener[],
matrix box,
tensor svir,
tensor fvir,
tensor vir,
tensor pres,
t_groups *grps,
rvec mu_tot, bool bNoseHoover)
{
static real *ttt=NULL;
static rvec *uuu=NULL;
int i,j,k,kk,m,n,gid;
real bs[NBOXS];
real tricl_bs[NTRICLBOXS];
real eee[egNR];
real ecopy[F_NRE];
real tmp;
copy_energy(ener,ecopy);
add_ebin(md->ebin,md->ie,f_nre,ecopy,step);
if (bPC || fabs(grps->cosacc.cos_accel)>GMX_REAL_MIN) {
if(bTricl) {
tricl_bs[0]=box[XX][XX];
tricl_bs[1]=box[YY][XX];
tricl_bs[2]=box[YY][YY];
tricl_bs[3]=box[ZZ][XX];
tricl_bs[4]=box[ZZ][YY];
tricl_bs[5]=box[ZZ][ZZ];
/* This is the volume */
tricl_bs[6]=tricl_bs[0]*tricl_bs[2]*tricl_bs[5];
/* This is the density */
tricl_bs[7] = (tmass*AMU)/(tricl_bs[6]*NANO*NANO*NANO);
} else {
for(m=0; (m<DIM); m++)
bs[m]=box[m][m];
/* This is the volume */
bs[3] = bs[XX]*bs[YY]*bs[ZZ];
/* This is the density */
bs[4] = (tmass*AMU)/(bs[3]*NANO*NANO*NANO);
}
}
if (bPC) {
/* This is pV (in kJ/mol) */
if(bTricl) {
tricl_bs[8] = tricl_bs[6]*ener[F_PRES]/PRESFAC;
add_ebin(md->ebin,md->ib,NTRICLBOXS,tricl_bs,step);
} else {
bs[5] = bs[3]*ener[F_PRES]/PRESFAC;
add_ebin(md->ebin,md->ib,NBOXS,bs,step);
}
}
if (bShake) {
add_ebin(md->ebin,md->isvir,9,svir[0],step);
add_ebin(md->ebin,md->ifvir,9,fvir[0],step);
}
add_ebin(md->ebin,md->ivir,9,vir[0],step);
add_ebin(md->ebin,md->ipres,9,pres[0],step);
tmp = (pres[ZZ][ZZ]-(pres[XX][XX]+pres[YY][YY])*0.5)*box[ZZ][ZZ];
add_ebin(md->ebin,md->isurft,1,&tmp,step);
add_ebin(md->ebin,md->imu,3,mu_tot,step);
if (fabs(grps->cosacc.cos_accel)>GMX_REAL_MIN) {
add_ebin(md->ebin,md->ivcos,1,&(grps->cosacc.vcos),step);
/* 1/viscosity, unit 1/(kg m^-1 s^-1) */
if(bTricl)
tmp = 1/(grps->cosacc.cos_accel/(grps->cosacc.vcos*PICO)
*tricl_bs[7]*sqr(box[ZZ][ZZ]*NANO/(2*M_PI)));
else
tmp = 1/(grps->cosacc.cos_accel/(grps->cosacc.vcos*PICO)
*bs[4]*sqr(box[ZZ][ZZ]*NANO/(2*M_PI)));
add_ebin(md->ebin,md->ivisc,1,&tmp,step);
}
if (md->nE > 1) {
n=0;
for(i=0; (i<md->nEg); i++) {
for(j=i; (j<md->nEg); j++) {
gid=GID(i,j,md->nEg);
for(k=kk=0; (k<egNR); k++)
if (bEInd[k])
eee[kk++]=grps->estat.ee[k][gid];
add_ebin(md->ebin,md->igrp[n],md->nEc,eee,step);
n++;
}
}
}
if(ttt == NULL)
snew(ttt,2*md->nTC);
for(i=0; (i<md->nTC); i++) {
ttt[2*i] = grps->tcstat[i].T;
if(bNoseHoover)
ttt[2*i+1] = grps->tcstat[i].xi;
else
ttt[2*i+1] = grps->tcstat[i].lambda;
}
add_ebin(md->ebin,md->itc,2*md->nTC,ttt,step);
if (md->nU > 1) {
if (uuu == NULL)
snew(uuu,md->nU);
for(i=0; (i<md->nU); i++)
copy_rvec(grps->grpstat[i].u,uuu[i]);
add_ebin(md->ebin,md->iu,3*md->nU,uuu[0],step);
}
if (fp_dgdl)
fprintf(fp_dgdl,"%g %g\n",time,ener[F_DVDL]+ener[F_DVDLKIN]);
}
void upd_mdebin(t_mdebin *md,FILE *fp_dgdl,
bool bSum,
real tmass,int step,real time,
gmx_enerdata_t *enerd,
t_state *state,
matrix box,
tensor svir,
tensor fvir,
tensor vir,
tensor pres,
gmx_ekindata_t *ekind,
rvec mu_tot,
gmx_constr_t constr)
{
static real *ttt=NULL;
static rvec *uuu=NULL;
int i,j,k,kk,m,n,gid;
real crmsd[2],bs[NBOXS],tmp6[6];
real tricl_bs[NTRICLBOXS];
real eee[egNR];
real ecopy[F_NRE];
real tmp;
/* Do NOT use the box in the state variable, but the separate box provided
* as an argument. This is because we sometimes need to write the box from
* the last timestep to match the trajectory frames.
*/
copy_energy(enerd->term,ecopy);
add_ebin(md->ebin,md->ie,f_nre,ecopy,bSum,step);
if (nCrmsd) {
crmsd[0] = constr_rmsd(constr,FALSE);
if (nCrmsd > 1)
crmsd[1] = constr_rmsd(constr,TRUE);
add_ebin(md->ebin,md->iconrmsd,nCrmsd,crmsd,FALSE,0);
}
if (bDynBox || ((ekind != NULL) && (ekind->cosacc.cos_accel != 0))) {
if(bTricl) {
tricl_bs[0]=box[XX][XX];
tricl_bs[1]=box[YY][XX];
tricl_bs[2]=box[YY][YY];
tricl_bs[3]=box[ZZ][XX];
tricl_bs[4]=box[ZZ][YY];
tricl_bs[5]=box[ZZ][ZZ];
/* This is the volume */
tricl_bs[6]=tricl_bs[0]*tricl_bs[2]*tricl_bs[5];
/* This is the density */
tricl_bs[7] = (tmass*AMU)/(tricl_bs[6]*NANO*NANO*NANO);
} else {
for(m=0; (m<DIM); m++)
bs[m]=box[m][m];
/* This is the volume */
bs[3] = bs[XX]*bs[YY]*bs[ZZ];
/* This is the density */
bs[4] = (tmass*AMU)/(bs[3]*NANO*NANO*NANO);
}
}
if (bDynBox) {
/* This is pV (in kJ/mol) */
if(bTricl) {
tricl_bs[8] = tricl_bs[6]*enerd->term[F_PRES]/PRESFAC;
add_ebin(md->ebin,md->ib,NTRICLBOXS,tricl_bs,bSum,step);
} else {
bs[5] = bs[3]*enerd->term[F_PRES]/PRESFAC;
add_ebin(md->ebin,md->ib,NBOXS,bs,bSum,step);
}
}
if (bConstrVir) {
add_ebin(md->ebin,md->isvir,9,svir[0],bSum,step);
add_ebin(md->ebin,md->ifvir,9,fvir[0],bSum,step);
}
add_ebin(md->ebin,md->ivir,9,vir[0],bSum,step);
add_ebin(md->ebin,md->ipres,9,pres[0],bSum,step);
tmp = (pres[ZZ][ZZ]-(pres[XX][XX]+pres[YY][YY])*0.5)*box[ZZ][ZZ];
add_ebin(md->ebin,md->isurft,1,&tmp,bSum,step);
if (epc == epcPARRINELLORAHMAN) {
tmp6[0] = state->boxv[XX][XX];
tmp6[1] = state->boxv[YY][YY];
tmp6[2] = state->boxv[ZZ][ZZ];
tmp6[3] = state->boxv[YY][XX];
tmp6[4] = state->boxv[ZZ][XX];
tmp6[5] = state->boxv[ZZ][YY];
add_ebin(md->ebin,md->ipc,bTricl ? 6 : 3,tmp6,bSum,step);
}
add_ebin(md->ebin,md->imu,3,mu_tot,bSum,step);
if (ekind && ekind->cosacc.cos_accel != 0) {
add_ebin(md->ebin,md->ivcos,1,&(ekind->cosacc.vcos),bSum,step);
/* 1/viscosity, unit 1/(kg m^-1 s^-1) */
if(bTricl)
tmp = 1/(ekind->cosacc.cos_accel/(ekind->cosacc.vcos*PICO)
*tricl_bs[7]*sqr(box[ZZ][ZZ]*NANO/(2*M_PI)));
else
tmp = 1/(ekind->cosacc.cos_accel/(ekind->cosacc.vcos*PICO)
*bs[4]*sqr(box[ZZ][ZZ]*NANO/(2*M_PI)));
add_ebin(md->ebin,md->ivisc,1,&tmp,bSum,step);
}
if (md->nE > 1) {
n=0;
for(i=0; (i<md->nEg); i++) {
for(j=i; (j<md->nEg); j++) {
gid=GID(i,j,md->nEg);
for(k=kk=0; (k<egNR); k++) {
if (bEInd[k]) {
eee[kk++] = enerd->grpp.ener[k][gid];
}
}
add_ebin(md->ebin,md->igrp[n],md->nEc,eee,bSum,step);
n++;
}
}
}
if (ekind) {
if(ttt == NULL)
snew(ttt,md->nTC);
for(i=0; (i<md->nTC); i++) {
ttt[i] = ekind->tcstat[i].T;
}
add_ebin(md->ebin,md->itemp,md->nTC,ttt,bSum,step);
if (etc == etcNOSEHOOVER) {
for(i=0; (i<md->nTC); i++)
ttt[i] = state->nosehoover_xi[i];
add_ebin(md->ebin,md->itc,md->nTC,ttt,bSum,step);
} else if (etc == etcBERENDSEN || etc == etcYES || etc == etcVRESCALE) {
for(i=0; (i<md->nTC); i++)
ttt[i] = ekind->tcstat[i].lambda;
add_ebin(md->ebin,md->itc,md->nTC,ttt,bSum,step);
}
}
if (ekind && md->nU > 1) {
if (uuu == NULL)
snew(uuu,md->nU);
for(i=0; (i<md->nU); i++)
copy_rvec(ekind->grpstat[i].u,uuu[i]);
add_ebin(md->ebin,md->iu,3*md->nU,uuu[0],bSum,step);
}
if (fp_dgdl)
fprintf(fp_dgdl,"%.4f %g\n",
time,
enerd->term[F_DVDL]+enerd->term[F_DKDL]+enerd->term[F_DGDL_CON]);
}
