static void boxv_trotter(t_inputrec *ir, real *veta, real dt, tensor box,
gmx_ekindata_t *ekind, tensor vir, real pcorr, real ecorr, t_extmass *MassQ)
{
real pscal;
double alpha;
int i,j,d,n,nwall;
real T,GW,vol;
tensor Winvm,ekinmod,localpres;
/* The heat bath is coupled to a separate barostat, the last temperature group. In the
2006 Tuckerman et al paper., the order is iL_{T_baro} iL {T_part}
*/
if (ir->epct==epctSEMIISOTROPIC)
{
nwall = 2;
}
else
{
nwall = 3;
}
/* eta is in pure units. veta is in units of ps^-1. GW is in
units of ps^-2. However, eta has a reference of 1 nm^3, so care must be
taken to use only RATIOS of eta in updating the volume. */
/* we take the partial pressure tensors, modify the
kinetic energy tensor, and recovert to pressure */
if (ir->opts.nrdf[0]==0)
{
gmx_fatal(FARGS,"Barostat is coupled to a T-group with no degrees of freedom\n");
}
/* alpha factor for phase space volume, then multiply by the ekin scaling factor. */
alpha = 1.0 + DIM/((double)ir->opts.nrdf[0]);
alpha *= ekind->tcstat[0].ekinscalef_nhc;
msmul(ekind->ekin,alpha,ekinmod);
/* for now, we use Elr = 0, because if you want to get it right, you
really should be using PME. Maybe print a warning? */
pscal = calc_pres(ir->ePBC,nwall,box,ekinmod,vir,localpres,0.0) + pcorr;
vol = det(box);
GW = (vol*(MassQ->Winv/PRESFAC))*(DIM*pscal - trace(ir->ref_p)); /* W is in ps^2 * bar * nm^3 */
*veta += 0.5*dt*GW;
}
void compute_globals(FILE *fplog, gmx_global_stat_t gstat, t_commrec *cr, t_inputrec *ir,
t_forcerec *fr, gmx_ekindata_t *ekind,
t_state *state, t_state *state_global, t_mdatoms *mdatoms,
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, gmx_bool bInterSimGS,
matrix box, gmx_mtop_t *top_global,
gmx_bool *bSumEkinhOld, int flags)
{
int i, gsi;
real gs_buf[eglsNR];
tensor corr_vir, corr_pres;
gmx_bool bEner, bPres, bTemp;
gmx_bool bStopCM, bGStat,
bReadEkin, bEkinAveVel, bScaleEkin, bConstrain;
real prescorr, enercorr, dvdlcorr, dvdl_ekin;
/* translate CGLO flags to gmx_booleans */
bStopCM = flags & CGLO_STOPCM;
bGStat = flags & CGLO_GSTAT;
bReadEkin = (flags & CGLO_READEKIN);
bScaleEkin = (flags & CGLO_SCALEEKIN);
bEner = flags & CGLO_ENERGY;
bTemp = flags & CGLO_TEMPERATURE;
bPres = (flags & CGLO_PRESSURE);
bConstrain = (flags & CGLO_CONSTRAINT);
/* we calculate a full state kinetic energy either with full-step velocity verlet
or half step where we need the pressure */
bEkinAveVel = (ir->eI == eiVV || (ir->eI == eiVVAK && bPres) || bReadEkin);
/* in initalization, it sums the shake virial in vv, and to
sums ekinh_old in leapfrog (or if we are calculating ekinh_old) for other reasons */
/* ########## Kinetic energy ############## */
if (bTemp)
{
/* Non-equilibrium MD: this is parallellized, but only does communication
* when there really is NEMD.
*/
if (PAR(cr) && (ekind->bNEMD))
{
accumulate_u(cr, &(ir->opts), ekind);
}
debug_gmx();
if (bReadEkin)
{
restore_ekinstate_from_state(cr, ekind, &state_global->ekinstate);
}
else
{
calc_ke_part(state, &(ir->opts), mdatoms, ekind, nrnb, bEkinAveVel);
}
debug_gmx();
}
/* Calculate center of mass velocity if necessary, also parallellized */
if (bStopCM)
{
calc_vcm_grp(0, mdatoms->homenr, mdatoms,
state->x, state->v, vcm);
}
if (bTemp || bStopCM || bPres || bEner || bConstrain)
{
if (!bGStat)
{
/* We will not sum ekinh_old,
* so signal that we still have to do it.
*/
*bSumEkinhOld = TRUE;
}
else
{
if (gs != NULL)
{
for (i = 0; i < eglsNR; i++)
{
gs_buf[i] = gs->sig[i];
}
}
if (PAR(cr))
{
wallcycle_start(wcycle, ewcMoveE);
global_stat(fplog, gstat, cr, enerd, force_vir, shake_vir, mu_tot,
ir, ekind, constr, bStopCM ? vcm : NULL,
gs != NULL ? eglsNR : 0, gs_buf,
top_global, state,
*bSumEkinhOld, flags);
wallcycle_stop(wcycle, ewcMoveE);
}
if (gs != NULL)
{
if (MULTISIM(cr) && bInterSimGS)
{
if (MASTER(cr))
{
/* Communicate the signals between the simulations */
gmx_sum_sim(eglsNR, gs_buf, cr->ms);
}
/* Communicate the signals form the master to the others */
gmx_bcast(eglsNR*sizeof(gs_buf[0]), gs_buf, cr);
}
for (i = 0; i < eglsNR; i++)
{
if (bInterSimGS || gs_simlocal[i])
{
/* Set the communicated signal only when it is non-zero,
* since signals might not be processed at each MD step.
*/
gsi = (gs_buf[i] >= 0 ?
(int)(gs_buf[i] + 0.5) :
(int)(gs_buf[i] - 0.5));
if (gsi != 0)
{
gs->set[i] = gsi;
}
/* Turn off the local signal */
gs->sig[i] = 0;
}
}
}
*bSumEkinhOld = FALSE;
}
}
if (!ekind->bNEMD && debug && bTemp && (vcm->nr > 0))
{
correct_ekin(debug,
0, mdatoms->homenr,
state->v, vcm->group_p[0],
mdatoms->massT, mdatoms->tmass, ekind->ekin);
}
/* Do center of mass motion removal */
if (bStopCM)
{
check_cm_grp(fplog, vcm, ir, 1);
do_stopcm_grp(0, mdatoms->homenr, mdatoms->cVCM,
state->x, state->v, vcm);
inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
}
if (bEner)
{
/* Calculate the amplitude of the cosine velocity profile */
ekind->cosacc.vcos = ekind->cosacc.mvcos/mdatoms->tmass;
}
if (bTemp)
{
/* Sum the kinetic energies of the groups & calc temp */
/* compute full step kinetic energies if vv, or if vv-avek and we are computing the pressure with IR_NPT_TROTTER */
/* three maincase: VV with AveVel (md-vv), vv with AveEkin (md-vv-avek), leap with AveEkin (md).
Leap with AveVel is not supported; it's not clear that it will actually work.
bEkinAveVel: If TRUE, we simply multiply ekin by ekinscale to get a full step kinetic energy.
If FALSE, we average ekinh_old and ekinh*ekinscale_nhc to get an averaged half step kinetic energy.
*/
enerd->term[F_TEMP] = sum_ekin(&(ir->opts), ekind, &dvdl_ekin,
bEkinAveVel, bScaleEkin);
enerd->dvdl_lin[efptMASS] = (double) dvdl_ekin;
enerd->term[F_EKIN] = trace(ekind->ekin);
}
/* ########## Long range energy information ###### */
if (bEner || bPres || bConstrain)
{
calc_dispcorr(ir, fr, top_global->natoms, box, state->lambda[efptVDW],
corr_pres, corr_vir, &prescorr, &enercorr, &dvdlcorr);
}
if (bEner)
{
enerd->term[F_DISPCORR] = enercorr;
enerd->term[F_EPOT] += enercorr;
enerd->term[F_DVDL_VDW] += dvdlcorr;
}
/* ########## Now pressure ############## */
if (bPres || bConstrain)
{
m_add(force_vir, shake_vir, total_vir);
/* Calculate pressure and apply LR correction if PPPM is used.
* Use the box from last timestep since we already called update().
*/
enerd->term[F_PRES] = calc_pres(fr->ePBC, ir->nwall, box, ekind->ekin, total_vir, pres);
/* Calculate long range corrections to pressure and energy */
/* this adds to enerd->term[F_PRES] and enerd->term[F_ETOT],
and computes enerd->term[F_DISPCORR]. Also modifies the
total_vir and pres tesors */
m_add(total_vir, corr_vir, total_vir);
m_add(pres, corr_pres, pres);
enerd->term[F_PDISPCORR] = prescorr;
enerd->term[F_PRES] += prescorr;
}
}
void parse_raw_data(ui08 *buf)
{
static fl64 analog2volts[3]={3.051757813E-4,1.525878906E-4,7629394531E-5};
si16 short_val;
si32 i,ifld,icv;
si32 data_tag, offset, data_size;
si32 int_val;
fl64 volts_val;
/* local variables used for calculations */
fl64 static_pres = BAD_VAL;
fl64 lat = BAD_VAL;
fl64 lon = BAD_VAL;
fl64 palt = BAD_VAL;
TimeStruct ts;
date_time_t dt;
DataDir *ddir;
/**********************************************************************/
ddir= (DataDir *)buf;
data_tag = (si32)ddir[0].tagNumber;
/* read each field in data dir directory and do necessary calculations */
i = 0;
while (data_tag!=LAST_TAG && data_tag!=NEXT_TAG && data_tag!=SAME_TAG) {
offset = (si32)ddir[i].dataOffset;
data_size = (si32)ddir[i].numberBytes;
/*if (Glob->params.debug) fprintf(stderr,"tag,offset,size are: %d %d %d\n",
data_tag,offset,data_size); */
/*------------> time field so parse out data and put into time struct */
if (data_tag == TIME_TAG) {
memcpy(&ts,buf+offset,data_size);
}
/*------------> Not time field so get out data into integer */
/* 2 byte value */
if (data_size == sizeof(si16)) {
memcpy(&short_val,buf+offset,sizeof(si16));
int_val = (si32)short_val;
}
/* 4 byte value */
if (data_size == sizeof(si32)) {
memcpy(&int_val,buf+offset,sizeof(si32));
}
/* Go through fields and find out location in aquisition/calculated
* variables table so that correct analog2volts may be applied.
* Then, do whatever calculations necessary to convert volts
* to engineering units. If these are not dependent on other fields! */
for (ifld = 0; ifld < Glob->num_raw_fields; ifld++) {
if (data_tag == Glob->acqtbl[ifld].tag) {
/*------------> Pressure variables SPRES*/
if (strncmp(Glob->acqtbl[ifld].var_type,SPRES,5) == 0) {
volts_val=(fl64)((fl64)(int_val)*analog2volts[Glob->acqtbl[ifld].para3]);
static_pres = calc_pres(volts_val,
Glob->fc[ifld].c1,
Glob->fc[ifld].c2);
/* -----------> PALT Pressure Altitude */
if ((icv = find_cvar(PALT,4)) != BAD_INDEX) {
palt= calc_palt(static_pres);
} /* endif palt is to be calculated */
} /* endif SPRES/PPRES variable */
/* -----------> LAT/LON variables */
if (strncmp(Glob->acqtbl[ifld].var_type,LAT,3) == 0) {
lat = calc_latlon(&int_val);
}
if (strncmp(Glob->acqtbl[ifld].var_type,LON,3) == 0) {
lon = calc_latlon(&int_val);
}
} /* end looking through fields for computation */
} /* end looking through tags */
/* check next tag */
i++;
data_tag = (si32)ddir[i].tagNumber;
} /* end while reading through valid tags */
if (lat != BAD_VAL && lon != BAD_VAL) {
if (lat != 0.0 || lon != 0) {
dt.year = ts.year;
dt.month = ts.mon;
dt.day = ts.day;
dt.hour = ts.hour;
dt.min = ts.min;
dt.sec = ts.sec;
uconvert_to_utime(&dt);
store_pos(&dt,lat,lon,palt,Glob->params.callsign);
}
}
}
/* TODO Specialize this routine into init-time and loop-time versions?
e.g. bReadEkin is only true when restoring from checkpoint */
void compute_globals(FILE *fplog, gmx_global_stat *gstat, t_commrec *cr, t_inputrec *ir,
t_forcerec *fr, gmx_ekindata_t *ekind,
t_state *state, t_mdatoms *mdatoms,
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,
gmx::SimulationSignaller *signalCoordinator,
matrix box, int *totalNumberOfBondedInteractions,
gmx_bool *bSumEkinhOld, int flags)
{
tensor corr_vir, corr_pres;
gmx_bool bEner, bPres, bTemp;
gmx_bool bStopCM, bGStat,
bReadEkin, bEkinAveVel, bScaleEkin, bConstrain;
real prescorr, enercorr, dvdlcorr, dvdl_ekin;
/* translate CGLO flags to gmx_booleans */
bStopCM = flags & CGLO_STOPCM;
bGStat = flags & CGLO_GSTAT;
bReadEkin = (flags & CGLO_READEKIN);
bScaleEkin = (flags & CGLO_SCALEEKIN);
bEner = flags & CGLO_ENERGY;
bTemp = flags & CGLO_TEMPERATURE;
bPres = (flags & CGLO_PRESSURE);
bConstrain = (flags & CGLO_CONSTRAINT);
/* we calculate a full state kinetic energy either with full-step velocity verlet
or half step where we need the pressure */
bEkinAveVel = (ir->eI == eiVV || (ir->eI == eiVVAK && bPres) || bReadEkin);
/* in initalization, it sums the shake virial in vv, and to
sums ekinh_old in leapfrog (or if we are calculating ekinh_old) for other reasons */
/* ########## Kinetic energy ############## */
if (bTemp)
{
/* Non-equilibrium MD: this is parallellized, but only does communication
* when there really is NEMD.
*/
if (PAR(cr) && (ekind->bNEMD))
{
accumulate_u(cr, &(ir->opts), ekind);
}
if (!bReadEkin)
{
calc_ke_part(state, &(ir->opts), mdatoms, ekind, nrnb, bEkinAveVel);
}
}
/* Calculate center of mass velocity if necessary, also parallellized */
if (bStopCM)
{
calc_vcm_grp(0, mdatoms->homenr, mdatoms,
state->x, state->v, vcm);
}
if (bTemp || bStopCM || bPres || bEner || bConstrain)
{
if (!bGStat)
{
/* We will not sum ekinh_old,
* so signal that we still have to do it.
*/
*bSumEkinhOld = TRUE;
}
else
{
gmx::ArrayRef<real> signalBuffer = signalCoordinator->getCommunicationBuffer();
if (PAR(cr))
{
wallcycle_start(wcycle, ewcMoveE);
global_stat(gstat, cr, enerd, force_vir, shake_vir, mu_tot,
ir, ekind, constr, bStopCM ? vcm : NULL,
signalBuffer.size(), signalBuffer.data(),
totalNumberOfBondedInteractions,
*bSumEkinhOld, flags);
wallcycle_stop(wcycle, ewcMoveE);
}
signalCoordinator->finalizeSignals();
*bSumEkinhOld = FALSE;
}
}
if (!ekind->bNEMD && debug && bTemp && (vcm->nr > 0))
{
correct_ekin(debug,
0, mdatoms->homenr,
state->v, vcm->group_p[0],
mdatoms->massT, mdatoms->tmass, ekind->ekin);
}
/* Do center of mass motion removal */
if (bStopCM)
{
check_cm_grp(fplog, vcm, ir, 1);
do_stopcm_grp(0, mdatoms->homenr, mdatoms->cVCM,
state->x, state->v, vcm);
inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
}
if (bEner)
{
/* Calculate the amplitude of the cosine velocity profile */
ekind->cosacc.vcos = ekind->cosacc.mvcos/mdatoms->tmass;
}
if (bTemp)
{
/* Sum the kinetic energies of the groups & calc temp */
/* compute full step kinetic energies if vv, or if vv-avek and we are computing the pressure with inputrecNptTrotter */
/* three maincase: VV with AveVel (md-vv), vv with AveEkin (md-vv-avek), leap with AveEkin (md).
Leap with AveVel is not supported; it's not clear that it will actually work.
bEkinAveVel: If TRUE, we simply multiply ekin by ekinscale to get a full step kinetic energy.
If FALSE, we average ekinh_old and ekinh*ekinscale_nhc to get an averaged half step kinetic energy.
*/
enerd->term[F_TEMP] = sum_ekin(&(ir->opts), ekind, &dvdl_ekin,
bEkinAveVel, bScaleEkin);
enerd->dvdl_lin[efptMASS] = (double) dvdl_ekin;
enerd->term[F_EKIN] = trace(ekind->ekin);
}
/* ########## Long range energy information ###### */
if (bEner || bPres || bConstrain)
{
calc_dispcorr(ir, fr, box, state->lambda[efptVDW],
corr_pres, corr_vir, &prescorr, &enercorr, &dvdlcorr);
}
if (bEner)
{
enerd->term[F_DISPCORR] = enercorr;
enerd->term[F_EPOT] += enercorr;
enerd->term[F_DVDL_VDW] += dvdlcorr;
}
/* ########## Now pressure ############## */
if (bPres || bConstrain)
{
m_add(force_vir, shake_vir, total_vir);
/* Calculate pressure and apply LR correction if PPPM is used.
* Use the box from last timestep since we already called update().
*/
enerd->term[F_PRES] = calc_pres(fr->ePBC, ir->nwall, box, ekind->ekin, total_vir, pres);
/* Calculate long range corrections to pressure and energy */
/* this adds to enerd->term[F_PRES] and enerd->term[F_ETOT],
and computes enerd->term[F_DISPCORR]. Also modifies the
total_vir and pres tesors */
m_add(total_vir, corr_vir, total_vir);
m_add(pres, corr_pres, pres);
enerd->term[F_PDISPCORR] = prescorr;
enerd->term[F_PRES] += prescorr;
}
}
