static void scale_velocities(t_state *state, real fac)
{
int i;
if (as_rvec_array(state->v.data()))
{
for (i = 0; i < state->natoms; i++)
{
svmul(fac, state->v[i], state->v[i]);
}
}
}
/* PLUMED HREX */
void exchange_state(const gmx_multisim_t *ms, int b, t_state *state)
/* END PLUMED HREX */
{
/* When t_state changes, this code should be updated. */
int ngtc, nnhpres;
ngtc = state->ngtc * state->nhchainlength;
nnhpres = state->nnhpres* state->nhchainlength;
exchange_rvecs(ms, b, state->box, DIM);
exchange_rvecs(ms, b, state->box_rel, DIM);
exchange_rvecs(ms, b, state->boxv, DIM);
exchange_reals(ms, b, &(state->veta), 1);
exchange_reals(ms, b, &(state->vol0), 1);
exchange_rvecs(ms, b, state->svir_prev, DIM);
exchange_rvecs(ms, b, state->fvir_prev, DIM);
exchange_rvecs(ms, b, state->pres_prev, DIM);
exchange_doubles(ms, b, state->nosehoover_xi.data(), ngtc);
exchange_doubles(ms, b, state->nosehoover_vxi.data(), ngtc);
exchange_doubles(ms, b, state->nhpres_xi.data(), nnhpres);
exchange_doubles(ms, b, state->nhpres_vxi.data(), nnhpres);
exchange_doubles(ms, b, state->therm_integral.data(), state->ngtc);
exchange_doubles(ms, b, &state->baros_integral, 1);
exchange_rvecs(ms, b, as_rvec_array(state->x.data()), state->natoms);
exchange_rvecs(ms, b, as_rvec_array(state->v.data()), state->natoms);
}
int gmx_pmeonly(struct gmx_pme_t *pme,
const t_commrec *cr, t_nrnb *mynrnb,
gmx_wallcycle *wcycle,
gmx_walltime_accounting_t walltime_accounting,
t_inputrec *ir, PmeRunMode runMode)
{
int ret;
int natoms = 0;
matrix box;
real lambda_q = 0;
real lambda_lj = 0;
int maxshift_x = 0, maxshift_y = 0;
real energy_q, energy_lj, dvdlambda_q, dvdlambda_lj;
matrix vir_q, vir_lj;
float cycles;
int count;
gmx_bool bEnerVir = FALSE;
int64_t step;
/* This data will only use with PME tuning, i.e. switching PME grids */
std::vector<gmx_pme_t *> pmedata;
pmedata.push_back(pme);
auto pme_pp = gmx_pme_pp_init(cr);
//TODO the variable below should be queried from the task assignment info
const bool useGpuForPme = (runMode == PmeRunMode::GPU) || (runMode == PmeRunMode::Mixed);
if (useGpuForPme)
{
changePinningPolicy(&pme_pp->chargeA, pme_get_pinning_policy());
changePinningPolicy(&pme_pp->x, pme_get_pinning_policy());
}
init_nrnb(mynrnb);
count = 0;
do /****** this is a quasi-loop over time steps! */
{
/* The reason for having a loop here is PME grid tuning/switching */
do
{
/* Domain decomposition */
ivec newGridSize;
bool atomSetChanged = false;
real ewaldcoeff_q = 0, ewaldcoeff_lj = 0;
ret = gmx_pme_recv_coeffs_coords(pme_pp.get(),
&natoms,
box,
&maxshift_x, &maxshift_y,
&lambda_q, &lambda_lj,
&bEnerVir,
&step,
&newGridSize,
&ewaldcoeff_q,
&ewaldcoeff_lj,
&atomSetChanged);
if (ret == pmerecvqxSWITCHGRID)
{
/* Switch the PME grid to newGridSize */
pme = gmx_pmeonly_switch(&pmedata, newGridSize, ewaldcoeff_q, ewaldcoeff_lj, cr, ir);
}
if (atomSetChanged)
{
gmx_pme_reinit_atoms(pme, natoms, pme_pp->chargeA.data());
}
if (ret == pmerecvqxRESETCOUNTERS)
{
/* Reset the cycle and flop counters */
reset_pmeonly_counters(wcycle, walltime_accounting, mynrnb, step, useGpuForPme);
}
}
while (ret == pmerecvqxSWITCHGRID || ret == pmerecvqxRESETCOUNTERS);
if (ret == pmerecvqxFINISH)
{
/* We should stop: break out of the loop */
break;
}
if (count == 0)
{
wallcycle_start(wcycle, ewcRUN);
walltime_accounting_start_time(walltime_accounting);
}
wallcycle_start(wcycle, ewcPMEMESH);
dvdlambda_q = 0;
dvdlambda_lj = 0;
clear_mat(vir_q);
clear_mat(vir_lj);
energy_q = 0;
energy_lj = 0;
// TODO Make a struct of array refs onto these per-atom fields
// of pme_pp (maybe box, energy and virial, too; and likewise
// from mdatoms for the other call to gmx_pme_do), so we have
// fewer lines of code and less parameter passing.
const int pmeFlags = GMX_PME_DO_ALL_F | (bEnerVir ? GMX_PME_CALC_ENER_VIR : 0);
gmx::ArrayRef<const gmx::RVec> forces;
if (useGpuForPme)
{
const bool boxChanged = false;
//TODO this should be set properly by gmx_pme_recv_coeffs_coords,
// or maybe use inputrecDynamicBox(ir), at the very least - change this when this codepath is tested!
pme_gpu_prepare_computation(pme, boxChanged, box, wcycle, pmeFlags);
pme_gpu_launch_spread(pme, pme_pp->x.rvec_array(), wcycle);
pme_gpu_launch_complex_transforms(pme, wcycle);
pme_gpu_launch_gather(pme, wcycle, PmeForceOutputHandling::Set);
pme_gpu_wait_finish_task(pme, wcycle, &forces, vir_q, &energy_q);
pme_gpu_reinit_computation(pme, wcycle);
}
else
{
gmx_pme_do(pme, 0, natoms, pme_pp->x.rvec_array(), as_rvec_array(pme_pp->f.data()),
pme_pp->chargeA.data(), pme_pp->chargeB.data(),
pme_pp->sqrt_c6A.data(), pme_pp->sqrt_c6B.data(),
pme_pp->sigmaA.data(), pme_pp->sigmaB.data(), box,
cr, maxshift_x, maxshift_y, mynrnb, wcycle,
vir_q, vir_lj,
&energy_q, &energy_lj, lambda_q, lambda_lj, &dvdlambda_q, &dvdlambda_lj,
pmeFlags);
forces = pme_pp->f;
}
cycles = wallcycle_stop(wcycle, ewcPMEMESH);
gmx_pme_send_force_vir_ener(pme_pp.get(), as_rvec_array(forces.data()),
vir_q, energy_q, vir_lj, energy_lj,
dvdlambda_q, dvdlambda_lj, cycles);
count++;
} /***** end of quasi-loop, we stop with the break above */
while (TRUE);
walltime_accounting_end_time(walltime_accounting);
return 0;
}
void dd_move_f_specat(gmx_domdec_t *dd, gmx_domdec_specat_comm_t *spac,
rvec *f, rvec *fshift)
{
gmx_specatsend_t *spas;
rvec *vbuf;
int n, n0, n1, dim, dir;
ivec vis;
int is;
gmx_bool bPBC, bScrew;
n = spac->at_end;
for (int d = dd->ndim - 1; d >= 0; d--)
{
dim = dd->dim[d];
if (dd->nc[dim] > 2)
{
/* Pulse the grid forward and backward */
spas = spac->spas[d];
n0 = spas[0].nrecv;
n1 = spas[1].nrecv;
n -= n1 + n0;
vbuf = as_rvec_array(spac->vbuf.data());
/* Send and receive the coordinates */
dd_sendrecv2_rvec(dd, d,
f + n + n1, n0, vbuf, spas[0].a.size(),
f + n, n1, vbuf + spas[0].a.size(),
spas[1].a.size());
for (dir = 0; dir < 2; dir++)
{
bPBC = ((dir == 0 && dd->ci[dim] == 0) ||
(dir == 1 && dd->ci[dim] == dd->nc[dim]-1));
bScrew = (bPBC && dd->bScrewPBC && dim == XX);
spas = &spac->spas[d][dir];
/* Sum the buffer into the required forces */
if (!bPBC || (!bScrew && fshift == nullptr))
{
for (int a : spas->a)
{
rvec_inc(f[a], *vbuf);
vbuf++;
}
}
else
{
clear_ivec(vis);
vis[dim] = (dir == 0 ? 1 : -1);
is = IVEC2IS(vis);
if (!bScrew)
{
/* Sum and add to shift forces */
for (int a : spas->a)
{
rvec_inc(f[a], *vbuf);
rvec_inc(fshift[is], *vbuf);
vbuf++;
}
}
else
{
/* Rotate the forces */
for (int a : spas->a)
{
f[a][XX] += (*vbuf)[XX];
f[a][YY] -= (*vbuf)[YY];
f[a][ZZ] -= (*vbuf)[ZZ];
if (fshift)
{
rvec_inc(fshift[is], *vbuf);
}
vbuf++;
}
}
}
}
}
else
{
/* Two cells, so we only need to communicate one way */
spas = &spac->spas[d][0];
n -= spas->nrecv;
/* Send and receive the coordinates */
ddSendrecv(dd, d, dddirForward,
f + n, spas->nrecv,
as_rvec_array(spac->vbuf.data()), spas->a.size());
/* Sum the buffer into the required forces */
if (dd->bScrewPBC && dim == XX &&
(dd->ci[dim] == 0 ||
dd->ci[dim] == dd->nc[dim]-1))
{
int i = 0;
for (int a : spas->a)
{
/* Rotate the force */
f[a][XX] += spac->vbuf[i][XX];
f[a][YY] -= spac->vbuf[i][YY];
f[a][ZZ] -= spac->vbuf[i][ZZ];
i++;
}
}
else
{
int i = 0;
for (int a : spas->a)
{
rvec_inc(f[a], spac->vbuf[i]);
i++;
}
}
}
}
}
void dd_move_x_specat(gmx_domdec_t *dd, gmx_domdec_specat_comm_t *spac,
const matrix box,
rvec *x0,
rvec *x1, gmx_bool bX1IsCoord)
{
gmx_specatsend_t *spas;
int nvec, v, n, nn, ns0, ns1, nr0, nr1, nr, d, dim, dir, i;
gmx_bool bPBC, bScrew = FALSE;
rvec shift = {0, 0, 0};
nvec = 1;
if (x1 != nullptr)
{
nvec++;
}
n = spac->at_start;
for (d = 0; d < dd->ndim; d++)
{
dim = dd->dim[d];
if (dd->nc[dim] > 2)
{
/* Pulse the grid forward and backward */
rvec *vbuf = as_rvec_array(spac->vbuf.data());
for (dir = 0; dir < 2; dir++)
{
if (dir == 0 && dd->ci[dim] == 0)
{
bPBC = TRUE;
bScrew = (dd->bScrewPBC && dim == XX);
copy_rvec(box[dim], shift);
}
else if (dir == 1 && dd->ci[dim] == dd->nc[dim]-1)
{
bPBC = TRUE;
bScrew = (dd->bScrewPBC && dim == XX);
for (i = 0; i < DIM; i++)
{
shift[i] = -box[dim][i];
}
}
else
{
bPBC = FALSE;
bScrew = FALSE;
}
spas = &spac->spas[d][dir];
for (v = 0; v < nvec; v++)
{
rvec *x = (v == 0 ? x0 : x1);
/* Copy the required coordinates to the send buffer */
if (!bPBC || (v == 1 && !bX1IsCoord))
{
/* Only copy */
for (int a : spas->a)
{
copy_rvec(x[a], *vbuf);
vbuf++;
}
}
else if (!bScrew)
{
/* Shift coordinates */
for (int a : spas->a)
{
rvec_add(x[a], shift, *vbuf);
vbuf++;
}
}
else
{
/* Shift and rotate coordinates */
for (int a : spas->a)
{
(*vbuf)[XX] = x[a][XX] + shift[XX];
(*vbuf)[YY] = box[YY][YY] - x[a][YY] + shift[YY];
(*vbuf)[ZZ] = box[ZZ][ZZ] - x[a][ZZ] + shift[ZZ];
vbuf++;
}
}
}
}
/* Send and receive the coordinates */
spas = spac->spas[d];
ns0 = spas[0].a.size();
nr0 = spas[0].nrecv;
ns1 = spas[1].a.size();
nr1 = spas[1].nrecv;
if (nvec == 1)
{
rvec *vbuf = as_rvec_array(spac->vbuf.data());
dd_sendrecv2_rvec(dd, d,
vbuf + ns0, ns1, x0 + n, nr1,
vbuf, ns0, x0 + n + nr1, nr0);
}
else
{
rvec *vbuf = as_rvec_array(spac->vbuf.data());
/* Communicate both vectors in one buffer */
rvec *rbuf = as_rvec_array(spac->vbuf2.data());
dd_sendrecv2_rvec(dd, d,
vbuf + 2*ns0, 2*ns1, rbuf, 2*nr1,
vbuf, 2*ns0, rbuf + 2*nr1, 2*nr0);
/* Split the buffer into the two vectors */
nn = n;
for (dir = 1; dir >= 0; dir--)
{
nr = spas[dir].nrecv;
for (v = 0; v < 2; v++)
{
rvec *x = (v == 0 ? x0 : x1);
for (i = 0; i < nr; i++)
{
copy_rvec(*rbuf, x[nn+i]);
rbuf++;
}
}
nn += nr;
}
}
n += nr0 + nr1;
}
else
{
spas = &spac->spas[d][0];
/* Copy the required coordinates to the send buffer */
rvec *vbuf = as_rvec_array(spac->vbuf.data());
for (v = 0; v < nvec; v++)
{
rvec *x = (v == 0 ? x0 : x1);
if (dd->bScrewPBC && dim == XX &&
(dd->ci[XX] == 0 || dd->ci[XX] == dd->nc[XX]-1))
{
/* Here we only perform the rotation, the rest of the pbc
* is handled in the constraint or viste routines.
*/
for (int a : spas->a)
{
(*vbuf)[XX] = x[a][XX];
(*vbuf)[YY] = box[YY][YY] - x[a][YY];
(*vbuf)[ZZ] = box[ZZ][ZZ] - x[a][ZZ];
vbuf++;
}
}
else
{
for (int a : spas->a)
{
copy_rvec(x[a], *vbuf);
vbuf++;
}
}
}
/* Send and receive the coordinates */
if (nvec == 1)
{
rvec *vbuf = as_rvec_array(spac->vbuf.data());
ddSendrecv(dd, d, dddirBackward,
vbuf, spas->a.size(), x0 + n, spas->nrecv);
}
else
{
rvec *vbuf = as_rvec_array(spac->vbuf.data());
/* Communicate both vectors in one buffer */
rvec *rbuf = as_rvec_array(spac->vbuf2.data());
ddSendrecv(dd, d, dddirBackward,
vbuf, 2*spas->a.size(), rbuf, 2*spas->nrecv);
/* Split the buffer into the two vectors */
nr = spas[0].nrecv;
for (v = 0; v < 2; v++)
{
rvec *x = (v == 0 ? x0 : x1);
for (i = 0; i < nr; i++)
{
copy_rvec(*rbuf, x[n+i]);
rbuf++;
}
}
}
n += spas->nrecv;
}
}
}
static void bcastPaddedRVecVector(const t_commrec *cr, PaddedRVecVector *v, unsigned int n)
{
(*v).resize(n + 1);
nblock_bc(cr, n, as_rvec_array(v->data()));
}
int gmx_convert_tpr(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] can edit run input files in three ways.[PAR]",
"[BB]1.[bb] by modifying the number of steps in a run input file",
"with options [TT]-extend[tt], [TT]-until[tt] or [TT]-nsteps[tt]",
"(nsteps=-1 means unlimited number of steps)[PAR]",
"[BB]2.[bb] by creating a [REF].tpx[ref] file for a subset of your original",
"tpx file, which is useful when you want to remove the solvent from",
"your [REF].tpx[ref] file, or when you want to make e.g. a pure C[GRK]alpha[grk] [REF].tpx[ref] file.",
"Note that you may need to use [TT]-nsteps -1[tt] (or similar) to get",
"this to work.",
"[BB]WARNING: this [REF].tpx[ref] file is not fully functional[bb].[PAR]",
"[BB]3.[bb] by setting the charges of a specified group",
"to zero. This is useful when doing free energy estimates",
"using the LIE (Linear Interaction Energy) method."
};
const char *top_fn;
int i;
gmx_int64_t nsteps_req, run_step;
double run_t, state_t;
gmx_bool bSel;
gmx_bool bNsteps, bExtend, bUntil;
gmx_mtop_t mtop;
t_atoms atoms;
t_inputrec *ir;
t_state state;
int gnx;
char *grpname;
int *index = NULL;
char buf[200], buf2[200];
gmx_output_env_t *oenv;
t_filenm fnm[] = {
{ efTPR, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efTPR, "-o", "tprout", ffWRITE }
};
#define NFILE asize(fnm)
/* Command line options */
static int nsteps_req_int = 0;
static real extend_t = 0.0, until_t = 0.0;
static gmx_bool bZeroQ = FALSE;
static t_pargs pa[] = {
{ "-extend", FALSE, etREAL, {&extend_t},
"Extend runtime by this amount (ps)" },
{ "-until", FALSE, etREAL, {&until_t},
"Extend runtime until this ending time (ps)" },
{ "-nsteps", FALSE, etINT, {&nsteps_req_int},
"Change the number of steps" },
{ "-zeroq", FALSE, etBOOL, {&bZeroQ},
"Set the charges of a group (from the index) to zero" }
};
/* Parse the command line */
if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
/* Convert int to gmx_int64_t */
nsteps_req = nsteps_req_int;
bNsteps = opt2parg_bSet("-nsteps", asize(pa), pa);
bExtend = opt2parg_bSet("-extend", asize(pa), pa);
bUntil = opt2parg_bSet("-until", asize(pa), pa);
top_fn = ftp2fn(efTPR, NFILE, fnm);
fprintf(stderr, "Reading toplogy and stuff from %s\n", top_fn);
gmx::MDModules mdModules;
ir = mdModules.inputrec();
read_tpx_state(top_fn, ir, &state, &mtop);
run_step = ir->init_step;
run_t = ir->init_step*ir->delta_t + ir->init_t;
if (bNsteps)
{
fprintf(stderr, "Setting nsteps to %s\n", gmx_step_str(nsteps_req, buf));
ir->nsteps = nsteps_req;
}
else
{
/* Determine total number of steps remaining */
if (bExtend)
{
ir->nsteps = ir->nsteps - (run_step - ir->init_step) + (gmx_int64_t)(extend_t/ir->delta_t + 0.5);
printf("Extending remaining runtime of by %g ps (now %s steps)\n",
extend_t, gmx_step_str(ir->nsteps, buf));
}
else if (bUntil)
{
printf("nsteps = %s, run_step = %s, current_t = %g, until = %g\n",
gmx_step_str(ir->nsteps, buf),
gmx_step_str(run_step, buf2),
run_t, until_t);
ir->nsteps = (gmx_int64_t)((until_t - run_t)/ir->delta_t + 0.5);
printf("Extending remaining runtime until %g ps (now %s steps)\n",
until_t, gmx_step_str(ir->nsteps, buf));
}
else
{
ir->nsteps -= run_step - ir->init_step;
/* Print message */
printf("%s steps (%g ps) remaining from first run.\n",
gmx_step_str(ir->nsteps, buf), ir->nsteps*ir->delta_t);
}
}
if (bNsteps || bZeroQ || (ir->nsteps > 0))
{
ir->init_step = run_step;
if (ftp2bSet(efNDX, NFILE, fnm) ||
!(bNsteps || bExtend || bUntil))
{
atoms = gmx_mtop_global_atoms(&mtop);
get_index(&atoms, ftp2fn_null(efNDX, NFILE, fnm), 1,
&gnx, &index, &grpname);
if (!bZeroQ)
{
bSel = (gnx != state.natoms);
for (i = 0; ((i < gnx) && (!bSel)); i++)
{
bSel = (i != index[i]);
}
}
else
{
bSel = FALSE;
}
if (bSel)
{
fprintf(stderr, "Will write subset %s of original tpx containing %d "
"atoms\n", grpname, gnx);
reduce_topology_x(gnx, index, &mtop, as_rvec_array(state.x.data()), as_rvec_array(state.v.data()));
state.natoms = gnx;
}
else if (bZeroQ)
{
zeroq(index, &mtop);
fprintf(stderr, "Zero-ing charges for group %s\n", grpname);
}
else
{
fprintf(stderr, "Will write full tpx file (no selection)\n");
}
}
state_t = ir->init_t + ir->init_step*ir->delta_t;
sprintf(buf, "Writing statusfile with starting step %s%s and length %s%s steps...\n", "%10", GMX_PRId64, "%10", GMX_PRId64);
fprintf(stderr, buf, ir->init_step, ir->nsteps);
fprintf(stderr, " time %10.3f and length %10.3f ps\n",
state_t, ir->nsteps*ir->delta_t);
write_tpx_state(opt2fn("-o", NFILE, fnm), ir, &state, &mtop);
}
else
{
printf("You've simulated long enough. Not writing tpr file\n");
}
return 0;
}
/* 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,
as_rvec_array(state->x.data()), as_rvec_array(state->v.data()), 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,
as_rvec_array(state->v.data()), 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,
as_rvec_array(state->x.data()), as_rvec_array(state->v.data()), 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;
}
}