gmx_fatal(FARGS,
"polarize can not be used with qA(%e) != qB(%e) for "
"atom %d of molecule block %zu",
- qS, atom[aS].qB, aS + 1, mb + 1);
+ qS,
+ atom[aS].qB,
+ aS + 1,
+ mb + 1);
}
shell[nsi].k += gmx::square(qS) * ONE_4PI_EPS0
/ ffparams->iparams[type].polarize.alpha;
gmx_fatal(FARGS,
"water_pol can not be used with qA(%e) != qB(%e) for "
"atom %d of molecule block %zu",
- qS, atom[aS].qB, aS + 1, mb + 1);
+ qS,
+ atom[aS].qB,
+ aS + 1,
+ mb + 1);
}
alpha = (ffparams->iparams[type].wpol.al_x
+ ffparams->iparams[type].wpol.al_y
ff2 = iprod(f[ind], f[ind]);
if (ff2 > ft2)
{
- fprintf(fp, "SHELL %5d, force %10.5f %10.5f %10.5f, |f| %10.5f\n", ind, f[ind][XX],
- f[ind][YY], f[ind][ZZ], std::sqrt(ff2));
+ fprintf(fp,
+ "SHELL %5d, force %10.5f %10.5f %10.5f, |f| %10.5f\n",
+ ind,
+ f[ind][XX],
+ f[ind][YY],
+ f[ind][ZZ],
+ std::sqrt(ff2));
}
}
}
bool needsLogging = false;
bool computeEnergy = false;
bool computeVirial = false;
- constr->apply(needsLogging, computeEnergy, step, 0, 1.0, xCurrent,
- shfc->adir_xnold.arrayRefWithPadding(), {}, box, lambda[efptBONDED],
- &(dvdlambda[efptBONDED]), {}, computeVirial, nullptr,
+ constr->apply(needsLogging,
+ computeEnergy,
+ step,
+ 0,
+ 1.0,
+ xCurrent,
+ shfc->adir_xnold.arrayRefWithPadding(),
+ {},
+ box,
+ lambda[efptBONDED],
+ &(dvdlambda[efptBONDED]),
+ {},
+ computeVirial,
+ nullptr,
gmx::ConstraintVariable::Positions);
- constr->apply(needsLogging, computeEnergy, step, 0, 1.0, xCurrent,
- shfc->adir_xnew.arrayRefWithPadding(), {}, box, lambda[efptBONDED],
- &(dvdlambda[efptBONDED]), {}, computeVirial, nullptr,
+ constr->apply(needsLogging,
+ computeEnergy,
+ step,
+ 0,
+ 1.0,
+ xCurrent,
+ shfc->adir_xnew.arrayRefWithPadding(),
+ {},
+ box,
+ lambda[efptBONDED],
+ &(dvdlambda[efptBONDED]),
+ {},
+ computeVirial,
+ nullptr,
gmx::ConstraintVariable::Positions);
for (n = 0; n < end; n++)
}
/* Project the acceleration on the old bond directions */
- constr->apply(needsLogging, computeEnergy, step, 0, 1.0, xOld, shfc->adir_xnew.arrayRefWithPadding(),
- acc_dir, box, lambda[efptBONDED], &(dvdlambda[efptBONDED]), {}, computeVirial,
- nullptr, gmx::ConstraintVariable::Deriv_FlexCon);
+ constr->apply(needsLogging,
+ computeEnergy,
+ step,
+ 0,
+ 1.0,
+ xOld,
+ shfc->adir_xnew.arrayRefWithPadding(),
+ acc_dir,
+ box,
+ lambda[efptBONDED],
+ &(dvdlambda[efptBONDED]),
+ {},
+ computeVirial,
+ nullptr,
+ gmx::ConstraintVariable::Deriv_FlexCon);
}
void relax_shell_flexcon(FILE* fplog,
* before do_force is called, which normally puts all
* charge groups in the box.
*/
- put_atoms_in_box_omp(fr->pbcType, box, x.subArray(0, md->homenr),
- gmx_omp_nthreads_get(emntDefault));
+ put_atoms_in_box_omp(
+ fr->pbcType, box, x.subArray(0, md->homenr), gmx_omp_nthreads_get(emntDefault));
}
if (nflexcon)
}
int shellfc_flags = force_flags | (bVerbose ? GMX_FORCE_ENERGY : 0);
gmx::ForceBuffersView forceViewInit = gmx::ForceBuffersView(forceWithPadding[Min], {}, false);
- do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession, pull_work, mdstep,
- nrnb, wcycle, top, box, xPadded, hist, &forceViewInit, force_vir, md, enerd, lambda,
- fr, runScheduleWork, vsite, mu_tot, t, nullptr,
- (bDoNS ? GMX_FORCE_NS : 0) | shellfc_flags, ddBalanceRegionHandler);
+ do_force(fplog,
+ cr,
+ ms,
+ inputrec,
+ nullptr,
+ enforcedRotation,
+ imdSession,
+ pull_work,
+ mdstep,
+ nrnb,
+ wcycle,
+ top,
+ box,
+ xPadded,
+ hist,
+ &forceViewInit,
+ force_vir,
+ md,
+ enerd,
+ lambda,
+ fr,
+ runScheduleWork,
+ vsite,
+ mu_tot,
+ t,
+ nullptr,
+ (bDoNS ? GMX_FORCE_NS : 0) | shellfc_flags,
+ ddBalanceRegionHandler);
sf_dir = 0;
if (nflexcon)
{
- init_adir(shfc, constr, inputrec, cr, dd_ac1, mdstep, md, end, shfc->x_old.arrayRefWithPadding(),
- x, xPadded, force[Min], shfc->acc_dir, box, lambda, &dum);
+ init_adir(shfc,
+ constr,
+ inputrec,
+ cr,
+ dd_ac1,
+ mdstep,
+ md,
+ end,
+ shfc->x_old.arrayRefWithPadding(),
+ x,
+ xPadded,
+ force[Min],
+ shfc->acc_dir,
+ box,
+ lambda,
+ &dum);
for (i = 0; i < end; i++)
{
* shell positions are updated, therefore the other particles must
* be set here, in advance.
*/
- std::copy(xPadded.paddedArrayRef().begin(), xPadded.paddedArrayRef().end(),
+ std::copy(xPadded.paddedArrayRef().begin(),
+ xPadded.paddedArrayRef().end(),
posWithPadding[Min].paddedArrayRef().begin());
- std::copy(xPadded.paddedArrayRef().begin(), xPadded.paddedArrayRef().end(),
+ std::copy(xPadded.paddedArrayRef().begin(),
+ xPadded.paddedArrayRef().end(),
posWithPadding[Try].paddedArrayRef().begin());
}
if (nflexcon)
{
- init_adir(shfc, constr, inputrec, cr, dd_ac1, mdstep, md, end,
- shfc->x_old.arrayRefWithPadding(), x, posWithPadding[Min], force[Min],
- shfc->acc_dir, box, lambda, &dum);
+ init_adir(shfc,
+ constr,
+ inputrec,
+ cr,
+ dd_ac1,
+ mdstep,
+ md,
+ end,
+ shfc->x_old.arrayRefWithPadding(),
+ x,
+ posWithPadding[Min],
+ force[Min],
+ shfc->acc_dir,
+ box,
+ lambda,
+ &dum);
directional_sd(pos[Min], pos[Try], shfc->acc_dir, end, fr->fc_stepsize);
}
}
/* Try the new positions */
gmx::ForceBuffersView forceViewTry = gmx::ForceBuffersView(forceWithPadding[Try], {}, false);
- do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession, pull_work, 1, nrnb, wcycle,
- top, box, posWithPadding[Try], hist, &forceViewTry, force_vir, md, enerd, lambda, fr,
- runScheduleWork, vsite, mu_tot, t, nullptr, shellfc_flags, ddBalanceRegionHandler);
+ do_force(fplog,
+ cr,
+ ms,
+ inputrec,
+ nullptr,
+ enforcedRotation,
+ imdSession,
+ pull_work,
+ 1,
+ nrnb,
+ wcycle,
+ top,
+ box,
+ posWithPadding[Try],
+ hist,
+ &forceViewTry,
+ force_vir,
+ md,
+ enerd,
+ lambda,
+ fr,
+ runScheduleWork,
+ vsite,
+ mu_tot,
+ t,
+ nullptr,
+ shellfc_flags,
+ ddBalanceRegionHandler);
accumulatePotentialEnergies(enerd, lambda, inputrec->fepvals);
if (gmx_debug_at)
{
sf_dir = 0;
if (nflexcon)
{
- init_adir(shfc, constr, inputrec, cr, dd_ac1, mdstep, md, end,
- shfc->x_old.arrayRefWithPadding(), x, posWithPadding[Try], force[Try],
- shfc->acc_dir, box, lambda, &dum);
+ init_adir(shfc,
+ constr,
+ inputrec,
+ cr,
+ dd_ac1,
+ mdstep,
+ md,
+ end,
+ shfc->x_old.arrayRefWithPadding(),
+ x,
+ posWithPadding[Try],
+ force[Try],
+ shfc->acc_dir,
+ box,
+ lambda,
+ &dum);
ArrayRef<const RVec> acc_dir = shfc->acc_dir;
for (i = 0; i < end; i++)
/* Note that the energies and virial are incorrect when not converged */
if (fplog)
{
- fprintf(fplog, "step %s: EM did not converge in %d iterations, RMS force %6.2e\n",
- gmx_step_str(mdstep, sbuf), number_steps, df[Min]);
+ fprintf(fplog,
+ "step %s: EM did not converge in %d iterations, RMS force %6.2e\n",
+ gmx_step_str(mdstep, sbuf),
+ number_steps,
+ df[Min]);
}
- fprintf(stderr, "step %s: EM did not converge in %d iterations, RMS force %6.2e\n",
- gmx_step_str(mdstep, sbuf), number_steps, df[Min]);
+ fprintf(stderr,
+ "step %s: EM did not converge in %d iterations, RMS force %6.2e\n",
+ gmx_step_str(mdstep, sbuf),
+ number_steps,
+ df[Min]);
}
/* Copy back the coordinates and the forces */
if (shfc && fplog && numSteps > 0)
{
double numStepsAsDouble = static_cast<double>(numSteps);
- fprintf(fplog, "Fraction of iterations that converged: %.2f %%\n",
+ fprintf(fplog,
+ "Fraction of iterations that converged: %.2f %%\n",
(shfc->numConvergedIterations * 100.0) / numStepsAsDouble);
- fprintf(fplog, "Average number of force evaluations per MD step: %.2f\n\n",
+ fprintf(fplog,
+ "Average number of force evaluations per MD step: %.2f\n\n",
shfc->numForceEvaluations / numStepsAsDouble);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff