set_warning_line(wi,mdparin,-1);
- /* BASIC CUT-OFF STUFF */
- if (ir->rcoulomb < 0)
- {
- warning_error(wi,"rcoulomb should be >= 0");
- }
- if (ir->rvdw < 0)
- {
- warning_error(wi,"rvdw should be >= 0");
- }
- if (ir->rlist < 0)
- {
- warning_error(wi,"rlist should be >= 0");
- }
- if (ir->rlist == 0 ||
- !((EEL_MIGHT_BE_ZERO_AT_CUTOFF(ir->coulombtype) && ir->rcoulomb > ir->rlist) ||
- (EVDW_MIGHT_BE_ZERO_AT_CUTOFF(ir->vdwtype) && ir->rvdw > ir->rlist))) {
- /* No switched potential and/or no twin-range:
- * we can set the long-range cut-off to the maximum of the other cut-offs.
- */
- ir->rlistlong = max_cutoff(ir->rlist,max_cutoff(ir->rvdw,ir->rcoulomb));
- } else if (ir->rlistlong < 0) {
- ir->rlistlong = max_cutoff(ir->rlist,max_cutoff(ir->rvdw,ir->rcoulomb));
- sprintf(warn_buf,"rlistlong was not set, setting it to %g (no buffer)",
- ir->rlistlong);
- warning(wi,warn_buf);
- }
- if (ir->rlistlong == 0 && ir->ePBC != epbcNONE) {
- warning_error(wi,"Can not have an infinite cut-off with PBC");
- }
- if (ir->rlistlong > 0 && (ir->rlist == 0 || ir->rlistlong < ir->rlist)) {
- warning_error(wi,"rlistlong can not be shorter than rlist");
- }
- if (IR_TWINRANGE(*ir) && ir->nstlist <= 0) {
- warning_error(wi,"Can not have nstlist<=0 with twin-range interactions");
- }
+ /* BASIC CUT-OFF STUFF */
+ if (ir->rcoulomb < 0)
+ {
+ warning_error(wi,"rcoulomb should be >= 0");
+ }
+ if (ir->rvdw < 0)
+ {
+ warning_error(wi,"rvdw should be >= 0");
+ }
+ if (ir->rlist < 0 &&
+ !(ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_drift > 0))
+ {
+ warning_error(wi,"rlist should be >= 0");
+ }
+
+ if (ir->cutoff_scheme == ecutsGROUP)
+ {
+ /* BASIC CUT-OFF STUFF */
+ if (ir->rlist == 0 ||
+ !((EEL_MIGHT_BE_ZERO_AT_CUTOFF(ir->coulombtype) && ir->rcoulomb > ir->rlist) ||
+ (EVDW_MIGHT_BE_ZERO_AT_CUTOFF(ir->vdwtype) && ir->rvdw > ir->rlist))) {
+ /* No switched potential and/or no twin-range:
+ * we can set the long-range cut-off to the maximum of the other cut-offs.
+ */
+ ir->rlistlong = max_cutoff(ir->rlist,max_cutoff(ir->rvdw,ir->rcoulomb));
+ }
+ else if (ir->rlistlong < 0)
+ {
+ ir->rlistlong = max_cutoff(ir->rlist,max_cutoff(ir->rvdw,ir->rcoulomb));
+ sprintf(warn_buf,"rlistlong was not set, setting it to %g (no buffer)",
+ ir->rlistlong);
+ warning(wi,warn_buf);
+ }
+ if (ir->rlistlong == 0 && ir->ePBC != epbcNONE)
+ {
+ warning_error(wi,"Can not have an infinite cut-off with PBC");
+ }
+ if (ir->rlistlong > 0 && (ir->rlist == 0 || ir->rlistlong < ir->rlist))
+ {
+ warning_error(wi,"rlistlong can not be shorter than rlist");
+ }
+ if (IR_TWINRANGE(*ir) && ir->nstlist <= 0)
+ {
+ warning_error(wi,"Can not have nstlist<=0 with twin-range interactions");
+ }
+ }
+
+ if (ir->cutoff_scheme == ecutsVERLET)
+ {
+ real rc_max;
+
+ /* Normal Verlet type neighbor-list, currently only limited feature support */
+ if (inputrec2nboundeddim(ir) < 3)
+ {
+ warning_error(wi,"With Verlet lists only full pbc or pbc=xy with walls is supported");
+ }
+ if (ir->rcoulomb != ir->rvdw)
+ {
+ warning_error(wi,"With Verlet lists rcoulomb!=rvdw is not supported");
+ }
+ if (ir->vdwtype != evdwCUT)
+ {
+ warning_error(wi,"With Verlet lists only cut-off LJ interactions are supported");
+ }
+ if (!(ir->coulombtype == eelCUT ||
+ (EEL_RF(ir->coulombtype) && ir->coulombtype != eelRF_NEC) ||
+ EEL_PME(ir->coulombtype) || ir->coulombtype == eelEWALD))
+ {
+ warning_error(wi,"With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported");
+ }
+
+ if (ir->nstlist <= 0)
+ {
+ warning_error(wi,"With Verlet lists nstlist should be larger than 0");
+ }
+
+ if (ir->nstlist < 10)
+ {
+ warning_note(wi,"With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation.");
+ }
+
+ rc_max = max(ir->rvdw,ir->rcoulomb);
+
+ if (ir->verletbuf_drift <= 0)
+ {
+ if (ir->verletbuf_drift == 0)
+ {
+ warning_error(wi,"Can not have an energy drift of exactly 0");
+ }
+
+ if (ir->rlist < rc_max)
+ {
+ warning_error(wi,"With verlet lists rlist can not be smaller than rvdw or rcoulomb");
+ }
+
+ if (ir->rlist == rc_max && ir->nstlist > 1)
+ {
+ warning_note(wi,"rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet buffer. The cluster pair list does have a buffering effect, but choosing a larger rlist might be necessary for good energy conservation.");
+ }
+ }
+ else
+ {
+ if (ir->rlist > rc_max)
+ {
+ warning_note(wi,"You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-drift > 0. Will set rlist using verlet-buffer-drift.");
+ }
+
+ if (ir->nstlist == 1)
+ {
+ /* No buffer required */
+ ir->rlist = rc_max;
+ }
+ else
+ {
+ if (EI_DYNAMICS(ir->eI))
+ {
+ if (EI_MD(ir->eI) && ir->etc == etcNO)
+ {
+ warning_error(wi,"Temperature coupling is required for calculating rlist using the energy drift with verlet-buffer-drift > 0. Either use temperature coupling or set rlist yourself together with verlet-buffer-drift = -1.");
+ }
+
+ if (inputrec2nboundeddim(ir) < 3)
+ {
+ warning_error(wi,"The box volume is required for calculating rlist from the energy drift with verlet-buffer-drift > 0. You are using at least one unbounded dimension, so no volume can be computed. Either use a finite box, or set rlist yourself together with verlet-buffer-drift = -1.");
+ }
+ /* Set rlist temporarily so we can continue processing */
+ ir->rlist = rc_max;
+ }
+ else
+ {
+ /* Set the buffer to 5% of the cut-off */
+ ir->rlist = 1.05*rc_max;
+ }
+ }
+ }
+
+ /* No twin-range calculations with Verlet lists */
+ ir->rlistlong = ir->rlist;
+ }
/* GENERAL INTEGRATOR STUFF */
if (!(ir->eI == eiMD || EI_VV(ir->eI)))
}
}
}
+ else if (ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy)
+ {
+ /* If the user sets nstenergy small, we should respect that */
+ sprintf(warn_buf,"Setting nstcalcenergy (%d) equal to nstenergy (%d)",ir->nstcalcenergy,ir->nstenergy);
+ ir->nstcalcenergy = ir->nstenergy;
+ }
+
if (ir->epc != epcNO)
{
if (ir->nstpcouple < 0)
CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
}
} else if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype)) {
- sprintf(err_buf,"With coulombtype = %s, rcoulomb must be >= rlist",
- eel_names[ir->coulombtype]);
- CHECK(ir->rlist > ir->rcoulomb);
+ if (ir->cutoff_scheme == ecutsGROUP) {
+ sprintf(err_buf,"With coulombtype = %s, rcoulomb must be >= rlist",
+ eel_names[ir->coulombtype]);
+ CHECK(ir->rlist > ir->rcoulomb);
+ }
}
if (EEL_FULL(ir->coulombtype)) {
sprintf(err_buf,"With coulombtype = %s, rcoulomb must be <= rlist",
eel_names[ir->coulombtype]);
CHECK(ir->rcoulomb > ir->rlist);
- } else {
+ } else if (ir->cutoff_scheme == ecutsGROUP) {
if (ir->coulombtype == eelPME || ir->coulombtype == eelP3M_AD) {
sprintf(err_buf,
"With coulombtype = %s, rcoulomb must be equal to rlist\n"
evdw_names[ir->vdwtype]);
CHECK(ir->rvdw_switch >= ir->rvdw);
} else if (ir->vdwtype == evdwCUT) {
- sprintf(err_buf,"With vdwtype = %s, rvdw must be >= rlist",evdw_names[ir->vdwtype]);
- CHECK(ir->rlist > ir->rvdw);
- }
- if (EEL_IS_ZERO_AT_CUTOFF(ir->coulombtype)
- && (ir->rlistlong <= ir->rcoulomb)) {
- sprintf(warn_buf,"For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rcoulomb.",
- IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
- warning_note(wi,warn_buf);
- }
- if (EVDW_SWITCHED(ir->vdwtype) && (ir->rlistlong <= ir->rvdw)) {
- sprintf(warn_buf,"For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rvdw.",
- IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
- warning_note(wi,warn_buf);
+ if (ir->cutoff_scheme == ecutsGROUP) {
+ sprintf(err_buf,"With vdwtype = %s, rvdw must be >= rlist",evdw_names[ir->vdwtype]);
+ CHECK(ir->rlist > ir->rvdw);
+ }
}
+ if (ir->cutoff_scheme == ecutsGROUP)
+ {
+ if (EEL_IS_ZERO_AT_CUTOFF(ir->coulombtype)
+ && (ir->rlistlong <= ir->rcoulomb))
+ {
+ sprintf(warn_buf,"For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rcoulomb.",
+ IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
+ warning_note(wi,warn_buf);
+ }
+ if (EVDW_SWITCHED(ir->vdwtype) && (ir->rlistlong <= ir->rvdw))
+ {
+ sprintf(warn_buf,"For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rvdw.",
+ IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
+ warning_note(wi,warn_buf);
+ }
+ }
if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO) {
warning_note(wi,"You have selected user tables with dispersion correction, the dispersion will be corrected to -C6/r^6 beyond rvdw_switch (the tabulated interaction between rvdw_switch and rvdw will not be double counted). Make sure that you really want dispersion correction to -C6/r^6.");
warning(wi,"Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
}
- /* ENERGY CONSERVATION */
- if (ir_NVE(ir))
- {
- if (!EVDW_MIGHT_BE_ZERO_AT_CUTOFF(ir->vdwtype) && ir->rvdw > 0)
- {
- sprintf(warn_buf,"You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = %s (possibly with DispCorr)",
- evdw_names[evdwSHIFT]);
- warning_note(wi,warn_buf);
- }
- if (!EEL_MIGHT_BE_ZERO_AT_CUTOFF(ir->coulombtype) && ir->rcoulomb > 0)
- {
- sprintf(warn_buf,"You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = %s or %s",
- eel_names[eelPMESWITCH],eel_names[eelRF_ZERO]);
- warning_note(wi,warn_buf);
- }
- }
+ /* ENERGY CONSERVATION */
+ if (ir_NVE(ir) && ir->cutoff_scheme == ecutsGROUP)
+ {
+ if (!EVDW_MIGHT_BE_ZERO_AT_CUTOFF(ir->vdwtype) && ir->rvdw > 0)
+ {
+ sprintf(warn_buf,"You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = %s (possibly with DispCorr)",
+ evdw_names[evdwSHIFT]);
+ warning_note(wi,warn_buf);
+ }
+ if (!EEL_MIGHT_BE_ZERO_AT_CUTOFF(ir->coulombtype) && ir->rcoulomb > 0)
+ {
+ sprintf(warn_buf,"You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = %s or %s",
+ eel_names[eelPMESWITCH],eel_names[eelRF_ZERO]);
+ warning_note(wi,warn_buf);
+ }
+ }
/* IMPLICIT SOLVENT */
if(ir->coulombtype==eelGB_NOTUSED)
}
- if (ir->bAdress && !EI_SD(ir->eI)){
- warning_error(wi,"AdresS simulation supports only stochastic dynamics");
- }
- if (ir->bAdress && ir->epc != epcNO){
- warning_error(wi,"AdresS simulation does not support pressure coupling");
- }
- if (ir->bAdress && (EEL_FULL(ir->coulombtype))){
- warning_error(wi,"AdresS simulation does not support long-range electrostatics");
- }
-
+ if (ir->bAdress)
+ {
+ if (ir->cutoff_scheme != ecutsGROUP)
+ {
+ warning_error(wi,"AdresS simulation supports only cutoff-scheme=group");
+ }
+ if (!EI_SD(ir->eI))
+ {
+ warning_error(wi,"AdresS simulation supports only stochastic dynamics");
+ }
+ if (ir->epc != epcNO)
+ {
+ warning_error(wi,"AdresS simulation does not support pressure coupling");
+ }
+ if (EEL_FULL(ir->coulombtype))
+ {
+ warning_error(wi,"AdresS simulation does not support long-range electrostatics");
+ }
+ }
}
/* count the number of text elemets separated by whitespace in a string.
CTYPE ("mode for center of mass motion removal");
EETYPE("comm-mode", ir->comm_mode, ecm_names);
CTYPE ("number of steps for center of mass motion removal");
- ITYPE ("nstcomm", ir->nstcomm, 10);
+ ITYPE ("nstcomm", ir->nstcomm, 100);
CTYPE ("group(s) for center of mass motion removal");
STYPE ("comm-grps", vcm, NULL);
ir->nstcheckpoint = 1000;
CTYPE ("Output frequency for energies to log file and energy file");
ITYPE ("nstlog", ir->nstlog, 1000);
- ITYPE ("nstcalcenergy",ir->nstcalcenergy, -1);
- ITYPE ("nstenergy", ir->nstenergy, 100);
+ ITYPE ("nstcalcenergy",ir->nstcalcenergy, 100);
+ ITYPE ("nstenergy", ir->nstenergy, 1000);
CTYPE ("Output frequency and precision for .xtc file");
ITYPE ("nstxtcout", ir->nstxtcout, 0);
RTYPE ("xtc-precision",ir->xtcprec, 1000.0);
/* Neighbor searching */
CCTYPE ("NEIGHBORSEARCHING PARAMETERS");
+ CTYPE ("cut-off scheme (group: using charge groups, Verlet: particle based cut-offs)");
+ EETYPE("cutoff-scheme", ir->cutoff_scheme, ecutscheme_names);
CTYPE ("nblist update frequency");
ITYPE ("nstlist", ir->nstlist, 10);
CTYPE ("ns algorithm (simple or grid)");
CTYPE ("Periodic boundary conditions: xyz, no, xy");
EETYPE("pbc", ir->ePBC, epbc_names);
EETYPE("periodic-molecules", ir->bPeriodicMols, yesno_names);
+ CTYPE ("Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom,");
+ CTYPE ("a value of -1 means: use rlist");
+ RTYPE("verlet-buffer-drift", ir->verletbuf_drift, 0.005);
CTYPE ("nblist cut-off");
RTYPE ("rlist", ir->rlist, -1);
CTYPE ("long-range cut-off for switched potentials");
CTYPE ("Seperate tables between energy group pairs");
STYPE ("energygrp-table", egptable, NULL);
CTYPE ("Spacing for the PME/PPPM FFT grid");
- RTYPE ("fourierspacing", opts->fourierspacing,0.12);
+ RTYPE ("fourierspacing", ir->fourier_spacing,0.12);
CTYPE ("FFT grid size, when a value is 0 fourierspacing will be used");
ITYPE ("fourier-nx", ir->nkx, 0);
ITYPE ("fourier-ny", ir->nky, 0);
sprintf(warn_buf,"With integrator %s tau-t should be larger than 0",ei_names[ir->eI]);
warning_error(wi,warn_buf);
}
- if ((ir->etc == etcVRESCALE && ir->opts.tau_t[i] >= 0) ||
- (ir->etc != etcVRESCALE && ir->opts.tau_t[i] > 0))
+
+ if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
+ {
+ warning_note(wi,"tau-t = -1 is the new value to signal that a group should not have temperature coupling. Treating your use of tau-t = 0 as if you used -1.");
+ }
+
+ if (ir->opts.tau_t[i] >= 0)
{
tau_min = min(tau_min,ir->opts.tau_t[i]);
}
snew(ir->opts.egp_flags,nr*nr);
bExcl = do_egp_flag(ir,groups,"energygrp-excl",egpexcl,EGP_EXCL);
+ if (bExcl && ir->cutoff_scheme == ecutsVERLET)
+ {
+ warning_error(wi,"Energy group exclusions are not (yet) implemented for the Verlet scheme");
+ }
if (bExcl && EEL_FULL(ir->coulombtype))
warning(wi,"Can not exclude the lattice Coulomb energy between energy groups");
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff