if (ir->cutoff_scheme == ecutsGROUP)
{
- if (ir->coulomb_modifier != eintmodNONE ||
- ir->vdw_modifier != eintmodNONE)
- {
- warning_error(wi,"potential modifiers are not supported (yet) with the group cut-off scheme");
- }
-
/* BASIC CUT-OFF STUFF */
if (ir->rlist == 0 ||
!((EEL_MIGHT_BE_ZERO_AT_CUTOFF(ir->coulombtype) && ir->rcoulomb > ir->rlist) ||
warning_error(wi,"Can not have nstlist<=0 with twin-range interactions");
}
}
-
+
+ if(ir->rlistlong == ir->rlist)
+ {
+ ir->nstcalclr = 0;
+ }
+ else if(ir->rlistlong>ir->rlist && ir->nstcalclr==0)
+ {
+ warning_error(wi,"With different cutoffs for electrostatics and VdW, nstcalclr must be -1 or a positive number");
+ }
+
if (ir->cutoff_scheme == ecutsVERLET)
{
real rc_max;
ir->rlistlong = ir->rlist;
}
+ if(ir->nstcalclr==-1)
+ {
+ /* if rlist=rlistlong, this will later be changed to nstcalclr=0 */
+ ir->nstcalclr = ir->nstlist;
+ }
+ else if(ir->nstcalclr>0)
+ {
+ if(ir->nstlist>0 && (ir->nstlist % ir->nstcalclr != 0))
+ {
+ warning_error(wi,"nstlist must be evenly divisible by nstcalclr. Use nstcalclr = -1 to automatically follow nstlist");
+ }
+ }
+ else if(ir->nstcalclr<-1)
+ {
+ warning_error(wi,"nstcalclr must be a positive number (divisor of nstcalclr), or -1 to follow nstlist.");
+ }
+
+ if(EEL_PME(ir->coulombtype) && ir->rcoulomb > ir->rvdw && ir->nstcalclr>1)
+ {
+ warning_error(wi,"When used with PME, the long-range component of twin-range interactions must be updated every step (nstcalclr)");
+ }
+
/* GENERAL INTEGRATOR STUFF */
if (!(ir->eI == eiMD || EI_VV(ir->eI)))
{
/* nstdhdl should be a multiple of nstcalcenergy */
check_nst("nstcalcenergy",ir->nstcalcenergy,
"nstdhdl",&ir->fepvals->nstdhdl,wi);
+ /* nstexpanded should be a multiple of nstcalcenergy */
+ check_nst("nstcalcenergy",ir->nstcalcenergy,
+ "nstdhdl",&ir->expandedvals->nstexpanded,wi);
}
}
}
/* More checks are in triple check (grompp.c) */
if (ir->coulombtype == eelSWITCH) {
- sprintf(warn_buf,"coulombtype = %s is only for testing purposes and can lead to serious artifacts, advice: use coulombtype = %s",
+ sprintf(warn_buf,"coulombtype = %s is only for testing purposes and can lead to serious "
+ "artifacts, advice: use coulombtype = %s",
eel_names[ir->coulombtype],
eel_names[eelRF_ZERO]);
warning(wi,warn_buf);
}
if (EEL_RF(ir->coulombtype) && ir->epsilon_rf==1 && ir->epsilon_r!=1) {
- sprintf(warn_buf,"epsilon-r = %g and epsilon-rf = 1 with reaction field, assuming old format and exchanging epsilon-r and epsilon-rf",ir->epsilon_r);
+ sprintf(warn_buf,"epsilon-r = %g and epsilon-rf = 1 with reaction field, proceeding assuming old format and exchanging epsilon-r and epsilon-rf",ir->epsilon_r);
warning(wi,warn_buf);
ir->epsilon_rf = ir->epsilon_r;
ir->epsilon_r = 1.0;
/* reaction field (at the cut-off) */
if (ir->coulombtype == eelRF_ZERO) {
- sprintf(err_buf,"With coulombtype = %s, epsilon-rf must be 0",
+ sprintf(warn_buf,"With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
eel_names[ir->coulombtype]);
- CHECK(ir->epsilon_rf != 0);
+ CHECK(ir->epsilon_rf != 0);
+ ir->epsilon_rf = 0.0;
}
sprintf(err_buf,"epsilon-rf must be >= epsilon-r");
if (EEL_MIGHT_BE_ZERO_AT_CUTOFF(ir->coulombtype)) {
if (EEL_SWITCHED(ir->coulombtype)) {
sprintf(err_buf,
- "With coulombtype = %s rcoulomb_switch must be < rcoulomb",
+ "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the potential modifier options!",
eel_names[ir->coulombtype]);
CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
}
} else if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype)) {
- if (ir->cutoff_scheme == ecutsGROUP) {
- sprintf(err_buf,"With coulombtype = %s, rcoulomb must be >= rlist",
+ if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE) {
+ sprintf(err_buf,"With coulombtype = %s, rcoulomb should be >= rlist unless you use a potential modifier",
eel_names[ir->coulombtype]);
CHECK(ir->rlist > ir->rcoulomb);
}
}
- if (EEL_FULL(ir->coulombtype)) {
- if (ir->coulombtype==eelPMESWITCH || ir->coulombtype==eelPMEUSER ||
- ir->coulombtype==eelPMEUSERSWITCH) {
- sprintf(err_buf,"With coulombtype = %s, rcoulomb must be <= rlist",
- eel_names[ir->coulombtype]);
- CHECK(ir->rcoulomb > ir->rlist);
- } 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"
- "If you want optimal energy conservation or exact integration use %s",
- eel_names[ir->coulombtype],eel_names[eelPMESWITCH]);
- } else {
- sprintf(err_buf,
- "With coulombtype = %s, rcoulomb must be equal to rlist",
- eel_names[ir->coulombtype]);
+ if(ir->coulombtype==eelSWITCH || ir->coulombtype==eelSHIFT ||
+ ir->vdwtype==evdwSWITCH || ir->vdwtype==evdwSHIFT)
+ {
+ sprintf(warn_buf,
+ "The switch/shift interaction settings are just for compatibility; you will get better"
+ "performance from applying potential modifiers to your interactions!\n");
+ warning_note(wi,warn_buf);
+ }
+
+ if (EEL_FULL(ir->coulombtype))
+ {
+ if (ir->coulombtype==eelPMESWITCH || ir->coulombtype==eelPMEUSER ||
+ ir->coulombtype==eelPMEUSERSWITCH)
+ {
+ sprintf(err_buf,"With coulombtype = %s, rcoulomb must be <= rlist",
+ eel_names[ir->coulombtype]);
+ CHECK(ir->rcoulomb > ir->rlist);
+ }
+ else if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
+ {
+ if (ir->coulombtype == eelPME || ir->coulombtype == eelP3M_AD)
+ {
+ sprintf(err_buf,
+ "With coulombtype = %s (without modifier), rcoulomb must be equal to rlist,\n"
+ "or rlistlong if nstcalclr=1. For optimal energy conservation,consider using\n"
+ "a potential modifier.",eel_names[ir->coulombtype]);
+ if(ir->nstcalclr==1)
+ {
+ CHECK(ir->rcoulomb != ir->rlist && ir->rcoulomb != ir->rlistlong);
+ }
+ else
+ {
+ CHECK(ir->rcoulomb != ir->rlist);
+ }
+ }
}
- CHECK(ir->rcoulomb != ir->rlist);
- }
}
if (EEL_PME(ir->coulombtype)) {
}
if (EVDW_SWITCHED(ir->vdwtype)) {
- sprintf(err_buf,"With vdwtype = %s rvdw-switch must be < rvdw",
+ sprintf(err_buf,"With vdwtype = %s rvdw-switch must be < rvdw. Or, better - use a potential modifier.",
evdw_names[ir->vdwtype]);
CHECK(ir->rvdw_switch >= ir->rvdw);
} else if (ir->vdwtype == evdwCUT) {
- if (ir->cutoff_scheme == ecutsGROUP) {
- sprintf(err_buf,"With vdwtype = %s, rvdw must be >= rlist",evdw_names[ir->vdwtype]);
+ if (ir->cutoff_scheme == ecutsGROUP && ir->vdw_modifier == eintmodNONE) {
+ sprintf(err_buf,"With vdwtype = %s, rvdw must be >= rlist unless you use a potential modifier",evdw_names[ir->vdwtype]);
CHECK(ir->rlist > ir->rvdw);
}
}
}
if (ir->nstlist == -1) {
- sprintf(err_buf,
- "nstlist=-1 only works with switched or shifted potentials,\n"
- "suggestion: use vdw-type=%s and coulomb-type=%s",
- evdw_names[evdwSHIFT],eel_names[eelPMESWITCH]);
- CHECK(!(EEL_MIGHT_BE_ZERO_AT_CUTOFF(ir->coulombtype) &&
- EVDW_MIGHT_BE_ZERO_AT_CUTOFF(ir->vdwtype)));
-
sprintf(err_buf,"With nstlist=-1 rvdw and rcoulomb should be smaller than rlist to account for diffusion and possibly charge-group radii");
CHECK(ir->rvdw >= ir->rlist || ir->rcoulomb >= ir->rlist);
}
/* ENERGY CONSERVATION */
if (ir_NVE(ir) && ir->cutoff_scheme == ecutsGROUP)
{
- if (!EVDW_MIGHT_BE_ZERO_AT_CUTOFF(ir->vdwtype) && ir->rvdw > 0)
+ if (!EVDW_MIGHT_BE_ZERO_AT_CUTOFF(ir->vdwtype) && ir->rvdw > 0 && ir->vdw_modifier == eintmodNONE)
{
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)
+ if (!EEL_MIGHT_BE_ZERO_AT_CUTOFF(ir->coulombtype) && ir->rcoulomb > 0 && ir->coulomb_modifier == eintmodNONE)
{
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]);
if (ir->bAdress)
{
+ warning_error(wi,"AdResS is currently disabled\n");
if (ir->cutoff_scheme != ecutsGROUP)
{
warning_error(wi,"AdresS simulation supports only cutoff-scheme=group");
/* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
}
if ((expand->nstexpanded < 0) && ir->bSimTemp) {
- expand->nstexpanded = ir->nstlist;
- /* if you don't specify nstexpanded when doing expanded ensemble simulated tempering, it is set to nstlist*/
+ expand->nstexpanded = 2*(int)(ir->opts.tau_t[0]/ir->delta_t);
+ /* if you don't specify nstexpanded when doing expanded ensemble simulated tempering, it is set to
+ 2*tau_t just to be careful so it's not to frequent */
}
}
RTYPE ("rlist", ir->rlist, -1);
CTYPE ("long-range cut-off for switched potentials");
RTYPE ("rlistlong", ir->rlistlong, -1);
+ ITYPE ("nstcalclr", ir->nstcalclr, -1);
/* Electrostatics */
CCTYPE ("OPTIONS FOR ELECTROSTATICS AND VDW");
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.");
+ warning_note(wi,"tau-t = -1 is the 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)
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff