void init_orires(FILE *fplog,const gmx_mtop_t *mtop,
rvec xref[],
const t_inputrec *ir,
const gmx_multisim_t *ms,t_oriresdata *od,
t_state *state)
{
int i,j,d,ex,nmol,nr,*nr_ex;
double mtot;
rvec com;
gmx_mtop_ilistloop_t iloop;
t_ilist *il;
gmx_mtop_atomloop_all_t aloop;
t_atom *atom;
od->fc = ir->orires_fc;
od->nex = 0;
od->S = NULL;
od->nr = gmx_mtop_ftype_count(mtop,F_ORIRES);
if (od->nr == 0)
{
return;
}
nr_ex = NULL;
iloop = gmx_mtop_ilistloop_init(mtop);
while (gmx_mtop_ilistloop_next(iloop,&il,&nmol))
{
for(i=0; i<il[F_ORIRES].nr; i+=3)
{
ex = mtop->ffparams.iparams[il[F_ORIRES].iatoms[i]].orires.ex;
if (ex >= od->nex)
{
srenew(nr_ex,ex+1);
for(j=od->nex; j<ex+1; j++)
{
nr_ex[j] = 0;
}
od->nex = ex+1;
}
nr_ex[ex]++;
}
}
snew(od->S,od->nex);
/* When not doing time averaging, the instaneous and time averaged data
* are indentical and the pointers can point to the same memory.
*/
snew(od->Dinsl,od->nr);
if (ms)
{
snew(od->Dins,od->nr);
}
else
{
od->Dins = od->Dinsl;
}
if (ir->orires_tau == 0)
{
od->Dtav = od->Dins;
od->edt = 0.0;
od->edt1 = 1.0;
}
else
{
snew(od->Dtav,od->nr);
od->edt = exp(-ir->delta_t/ir->orires_tau);
od->edt1 = 1.0 - od->edt;
/* Extend the state with the orires history */
state->flags |= (1<<estORIRE_INITF);
state->hist.orire_initf = 1;
state->flags |= (1<<estORIRE_DTAV);
state->hist.norire_Dtav = od->nr*5;
snew(state->hist.orire_Dtav,state->hist.norire_Dtav);
}
snew(od->oinsl,od->nr);
if (ms)
{
snew(od->oins,od->nr);
}
else
{
od->oins = od->oinsl;
}
if (ir->orires_tau == 0) {
od->otav = od->oins;
}
else
{
snew(od->otav,od->nr);
}
snew(od->tmp,od->nex);
snew(od->TMP,od->nex);
for(ex=0; ex<od->nex; ex++)
{
snew(od->TMP[ex],5);
for(i=0; i<5; i++)
{
snew(od->TMP[ex][i],5);
}
}
od->nref = 0;
for(i=0; i<mtop->natoms; i++)
{
if (ggrpnr(&mtop->groups,egcORFIT,i) == 0)
{
od->nref++;
}
}
snew(od->mref,od->nref);
snew(od->xref,od->nref);
snew(od->xtmp,od->nref);
snew(od->eig,od->nex*12);
/* Determine the reference structure on the master node.
* Copy it to the other nodes after checking multi compatibility,
* so we are sure the subsystems match before copying.
*/
clear_rvec(com);
mtot = 0.0;
j = 0;
aloop = gmx_mtop_atomloop_all_init(mtop);
while(gmx_mtop_atomloop_all_next(aloop,&i,&atom))
{
if (mtop->groups.grpnr[egcORFIT] == NULL ||
mtop->groups.grpnr[egcORFIT][i] == 0)
{
/* Not correct for free-energy with changing masses */
od->mref[j] = atom->m;
if (ms==NULL || MASTERSIM(ms))
{
copy_rvec(xref[i],od->xref[j]);
for(d=0; d<DIM; d++)
{
com[d] += od->mref[j]*xref[i][d];
}
}
mtot += od->mref[j];
j++;
}
}
svmul(1.0/mtot,com,com);
if (ms==NULL || MASTERSIM(ms))
{
for(j=0; j<od->nref; j++)
{
rvec_dec(od->xref[j],com);
}
}
fprintf(fplog,"Found %d orientation experiments\n",od->nex);
for(i=0; i<od->nex; i++)
{
fprintf(fplog," experiment %d has %d restraints\n",i+1,nr_ex[i]);
}
sfree(nr_ex);
fprintf(fplog," the fit group consists of %d atoms and has total mass %g\n",
od->nref,mtot);
if (ms)
{
fprintf(fplog," the orientation restraints are ensemble averaged over %d systems\n",ms->nsim);
check_multi_int(fplog,ms,od->nr,
"the number of orientation restraints");
check_multi_int(fplog,ms,od->nref,
"the number of fit atoms for orientation restraining");
check_multi_int(fplog,ms,ir->nsteps,"nsteps");
/* Copy the reference coordinates from the master to the other nodes */
gmx_sum_sim(DIM*od->nref,od->xref[0],ms);
}
please_cite(fplog,"Hess2003");
}
gmx_repl_ex_t init_replica_exchange(FILE *fplog,
const gmx_multisim_t *ms,
const t_state *state,
const t_inputrec *ir,
int nst, int nex, int init_seed)
{
real temp, pres;
int i, j, k;
struct gmx_repl_ex *re;
gmx_bool bTemp;
gmx_bool bLambda = FALSE;
fprintf(fplog, "\nInitializing Replica Exchange\n");
if (ms == NULL || ms->nsim == 1)
{
gmx_fatal(FARGS, "Nothing to exchange with only one replica, maybe you forgot to set the -multi option of mdrun?");
}
if (!EI_DYNAMICS(ir->eI))
{
gmx_fatal(FARGS, "Replica exchange is only supported by dynamical simulations");
/* Note that PAR(cr) is defined by cr->nnodes > 1, which is
* distinct from MULTISIM(cr). A multi-simulation only runs
* with real MPI parallelism, but this does not imply PAR(cr)
* is true!
*
* Since we are using a dynamical integrator, the only
* decomposition is DD, so PAR(cr) and DOMAINDECOMP(cr) are
* synonymous. The only way for cr->nnodes > 1 to be true is
* if we are using DD. */
}
snew(re, 1);
re->repl = ms->sim;
re->nrepl = ms->nsim;
snew(re->q, ereENDSINGLE);
fprintf(fplog, "Repl There are %d replicas:\n", re->nrepl);
check_multi_int(fplog, ms, state->natoms, "the number of atoms", FALSE);
check_multi_int(fplog, ms, ir->eI, "the integrator", FALSE);
check_multi_int64(fplog, ms, ir->init_step+ir->nsteps, "init_step+nsteps", FALSE);
check_multi_int64(fplog, ms, (ir->init_step+nst-1)/nst,
"first exchange step: init_step/-replex", FALSE);
check_multi_int(fplog, ms, ir->etc, "the temperature coupling", FALSE);
check_multi_int(fplog, ms, ir->opts.ngtc,
"the number of temperature coupling groups", FALSE);
check_multi_int(fplog, ms, ir->epc, "the pressure coupling", FALSE);
check_multi_int(fplog, ms, ir->efep, "free energy", FALSE);
check_multi_int(fplog, ms, ir->fepvals->n_lambda, "number of lambda states", FALSE);
re->temp = ir->opts.ref_t[0];
for (i = 1; (i < ir->opts.ngtc); i++)
{
if (ir->opts.ref_t[i] != re->temp)
{
fprintf(fplog, "\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
fprintf(stderr, "\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
}
}
re->type = -1;
bTemp = repl_quantity(ms, re, ereTEMP, re->temp);
if (ir->efep != efepNO)
{
bLambda = repl_quantity(ms, re, ereLAMBDA, (real)ir->fepvals->init_fep_state);
}
if (re->type == -1) /* nothing was assigned */
{
gmx_fatal(FARGS, "The properties of the %d systems are all the same, there is nothing to exchange", re->nrepl);
}
if (bLambda && bTemp)
{
re->type = ereTL;
}
if (bTemp)
{
please_cite(fplog, "Sugita1999a");
if (ir->epc != epcNO)
{
re->bNPT = TRUE;
fprintf(fplog, "Repl Using Constant Pressure REMD.\n");
please_cite(fplog, "Okabe2001a");
}
if (ir->etc == etcBERENDSEN)
{
gmx_fatal(FARGS, "REMD with the %s thermostat does not produce correct potential energy distributions, consider using the %s thermostat instead",
ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
}
}
if (bLambda)
{
if (ir->fepvals->delta_lambda != 0) /* check this? */
{
gmx_fatal(FARGS, "delta_lambda is not zero");
}
}
if (re->bNPT)
{
snew(re->pres, re->nrepl);
if (ir->epct == epctSURFACETENSION)
{
pres = ir->ref_p[ZZ][ZZ];
}
else
{
pres = 0;
j = 0;
for (i = 0; i < DIM; i++)
{
if (ir->compress[i][i] != 0)
{
pres += ir->ref_p[i][i];
j++;
}
}
pres /= j;
}
re->pres[re->repl] = pres;
gmx_sum_sim(re->nrepl, re->pres, ms);
}
/* Make an index for increasing replica order */
/* only makes sense if one or the other is varying, not both!
if both are varying, we trust the order the person gave. */
snew(re->ind, re->nrepl);
for (i = 0; i < re->nrepl; i++)
{
re->ind[i] = i;
}
if (re->type < ereENDSINGLE)
{
for (i = 0; i < re->nrepl; i++)
{
for (j = i+1; j < re->nrepl; j++)
{
if (re->q[re->type][re->ind[j]] < re->q[re->type][re->ind[i]])
{
k = re->ind[i];
re->ind[i] = re->ind[j];
re->ind[j] = k;
}
else if (re->q[re->type][re->ind[j]] == re->q[re->type][re->ind[i]])
{
gmx_fatal(FARGS, "Two replicas have identical %ss", erename[re->type]);
}
}
}
}
/* keep track of all the swaps, starting with the initial placement. */
snew(re->allswaps, re->nrepl);
for (i = 0; i < re->nrepl; i++)
{
re->allswaps[i] = re->ind[i];
}
switch (re->type)
{
case ereTEMP:
fprintf(fplog, "\nReplica exchange in temperature\n");
for (i = 0; i < re->nrepl; i++)
{
fprintf(fplog, " %5.1f", re->q[re->type][re->ind[i]]);
}
fprintf(fplog, "\n");
break;
case ereLAMBDA:
fprintf(fplog, "\nReplica exchange in lambda\n");
for (i = 0; i < re->nrepl; i++)
{
fprintf(fplog, " %3d", (int)re->q[re->type][re->ind[i]]);
}
fprintf(fplog, "\n");
break;
case ereTL:
fprintf(fplog, "\nReplica exchange in temperature and lambda state\n");
for (i = 0; i < re->nrepl; i++)
{
fprintf(fplog, " %5.1f", re->q[ereTEMP][re->ind[i]]);
}
fprintf(fplog, "\n");
for (i = 0; i < re->nrepl; i++)
{
fprintf(fplog, " %5d", (int)re->q[ereLAMBDA][re->ind[i]]);
}
fprintf(fplog, "\n");
break;
default:
gmx_incons("Unknown replica exchange quantity");
}
if (re->bNPT)
{
fprintf(fplog, "\nRepl p");
for (i = 0; i < re->nrepl; i++)
{
fprintf(fplog, " %5.2f", re->pres[re->ind[i]]);
}
for (i = 0; i < re->nrepl; i++)
{
if ((i > 0) && (re->pres[re->ind[i]] < re->pres[re->ind[i-1]]))
{
fprintf(fplog, "\nWARNING: The reference pressures decrease with increasing temperatures\n\n");
fprintf(stderr, "\nWARNING: The reference pressures decrease with increasing temperatures\n\n");
}
}
}
re->nst = nst;
if (init_seed == -1)
{
if (MASTERSIM(ms))
{
re->seed = (int)gmx_rng_make_seed();
}
else
{
re->seed = 0;
}
gmx_sumi_sim(1, &(re->seed), ms);
}
else
{
re->seed = init_seed;
}
fprintf(fplog, "\nReplica exchange interval: %d\n", re->nst);
fprintf(fplog, "\nReplica random seed: %d\n", re->seed);
re->rng = gmx_rng_init(re->seed);
re->nattempt[0] = 0;
re->nattempt[1] = 0;
snew(re->prob_sum, re->nrepl);
snew(re->nexchange, re->nrepl);
snew(re->nmoves, re->nrepl);
for (i = 0; i < re->nrepl; i++)
{
snew(re->nmoves[i], re->nrepl);
}
fprintf(fplog, "Replica exchange information below: x=exchange, pr=probability\n");
/* generate space for the helper functions so we don't have to snew each time */
snew(re->destinations, re->nrepl);
snew(re->incycle, re->nrepl);
snew(re->tmpswap, re->nrepl);
snew(re->cyclic, re->nrepl);
snew(re->order, re->nrepl);
for (i = 0; i < re->nrepl; i++)
{
snew(re->cyclic[i], re->nrepl);
snew(re->order[i], re->nrepl);
}
/* allocate space for the functions storing the data for the replicas */
/* not all of these arrays needed in all cases, but they don't take
up much space, since the max size is nrepl**2 */
snew(re->prob, re->nrepl);
snew(re->bEx, re->nrepl);
snew(re->beta, re->nrepl);
snew(re->Vol, re->nrepl);
snew(re->Epot, re->nrepl);
snew(re->de, re->nrepl);
for (i = 0; i < re->nrepl; i++)
{
snew(re->de[i], re->nrepl);
}
re->nex = nex;
return re;
}
gmx_repl_ex_t init_replica_exchange(FILE *fplog,
const gmx_multisim_t *ms,
const t_state *state,
const t_inputrec *ir,
int nst,int init_seed)
{
real temp,pres;
int i,j,k;
struct gmx_repl_ex *re;
fprintf(fplog,"\nInitializing Replica Exchange\n");
if (ms == NULL || ms->nsim == 1)
{
gmx_fatal(FARGS,"Nothing to exchange with only one replica, maybe you forgot to set the -multi option of mdrun?");
}
snew(re,1);
re->repl = ms->sim;
re->nrepl = ms->nsim;
fprintf(fplog,"Repl There are %d replicas:\n",re->nrepl);
check_multi_int(fplog,ms,state->natoms,"the number of atoms");
check_multi_int(fplog,ms,ir->eI,"the integrator");
check_multi_large_int(fplog,ms,ir->init_step+ir->nsteps,"init_step+nsteps");
check_multi_large_int(fplog,ms,(ir->init_step+nst-1)/nst,
"first exchange step: init_step/-replex");
check_multi_int(fplog,ms,ir->etc,"the temperature coupling");
check_multi_int(fplog,ms,ir->opts.ngtc,
"the number of temperature coupling groups");
check_multi_int(fplog,ms,ir->epc,"the pressure coupling");
check_multi_int(fplog,ms,ir->efep,"free energy");
re->temp = ir->opts.ref_t[0];
for(i=1; (i<ir->opts.ngtc); i++)
{
if (ir->opts.ref_t[i] != re->temp)
{
fprintf(fplog,"\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
fprintf(stderr,"\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
}
}
re->type = -1;
for(i=0; i<ereNR; i++)
{
switch (i)
{
case ereTEMP:
repl_quantity(fplog,ms,re,i,re->temp);
break;
case ereLAMBDA:
if (ir->efep != efepNO)
{
repl_quantity(fplog,ms,re,i,ir->init_lambda);
}
break;
default:
gmx_incons("Unknown replica exchange quantity");
}
}
if (re->type == -1)
{
gmx_fatal(FARGS,"The properties of the %d systems are all the same, there is nothing to exchange",re->nrepl);
}
switch (re->type)
{
case ereTEMP:
please_cite(fplog,"Hukushima96a");
if (ir->epc != epcNO)
{
re->bNPT = TRUE;
fprintf(fplog,"Repl Using Constant Pressure REMD.\n");
please_cite(fplog,"Okabe2001a");
}
if (ir->etc == etcBERENDSEN)
{
gmx_fatal(FARGS,"REMD with the %s thermostat does not produce correct potential energy distributions, consider using the %s thermostat instead",
ETCOUPLTYPE(ir->etc),ETCOUPLTYPE(etcVRESCALE));
}
break;
case ereLAMBDA:
if (ir->delta_lambda != 0)
{
gmx_fatal(FARGS,"delta_lambda is not zero");
}
break;
}
if (re->bNPT)
{
snew(re->pres,re->nrepl);
if (ir->epct == epctSURFACETENSION)
{
pres = ir->ref_p[ZZ][ZZ];
}
else
{
pres = 0;
j = 0;
for(i=0; i<DIM; i++)
{
if (ir->compress[i][i] != 0)
{
pres += ir->ref_p[i][i];
j++;
}
}
pres /= j;
}
re->pres[re->repl] = pres;
gmx_sum_sim(re->nrepl,re->pres,ms);
}
snew(re->ind,re->nrepl);
/* Make an index for increasing temperature order */
for(i=0; i<re->nrepl; i++)
{
re->ind[i] = i;
}
for(i=0; i<re->nrepl; i++)
{
for(j=i+1; j<re->nrepl; j++)
{
if (re->q[re->ind[j]] < re->q[re->ind[i]])
{
k = re->ind[i];
re->ind[i] = re->ind[j];
re->ind[j] = k;
}
else if (re->q[re->ind[j]] == re->q[re->ind[i]])
{
gmx_fatal(FARGS,"Two replicas have identical %ss",erename[re->type]);
}
}
}
fprintf(fplog,"Repl ");
for(i=0; i<re->nrepl; i++)
{
fprintf(fplog," %3d ",re->ind[i]);
}
switch (re->type)
{
case ereTEMP:
fprintf(fplog,"\nRepl T");
for(i=0; i<re->nrepl; i++)
{
fprintf(fplog," %5.1f",re->q[re->ind[i]]);
}
break;
case ereLAMBDA:
fprintf(fplog,"\nRepl l");
for(i=0; i<re->nrepl; i++)
{
fprintf(fplog," %5.3f",re->q[re->ind[i]]);
}
break;
default:
gmx_incons("Unknown replica exchange quantity");
}
if (re->bNPT)
{
fprintf(fplog,"\nRepl p");
for(i=0; i<re->nrepl; i++)
{
fprintf(fplog," %5.2f",re->pres[re->ind[i]]);
}
for(i=0; i<re->nrepl; i++)
{
if ((i > 0) && (re->pres[re->ind[i]] < re->pres[re->ind[i-1]]))
{
gmx_fatal(FARGS,"The reference pressure decreases with increasing temperature");
}
}
}
fprintf(fplog,"\nRepl ");
re->nst = nst;
if (init_seed == -1)
{
if (MASTERSIM(ms))
{
re->seed = make_seed();
}
else
{
re->seed = 0;
}
gmx_sumi_sim(1,&(re->seed),ms);
}
else
{
re->seed = init_seed;
}
fprintf(fplog,"\nRepl exchange interval: %d\n",re->nst);
fprintf(fplog,"\nRepl random seed: %d\n",re->seed);
re->nattempt[0] = 0;
re->nattempt[1] = 0;
snew(re->prob_sum,re->nrepl);
snew(re->nexchange,re->nrepl);
fprintf(fplog,"Repl below: x=exchange, pr=probability\n");
return re;
}