t_mdatoms *init_mdatoms(FILE *fp, gmx_mtop_t *mtop, gmx_bool bFreeEnergy)
{
int mb, a, g, nmol;
double tmA, tmB;
t_atom *atom;
t_mdatoms *md;
gmx_mtop_atomloop_all_t aloop;
t_ilist *ilist;
snew(md, 1);
md->nenergrp = mtop->groups.grps[egcENER].nr;
md->bVCMgrps = FALSE;
tmA = 0.0;
tmB = 0.0;
aloop = gmx_mtop_atomloop_all_init(mtop);
while (gmx_mtop_atomloop_all_next(aloop, &a, &atom))
{
if (ggrpnr(&mtop->groups, egcVCM, a) > 0)
{
md->bVCMgrps = TRUE;
}
if (bFreeEnergy && PERTURBED(*atom))
{
md->nPerturbed++;
if (atom->mB != atom->m)
{
md->nMassPerturbed++;
}
if (atom->qB != atom->q)
{
md->nChargePerturbed++;
}
if (atom->typeB != atom->type)
{
md->nTypePerturbed++;
}
}
tmA += atom->m;
tmB += atom->mB;
}
md->tmassA = tmA;
md->tmassB = tmB;
if (bFreeEnergy && fp)
{
fprintf(fp,
"There are %d atoms and %d charges for free energy perturbation\n",
md->nPerturbed, md->nChargePerturbed);
}
md->bOrires = gmx_mtop_ftype_count(mtop, F_ORIRES);
return md;
}
void print_atoms(FILE *out, gpp_atomtype_t atype, t_atoms *at, int *cgnr,
gmx_bool bRTPresname)
{
int i, ri;
int tpA, tpB;
const char *as;
char *tpnmA, *tpnmB;
double qres, qtot;
as = dir2str(d_atoms);
fprintf(out, "[ %s ]\n", as);
fprintf(out, "; %4s %10s %6s %7s%6s %6s %10s %10s %6s %10s %10s\n",
"nr", "type", "resnr", "residue", "atom", "cgnr", "charge", "mass", "typeB", "chargeB", "massB");
qtot = 0;
if (debug)
{
fprintf(debug, "This molecule has %d atoms and %d residues\n",
at->nr, at->nres);
}
if (at->nres)
{
/* if the information is present... */
for (i = 0; (i < at->nr); i++)
{
ri = at->atom[i].resind;
if ((i == 0 || ri != at->atom[i-1].resind) &&
at->resinfo[ri].rtp != NULL)
{
qres = get_residue_charge(at, i);
fprintf(out, "; residue %3d %-3s rtp %-4s q ",
at->resinfo[ri].nr,
*at->resinfo[ri].name,
*at->resinfo[ri].rtp);
if (fabs(qres) < 0.001)
{
fprintf(out, " %s", "0.0");
}
else
{
fprintf(out, "%+3.1f", qres);
}
fprintf(out, "\n");
}
tpA = at->atom[i].type;
if ((tpnmA = get_atomtype_name(tpA, atype)) == NULL)
{
gmx_fatal(FARGS, "tpA = %d, i= %d in print_atoms", tpA, i);
}
fprintf(out, "%6d %10s %6d%c %5s %6s %6d %10g %10g",
i+1, tpnmA,
at->resinfo[ri].nr,
at->resinfo[ri].ic,
bRTPresname ?
*(at->resinfo[at->atom[i].resind].rtp) :
*(at->resinfo[at->atom[i].resind].name),
*(at->atomname[i]), cgnr[i],
at->atom[i].q, at->atom[i].m);
if (PERTURBED(at->atom[i]))
{
tpB = at->atom[i].typeB;
if ((tpnmB = get_atomtype_name(tpB, atype)) == NULL)
{
gmx_fatal(FARGS, "tpB = %d, i= %d in print_atoms", tpB, i);
}
fprintf(out, " %6s %10g %10g",
tpnmB, at->atom[i].qB, at->atom[i].mB);
}
qtot += (double)at->atom[i].q;
if (fabs(qtot) < 4*GMX_REAL_EPS)
{
qtot = 0;
}
fprintf(out, " ; qtot %.4g\n", qtot);
}
}
fprintf(out, "\n");
fflush(out);
}
void atoms2md(const gmx_mtop_t *mtop, const t_inputrec *ir,
int nindex, const int *index,
int homenr,
t_mdatoms *md)
{
gmx_bool bLJPME;
gmx_mtop_atomlookup_t alook;
int i;
const t_grpopts *opts;
const gmx_groups_t *groups;
int nthreads gmx_unused;
const real oneOverSix = 1.0 / 6.0;
bLJPME = EVDW_PME(ir->vdwtype);
opts = &ir->opts;
groups = &mtop->groups;
/* Index==NULL indicates no DD (unless we have a DD node with no
* atoms), so also check for homenr. This should be
* signaled properly with an extra parameter or nindex==-1.
*/
if (index == NULL && (homenr > 0))
{
md->nr = mtop->natoms;
}
else
{
md->nr = nindex;
}
if (md->nr > md->nalloc)
{
md->nalloc = over_alloc_dd(md->nr);
if (md->nMassPerturbed)
{
srenew(md->massA, md->nalloc);
srenew(md->massB, md->nalloc);
}
srenew(md->massT, md->nalloc);
srenew(md->invmass, md->nalloc);
srenew(md->chargeA, md->nalloc);
srenew(md->typeA, md->nalloc);
if (md->nPerturbed)
{
srenew(md->chargeB, md->nalloc);
srenew(md->typeB, md->nalloc);
}
if (bLJPME)
{
srenew(md->sqrt_c6A, md->nalloc);
srenew(md->sigmaA, md->nalloc);
srenew(md->sigma3A, md->nalloc);
if (md->nPerturbed)
{
srenew(md->sqrt_c6B, md->nalloc);
srenew(md->sigmaB, md->nalloc);
srenew(md->sigma3B, md->nalloc);
}
}
srenew(md->ptype, md->nalloc);
if (opts->ngtc > 1)
{
srenew(md->cTC, md->nalloc);
/* We always copy cTC with domain decomposition */
}
srenew(md->cENER, md->nalloc);
if (opts->ngacc > 1)
{
srenew(md->cACC, md->nalloc);
}
if (opts->nFreeze &&
(opts->ngfrz > 1 ||
opts->nFreeze[0][XX] || opts->nFreeze[0][YY] || opts->nFreeze[0][ZZ]))
{
srenew(md->cFREEZE, md->nalloc);
}
if (md->bVCMgrps)
{
srenew(md->cVCM, md->nalloc);
}
if (md->bOrires)
{
srenew(md->cORF, md->nalloc);
}
if (md->nPerturbed)
{
srenew(md->bPerturbed, md->nalloc);
}
/* Note that these user t_mdatoms array pointers are NULL
* when there is only one group present.
* Therefore, when adding code, the user should use something like:
* gprnrU1 = (md->cU1==NULL ? 0 : md->cU1[localatindex])
*/
if (mtop->groups.grpnr[egcUser1] != NULL)
{
srenew(md->cU1, md->nalloc);
}
if (mtop->groups.grpnr[egcUser2] != NULL)
{
srenew(md->cU2, md->nalloc);
}
if (ir->bQMMM)
{
srenew(md->bQM, md->nalloc);
}
if (ir->bAdress)
{
srenew(md->wf, md->nalloc);
srenew(md->tf_table_index, md->nalloc);
}
}
alook = gmx_mtop_atomlookup_init(mtop);
// cppcheck-suppress unreadVariable
nthreads = gmx_omp_nthreads_get(emntDefault);
#pragma omp parallel for num_threads(nthreads) schedule(static)
for (i = 0; i < md->nr; i++)
{
try
{
int g, ag;
real mA, mB, fac;
real c6, c12;
t_atom *atom;
if (index == NULL)
{
ag = i;
}
else
{
ag = index[i];
}
gmx_mtop_atomnr_to_atom(alook, ag, &atom);
if (md->cFREEZE)
{
md->cFREEZE[i] = ggrpnr(groups, egcFREEZE, ag);
}
if (EI_ENERGY_MINIMIZATION(ir->eI))
{
/* Displacement is proportional to F, masses used for constraints */
mA = 1.0;
mB = 1.0;
}
else if (ir->eI == eiBD)
{
/* With BD the physical masses are irrelevant.
* To keep the code simple we use most of the normal MD code path
* for BD. Thus for constraining the masses should be proportional
* to the friction coefficient. We set the absolute value such that
* m/2<(dx/dt)^2> = m/2*2kT/fric*dt = kT/2 => m=fric*dt/2
* Then if we set the (meaningless) velocity to v=dx/dt, we get the
* correct kinetic energy and temperature using the usual code path.
* Thus with BD v*dt will give the displacement and the reported
* temperature can signal bad integration (too large time step).
*/
if (ir->bd_fric > 0)
{
mA = 0.5*ir->bd_fric*ir->delta_t;
mB = 0.5*ir->bd_fric*ir->delta_t;
}
else
{
/* The friction coefficient is mass/tau_t */
fac = ir->delta_t/opts->tau_t[md->cTC ? groups->grpnr[egcTC][ag] : 0];
mA = 0.5*atom->m*fac;
mB = 0.5*atom->mB*fac;
}
}
else
{
mA = atom->m;
mB = atom->mB;
}
if (md->nMassPerturbed)
{
md->massA[i] = mA;
md->massB[i] = mB;
}
md->massT[i] = mA;
if (mA == 0.0)
{
md->invmass[i] = 0;
}
else if (md->cFREEZE)
{
g = md->cFREEZE[i];
if (opts->nFreeze[g][XX] && opts->nFreeze[g][YY] && opts->nFreeze[g][ZZ])
{
/* Set the mass of completely frozen particles to ALMOST_ZERO iso 0
* to avoid div by zero in lincs or shake.
* Note that constraints can still move a partially frozen particle.
*/
md->invmass[i] = ALMOST_ZERO;
}
else
{
md->invmass[i] = 1.0/mA;
}
}
else
{
md->invmass[i] = 1.0/mA;
}
md->chargeA[i] = atom->q;
md->typeA[i] = atom->type;
if (bLJPME)
{
c6 = mtop->ffparams.iparams[atom->type*(mtop->ffparams.atnr+1)].lj.c6;
c12 = mtop->ffparams.iparams[atom->type*(mtop->ffparams.atnr+1)].lj.c12;
md->sqrt_c6A[i] = sqrt(c6);
if (c6 == 0.0 || c12 == 0)
{
md->sigmaA[i] = 1.0;
}
else
{
md->sigmaA[i] = pow(c12/c6, oneOverSix);
}
md->sigma3A[i] = 1/(md->sigmaA[i]*md->sigmaA[i]*md->sigmaA[i]);
}
if (md->nPerturbed)
{
md->bPerturbed[i] = PERTURBED(*atom);
md->chargeB[i] = atom->qB;
md->typeB[i] = atom->typeB;
if (bLJPME)
{
c6 = mtop->ffparams.iparams[atom->typeB*(mtop->ffparams.atnr+1)].lj.c6;
c12 = mtop->ffparams.iparams[atom->typeB*(mtop->ffparams.atnr+1)].lj.c12;
md->sqrt_c6B[i] = sqrt(c6);
if (c6 == 0.0 || c12 == 0)
{
md->sigmaB[i] = 1.0;
}
else
{
md->sigmaB[i] = pow(c12/c6, oneOverSix);
}
md->sigma3B[i] = 1/(md->sigmaB[i]*md->sigmaB[i]*md->sigmaB[i]);
}
}
md->ptype[i] = atom->ptype;
if (md->cTC)
{
md->cTC[i] = groups->grpnr[egcTC][ag];
}
md->cENER[i] =
(groups->grpnr[egcENER] ? groups->grpnr[egcENER][ag] : 0);
if (md->cACC)
{
md->cACC[i] = groups->grpnr[egcACC][ag];
}
if (md->cVCM)
{
md->cVCM[i] = groups->grpnr[egcVCM][ag];
}
if (md->cORF)
{
md->cORF[i] = groups->grpnr[egcORFIT][ag];
}
if (md->cU1)
{
md->cU1[i] = groups->grpnr[egcUser1][ag];
}
if (md->cU2)
{
md->cU2[i] = groups->grpnr[egcUser2][ag];
}
if (ir->bQMMM)
{
if (groups->grpnr[egcQMMM] == 0 ||
groups->grpnr[egcQMMM][ag] < groups->grps[egcQMMM].nr-1)
{
md->bQM[i] = TRUE;
}
else
{
md->bQM[i] = FALSE;
}
}
/* Initialize AdResS weighting functions to adressw */
if (ir->bAdress)
{
md->wf[i] = 1.0;
/* if no tf table groups specified, use default table */
md->tf_table_index[i] = DEFAULT_TF_TABLE;
if (ir->adress->n_tf_grps > 0)
{
/* if tf table groups specified, tf is only applied to thoose energy groups*/
md->tf_table_index[i] = NO_TF_TABLE;
/* check wether atom is in one of the relevant energy groups and assign a table index */
for (g = 0; g < ir->adress->n_tf_grps; g++)
{
if (md->cENER[i] == ir->adress->tf_table_index[g])
{
md->tf_table_index[i] = g;
}
}
}
}
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}
gmx_mtop_atomlookup_destroy(alook);
md->homenr = homenr;
md->lambda = 0;
}
void atoms2md(gmx_mtop_t *mtop,t_inputrec *ir,
int nindex,int *index,
int start,int homenr,
t_mdatoms *md)
{
t_atoms *atoms_mol;
int i,g,ag,as,ae,molb;
real mA,mB,fac;
t_atom *atom;
t_grpopts *opts;
gmx_groups_t *groups;
gmx_molblock_t *molblock;
opts = &ir->opts;
groups = &mtop->groups;
molblock = mtop->molblock;
if (index == NULL) {
md->nr = mtop->natoms;
} else {
md->nr = nindex;
}
if (md->nr > md->nalloc) {
md->nalloc = over_alloc_dd(md->nr);
if (md->nMassPerturbed) {
srenew(md->massA,md->nalloc);
srenew(md->massB,md->nalloc);
}
srenew(md->massT,md->nalloc);
srenew(md->invmass,md->nalloc);
srenew(md->chargeA,md->nalloc);
if (md->nPerturbed) {
srenew(md->chargeB,md->nalloc);
}
srenew(md->typeA,md->nalloc);
if (md->nPerturbed) {
srenew(md->typeB,md->nalloc);
}
srenew(md->ptype,md->nalloc);
if (opts->ngtc > 1) {
srenew(md->cTC,md->nalloc);
/* We always copy cTC with domain decomposition */
}
srenew(md->cENER,md->nalloc);
if (opts->ngacc > 1)
srenew(md->cACC,md->nalloc);
if (opts->nFreeze &&
(opts->ngfrz > 1 ||
opts->nFreeze[0][XX] || opts->nFreeze[0][YY] || opts->nFreeze[0][ZZ]))
srenew(md->cFREEZE,md->nalloc);
if (md->bVCMgrps)
srenew(md->cVCM,md->nalloc);
if (md->bOrires)
srenew(md->cORF,md->nalloc);
if (md->nPerturbed)
srenew(md->bPerturbed,md->nalloc);
/* Note that these user t_mdatoms array pointers are NULL
* when there is only one group present.
* Therefore, when adding code, the user should use something like:
* gprnrU1 = (md->cU1==NULL ? 0 : md->cU1[localatindex])
*/
if (mtop->groups.grpnr[egcUser1] != NULL)
srenew(md->cU1,md->nalloc);
if (mtop->groups.grpnr[egcUser2] != NULL)
srenew(md->cU2,md->nalloc);
if (ir->bQMMM)
srenew(md->bQM,md->nalloc);
}
for(i=0; (i<md->nr); i++) {
if (index == NULL) {
ag = i;
gmx_mtop_atomnr_to_atom(mtop,ag,&atom);
} else {
ag = index[i];
molb = -1;
ae = 0;
do {
molb++;
as = ae;
ae = as + molblock[molb].nmol*molblock[molb].natoms_mol;
} while (ag >= ae);
atoms_mol = &mtop->moltype[molblock[molb].type].atoms;
atom = &atoms_mol->atom[(ag - as) % atoms_mol->nr];
}
if (md->cFREEZE) {
md->cFREEZE[i] = ggrpnr(groups,egcFREEZE,ag);
}
if (EI_ENERGY_MINIMIZATION(ir->eI)) {
mA = 1.0;
mB = 1.0;
} else if (ir->eI == eiBD) {
/* Make the mass proportional to the friction coefficient for BD.
* This is necessary for the constraint algorithms.
*/
if (ir->bd_fric) {
mA = ir->bd_fric*ir->delta_t;
mB = ir->bd_fric*ir->delta_t;
} else {
fac = ir->delta_t/opts->tau_t[md->cTC ? groups->grpnr[egcTC][ag] : 0];
mA = atom->m*fac;
mB = atom->mB*fac;
}
} else {
mA = atom->m;
mB = atom->mB;
}
if (md->nMassPerturbed) {
md->massA[i] = mA;
md->massB[i] = mB;
}
md->massT[i] = mA;
if (mA == 0.0) {
md->invmass[i] = 0;
} else if (md->cFREEZE) {
g = md->cFREEZE[i];
if (opts->nFreeze[g][XX] && opts->nFreeze[g][YY] && opts->nFreeze[g][ZZ])
/* Set the mass of completely frozen particles to ALMOST_ZERO iso 0
* to avoid div by zero in lincs or shake.
* Note that constraints can still move a partially frozen particle.
*/
md->invmass[i] = ALMOST_ZERO;
else
md->invmass[i] = 1.0/mA;
} else {
md->invmass[i] = 1.0/mA;
}
md->chargeA[i] = atom->q;
md->typeA[i] = atom->type;
if (md->nPerturbed) {
md->chargeB[i] = atom->qB;
md->typeB[i] = atom->typeB;
md->bPerturbed[i] = PERTURBED(*atom);
}
md->ptype[i] = atom->ptype;
if (md->cTC)
md->cTC[i] = groups->grpnr[egcTC][ag];
md->cENER[i] =
(groups->grpnr[egcENER] ? groups->grpnr[egcENER][ag] : 0);
if (md->cACC)
md->cACC[i] = groups->grpnr[egcACC][ag];
if (md->cVCM)
md->cVCM[i] = groups->grpnr[egcVCM][ag];
if (md->cORF)
md->cORF[i] = groups->grpnr[egcORFIT][ag];
if (md->cU1)
md->cU1[i] = groups->grpnr[egcUser1][ag];
if (md->cU2)
md->cU2[i] = groups->grpnr[egcUser2][ag];
if (ir->bQMMM) {
if (groups->grpnr[egcQMMM] == 0 ||
groups->grpnr[egcQMMM][ag] < groups->grps[egcQMMM].nr-1) {
md->bQM[i] = TRUE;
} else {
md->bQM[i] = FALSE;
}
}
}
md->start = start;
md->homenr = homenr;
md->lambda = 0;
}
