void writeSystemInformation(TextWriter *writer, const gmx_mtop_t &top, bool writeFormattedText)
{
int nmol, nvsite = 0;
gmx_mtop_atomloop_block_t aloop;
const t_atom *atom;
writeHeader(writer, "Simulation system", "subsection", writeFormattedText);
aloop = gmx_mtop_atomloop_block_init(&top);
while (gmx_mtop_atomloop_block_next(aloop, &atom, &nmol))
{
if (atom->ptype == eptVSite)
{
nvsite += nmol;
}
}
{
writer->writeLine(formatString("A system of %d molecules (%d atoms) was simulated.",
gmx_mtop_num_molecules(top), top.natoms-nvsite));
}
if (nvsite)
{
writer->writeLine(formatString("Virtual sites were used in some of the molecules."));
}
writer->ensureEmptyLine();
}
/*! \brief Count the different particle types in a system
*
* Routine prints a warning to stderr in case an unknown particle type
* is encountered.
* \param[in] fplog Print what we have found if not NULL
* \param[in] mtop Molecular topology.
* \returns Array holding the number of particles of a type
*/
static std::array<int, eptNR> countPtypes(FILE *fplog,
gmx_mtop_t *mtop)
{
std::array<int, eptNR> nptype = { { 0 } };
/* Count number of shells, and find their indices */
for (int i = 0; (i < eptNR); i++)
{
nptype[i] = 0;
}
gmx_mtop_atomloop_block_t aloopb = gmx_mtop_atomloop_block_init(mtop);
int nmol;
t_atom *atom;
while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
{
switch (atom->ptype)
{
case eptAtom:
case eptVSite:
case eptShell:
nptype[atom->ptype] += nmol;
break;
default:
fprintf(stderr, "Warning unsupported particle type %d in countPtypes",
static_cast<int>(atom->ptype));
}
}
if (fplog)
{
/* Print the number of each particle type */
int n = 0;
for (const auto &i : nptype)
{
if (i != 0)
{
fprintf(fplog, "There are: %d %ss\n", i, ptype_str[n]);
}
n++;
}
}
return nptype;
}
static void tpx2system(FILE *fp, gmx_mtop_t *mtop)
{
int i, nmol, nvsite = 0;
gmx_mtop_atomloop_block_t aloop;
t_atom *atom;
fprintf(fp, "\\subsection{Simulation system}\n");
aloop = gmx_mtop_atomloop_block_init(mtop);
while (gmx_mtop_atomloop_block_next(aloop, &atom, &nmol))
{
if (atom->ptype == eptVSite)
{
nvsite += nmol;
}
}
fprintf(fp, "A system of %d molecules (%d atoms) was simulated.\n",
mtop->mols.nr, mtop->natoms-nvsite);
if (nvsite)
{
fprintf(fp, "Virtual sites were used in some of the molecules.\n");
}
fprintf(fp, "\n\n");
}
gmx_shellfc_t init_shell_flexcon(FILE *fplog,
gmx_bool bCutoffSchemeIsVerlet,
gmx_mtop_t *mtop, int nflexcon,
rvec *x)
{
struct gmx_shellfc *shfc;
t_shell *shell;
int *shell_index = NULL, *at2cg;
t_atom *atom;
int n[eptNR], ns, nshell, nsi;
int i, j, nmol, type, mb, mt, a_offset, cg, mol, ftype, nra;
real qS, alpha;
int aS, aN = 0; /* Shell and nucleus */
int bondtypes[] = { F_BONDS, F_HARMONIC, F_CUBICBONDS, F_POLARIZATION, F_ANHARM_POL, F_WATER_POL };
#define NBT asize(bondtypes)
t_iatom *ia;
gmx_mtop_atomloop_block_t aloopb;
gmx_mtop_atomloop_all_t aloop;
gmx_ffparams_t *ffparams;
gmx_molblock_t *molb;
gmx_moltype_t *molt;
t_block *cgs;
/* Count number of shells, and find their indices */
for (i = 0; (i < eptNR); i++)
{
n[i] = 0;
}
aloopb = gmx_mtop_atomloop_block_init(mtop);
while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
{
n[atom->ptype] += nmol;
}
if (fplog)
{
/* Print the number of each particle type */
for (i = 0; (i < eptNR); i++)
{
if (n[i] != 0)
{
fprintf(fplog, "There are: %d %ss\n", n[i], ptype_str[i]);
}
}
}
nshell = n[eptShell];
if (nshell == 0 && nflexcon == 0)
{
/* We're not doing shells or flexible constraints */
return NULL;
}
if (bCutoffSchemeIsVerlet)
{
gmx_fatal(FARGS, "The shell code does not work with the Verlet cut-off scheme.\n");
}
snew(shfc, 1);
shfc->nflexcon = nflexcon;
if (nshell == 0)
{
return shfc;
}
/* We have shells: fill the shell data structure */
/* Global system sized array, this should be avoided */
snew(shell_index, mtop->natoms);
aloop = gmx_mtop_atomloop_all_init(mtop);
nshell = 0;
while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
{
if (atom->ptype == eptShell)
{
shell_index[i] = nshell++;
}
}
snew(shell, nshell);
/* Initiate the shell structures */
for (i = 0; (i < nshell); i++)
{
shell[i].shell = NO_ATID;
shell[i].nnucl = 0;
shell[i].nucl1 = NO_ATID;
shell[i].nucl2 = NO_ATID;
shell[i].nucl3 = NO_ATID;
/* shell[i].bInterCG=FALSE; */
shell[i].k_1 = 0;
shell[i].k = 0;
}
ffparams = &mtop->ffparams;
/* Now fill the structures */
shfc->bInterCG = FALSE;
ns = 0;
a_offset = 0;
for (mb = 0; mb < mtop->nmolblock; mb++)
{
molb = &mtop->molblock[mb];
molt = &mtop->moltype[molb->type];
cgs = &molt->cgs;
snew(at2cg, molt->atoms.nr);
for (cg = 0; cg < cgs->nr; cg++)
{
for (i = cgs->index[cg]; i < cgs->index[cg+1]; i++)
{
at2cg[i] = cg;
}
}
atom = molt->atoms.atom;
for (mol = 0; mol < molb->nmol; mol++)
{
for (j = 0; (j < NBT); j++)
{
ia = molt->ilist[bondtypes[j]].iatoms;
for (i = 0; (i < molt->ilist[bondtypes[j]].nr); )
{
type = ia[0];
ftype = ffparams->functype[type];
nra = interaction_function[ftype].nratoms;
/* Check whether we have a bond with a shell */
aS = NO_ATID;
switch (bondtypes[j])
{
case F_BONDS:
case F_HARMONIC:
case F_CUBICBONDS:
case F_POLARIZATION:
case F_ANHARM_POL:
if (atom[ia[1]].ptype == eptShell)
{
aS = ia[1];
aN = ia[2];
}
else if (atom[ia[2]].ptype == eptShell)
{
aS = ia[2];
aN = ia[1];
}
break;
case F_WATER_POL:
aN = ia[4]; /* Dummy */
aS = ia[5]; /* Shell */
break;
default:
gmx_fatal(FARGS, "Death Horror: %s, %d", __FILE__, __LINE__);
}
if (aS != NO_ATID)
{
qS = atom[aS].q;
/* Check whether one of the particles is a shell... */
nsi = shell_index[a_offset+aS];
if ((nsi < 0) || (nsi >= nshell))
{
gmx_fatal(FARGS, "nsi is %d should be within 0 - %d. aS = %d",
nsi, nshell, aS);
}
if (shell[nsi].shell == NO_ATID)
{
shell[nsi].shell = a_offset + aS;
ns++;
}
else if (shell[nsi].shell != a_offset+aS)
{
gmx_fatal(FARGS, "Weird stuff in %s, %d", __FILE__, __LINE__);
}
if (shell[nsi].nucl1 == NO_ATID)
{
shell[nsi].nucl1 = a_offset + aN;
}
else if (shell[nsi].nucl2 == NO_ATID)
{
shell[nsi].nucl2 = a_offset + aN;
}
else if (shell[nsi].nucl3 == NO_ATID)
{
shell[nsi].nucl3 = a_offset + aN;
}
else
{
if (fplog)
{
pr_shell(fplog, ns, shell);
}
gmx_fatal(FARGS, "Can not handle more than three bonds per shell\n");
}
if (at2cg[aS] != at2cg[aN])
{
/* shell[nsi].bInterCG = TRUE; */
shfc->bInterCG = TRUE;
}
switch (bondtypes[j])
{
case F_BONDS:
case F_HARMONIC:
shell[nsi].k += ffparams->iparams[type].harmonic.krA;
break;
case F_CUBICBONDS:
shell[nsi].k += ffparams->iparams[type].cubic.kb;
break;
case F_POLARIZATION:
case F_ANHARM_POL:
if (!gmx_within_tol(qS, atom[aS].qB, GMX_REAL_EPS*10))
{
gmx_fatal(FARGS, "polarize can not be used with qA(%e) != qB(%e) for atom %d of molecule block %d", qS, atom[aS].qB, aS+1, mb+1);
}
shell[nsi].k += sqr(qS)*ONE_4PI_EPS0/
ffparams->iparams[type].polarize.alpha;
break;
case F_WATER_POL:
if (!gmx_within_tol(qS, atom[aS].qB, GMX_REAL_EPS*10))
{
gmx_fatal(FARGS, "water_pol can not be used with qA(%e) != qB(%e) for atom %d of molecule block %d", qS, atom[aS].qB, aS+1, mb+1);
}
alpha = (ffparams->iparams[type].wpol.al_x+
ffparams->iparams[type].wpol.al_y+
ffparams->iparams[type].wpol.al_z)/3.0;
shell[nsi].k += sqr(qS)*ONE_4PI_EPS0/alpha;
break;
default:
gmx_fatal(FARGS, "Death Horror: %s, %d", __FILE__, __LINE__);
}
shell[nsi].nnucl++;
}
ia += nra+1;
i += nra+1;
}
}
a_offset += molt->atoms.nr;
}
/* Done with this molecule type */
sfree(at2cg);
}
/* Verify whether it's all correct */
if (ns != nshell)
{
gmx_fatal(FARGS, "Something weird with shells. They may not be bonded to something");
}
for (i = 0; (i < ns); i++)
{
shell[i].k_1 = 1.0/shell[i].k;
}
if (debug)
{
pr_shell(debug, ns, shell);
}
shfc->nshell_gl = ns;
shfc->shell_gl = shell;
shfc->shell_index_gl = shell_index;
shfc->bPredict = (getenv("GMX_NOPREDICT") == NULL);
shfc->bRequireInit = FALSE;
if (!shfc->bPredict)
{
if (fplog)
{
fprintf(fplog, "\nWill never predict shell positions\n");
}
}
else
{
shfc->bRequireInit = (getenv("GMX_REQUIRE_SHELL_INIT") != NULL);
if (shfc->bRequireInit && fplog)
{
fprintf(fplog, "\nWill always initiate shell positions\n");
}
}
if (shfc->bPredict)
{
if (x)
{
predict_shells(fplog, x, NULL, 0, shfc->nshell_gl, shfc->shell_gl,
NULL, mtop, TRUE);
}
if (shfc->bInterCG)
{
if (fplog)
{
fprintf(fplog, "\nNOTE: there all shells that are connected to particles outside thier own charge group, will not predict shells positions during the run\n\n");
}
shfc->bPredict = FALSE;
}
}
return shfc;
}
