#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
-typedef struct {
- int nnucl;
- int shell; /* The shell id */
- int nucl1, nucl2, nucl3; /* The nuclei connected to the shell */
- /* gmx_bool bInterCG; */ /* Coupled to nuclei outside cg? */
- real k; /* force constant */
- real k_1; /* 1 over force constant */
- rvec xold;
- rvec fold;
- rvec step;
+typedef struct
+{
+ int nnucl;
+ int shell; /* The shell id */
+ int nucl1, nucl2, nucl3; /* The nuclei connected to the shell */
+ /* gmx_bool bInterCG; */ /* Coupled to nuclei outside cg? */
+ real k; /* force constant */
+ real k_1; /* 1 over force constant */
+ rvec xold;
+ rvec fold;
+ rvec step;
} t_shell;
-struct gmx_shellfc_t {
+struct gmx_shellfc_t
+{
/* Shell counts, indices, parameters and working data */
- int nshell_gl; /* The number of shells in the system */
- t_shell *shell_gl; /* All the shells (for DD only) */
- int *shell_index_gl; /* Global shell index (for DD only) */
- gmx_bool bInterCG; /* Are there inter charge-group shells? */
- int nshell; /* The number of local shells */
- t_shell *shell; /* The local shells */
- int shell_nalloc; /* The allocation size of shell */
- gmx_bool bPredict; /* Predict shell positions */
- gmx_bool bRequireInit; /* Require initialization of shell positions */
- int nflexcon; /* The number of flexible constraints */
+ int nshell_gl; /* The number of shells in the system */
+ t_shell* shell_gl; /* All the shells (for DD only) */
+ int* shell_index_gl; /* Global shell index (for DD only) */
+ gmx_bool bInterCG; /* Are there inter charge-group shells? */
+ int nshell; /* The number of local shells */
+ t_shell* shell; /* The local shells */
+ int shell_nalloc; /* The allocation size of shell */
+ gmx_bool bPredict; /* Predict shell positions */
+ gmx_bool bRequireInit; /* Require initialization of shell positions */
+ int nflexcon; /* The number of flexible constraints */
/* Temporary arrays, should be fixed size 2 when fully converted to C++ */
- PaddedHostVector<gmx::RVec> *x; /* Array for iterative minimization */
- PaddedHostVector<gmx::RVec> *f; /* Array for iterative minimization */
+ PaddedHostVector<gmx::RVec>* x; /* Array for iterative minimization */
+ PaddedHostVector<gmx::RVec>* f; /* Array for iterative minimization */
/* Flexible constraint working data */
- rvec *acc_dir; /* Acceleration direction for flexcon */
- rvec *x_old; /* Old coordinates for flexcon */
+ rvec* acc_dir; /* Acceleration direction for flexcon */
+ rvec* x_old; /* Old coordinates for flexcon */
int flex_nalloc; /* The allocation size of acc_dir and x_old */
- rvec *adir_xnold; /* Work space for init_adir */
- rvec *adir_xnew; /* Work space for init_adir */
+ rvec* adir_xnold; /* Work space for init_adir */
+ rvec* adir_xnew; /* Work space for init_adir */
int adir_nalloc; /* Work space for init_adir */
std::int64_t numForceEvaluations; /* Total number of force evaluations */
int numConvergedIterations; /* Total number of iterations that converged */
};
-static void pr_shell(FILE *fplog, int ns, t_shell s[])
+static void pr_shell(FILE* fplog, int ns, t_shell s[])
{
int i;
fprintf(fplog, "SHELL DATA\n");
- fprintf(fplog, "%5s %8s %5s %5s %5s\n",
- "Shell", "Force k", "Nucl1", "Nucl2", "Nucl3");
+ fprintf(fplog, "%5s %8s %5s %5s %5s\n", "Shell", "Force k", "Nucl1", "Nucl2", "Nucl3");
for (i = 0; (i < ns); i++)
{
- fprintf(fplog, "%5d %8.3f %5d", s[i].shell, 1.0/s[i].k_1, s[i].nucl1);
+ fprintf(fplog, "%5d %8.3f %5d", s[i].shell, 1.0 / s[i].k_1, s[i].nucl1);
if (s[i].nnucl == 2)
{
fprintf(fplog, " %5d\n", s[i].nucl2);
* started, but even when called, the prediction was always
* over-written by a subsequent call in the MD loop, so has been
* removed. */
-static void predict_shells(FILE *fplog, rvec x[], rvec v[], real dt,
- int ns, t_shell s[],
- const real mass[], gmx_mtop_t *mtop, gmx_bool bInit)
+static void predict_shells(FILE* fplog,
+ rvec x[],
+ rvec v[],
+ real dt,
+ int ns,
+ t_shell s[],
+ const real mass[],
+ gmx_mtop_t* mtop,
+ gmx_bool bInit)
{
- int i, m, s1, n1, n2, n3;
- real dt_1, fudge, tm, m1, m2, m3;
- rvec *ptr;
+ int i, m, s1, n1, n2, n3;
+ real dt_1, fudge, tm, m1, m2, m3;
+ rvec* ptr;
GMX_RELEASE_ASSERT(mass || mtop, "Must have masses or a way to look them up");
else
{
ptr = v;
- dt_1 = fudge*dt;
+ dt_1 = fudge * dt;
}
int molb = 0;
n1 = s[i].nucl1;
for (m = 0; (m < DIM); m++)
{
- x[s1][m] += ptr[n1][m]*dt_1;
+ x[s1][m] += ptr[n1][m] * dt_1;
}
break;
case 2:
m1 = mtopGetAtomMass(mtop, n1, &molb);
m2 = mtopGetAtomMass(mtop, n2, &molb);
}
- tm = dt_1/(m1+m2);
+ tm = dt_1 / (m1 + m2);
for (m = 0; (m < DIM); m++)
{
- x[s1][m] += (m1*ptr[n1][m]+m2*ptr[n2][m])*tm;
+ x[s1][m] += (m1 * ptr[n1][m] + m2 * ptr[n2][m]) * tm;
}
break;
case 3:
m2 = mtopGetAtomMass(mtop, n2, &molb);
m3 = mtopGetAtomMass(mtop, n3, &molb);
}
- tm = dt_1/(m1+m2+m3);
+ tm = dt_1 / (m1 + m2 + m3);
for (m = 0; (m < DIM); m++)
{
- x[s1][m] += (m1*ptr[n1][m]+m2*ptr[n2][m]+m3*ptr[n3][m])*tm;
+ x[s1][m] += (m1 * ptr[n1][m] + m2 * ptr[n2][m] + m3 * ptr[n3][m]) * tm;
}
break;
- default:
- gmx_fatal(FARGS, "Shell %d has %d nuclei!", i, s[i].nnucl);
+ default: gmx_fatal(FARGS, "Shell %d has %d nuclei!", i, s[i].nnucl);
}
}
}
* \param[in] mtop Molecular topology.
* \returns Array holding the number of particles of a type
*/
-std::array<int, eptNR> countPtypes(FILE *fplog,
- const gmx_mtop_t *mtop)
+std::array<int, eptNR> countPtypes(FILE* fplog, const gmx_mtop_t* mtop)
{
std::array<int, eptNR> nptype = { { 0 } };
/* Count number of shells, and find their indices */
nptype[i] = 0;
}
- gmx_mtop_atomloop_block_t aloopb = gmx_mtop_atomloop_block_init(mtop);
- int nmol;
- const t_atom *atom;
+ gmx_mtop_atomloop_block_t aloopb = gmx_mtop_atomloop_block_init(mtop);
+ int nmol;
+ const 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;
+ case eptShell: nptype[atom->ptype] += nmol; break;
default:
fprintf(stderr, "Warning unsupported particle type %d in countPtypes",
static_cast<int>(atom->ptype));
{
/* Print the number of each particle type */
int n = 0;
- for (const auto &i : nptype)
+ for (const auto& i : nptype)
{
if (i != 0)
{
return nptype;
}
-gmx_shellfc_t *init_shell_flexcon(FILE *fplog,
- const gmx_mtop_t *mtop, int nflexcon,
- int nstcalcenergy,
- bool usingDomainDecomposition)
+gmx_shellfc_t* init_shell_flexcon(FILE* fplog, const gmx_mtop_t* mtop, int nflexcon, int nstcalcenergy, bool usingDomainDecomposition)
{
- gmx_shellfc_t *shfc;
- t_shell *shell;
- int *shell_index = nullptr;
-
- int ns, nshell, nsi;
- int i, j, type, a_offset, 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 };
+ gmx_shellfc_t* shfc;
+ t_shell* shell;
+ int* shell_index = nullptr;
+
+ int ns, nshell, nsi;
+ int i, j, type, a_offset, 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)
- const gmx_ffparams_t *ffparams;
+ const gmx_ffparams_t* ffparams;
- std::array<int, eptNR> n = countPtypes(fplog, mtop);
- nshell = n[eptShell];
+ std::array<int, eptNR> n = countPtypes(fplog, mtop);
+ nshell = n[eptShell];
if (nshell == 0 && nflexcon == 0)
{
if (nstcalcenergy != 1)
{
- gmx_fatal(FARGS, "You have nstcalcenergy set to a value (%d) that is different from 1.\nThis is not supported in combination with shell particles.\nPlease make a new tpr file.", nstcalcenergy);
+ gmx_fatal(FARGS,
+ "You have nstcalcenergy set to a value (%d) that is different from 1.\nThis is "
+ "not supported in combination with shell particles.\nPlease make a new tpr file.",
+ nstcalcenergy);
}
if (usingDomainDecomposition)
{
- gmx_fatal(FARGS, "Shell particles are not implemented with domain decomposition, use a single rank");
+ gmx_fatal(
+ FARGS,
+ "Shell particles are not implemented with domain decomposition, use a single rank");
}
/* We have shells: fill the shell data structure */
nshell = 0;
for (const AtomProxy atomP : AtomRange(*mtop))
{
- const t_atom &local = atomP.atom();
+ const t_atom& local = atomP.atom();
int i = atomP.globalAtomNumber();
if (local.ptype == eptShell)
{
shell[i].nucl2 = -1;
shell[i].nucl3 = -1;
/* shell[i].bInterCG=FALSE; */
- shell[i].k_1 = 0;
- shell[i].k = 0;
+ shell[i].k_1 = 0;
+ shell[i].k = 0;
}
ffparams = &mtop->ffparams;
a_offset = 0;
for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
{
- const gmx_molblock_t *molb = &mtop->molblock[mb];
- const gmx_moltype_t *molt = &mtop->moltype[molb->type];
+ const gmx_molblock_t* molb = &mtop->molblock[mb];
+ const gmx_moltype_t* molt = &mtop->moltype[molb->type];
- const t_atom *atom = molt->atoms.atom;
+ const t_atom* atom = molt->atoms.atom;
for (mol = 0; mol < molb->nmol; mol++)
{
for (j = 0; (j < NBT); j++)
{
- const int *ia = molt->ilist[bondtypes[j]].iatoms.data();
- for (i = 0; (i < molt->ilist[bondtypes[j]].size()); )
+ const int* ia = molt->ilist[bondtypes[j]].iatoms.data();
+ for (i = 0; (i < molt->ilist[bondtypes[j]].size());)
{
type = ia[0];
ftype = ffparams->functype[type];
}
break;
case F_WATER_POL:
- aN = ia[4]; /* Dummy */
- aS = ia[5]; /* Shell */
+ aN = ia[4]; /* Dummy */
+ aS = ia[5]; /* Shell */
break;
- default:
- gmx_fatal(FARGS, "Death Horror: %s, %d", __FILE__, __LINE__);
+ default: gmx_fatal(FARGS, "Death Horror: %s, %d", __FILE__, __LINE__);
}
if (aS != -1)
qS = atom[aS].q;
/* Check whether one of the particles is a shell... */
- nsi = shell_index[a_offset+aS];
+ 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);
+ gmx_fatal(FARGS, "nsi is %d should be within 0 - %d. aS = %d", nsi, nshell, aS);
}
if (shell[nsi].shell == -1)
{
shell[nsi].shell = a_offset + aS;
ns++;
}
- else if (shell[nsi].shell != a_offset+aS)
+ else if (shell[nsi].shell != a_offset + aS)
{
gmx_fatal(FARGS, "Weird stuff in %s, %d", __FILE__, __LINE__);
}
- if (shell[nsi].nucl1 == -1)
+ if (shell[nsi].nucl1 == -1)
{
shell[nsi].nucl1 = a_offset + aN;
}
{
case F_BONDS:
case F_HARMONIC:
- shell[nsi].k += ffparams->iparams[type].harmonic.krA;
+ shell[nsi].k += ffparams->iparams[type].harmonic.krA;
break;
case F_CUBICBONDS:
- shell[nsi].k += ffparams->iparams[type].cubic.kb;
+ 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))
+ 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 %zu", qS, atom[aS].qB, aS+1, mb+1);
+ gmx_fatal(FARGS,
+ "polarize can not be used with qA(%e) != qB(%e) for "
+ "atom %d of molecule block %zu",
+ qS, atom[aS].qB, aS + 1, mb + 1);
}
- shell[nsi].k += gmx::square(qS)*ONE_4PI_EPS0/
- ffparams->iparams[type].polarize.alpha;
+ shell[nsi].k += gmx::square(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))
+ 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 %zu", qS, atom[aS].qB, aS+1, mb+1);
+ gmx_fatal(FARGS,
+ "water_pol can not be used with qA(%e) != qB(%e) for "
+ "atom %d of molecule block %zu",
+ 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 += gmx::square(qS)*ONE_4PI_EPS0/alpha;
+ alpha = (ffparams->iparams[type].wpol.al_x
+ + ffparams->iparams[type].wpol.al_y
+ + ffparams->iparams[type].wpol.al_z)
+ / 3.0;
+ shell[nsi].k += gmx::square(qS) * ONE_4PI_EPS0 / alpha;
break;
- default:
- gmx_fatal(FARGS, "Death Horror: %s, %d", __FILE__, __LINE__);
+ default: gmx_fatal(FARGS, "Death Horror: %s, %d", __FILE__, __LINE__);
}
shell[nsi].nnucl++;
}
- ia += nra+1;
- i += nra+1;
+ ia += nra + 1;
+ i += nra + 1;
}
}
a_offset += molt->atoms.nr;
for (i = 0; (i < ns); i++)
{
- shell[i].k_1 = 1.0/shell[i].k;
+ shell[i].k_1 = 1.0 / shell[i].k;
}
if (debug)
{
if (fplog)
{
- fprintf(fplog, "\nNOTE: in the current version shell prediction during the crun is disabled\n\n");
+ fprintf(fplog,
+ "\nNOTE: in the current version shell prediction during the crun is "
+ "disabled\n\n");
}
/* Prediction improves performance, so we should implement either:
* 1. communication for the atoms needed for prediction
return shfc;
}
-void make_local_shells(const t_commrec *cr,
- const t_mdatoms *md,
- gmx_shellfc_t *shfc)
+void make_local_shells(const t_commrec* cr, const t_mdatoms* md, gmx_shellfc_t* shfc)
{
- t_shell *shell;
+ t_shell* shell;
int a0, a1, *ind, nshell, i;
- gmx_domdec_t *dd = nullptr;
+ gmx_domdec_t* dd = nullptr;
if (DOMAINDECOMP(cr))
{
{
if (md->ptype[i] == eptShell)
{
- if (nshell+1 > shfc->shell_nalloc)
+ if (nshell + 1 > shfc->shell_nalloc)
{
- shfc->shell_nalloc = over_alloc_dd(nshell+1);
+ shfc->shell_nalloc = over_alloc_dd(nshell + 1);
srenew(shell, shfc->shell_nalloc);
}
if (dd)
*/
if (!shfc->bInterCG)
{
- shell[nshell].nucl1 = i + shell[nshell].nucl1 - shell[nshell].shell;
+ shell[nshell].nucl1 = i + shell[nshell].nucl1 - shell[nshell].shell;
if (shell[nshell].nnucl > 1)
{
shell[nshell].nucl2 = i + shell[nshell].nucl2 - shell[nshell].shell;
yo = xold[YY];
zo = xold[ZZ];
- dx = f[XX]*step;
- dy = f[YY]*step;
- dz = f[ZZ]*step;
+ dx = f[XX] * step;
+ dy = f[YY] * step;
+ dz = f[ZZ] * step;
- xnew[XX] = xo+dx;
- xnew[YY] = yo+dy;
- xnew[ZZ] = zo+dz;
+ xnew[XX] = xo + dx;
+ xnew[YY] = yo + dy;
+ xnew[ZZ] = zo + dz;
}
static void do_1pos3(rvec xnew, const rvec xold, const rvec f, const rvec step)
yo = xold[YY];
zo = xold[ZZ];
- dx = f[XX]*step[XX];
- dy = f[YY]*step[YY];
- dz = f[ZZ]*step[ZZ];
+ dx = f[XX] * step[XX];
+ dy = f[YY] * step[YY];
+ dz = f[ZZ] * step[ZZ];
- xnew[XX] = xo+dx;
- xnew[YY] = yo+dy;
- xnew[ZZ] = zo+dz;
+ xnew[XX] = xo + dx;
+ xnew[YY] = yo + dy;
+ xnew[ZZ] = zo + dz;
}
static void directional_sd(gmx::ArrayRef<const gmx::RVec> xold,
- gmx::ArrayRef<gmx::RVec> xnew,
- const rvec acc_dir[], int homenr, real step)
+ gmx::ArrayRef<gmx::RVec> xnew,
+ const rvec acc_dir[],
+ int homenr,
+ real step)
{
- const rvec *xo = as_rvec_array(xold.data());
- rvec *xn = as_rvec_array(xnew.data());
+ const rvec* xo = as_rvec_array(xold.data());
+ rvec* xn = as_rvec_array(xnew.data());
for (int i = 0; i < homenr; i++)
{
}
static void shell_pos_sd(gmx::ArrayRef<const gmx::RVec> xcur,
- gmx::ArrayRef<gmx::RVec> xnew,
+ gmx::ArrayRef<gmx::RVec> xnew,
gmx::ArrayRef<const gmx::RVec> f,
- int ns, t_shell s[], int count)
+ int ns,
+ t_shell s[],
+ int count)
{
- const real step_scale_min = 0.8,
- step_scale_increment = 0.2,
- step_scale_max = 1.2,
- step_scale_multiple = (step_scale_max - step_scale_min) / step_scale_increment;
+ const real step_scale_min = 0.8, step_scale_increment = 0.2, step_scale_max = 1.2,
+ step_scale_multiple = (step_scale_max - step_scale_min) / step_scale_increment;
int i, shell, d;
real dx, df, k_est;
const real zero = 0;
#ifdef PRINT_STEP
- real step_min, step_max;
+ real step_min, step_max;
step_min = 1e30;
step_max = 0;
for (d = 0; d < DIM; d++)
{
dx = xcur[shell][d] - s[i].xold[d];
- df = f[shell][d] - s[i].fold[d];
+ df = f[shell][d] - s[i].fold[d];
/* -dx/df gets used to generate an interpolated value, but would
* cause a NaN if df were binary-equal to zero. Values close to
* zero won't cause problems (because of the min() and max()), so
* just testing for binary inequality is OK. */
if (zero != df)
{
- k_est = -dx/df;
+ k_est = -dx / df;
/* Scale the step size by a factor interpolated from
* step_scale_min to step_scale_max, as k_est goes from 0 to
* step_scale_multiple * s[i].step[d] */
- s[i].step[d] =
- step_scale_min * s[i].step[d] +
- step_scale_increment * std::min(step_scale_multiple * s[i].step[d], std::max(k_est, zero));
+ s[i].step[d] = step_scale_min * s[i].step[d]
+ + step_scale_increment
+ * std::min(step_scale_multiple * s[i].step[d],
+ std::max(k_est, zero));
}
else
{
#endif
}
}
- copy_rvec(xcur [shell], s[i].xold);
- copy_rvec(f[shell], s[i].fold);
+ copy_rvec(xcur[shell], s[i].xold);
+ copy_rvec(f[shell], s[i].fold);
do_1pos3(xnew[shell], xcur[shell], f[shell], s[i].step);
}
}
-static void print_epot(FILE *fp, int64_t mdstep, int count, real epot, real df,
- int ndir, real sf_dir)
+static void print_epot(FILE* fp, int64_t mdstep, int count, real epot, real df, int ndir, real sf_dir)
{
char buf[22];
- fprintf(fp, "MDStep=%5s/%2d EPot: %12.8e, rmsF: %6.2e",
- gmx_step_str(mdstep, buf), count, epot, df);
+ fprintf(fp, "MDStep=%5s/%2d EPot: %12.8e, rmsF: %6.2e", gmx_step_str(mdstep, buf), count, epot, df);
if (ndir)
{
- fprintf(fp, ", dir. rmsF: %6.2e\n", std::sqrt(sf_dir/ndir));
+ fprintf(fp, ", dir. rmsF: %6.2e\n", std::sqrt(sf_dir / ndir));
}
else
{
}
-static real rms_force(const t_commrec *cr, gmx::ArrayRef<const gmx::RVec> force, int ns, t_shell s[],
- int ndir, real *sf_dir, real *Epot)
+static real rms_force(const t_commrec* cr,
+ gmx::ArrayRef<const gmx::RVec> force,
+ int ns,
+ t_shell s[],
+ int ndir,
+ real* sf_dir,
+ real* Epot)
{
double buf[4];
- const rvec *f = as_rvec_array(force.data());
+ const rvec* f = as_rvec_array(force.data());
buf[0] = *sf_dir;
for (int i = 0; i < ns; i++)
{
- int shell = s[i].shell;
- buf[0] += norm2(f[shell]);
+ int shell = s[i].shell;
+ buf[0] += norm2(f[shell]);
}
int ntot = ns;
}
ntot += ndir;
- return (ntot ? std::sqrt(buf[0]/ntot) : 0);
+ return (ntot ? std::sqrt(buf[0] / ntot) : 0);
}
-static void dump_shells(FILE *fp, gmx::ArrayRef<gmx::RVec> f, real ftol, int ns, t_shell s[])
+static void dump_shells(FILE* fp, gmx::ArrayRef<gmx::RVec> f, real ftol, int ns, t_shell s[])
{
int i, shell;
real ft2, ff2;
ff2 = iprod(f[shell], f[shell]);
if (ff2 > ft2)
{
- fprintf(fp, "SHELL %5d, force %10.5f %10.5f %10.5f, |f| %10.5f\n",
- shell, f[shell][XX], f[shell][YY], f[shell][ZZ], std::sqrt(ff2));
+ fprintf(fp, "SHELL %5d, force %10.5f %10.5f %10.5f, |f| %10.5f\n", shell,
+ f[shell][XX], f[shell][YY], f[shell][ZZ], std::sqrt(ff2));
}
}
}
-static void init_adir(gmx_shellfc_t *shfc,
- gmx::Constraints *constr,
- const t_inputrec *ir,
- const t_commrec *cr,
+static void init_adir(gmx_shellfc_t* shfc,
+ gmx::Constraints* constr,
+ const t_inputrec* ir,
+ const t_commrec* cr,
int dd_ac1,
int64_t step,
- const t_mdatoms *md,
+ const t_mdatoms* md,
int end,
- rvec *x_old,
- rvec *x_init,
- rvec *x,
- rvec *f,
- rvec *acc_dir,
+ rvec* x_old,
+ rvec* x_init,
+ rvec* x,
+ rvec* f,
+ rvec* acc_dir,
const matrix box,
gmx::ArrayRef<const real> lambda,
- real *dvdlambda)
+ real* dvdlambda)
{
- rvec *xnold, *xnew;
+ rvec * xnold, *xnew;
double dt, w_dt;
int n, d;
- unsigned short *ptype;
+ unsigned short* ptype;
if (DOMAINDECOMP(cr))
{
/* Does NOT work with freeze or acceleration groups (yet) */
for (n = 0; n < end; n++)
{
- w_dt = md->invmass[n]*dt;
+ w_dt = md->invmass[n] * dt;
for (d = 0; d < DIM; d++)
{
if ((ptype[n] != eptVSite) && (ptype[n] != eptShell))
{
xnold[n][d] = x[n][d] - (x_init[n][d] - x_old[n][d]);
- xnew[n][d] = 2*x[n][d] - x_old[n][d] + f[n][d]*w_dt*dt;
+ xnew[n][d] = 2 * x[n][d] - x_old[n][d] + f[n][d] * w_dt * dt;
}
else
{
}
}
}
- constr->apply(FALSE, FALSE, step, 0, 1.0,
- x, xnold, nullptr, box,
- lambda[efptBONDED], &(dvdlambda[efptBONDED]),
- nullptr, nullptr, gmx::ConstraintVariable::Positions);
- constr->apply(FALSE, FALSE, step, 0, 1.0,
- x, xnew, nullptr, box,
- lambda[efptBONDED], &(dvdlambda[efptBONDED]),
- nullptr, nullptr, gmx::ConstraintVariable::Positions);
+ constr->apply(FALSE, FALSE, step, 0, 1.0, x, xnold, nullptr, box, lambda[efptBONDED],
+ &(dvdlambda[efptBONDED]), nullptr, nullptr, gmx::ConstraintVariable::Positions);
+ constr->apply(FALSE, FALSE, step, 0, 1.0, x, xnew, nullptr, box, lambda[efptBONDED],
+ &(dvdlambda[efptBONDED]), nullptr, nullptr, gmx::ConstraintVariable::Positions);
for (n = 0; n < end; n++)
{
for (d = 0; d < DIM; d++)
{
- xnew[n][d] =
- -(2*x[n][d]-xnold[n][d]-xnew[n][d])/gmx::square(dt)
- - f[n][d]*md->invmass[n];
+ xnew[n][d] = -(2 * x[n][d] - xnold[n][d] - xnew[n][d]) / gmx::square(dt)
+ - f[n][d] * md->invmass[n];
}
clear_rvec(acc_dir[n]);
}
/* Project the acceleration on the old bond directions */
- constr->apply(FALSE, FALSE, step, 0, 1.0,
- x_old, xnew, acc_dir, box,
- lambda[efptBONDED], &(dvdlambda[efptBONDED]),
- nullptr, nullptr, gmx::ConstraintVariable::Deriv_FlexCon);
+ constr->apply(FALSE, FALSE, step, 0, 1.0, x_old, xnew, acc_dir, box, lambda[efptBONDED],
+ &(dvdlambda[efptBONDED]), nullptr, nullptr, gmx::ConstraintVariable::Deriv_FlexCon);
}
-void relax_shell_flexcon(FILE *fplog,
- const t_commrec *cr,
- const gmx_multisim_t *ms,
- gmx_bool bVerbose,
- gmx_enfrot *enforcedRotation,
- int64_t mdstep,
- const t_inputrec *inputrec,
- gmx::ImdSession *imdSession,
- pull_t *pull_work,
- gmx_bool bDoNS,
- int force_flags,
- const gmx_localtop_t *top,
- gmx::Constraints *constr,
- gmx_enerdata_t *enerd,
- t_fcdata *fcd,
- int natoms,
- gmx::ArrayRefWithPadding<gmx::RVec> x,
- gmx::ArrayRefWithPadding<gmx::RVec> v,
- const matrix box,
- gmx::ArrayRef<real> lambda,
- history_t *hist,
- gmx::ArrayRefWithPadding<gmx::RVec> f,
- tensor force_vir,
- const t_mdatoms *md,
- t_nrnb *nrnb,
- gmx_wallcycle_t wcycle,
- t_graph *graph,
- gmx_shellfc_t *shfc,
- t_forcerec *fr,
- gmx::MdrunScheduleWorkload *runScheduleWork,
- double t,
- rvec mu_tot,
- const gmx_vsite_t *vsite,
- const DDBalanceRegionHandler &ddBalanceRegionHandler)
+void relax_shell_flexcon(FILE* fplog,
+ const t_commrec* cr,
+ const gmx_multisim_t* ms,
+ gmx_bool bVerbose,
+ gmx_enfrot* enforcedRotation,
+ int64_t mdstep,
+ const t_inputrec* inputrec,
+ gmx::ImdSession* imdSession,
+ pull_t* pull_work,
+ gmx_bool bDoNS,
+ int force_flags,
+ const gmx_localtop_t* top,
+ gmx::Constraints* constr,
+ gmx_enerdata_t* enerd,
+ t_fcdata* fcd,
+ int natoms,
+ gmx::ArrayRefWithPadding<gmx::RVec> x,
+ gmx::ArrayRefWithPadding<gmx::RVec> v,
+ const matrix box,
+ gmx::ArrayRef<real> lambda,
+ history_t* hist,
+ gmx::ArrayRefWithPadding<gmx::RVec> f,
+ tensor force_vir,
+ const t_mdatoms* md,
+ t_nrnb* nrnb,
+ gmx_wallcycle_t wcycle,
+ t_graph* graph,
+ gmx_shellfc_t* shfc,
+ t_forcerec* fr,
+ gmx::MdrunScheduleWorkload* runScheduleWork,
+ double t,
+ rvec mu_tot,
+ const gmx_vsite_t* vsite,
+ const DDBalanceRegionHandler& ddBalanceRegionHandler)
{
- auto xRvec = as_rvec_array(x.paddedArrayRef().data());
- auto vRvec = as_rvec_array(v.paddedArrayRef().data());
+ auto xRvec = as_rvec_array(x.paddedArrayRef().data());
+ auto vRvec = as_rvec_array(v.paddedArrayRef().data());
int nshell;
- t_shell *shell;
- const t_idef *idef;
- rvec *acc_dir = nullptr, *x_old = nullptr;
+ t_shell* shell;
+ const t_idef* idef;
+ rvec * acc_dir = nullptr, *x_old = nullptr;
real Epot[2], df[2];
real sf_dir, invdt;
real ftol, dum = 0;
int nat, dd_ac0, dd_ac1 = 0, i;
int homenr = md->homenr, end = homenr;
int nflexcon, number_steps, d, Min = 0, count = 0;
-#define Try (1-Min) /* At start Try = 1 */
+#define Try (1 - Min) /* At start Try = 1 */
bCont = (mdstep == inputrec->init_step) && inputrec->bContinuation;
bInit = (mdstep == inputrec->init_step) || shfc->bRequireInit;
* charge groups in the box.
*/
auto xRef = x.paddedArrayRef();
- put_atoms_in_box_omp(fr->ePBC, box, xRef.subArray(0, md->homenr), gmx_omp_nthreads_get(emntDefault));
+ put_atoms_in_box_omp(fr->ePBC, box, xRef.subArray(0, md->homenr),
+ gmx_omp_nthreads_get(emntDefault));
if (graph)
{
srenew(shfc->acc_dir, shfc->flex_nalloc);
srenew(shfc->x_old, shfc->flex_nalloc);
}
- acc_dir = shfc->acc_dir;
- x_old = shfc->x_old;
+ acc_dir = shfc->acc_dir;
+ x_old = shfc->x_old;
auto xArrayRef = x.paddedArrayRef();
auto vArrayRef = v.paddedArrayRef();
for (i = 0; i < homenr; i++)
{
for (d = 0; d < DIM; d++)
{
- shfc->x_old[i][d] =
- xArrayRef[i][d] - vArrayRef[i][d]*inputrec->delta_t;
+ shfc->x_old[i][d] = xArrayRef[i][d] - vArrayRef[i][d] * inputrec->delta_t;
}
}
}
*/
if (shfc->bPredict && !bCont && (EI_STATE_VELOCITY(inputrec->eI) || bInit))
{
- predict_shells(fplog, xRvec, vRvec, inputrec->delta_t, nshell, shell,
- md->massT, nullptr, bInit);
+ predict_shells(fplog, xRvec, vRvec, inputrec->delta_t, nshell, shell, md->massT, nullptr, bInit);
}
/* do_force expected the charge groups to be in the box */
pr_rvecs(debug, 0, "x b4 do_force", xRvec, homenr);
}
int shellfc_flags = force_flags | (bVerbose ? GMX_FORCE_ENERGY : 0);
- do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession,
- pull_work,
- mdstep, nrnb, wcycle, top,
- box, x, hist,
- forceWithPadding[Min], force_vir, md, enerd, fcd,
- lambda, graph,
- fr, runScheduleWork, vsite, mu_tot, t, nullptr,
- (bDoNS ? GMX_FORCE_NS : 0) | shellfc_flags,
- ddBalanceRegionHandler);
+ do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession, pull_work, mdstep,
+ nrnb, wcycle, top, box, x, hist, forceWithPadding[Min], force_vir, md, enerd, fcd,
+ lambda, graph, fr, runScheduleWork, vsite, mu_tot, t, nullptr,
+ (bDoNS ? GMX_FORCE_NS : 0) | shellfc_flags, ddBalanceRegionHandler);
sf_dir = 0;
if (nflexcon)
{
- init_adir(shfc,
- constr, inputrec, cr, dd_ac1, mdstep, md, end,
- shfc->x_old, xRvec, xRvec, as_rvec_array(force[Min].data()),
- shfc->acc_dir,
- box, lambda, &dum);
+ init_adir(shfc, constr, inputrec, cr, dd_ac1, mdstep, md, end, shfc->x_old, xRvec, xRvec,
+ as_rvec_array(force[Min].data()), shfc->acc_dir, box, lambda, &dum);
for (i = 0; i < end; i++)
{
- sf_dir += md->massT[i]*norm2(shfc->acc_dir[i]);
+ sf_dir += md->massT[i] * norm2(shfc->acc_dir[i]);
}
}
sum_epot(&(enerd->grpp), enerd->term);
Epot[Min] = enerd->term[F_EPOT];
- df[Min] = rms_force(cr, forceWithPadding[Min].paddedArrayRef(), nshell, shell, nflexcon, &sf_dir, &Epot[Min]);
+ df[Min] = rms_force(cr, forceWithPadding[Min].paddedArrayRef(), nshell, shell, nflexcon,
+ &sf_dir, &Epot[Min]);
df[Try] = 0;
if (debug)
{
pr_rvecs(debug, 0, "force0", as_rvec_array(force[Min].data()), md->nr);
}
- if (nshell+nflexcon > 0)
+ if (nshell + nflexcon > 0)
{
/* Copy x to pos[Min] & pos[Try]: during minimization only the
* shell positions are updated, therefore the other particles must
* be set here, in advance.
*/
- std::copy(x.paddedArrayRef().begin(),
- x.paddedArrayRef().end(),
+ std::copy(x.paddedArrayRef().begin(), x.paddedArrayRef().end(),
posWithPadding[Min].paddedArrayRef().begin());
- std::copy(x.paddedArrayRef().begin(),
- x.paddedArrayRef().end(),
+ std::copy(x.paddedArrayRef().begin(), x.paddedArrayRef().end(),
posWithPadding[Try].paddedArrayRef().begin());
}
if (debug)
{
- fprintf(debug, "%17s: %14.10e\n",
- interaction_function[F_EKIN].longname, enerd->term[F_EKIN]);
- fprintf(debug, "%17s: %14.10e\n",
- interaction_function[F_EPOT].longname, enerd->term[F_EPOT]);
- fprintf(debug, "%17s: %14.10e\n",
- interaction_function[F_ETOT].longname, enerd->term[F_ETOT]);
+ fprintf(debug, "%17s: %14.10e\n", interaction_function[F_EKIN].longname, enerd->term[F_EKIN]);
+ fprintf(debug, "%17s: %14.10e\n", interaction_function[F_EPOT].longname, enerd->term[F_EPOT]);
+ fprintf(debug, "%17s: %14.10e\n", interaction_function[F_ETOT].longname, enerd->term[F_ETOT]);
fprintf(debug, "SHELLSTEP %s\n", gmx_step_str(mdstep, sbuf));
}
{
if (vsite)
{
- construct_vsites(vsite, as_rvec_array(pos[Min].data()),
- inputrec->delta_t, vRvec,
- idef->iparams, idef->il,
- fr->ePBC, fr->bMolPBC, cr, box);
+ construct_vsites(vsite, as_rvec_array(pos[Min].data()), inputrec->delta_t, vRvec,
+ idef->iparams, idef->il, fr->ePBC, fr->bMolPBC, cr, box);
}
if (nflexcon)
{
- init_adir(shfc,
- constr, inputrec, cr, dd_ac1, mdstep, md, end,
- x_old, xRvec,
- as_rvec_array(pos[Min].data()),
- as_rvec_array(force[Min].data()), acc_dir,
+ init_adir(shfc, constr, inputrec, cr, dd_ac1, mdstep, md, end, x_old, xRvec,
+ as_rvec_array(pos[Min].data()), as_rvec_array(force[Min].data()), acc_dir,
box, lambda, &dum);
directional_sd(pos[Min], pos[Try], acc_dir, end, fr->fc_stepsize);
pr_rvecs(debug, 0, "RELAX: pos[Try] ", as_rvec_array(pos[Try].data()), homenr);
}
/* Try the new positions */
- do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession,
- pull_work,
- 1, nrnb, wcycle,
- top, box, posWithPadding[Try], hist,
- forceWithPadding[Try], force_vir,
- md, enerd, fcd, lambda, graph,
- fr, runScheduleWork, vsite, mu_tot, t, nullptr,
- shellfc_flags,
- ddBalanceRegionHandler);
+ do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession, pull_work, 1, nrnb,
+ wcycle, top, box, posWithPadding[Try], hist, forceWithPadding[Try], force_vir, md,
+ enerd, fcd, lambda, graph, fr, runScheduleWork, vsite, mu_tot, t, nullptr,
+ shellfc_flags, ddBalanceRegionHandler);
sum_epot(&(enerd->grpp), enerd->term);
if (gmx_debug_at)
{
sf_dir = 0;
if (nflexcon)
{
- init_adir(shfc,
- constr, inputrec, cr, dd_ac1, mdstep, md, end,
- x_old, xRvec,
- as_rvec_array(pos[Try].data()),
- as_rvec_array(force[Try].data()),
- acc_dir, box, lambda, &dum);
+ init_adir(shfc, constr, inputrec, cr, dd_ac1, mdstep, md, end, x_old, xRvec,
+ as_rvec_array(pos[Try].data()), as_rvec_array(force[Try].data()), acc_dir,
+ box, lambda, &dum);
for (i = 0; i < end; i++)
{
- sf_dir += md->massT[i]*norm2(acc_dir[i]);
+ sf_dir += md->massT[i] * norm2(acc_dir[i]);
}
}
if (nflexcon)
{
/* Correct the velocities for the flexible constraints */
- invdt = 1/inputrec->delta_t;
+ invdt = 1 / inputrec->delta_t;
auto vArrayRef = v.paddedArrayRef();
for (i = 0; i < end; i++)
{
for (d = 0; d < DIM; d++)
{
- vArrayRef[i][d] += (pos[Try][i][d] - pos[Min][i][d])*invdt;
+ vArrayRef[i][d] += (pos[Try][i][d] - pos[Min][i][d]) * invdt;
}
}
}
- Min = Try;
+ Min = Try;
}
else
{
/* Note that the energies and virial are incorrect when not converged */
if (fplog)
{
- fprintf(fplog,
- "step %s: EM did not converge in %d iterations, RMS force %6.2e\n",
+ fprintf(fplog, "step %s: EM did not converge in %d iterations, RMS force %6.2e\n",
gmx_step_str(mdstep, sbuf), number_steps, df[Min]);
}
- fprintf(stderr,
- "step %s: EM did not converge in %d iterations, RMS force %6.2e\n",
+ fprintf(stderr, "step %s: EM did not converge in %d iterations, RMS force %6.2e\n",
gmx_step_str(mdstep, sbuf), number_steps, df[Min]);
}
std::copy(force[Min].begin(), force[Min].end(), f.unpaddedArrayRef().begin());
}
-void done_shellfc(FILE *fplog, gmx_shellfc_t *shfc, int64_t numSteps)
+void done_shellfc(FILE* fplog, gmx_shellfc_t* shfc, int64_t numSteps)
{
if (shfc && fplog && numSteps > 0)
{
double numStepsAsDouble = static_cast<double>(numSteps);
fprintf(fplog, "Fraction of iterations that converged: %.2f %%\n",
- (shfc->numConvergedIterations*100.0)/numStepsAsDouble);
+ (shfc->numConvergedIterations * 100.0) / numStepsAsDouble);
fprintf(fplog, "Average number of force evaluations per MD step: %.2f\n\n",
- shfc->numForceEvaluations/numStepsAsDouble);
+ shfc->numForceEvaluations / numStepsAsDouble);
}
// TODO Deallocate memory in shfc
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff