#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
-#include "gromacs/utility/smalloc.h"
-typedef struct
+using gmx::ArrayRef;
+using gmx::ArrayRefWithPadding;
+using gmx::RVec;
+
+struct t_shell
{
- 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;
+ int nnucl = 0; /* The number of nuclei */
+ int shellIndex = -1; /* The shell index */
+ int nucl1 = -1; /* The first nuclei connected to the shell */
+ int nucl2 = -1; /* The second nuclei connected to the shell */
+ int nucl3 = -1; /* The third nuclei connected to the shell */
+ real k = 0; /* force constant */
+ real k_1 = 0; /* 1 over force constant */
+ rvec xold; /* The old shell coordinates */
+ rvec fold; /* The old force on the shell */
+ rvec step; /* Step size for steepest descents */
+};
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 */
-
- /* 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 */
+ std::vector<t_shell> shell_gl; /* All the shells (for DD only) */
+ std::vector<int> shell_index_gl; /* Global shell index (for DD only) */
+ gmx_bool bInterCG; /* Are there inter charge-group shells? */
+ std::vector<t_shell> shells; /* The local shells */
+ bool predictShells = false; /* Predict shell positions */
+ bool requireInit = false; /* Require initialization of shell positions */
+ int nflexcon = 0; /* The number of flexible constraints */
+
+ std::array<PaddedHostVector<RVec>, 2> x; /* Coordinate buffers for iterative minimization */
+ std::array<PaddedHostVector<RVec>, 2> f; /* Force buffers for iterative minimization */
/* Flexible constraint working data */
- 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 */
- 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 */
+ std::vector<RVec> acc_dir; /* Acceleration direction for flexcon */
+ gmx::PaddedVector<RVec> x_old; /* Old coordinates for flexcon */
+ gmx::PaddedVector<RVec> adir_xnold; /* Work space for init_adir */
+ gmx::PaddedVector<RVec> adir_xnew; /* 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, ArrayRef<const t_shell> shells)
{
- int i;
-
fprintf(fplog, "SHELL DATA\n");
fprintf(fplog, "%5s %8s %5s %5s %5s\n", "Shell", "Force k", "Nucl1", "Nucl2", "Nucl3");
- for (i = 0; (i < ns); i++)
+ for (const t_shell& shell : shells)
{
- 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 %8.3f %5d", shell.shellIndex, 1.0 / shell.k_1, shell.nucl1);
+ if (shell.nnucl == 2)
{
- fprintf(fplog, " %5d\n", s[i].nucl2);
+ fprintf(fplog, " %5d\n", shell.nucl2);
}
- else if (s[i].nnucl == 3)
+ else if (shell.nnucl == 3)
{
- fprintf(fplog, " %5d %5d\n", s[i].nucl2, s[i].nucl3);
+ fprintf(fplog, " %5d %5d\n", shell.nucl2, shell.nucl3);
}
else
{
* 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,
+ ArrayRef<RVec> x,
+ ArrayRef<RVec> v,
+ real dt,
+ ArrayRef<const t_shell> shells,
+ 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 m, n1, n2, n3;
+ real dt_1, fudge, tm, m1, m2, m3;
GMX_RELEASE_ASSERT(mass || mtop, "Must have masses or a way to look them up");
*/
fudge = 1.0;
+ ArrayRef<RVec> xOrV;
if (bInit)
{
if (fplog)
{
fprintf(fplog, "RELAX: Using prediction for initial shell placement\n");
}
- ptr = x;
+ xOrV = x;
dt_1 = 1;
}
else
{
- ptr = v;
+ xOrV = v;
dt_1 = fudge * dt;
}
int molb = 0;
- for (i = 0; (i < ns); i++)
+ for (const t_shell& shell : shells)
{
- s1 = s[i].shell;
+ const int s1 = shell.shellIndex;
if (bInit)
{
clear_rvec(x[s1]);
}
- switch (s[i].nnucl)
+ switch (shell.nnucl)
{
case 1:
- n1 = s[i].nucl1;
+ n1 = shell.nucl1;
for (m = 0; (m < DIM); m++)
{
- x[s1][m] += ptr[n1][m] * dt_1;
+ x[s1][m] += xOrV[n1][m] * dt_1;
}
break;
case 2:
- n1 = s[i].nucl1;
- n2 = s[i].nucl2;
+ n1 = shell.nucl1;
+ n2 = shell.nucl2;
if (mass)
{
m1 = mass[n1];
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 * xOrV[n1][m] + m2 * xOrV[n2][m]) * tm;
}
break;
case 3:
- n1 = s[i].nucl1;
- n2 = s[i].nucl2;
- n3 = s[i].nucl3;
+ n1 = shell.nucl1;
+ n2 = shell.nucl2;
+ n3 = shell.nucl3;
if (mass)
{
m1 = mass[n1];
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 * xOrV[n1][m] + m2 * xOrV[n2][m] + m3 * xOrV[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!", s1, shell.nnucl);
}
}
}
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;
return nullptr;
}
- snew(shfc, 1);
- shfc->x = new PaddedHostVector<gmx::RVec>[2] {};
- shfc->f = new PaddedHostVector<gmx::RVec>[2] {};
+ shfc = new gmx_shellfc_t;
shfc->nflexcon = nflexcon;
if (nshell == 0)
/* Only flexible constraints, no shells.
* Note that make_local_shells() does not need to be called.
*/
- shfc->nshell = 0;
- shfc->bPredict = FALSE;
-
return shfc;
}
/* We have shells: fill the shell data structure */
/* Global system sized array, this should be avoided */
- snew(shell_index, mtop->natoms);
+ std::vector<int> shell_index(mtop->natoms);
nshell = 0;
for (const AtomProxy atomP : AtomRange(*mtop))
}
}
- snew(shell, nshell);
-
- /* Initiate the shell structures */
- for (i = 0; (i < nshell); i++)
- {
- shell[i].shell = -1;
- shell[i].nnucl = 0;
- shell[i].nucl1 = -1;
- shell[i].nucl2 = -1;
- shell[i].nucl3 = -1;
- /* shell[i].bInterCG=FALSE; */
- shell[i].k_1 = 0;
- shell[i].k = 0;
- }
+ std::vector<t_shell> shell(nshell);
ffparams = &mtop->ffparams;
{
gmx_fatal(FARGS, "nsi is %d should be within 0 - %d. aS = %d", nsi, nshell, aS);
}
- if (shell[nsi].shell == -1)
+ if (shell[nsi].shellIndex == -1)
{
- shell[nsi].shell = a_offset + aS;
+ shell[nsi].shellIndex = a_offset + aS;
ns++;
}
- else if (shell[nsi].shell != a_offset + aS)
+ else if (shell[nsi].shellIndex != a_offset + aS)
{
gmx_fatal(FARGS, "Weird stuff in %s, %d", __FILE__, __LINE__);
}
{
if (fplog)
{
- pr_shell(fplog, ns, shell);
+ pr_shell(fplog, shell);
}
gmx_fatal(FARGS, "Can not handle more than three bonds per shell\n");
}
if (debug)
{
- pr_shell(debug, ns, shell);
+ pr_shell(debug, shell);
}
- shfc->nshell_gl = ns;
shfc->shell_gl = shell;
shfc->shell_index_gl = shell_index;
- shfc->bPredict = (getenv("GMX_NOPREDICT") == nullptr);
- shfc->bRequireInit = FALSE;
- if (!shfc->bPredict)
+ shfc->predictShells = (getenv("GMX_NOPREDICT") == nullptr);
+ shfc->requireInit = false;
+ if (!shfc->predictShells)
{
if (fplog)
{
}
else
{
- shfc->bRequireInit = (getenv("GMX_REQUIRE_SHELL_INIT") != nullptr);
- if (shfc->bRequireInit && fplog)
+ shfc->requireInit = (getenv("GMX_REQUIRE_SHELL_INIT") != nullptr);
+ if (shfc->requireInit && fplog)
{
fprintf(fplog, "\nWill always initiate shell positions\n");
}
}
- if (shfc->bPredict)
+ if (shfc->predictShells)
{
if (shfc->bInterCG)
{
* shell velocities are zeroed, it's a bit tricky to keep
* track of the shell displacements and thus the velocity.
*/
- shfc->bPredict = FALSE;
+ shfc->predictShells = false;
}
}
void make_local_shells(const t_commrec* cr, const t_mdatoms* md, gmx_shellfc_t* shfc)
{
- t_shell* shell;
- int a0, a1, *ind, nshell, i;
+ int a0, a1;
gmx_domdec_t* dd = nullptr;
if (DOMAINDECOMP(cr))
}
else
{
- /* Single node: we need all shells, just copy the pointer */
- shfc->nshell = shfc->nshell_gl;
- shfc->shell = shfc->shell_gl;
+ /* Single node: we need all shells, copy them */
+ shfc->shells = shfc->shell_gl;
return;
}
- ind = shfc->shell_index_gl;
+ ArrayRef<const int> ind = shfc->shell_index_gl;
- nshell = 0;
- shell = shfc->shell;
- for (i = a0; i < a1; i++)
+ std::vector<t_shell>& shells = shfc->shells;
+ shells.clear();
+ for (int i = a0; i < a1; i++)
{
if (md->ptype[i] == eptShell)
{
- if (nshell + 1 > shfc->shell_nalloc)
- {
- shfc->shell_nalloc = over_alloc_dd(nshell + 1);
- srenew(shell, shfc->shell_nalloc);
- }
if (dd)
{
- shell[nshell] = shfc->shell_gl[ind[dd->globalAtomIndices[i]]];
+ shells.push_back(shfc->shell_gl[ind[dd->globalAtomIndices[i]]]);
}
else
{
- shell[nshell] = shfc->shell_gl[ind[i]];
+ shells.push_back(shfc->shell_gl[ind[i]]);
}
+ t_shell& shell = shells.back();
/* With inter-cg shells we can no do shell prediction,
* so we do not need the nuclei numbers.
*/
if (!shfc->bInterCG)
{
- shell[nshell].nucl1 = i + shell[nshell].nucl1 - shell[nshell].shell;
- if (shell[nshell].nnucl > 1)
+ shell.nucl1 = i + shell.nucl1 - shell.shellIndex;
+ if (shell.nnucl > 1)
{
- shell[nshell].nucl2 = i + shell[nshell].nucl2 - shell[nshell].shell;
+ shell.nucl2 = i + shell.nucl2 - shell.shellIndex;
}
- if (shell[nshell].nnucl > 2)
+ if (shell.nnucl > 2)
{
- shell[nshell].nucl3 = i + shell[nshell].nucl3 - shell[nshell].shell;
+ shell.nucl3 = i + shell.nucl3 - shell.shellIndex;
}
}
- shell[nshell].shell = i;
- nshell++;
+ shell.shellIndex = i;
}
}
-
- shfc->nshell = nshell;
- shfc->shell = shell;
}
static void do_1pos(rvec xnew, const rvec xold, const rvec f, real step)
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)
+static void directional_sd(ArrayRef<const RVec> xold,
+ ArrayRef<RVec> xnew,
+ ArrayRef<const RVec> acc_dir,
+ int homenr,
+ real step)
{
const rvec* xo = as_rvec_array(xold.data());
rvec* xn = as_rvec_array(xnew.data());
}
}
-static void shell_pos_sd(gmx::ArrayRef<const gmx::RVec> xcur,
- gmx::ArrayRef<gmx::RVec> xnew,
- gmx::ArrayRef<const gmx::RVec> f,
- int ns,
- t_shell s[],
- int count)
+static void shell_pos_sd(ArrayRef<const RVec> xcur,
+ ArrayRef<RVec> xnew,
+ ArrayRef<const RVec> f,
+ ArrayRef<t_shell> shells,
+ 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;
- int i, shell, d;
+ int d;
real dx, df, k_est;
const real zero = 0;
#ifdef PRINT_STEP
step_min = 1e30;
step_max = 0;
#endif
- for (i = 0; (i < ns); i++)
+ for (t_shell& shell : shells)
{
- shell = s[i].shell;
+ const int ind = shell.shellIndex;
if (count == 1)
{
for (d = 0; d < DIM; d++)
{
- s[i].step[d] = s[i].k_1;
+ shell.step[d] = shell.k_1;
#ifdef PRINT_STEP
- step_min = std::min(step_min, s[i].step[d]);
- step_max = std::max(step_max, s[i].step[d]);
+ step_min = std::min(step_min, shell.step[d]);
+ step_max = std::max(step_max, shell.step[d]);
#endif
}
}
{
for (d = 0; d < DIM; d++)
{
- dx = xcur[shell][d] - s[i].xold[d];
- df = f[shell][d] - s[i].fold[d];
+ dx = xcur[ind][d] - shell.xold[d];
+ df = f[ind][d] - shell.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
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));
+ * step_scale_multiple * shell.step[d] */
+ shell.step[d] = step_scale_min * shell.step[d]
+ + step_scale_increment
+ * std::min(step_scale_multiple * shell.step[d],
+ std::max(k_est, zero));
}
else
{
}
else /* 0 != dx */
{
- s[i].step[d] *= step_scale_max;
+ shell.step[d] *= step_scale_max;
}
}
#ifdef PRINT_STEP
- step_min = std::min(step_min, s[i].step[d]);
- step_max = std::max(step_max, s[i].step[d]);
+ step_min = std::min(step_min, shell.step[d]);
+ step_max = std::max(step_max, shell.step[d]);
#endif
}
}
- copy_rvec(xcur[shell], s[i].xold);
- copy_rvec(f[shell], s[i].fold);
+ copy_rvec(xcur[ind], shell.xold);
+ copy_rvec(f[ind], shell.fold);
- do_1pos3(xnew[shell], xcur[shell], f[shell], s[i].step);
+ do_1pos3(xnew[ind], xcur[ind], f[ind], shell.step);
if (gmx_debug_at)
{
- fprintf(debug, "shell[%d] = %d\n", i, shell);
- pr_rvec(debug, 0, "fshell", f[shell], DIM, TRUE);
- pr_rvec(debug, 0, "xold", xcur[shell], DIM, TRUE);
- pr_rvec(debug, 0, "step", s[i].step, DIM, TRUE);
- pr_rvec(debug, 0, "xnew", xnew[shell], DIM, TRUE);
+ fprintf(debug, "shell = %d\n", ind);
+ pr_rvec(debug, 0, "fshell", f[ind], DIM, TRUE);
+ pr_rvec(debug, 0, "xold", xcur[ind], DIM, TRUE);
+ pr_rvec(debug, 0, "step", shell.step, DIM, TRUE);
+ pr_rvec(debug, 0, "xnew", xnew[ind], DIM, TRUE);
}
}
#ifdef PRINT_STEP
#endif
}
-static void decrease_step_size(int nshell, t_shell s[])
+static void decrease_step_size(ArrayRef<t_shell> shells)
{
- int i;
-
- for (i = 0; i < nshell; i++)
+ for (t_shell& shell : shells)
{
- svmul(0.8, s[i].step, s[i].step);
+ svmul(0.8, shell.step, shell.step);
}
}
}
-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,
+ ArrayRef<const RVec> force,
+ ArrayRef<const t_shell> shells,
+ int ndir,
+ real* sf_dir,
+ real* Epot)
{
double buf[4];
const rvec* f = as_rvec_array(force.data());
buf[0] = *sf_dir;
- for (int i = 0; i < ns; i++)
+ for (const t_shell& shell : shells)
{
- int shell = s[i].shell;
- buf[0] += norm2(f[shell]);
+ buf[0] += norm2(f[shell.shellIndex]);
}
- int ntot = ns;
+ int ntot = shells.ssize();
if (PAR(cr))
{
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, ArrayRef<RVec> f, real ftol, ArrayRef<const t_shell> shells)
{
- int i, shell;
real ft2, ff2;
ft2 = gmx::square(ftol);
- for (i = 0; (i < ns); i++)
+ for (const t_shell& shell : shells)
{
- shell = s[i].shell;
- ff2 = iprod(f[shell], f[shell]);
+ const int ind = shell.shellIndex;
+ ff2 = iprod(f[ind], f[ind]);
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", ind, f[ind][XX],
+ f[ind][YY], f[ind][ZZ], std::sqrt(ff2));
}
}
}
int64_t step,
const t_mdatoms* md,
int end,
- rvec* x_old,
- rvec* x_init,
- rvec* x,
- rvec* f,
- rvec* acc_dir,
+ ArrayRefWithPadding<RVec> xOld,
+ ArrayRef<RVec> x_init,
+ ArrayRefWithPadding<RVec> xCurrent,
+ ArrayRef<RVec> f,
+ ArrayRef<RVec> acc_dir,
const matrix box,
- gmx::ArrayRef<const real> lambda,
+ ArrayRef<const real> lambda,
real* dvdlambda)
{
- rvec * xnold, *xnew;
double dt, w_dt;
int n, d;
unsigned short* ptype;
{
n = end;
}
- if (n > shfc->adir_nalloc)
- {
- shfc->adir_nalloc = over_alloc_dd(n);
- srenew(shfc->adir_xnold, shfc->adir_nalloc);
- srenew(shfc->adir_xnew, shfc->adir_nalloc);
- }
- xnold = shfc->adir_xnold;
- xnew = shfc->adir_xnew;
+ shfc->adir_xnold.resizeWithPadding(n);
+ shfc->adir_xnew.resizeWithPadding(n);
+ rvec* xnold = as_rvec_array(shfc->adir_xnold.data());
+ rvec* xnew = as_rvec_array(shfc->adir_xnew.data());
+ rvec* x_old = as_rvec_array(xOld.paddedArrayRef().data());
+ rvec* x = as_rvec_array(xCurrent.paddedArrayRef().data());
ptype = md->ptype;
}
}
}
- 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, xCurrent, shfc->adir_xnold.arrayRefWithPadding(), {},
+ box, lambda[efptBONDED], &(dvdlambda[efptBONDED]), {}, nullptr,
+ gmx::ConstraintVariable::Positions);
+ constr->apply(FALSE, FALSE, step, 0, 1.0, xCurrent, shfc->adir_xnew.arrayRefWithPadding(), {},
+ box, lambda[efptBONDED], &(dvdlambda[efptBONDED]), {}, nullptr,
+ gmx::ConstraintVariable::Positions);
for (n = 0; n < end; 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, xOld, shfc->adir_xnew.arrayRefWithPadding(), acc_dir,
+ box, lambda[efptBONDED], &(dvdlambda[efptBONDED]), {}, 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,
+ ArrayRefWithPadding<RVec> xPadded,
+ ArrayRefWithPadding<RVec> vPadded,
+ const matrix box,
+ ArrayRef<real> lambda,
+ history_t* hist,
+ ArrayRefWithPadding<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());
-
- int nshell;
- 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;
- char sbuf[22];
- gmx_bool bCont, bInit, bConverged;
- int nat, dd_ac0, dd_ac1 = 0, i;
- int homenr = md->homenr, end = homenr;
- int nflexcon, number_steps, d, Min = 0, count = 0;
+ real Epot[2], df[2];
+ real sf_dir, invdt;
+ real dum = 0;
+ char sbuf[22];
+ int nat, dd_ac0, dd_ac1 = 0, i;
+ int homenr = md->homenr, end = homenr;
+ int d, Min = 0, count = 0;
#define Try (1 - Min) /* At start Try = 1 */
- bCont = (mdstep == inputrec->init_step) && inputrec->bContinuation;
- bInit = (mdstep == inputrec->init_step) || shfc->bRequireInit;
- ftol = inputrec->em_tol;
- number_steps = inputrec->niter;
- nshell = shfc->nshell;
- shell = shfc->shell;
- nflexcon = shfc->nflexcon;
+ const bool bCont = (mdstep == inputrec->init_step) && inputrec->bContinuation;
+ const bool bInit = (mdstep == inputrec->init_step) || shfc->requireInit;
+ const real ftol = inputrec->em_tol;
+ const int number_steps = inputrec->niter;
+ ArrayRef<t_shell> shells = shfc->shells;
+ const int nflexcon = shfc->nflexcon;
- idef = &top->idef;
+ const t_idef* idef = &top->idef;
if (DOMAINDECOMP(cr))
{
shfc->f[i].resizeWithPadding(nat);
}
- /* Create views that we can swap */
- gmx::ArrayRefWithPadding<gmx::RVec> posWithPadding[2];
- gmx::ArrayRefWithPadding<gmx::RVec> forceWithPadding[2];
- gmx::ArrayRef<gmx::RVec> pos[2];
- gmx::ArrayRef<gmx::RVec> force[2];
+ /* Create views that we can swap for trail and minimum for positions and forces */
+ ArrayRefWithPadding<RVec> posWithPadding[2];
+ ArrayRefWithPadding<RVec> forceWithPadding[2];
+ ArrayRef<RVec> pos[2];
+ ArrayRef<RVec> force[2];
for (i = 0; (i < 2); i++)
{
posWithPadding[i] = shfc->x[i].arrayRefWithPadding();
force[i] = forceWithPadding[i].paddedArrayRef();
}
- if (bDoNS && inputrec->ePBC != epbcNONE && !DOMAINDECOMP(cr))
+ ArrayRef<RVec> x = xPadded.unpaddedArrayRef();
+ ArrayRef<RVec> v = vPadded.unpaddedArrayRef();
+
+ if (bDoNS && inputrec->pbcType != PbcType::No && !DOMAINDECOMP(cr))
{
/* This is the only time where the coordinates are used
* before do_force is called, which normally puts all
* charge groups in the box.
*/
- auto xRef = x.paddedArrayRef();
- put_atoms_in_box_omp(fr->ePBC, box, xRef.subArray(0, md->homenr),
+ put_atoms_in_box_omp(fr->pbcType, box, x.subArray(0, md->homenr),
gmx_omp_nthreads_get(emntDefault));
if (graph)
{
- mk_mshift(fplog, graph, fr->ePBC, box, xRvec);
+ mk_mshift(fplog, graph, fr->pbcType, box, as_rvec_array(x.data()));
}
}
/* After this all coordinate arrays will contain whole charge groups */
if (graph)
{
- shift_self(graph, box, xRvec);
+ shift_self(graph, box, as_rvec_array(x.data()));
}
if (nflexcon)
{
- if (nat > shfc->flex_nalloc)
- {
- shfc->flex_nalloc = over_alloc_dd(nat);
- srenew(shfc->acc_dir, shfc->flex_nalloc);
- srenew(shfc->x_old, shfc->flex_nalloc);
- }
- acc_dir = shfc->acc_dir;
- x_old = shfc->x_old;
- auto xArrayRef = x.paddedArrayRef();
- auto vArrayRef = v.paddedArrayRef();
+ shfc->acc_dir.resize(nat);
+ shfc->x_old.resizeWithPadding(nat);
+ ArrayRef<RVec> x_old = shfc->x_old.arrayRefWithPadding().unpaddedArrayRef();
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;
+ x_old[i][d] = x[i][d] - v[i][d] * inputrec->delta_t;
}
}
}
/* Do a prediction of the shell positions, when appropriate.
* Without velocities (EM, NM, BD) we only do initial prediction.
*/
- if (shfc->bPredict && !bCont && (EI_STATE_VELOCITY(inputrec->eI) || bInit))
+ if (shfc->predictShells && !bCont && (EI_STATE_VELOCITY(inputrec->eI) || bInit))
{
- predict_shells(fplog, xRvec, vRvec, inputrec->delta_t, nshell, shell, md->massT, nullptr, bInit);
+ predict_shells(fplog, x, v, inputrec->delta_t, shells, md->massT, nullptr, bInit);
}
/* do_force expected the charge groups to be in the box */
if (graph)
{
- unshift_self(graph, box, xRvec);
+ unshift_self(graph, box, as_rvec_array(x.data()));
}
/* Calculate the forces first time around */
if (gmx_debug_at)
{
- pr_rvecs(debug, 0, "x b4 do_force", xRvec, homenr);
+ pr_rvecs(debug, 0, "x b4 do_force", as_rvec_array(x.data()), 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,
+ nrnb, wcycle, top, box, xPadded, 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.arrayRefWithPadding(),
+ x, xPadded, force[Min], shfc->acc_dir, box, lambda, &dum);
for (i = 0; i < end; 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(), shells, 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 (!shells.empty() || 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(xPadded.paddedArrayRef().begin(), xPadded.paddedArrayRef().end(),
posWithPadding[Min].paddedArrayRef().begin());
- std::copy(x.paddedArrayRef().begin(), x.paddedArrayRef().end(),
+ std::copy(xPadded.paddedArrayRef().begin(), xPadded.paddedArrayRef().end(),
posWithPadding[Try].paddedArrayRef().begin());
}
/* First check whether we should do shells, or whether the force is
* low enough even without minimization.
*/
- bConverged = (df[Min] < ftol);
+ bool bConverged = (df[Min] < ftol);
for (count = 1; (!(bConverged) && (count < number_steps)); count++)
{
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,
+ as_rvec_array(v.data()), idef->iparams, idef->il, fr->pbcType,
+ 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,
- box, lambda, &dum);
+ init_adir(shfc, constr, inputrec, cr, dd_ac1, mdstep, md, end,
+ shfc->x_old.arrayRefWithPadding(), x, posWithPadding[Min], force[Min],
+ shfc->acc_dir, box, lambda, &dum);
- directional_sd(pos[Min], pos[Try], acc_dir, end, fr->fc_stepsize);
+ directional_sd(pos[Min], pos[Try], shfc->acc_dir, end, fr->fc_stepsize);
}
/* New positions, Steepest descent */
- shell_pos_sd(pos[Min], pos[Try], force[Min], nshell, shell, count);
+ shell_pos_sd(pos[Min], pos[Try], force[Min], shells, count);
/* do_force expected the charge groups to be in the box */
if (graph)
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,
+ shfc->x_old.arrayRefWithPadding(), x, posWithPadding[Try], force[Try],
+ shfc->acc_dir, box, lambda, &dum);
+ ArrayRef<const RVec> acc_dir = shfc->acc_dir;
for (i = 0; i < end; i++)
{
sf_dir += md->massT[i] * norm2(acc_dir[i]);
Epot[Try] = enerd->term[F_EPOT];
- df[Try] = rms_force(cr, force[Try], nshell, shell, nflexcon, &sf_dir, &Epot[Try]);
+ df[Try] = rms_force(cr, force[Try], shells, nflexcon, &sf_dir, &Epot[Try]);
if (debug)
{
if (gmx_debug_at)
{
fprintf(debug, "SHELL ITER %d\n", count);
- dump_shells(debug, force[Try], ftol, nshell, shell);
+ dump_shells(debug, force[Try], ftol, shells);
}
}
if (nflexcon)
{
/* Correct the velocities for the flexible constraints */
- invdt = 1 / inputrec->delta_t;
- auto vArrayRef = v.paddedArrayRef();
+ invdt = 1 / inputrec->delta_t;
for (i = 0; i < end; i++)
{
for (d = 0; d < DIM; d++)
{
- vArrayRef[i][d] += (pos[Try][i][d] - pos[Min][i][d]) * invdt;
+ v[i][d] += (pos[Try][i][d] - pos[Min][i][d]) * invdt;
}
}
}
}
else
{
- decrease_step_size(nshell, shell);
+ decrease_step_size(shells);
}
}
shfc->numForceEvaluations += count;
}
/* Copy back the coordinates and the forces */
- std::copy(pos[Min].begin(), pos[Min].end(), x.paddedArrayRef().data());
+ std::copy(pos[Min].begin(), pos[Min].end(), x.data());
std::copy(force[Min].begin(), force[Min].end(), f.unpaddedArrayRef().begin());
}
shfc->numForceEvaluations / numStepsAsDouble);
}
- // TODO Deallocate memory in shfc
+ delete shfc;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff