*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/domdec/mdsetup.h"
-#include "gromacs/gmxlib/chargegroup.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/math/vecdump.h"
#include "gromacs/mdlib/constr.h"
#include "gromacs/mdlib/force.h"
#include "gromacs/mdlib/force_flags.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
-#include "gromacs/mdlib/mdatoms.h"
#include "gromacs/mdlib/vsite.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/enerdata.h"
+#include "gromacs/mdtypes/forcebuffers.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/mdtypes/state.h"
-#include "gromacs/pbcutil/mshift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.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;
-} t_shell;
-
-struct gmx_shellfc_t {
+#include "gromacs/utility/gmxassert.h"
+
+using gmx::ArrayRef;
+using gmx::ArrayRefWithPadding;
+using gmx::RVec;
+
+struct 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++ */
- PaddedVector<gmx::RVec> *x; /* Array for iterative minimization */
- PaddedVector<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++)
+ fprintf(fplog, "%5s %8s %5s %5s %5s\n", "Shell", "Force k", "Nucl1", "Nucl2", "Nucl3");
+ 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,
+ gmx::ArrayRef<const real> mass,
+ 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;
/* We introduce a fudge factor for performance reasons: with this choice
* the initial force on the shells is about a factor of two lower than
*/
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;
- dt_1 = fudge*dt;
+ 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;
- if (mass)
- {
- m1 = mass[n1];
- m2 = mass[n2];
- }
- else
- {
- /* Not the correct masses with FE, but it is just a prediction... */
- m1 = mtopGetAtomMass(mtop, n1, &molb);
- m2 = mtopGetAtomMass(mtop, n2, &molb);
- }
- tm = dt_1/(m1+m2);
+ n1 = shell.nucl1;
+ n2 = shell.nucl2;
+ m1 = mass[n1];
+ m2 = mass[n2];
+ 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;
- if (mass)
- {
- m1 = mass[n1];
- m2 = mass[n2];
- m3 = mass[n3];
- }
- else
- {
- /* Not the correct masses with FE, but it is just a prediction... */
- m1 = mtopGetAtomMass(mtop, n1, &molb);
- m2 = mtopGetAtomMass(mtop, n2, &molb);
- m3 = mtopGetAtomMass(mtop, n3, &molb);
- }
- tm = dt_1/(m1+m2+m3);
+ n1 = shell.nucl1;
+ n2 = shell.nucl2;
+ n3 = shell.nucl3;
+ m1 = mass[n1];
+ m2 = mass[n2];
+ m3 = mass[n3];
+ 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);
}
}
}
-/*! \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,
- const gmx_mtop_t *mtop)
+gmx_shellfc_t* init_shell_flexcon(FILE* fplog,
+ const gmx_mtop_t& mtop,
+ int nflexcon,
+ int nstcalcenergy,
+ bool usingDomainDecomposition,
+ bool usingPmeOnGpu)
{
- 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_shellfc_t* shfc;
- 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;
- default:
- fprintf(stderr, "Warning unsupported particle type %d in countPtypes",
- static_cast<int>(atom->ptype));
- }
- }
+ 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::EnumerationArray<ParticleType, int> numParticles = gmx_mtop_particletype_count(mtop);
if (fplog)
{
/* Print the number of each particle type */
- int n = 0;
- for (const auto &i : nptype)
+ for (const auto entry : gmx::keysOf(numParticles))
{
- if (i != 0)
+ const int number = numParticles[entry];
+ if (number != 0)
{
- fprintf(fplog, "There are: %d %ss\n", i, ptype_str[n]);
+ fprintf(fplog, "There are: %d %ss\n", number, enumValueToString(entry));
}
- n++;
}
}
- return nptype;
-}
-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, *at2cg;
-
- int ns, nshell, nsi;
- int i, j, type, 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)
- const gmx_ffparams_t *ffparams;
-
- std::array<int, eptNR> n = countPtypes(fplog, mtop);
- nshell = n[eptShell];
+ nshell = numParticles[ParticleType::Shell];
if (nshell == 0 && nflexcon == 0)
{
return nullptr;
}
- snew(shfc, 1);
- shfc->x = new PaddedVector<gmx::RVec>[2] {};
- shfc->f = new PaddedVector<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;
}
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)
+ if (nshell > 0 && 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 */
/* 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))
+ 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)
+ if (local.ptype == ParticleType::Shell)
{
shell_index[i] = nshell++;
}
}
- snew(shell, nshell);
+ std::vector<t_shell> 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;
- }
-
- ffparams = &mtop->ffparams;
+ ffparams = &mtop.ffparams;
/* Now fill the structures */
+ /* TODO: See if we can use update groups that cover shell constructions */
shfc->bInterCG = FALSE;
ns = 0;
a_offset = 0;
- for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
+ 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 t_block *cgs = &molt->cgs;
+ const gmx_molblock_t& molb = mtop.molblock[mb];
+ const gmx_moltype_t& molt = mtop.moltype[molb.type];
- 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;
- }
- }
-
- const t_atom *atom = molt->atoms.atom;
- for (mol = 0; mol < molb->nmol; mol++)
+ 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];
case F_CUBICBONDS:
case F_POLARIZATION:
case F_ANHARM_POL:
- if (atom[ia[1]].ptype == eptShell)
+ if (atom[ia[1]].ptype == ParticleType::Shell)
{
aS = ia[1];
aN = ia[2];
}
- else if (atom[ia[2]].ptype == eptShell)
+ else if (atom[ia[2]].ptype == ParticleType::Shell)
{
aS = ia[2];
aN = ia[1];
}
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)
+ 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 (shell[nsi].nucl1 == -1)
+ if (shell[nsi].nucl1 == -1)
{
shell[nsi].nucl1 = a_offset + aN;
}
{
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 (at2cg[aS] != at2cg[aN])
+ if (aS != aN)
{
/* shell[nsi].bInterCG = TRUE; */
shfc->bInterCG = TRUE;
{
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) * gmx::c_one4PiEps0
+ / 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) * gmx::c_one4PiEps0 / 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;
+ a_offset += molt.atoms.nr;
}
/* Done with this molecule type */
- sfree(at2cg);
}
/* Verify whether it's all correct */
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)
{
- 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)
{
if (fplog)
{
- fprintf(fplog, "\nNOTE: there are shells that are connected to particles outside their own charge group, will not predict shells positions during the run\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
* 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;
+ }
+ }
+
+ /* shfc->x is used as a coordinate buffer for the sim_util's `do_force` function, and
+ * when using PME it must be pinned. */
+ if (usingPmeOnGpu)
+ {
+ for (i = 0; i < 2; i++)
+ {
+ changePinningPolicy(&shfc->x[i], gmx::PinningPolicy::PinnedIfSupported);
}
}
return shfc;
}
-void make_local_shells(const t_commrec *cr,
- const t_mdatoms *md,
- gmx_shellfc_t *shfc)
+void gmx::make_local_shells(const t_commrec* cr, const t_mdatoms& md, gmx_shellfc_t* shfc)
{
- t_shell *shell;
- int a0, a1, *ind, nshell, i;
- gmx_domdec_t *dd = nullptr;
+ int a0, a1;
+ gmx_domdec_t* dd = nullptr;
- if (DOMAINDECOMP(cr))
+ if (haveDDAtomOrdering(*cr))
{
dd = cr->dd;
a0 = 0;
}
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();
+ auto* ptype = md.ptype;
+ for (int i = a0; i < a1; i++)
{
- if (md->ptype[i] == eptShell)
+ if (ptype[i] == ParticleType::Shell)
{
- 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)
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)
+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());
+ 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<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;
+ 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 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;
#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
* 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));
+ * 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 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,
+ 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());
+ 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))
{
}
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, 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));
}
}
}
-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,
- matrix box,
- gmx::ArrayRef<const real> lambda,
- real *dvdlambda)
+ ArrayRefWithPadding<RVec> xOld,
+ ArrayRef<RVec> x_init,
+ ArrayRefWithPadding<RVec> xCurrent,
+ ArrayRef<RVec> f,
+ ArrayRef<RVec> acc_dir,
+ const matrix box,
+ ArrayRef<const real> lambda,
+ real* dvdlambda)
{
- rvec *xnold, *xnew;
- double dt, w_dt;
- int n, d;
- unsigned short *ptype;
+ double dt, w_dt;
+ int n, d;
- if (DOMAINDECOMP(cr))
+ if (haveDDAtomOrdering(*cr))
{
n = dd_ac1;
}
{
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;
-
- ptype = md->ptype;
+ 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());
- dt = ir->delta_t;
+ auto* ptype = md.ptype;
+ auto invmass = gmx::arrayRefFromArray(md.invmass, md.nr);
+ dt = ir->delta_t;
/* Does NOT work with freeze or acceleration groups (yet) */
for (n = 0; n < end; n++)
{
- w_dt = md->invmass[n]*dt;
+ w_dt = invmass[n] * dt;
for (d = 0; d < DIM; d++)
{
- if ((ptype[n] != eptVSite) && (ptype[n] != eptShell))
+ if ((ptype[n] != ParticleType::VSite) && (ptype[n] != ParticleType::Shell))
{
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);
+ bool needsLogging = false;
+ bool computeEnergy = false;
+ bool computeVirial = false;
+ constr->apply(needsLogging,
+ computeEnergy,
+ step,
+ 0,
+ 1.0,
+ xCurrent,
+ shfc->adir_xnold.arrayRefWithPadding(),
+ {},
+ box,
+ lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Bonded)],
+ &(dvdlambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Bonded)]),
+ {},
+ computeVirial,
+ nullptr,
+ gmx::ConstraintVariable::Positions);
+ constr->apply(needsLogging,
+ computeEnergy,
+ step,
+ 0,
+ 1.0,
+ xCurrent,
+ shfc->adir_xnew.arrayRefWithPadding(),
+ {},
+ box,
+ lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Bonded)],
+ &(dvdlambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Bonded)]),
+ {},
+ computeVirial,
+ 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] * 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(needsLogging,
+ computeEnergy,
+ step,
+ 0,
+ 1.0,
+ xOld,
+ shfc->adir_xnew.arrayRefWithPadding(),
+ acc_dir,
+ box,
+ lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Bonded)],
+ &(dvdlambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Bonded)]),
+ {},
+ computeVirial,
+ 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,
- gmx_bool bDoNS,
- int force_flags,
- gmx_localtop_t *top,
- gmx::Constraints *constr,
- gmx_enerdata_t *enerd,
- t_fcdata *fcd,
- t_state *state,
- 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::PpForceWorkload *ppForceWorkload,
- 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,
+ int natoms,
+ ArrayRefWithPadding<RVec> xPadded,
+ ArrayRefWithPadding<RVec> vPadded,
+ const matrix box,
+ ArrayRef<real> lambda,
+ const history_t* hist,
+ gmx::ForceBuffersView* f,
+ tensor force_vir,
+ const t_mdatoms& md,
+ CpuPpLongRangeNonbondeds* longRangeNonbondeds,
+ t_nrnb* nrnb,
+ gmx_wallcycle* wcycle,
+ gmx_shellfc_t* shfc,
+ t_forcerec* fr,
+ gmx::MdrunScheduleWorkload* runScheduleWork,
+ double t,
+ rvec mu_tot,
+ gmx::VirtualSitesHandler* vsite,
+ const DDBalanceRegionHandler& ddBalanceRegionHandler)
{
- 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, cg0, cg1;
- int nflexcon, number_steps, 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;
-
- idef = &top->idef;
-
- if (DOMAINDECOMP(cr))
+ 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 */
+
+ 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;
+
+ if (haveDDAtomOrdering(*cr))
{
- nat = dd_natoms_vsite(cr->dd);
+ nat = dd_natoms_vsite(*cr->dd);
if (nflexcon > 0)
{
- dd_get_constraint_range(cr->dd, &dd_ac0, &dd_ac1);
+ dd_get_constraint_range(*cr->dd, &dd_ac0, &dd_ac1);
nat = std::max(nat, dd_ac1);
}
}
else
{
- nat = state->natoms;
+ nat = natoms;
}
for (i = 0; (i < 2); i++)
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 && !haveDDAtomOrdering(*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.
*/
- if (inputrec->cutoff_scheme == ecutsVERLET)
- {
- auto xRef = state->x.arrayRefWithPadding().paddedArrayRef();
- put_atoms_in_box_omp(fr->ePBC, state->box, xRef.subArray(0, md->homenr), gmx_omp_nthreads_get(emntDefault));
- }
- else
- {
- cg0 = 0;
- cg1 = top->cgs.nr;
- put_charge_groups_in_box(fplog, cg0, cg1, fr->ePBC, state->box,
- &(top->cgs), state->x.rvec_array(), fr->cg_cm);
- }
-
- if (graph)
- {
- mk_mshift(fplog, graph, fr->ePBC, state->box, state->x.rvec_array());
- }
- }
-
- /* After this all coordinate arrays will contain whole charge groups */
- if (graph)
- {
- shift_self(graph, state->box, state->x.rvec_array());
+ put_atoms_in_box_omp(
+ fr->pbcType, box, x.subArray(0, md.homenr), gmx_omp_nthreads_get(ModuleMultiThread::Default));
}
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 x = makeArrayRef(state->x);
- auto v = makeArrayRef(state->v);
+ 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] =
- x[i][d] - v[i][d]*inputrec->delta_t;
+ x_old[i][d] = x[i][d] - v[i][d] * inputrec->delta_t;
}
}
}
+ auto massT = gmx::arrayRefFromArray(md.massT, md.nr);
/* 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))
- {
- predict_shells(fplog, state->x.rvec_array(), state->v.rvec_array(), inputrec->delta_t, nshell, shell,
- md->massT, nullptr, bInit);
- }
-
- /* do_force expected the charge groups to be in the box */
- if (graph)
+ if (shfc->predictShells && !bCont && (EI_STATE_VELOCITY(inputrec->eI) || bInit))
{
- unshift_self(graph, state->box, state->x.rvec_array());
+ predict_shells(fplog, x, v, inputrec->delta_t, shells, massT, bInit);
}
/* Calculate the forces first time around */
if (gmx_debug_at)
{
- pr_rvecs(debug, 0, "x b4 do_force", state->x.rvec_array(), 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,
- mdstep, nrnb, wcycle, top,
- state->box, state->x.arrayRefWithPadding(), &state->hist,
- forceWithPadding[Min], force_vir, md, enerd, fcd,
- state->lambda, graph,
- fr, ppForceWorkload, vsite, mu_tot, t, nullptr,
+ int shellfc_flags = force_flags | (bVerbose ? GMX_FORCE_ENERGY : 0);
+ gmx::ForceBuffersView forceViewInit = gmx::ForceBuffersView(forceWithPadding[Min], {}, false);
+ do_force(fplog,
+ cr,
+ ms,
+ *inputrec,
+ nullptr,
+ enforcedRotation,
+ imdSession,
+ pull_work,
+ mdstep,
+ nrnb,
+ wcycle,
+ top,
+ box,
+ xPadded,
+ hist,
+ &forceViewInit,
+ force_vir,
+ &md,
+ enerd,
+ lambda,
+ fr,
+ runScheduleWork,
+ vsite,
+ mu_tot,
+ t,
+ nullptr,
+ longRangeNonbondeds,
(bDoNS ? GMX_FORCE_NS : 0) | shellfc_flags,
ddBalanceRegionHandler);
if (nflexcon)
{
init_adir(shfc,
- constr, inputrec, cr, dd_ac1, mdstep, md, end,
- shfc->x_old, state->x.rvec_array(), state->x.rvec_array(), as_rvec_array(force[Min].data()),
+ constr,
+ inputrec,
+ cr,
+ dd_ac1,
+ mdstep,
+ md,
+ end,
+ shfc->x_old.arrayRefWithPadding(),
+ x,
+ xPadded,
+ force[Min],
shfc->acc_dir,
- state->box, state->lambda, &dum);
+ box,
+ lambda,
+ &dum);
for (i = 0; i < end; i++)
{
- sf_dir += md->massT[i]*norm2(shfc->acc_dir[i]);
+ sf_dir += massT[i] * norm2(shfc->acc_dir[i]);
}
}
- sum_epot(&(enerd->grpp), enerd->term);
+ accumulatePotentialEnergies(enerd, lambda, inputrec->fepvals.get());
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)
{
if (gmx_debug_at)
{
- pr_rvecs(debug, 0, "force0", as_rvec_array(force[Min].data()), md->nr);
+ 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(state->x.begin(),
- state->x.end(),
+ std::copy(xPadded.paddedArrayRef().begin(),
+ xPadded.paddedArrayRef().end(),
posWithPadding[Min].paddedArrayRef().begin());
- std::copy(state->x.begin(),
- state->x.end(),
+ std::copy(xPadded.paddedArrayRef().begin(),
+ xPadded.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));
}
/* 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, state->v.rvec_array(),
- idef->iparams, idef->il,
- fr->ePBC, fr->bMolPBC, cr, state->box);
+ vsite->construct(pos[Min], v, box, gmx::VSiteOperation::PositionsAndVelocities);
}
if (nflexcon)
{
init_adir(shfc,
- constr, inputrec, cr, dd_ac1, mdstep, md, end,
- x_old, state->x.rvec_array(),
- as_rvec_array(pos[Min].data()),
- as_rvec_array(force[Min].data()), acc_dir,
- state->box, state->lambda, &dum);
-
- directional_sd(pos[Min], pos[Try], acc_dir, end, fr->fc_stepsize);
+ 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], shfc->acc_dir, end, fr->fc_stepsize);
}
/* New positions, Steepest descent */
- shell_pos_sd(pos[Min], pos[Try], force[Min], nshell, shell, count);
-
- /* do_force expected the charge groups to be in the box */
- if (graph)
- {
- unshift_self(graph, state->box, as_rvec_array(pos[Try].data()));
- }
+ shell_pos_sd(pos[Min], pos[Try], force[Min], shells, count);
if (gmx_debug_at)
{
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,
- 1, nrnb, wcycle,
- top, state->box, posWithPadding[Try], &state->hist,
- forceWithPadding[Try], force_vir,
- md, enerd, fcd, state->lambda, graph,
- fr, ppForceWorkload, vsite, mu_tot, t, nullptr,
+ gmx::ForceBuffersView forceViewTry = gmx::ForceBuffersView(forceWithPadding[Try], {}, false);
+ do_force(fplog,
+ cr,
+ ms,
+ *inputrec,
+ nullptr,
+ enforcedRotation,
+ imdSession,
+ pull_work,
+ 1,
+ nrnb,
+ wcycle,
+ top,
+ box,
+ posWithPadding[Try],
+ hist,
+ &forceViewTry,
+ force_vir,
+ &md,
+ enerd,
+ lambda,
+ fr,
+ runScheduleWork,
+ vsite,
+ mu_tot,
+ t,
+ nullptr,
+ longRangeNonbondeds,
shellfc_flags,
ddBalanceRegionHandler);
- sum_epot(&(enerd->grpp), enerd->term);
+ accumulatePotentialEnergies(enerd, lambda, inputrec->fepvals.get());
if (gmx_debug_at)
{
pr_rvecs(debug, 0, "RELAX: force[Min]", as_rvec_array(force[Min].data()), homenr);
if (nflexcon)
{
init_adir(shfc,
- constr, inputrec, cr, dd_ac1, mdstep, md, end,
- x_old, state->x.rvec_array(),
- as_rvec_array(pos[Try].data()),
- as_rvec_array(force[Try].data()),
- acc_dir, state->box, state->lambda, &dum);
-
+ 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]);
+ sf_dir += 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 v = makeArrayRef(state->v);
+ invdt = 1 / inputrec->delta_t;
for (i = 0; i < end; i++)
{
for (d = 0; d < DIM; d++)
{
- v[i][d] += (pos[Try][i][d] - pos[Min][i][d])*invdt;
+ v[i][d] += (pos[Try][i][d] - pos[Min][i][d]) * invdt;
}
}
}
- Min = Try;
+ Min = Try;
}
else
{
- decrease_step_size(nshell, shell);
+ decrease_step_size(shells);
}
}
shfc->numForceEvaluations += count;
{
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]);
+ 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",
- gmx_step_str(mdstep, sbuf), number_steps, df[Min]);
+ gmx_step_str(mdstep, sbuf),
+ number_steps,
+ df[Min]);
}
/* Copy back the coordinates and the forces */
- std::copy(pos[Min].begin(), pos[Min].end(), makeArrayRef(state->x).data());
- std::copy(force[Min].begin(), force[Min].end(), f.unpaddedArrayRef().begin());
+ std::copy(pos[Min].begin(), pos[Min].end(), x.data());
+ std::copy(force[Min].begin(), force[Min].end(), f->force().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);
- fprintf(fplog, "Average number of force evaluations per MD step: %.2f\n\n",
- shfc->numForceEvaluations/numStepsAsDouble);
+ fprintf(fplog,
+ "Fraction of iterations that converged: %.2f %%\n",
+ (shfc->numConvergedIterations * 100.0) / numStepsAsDouble);
+ fprintf(fplog,
+ "Average number of force evaluations per MD step: %.2f\n\n",
+ shfc->numForceEvaluations / numStepsAsDouble);
}
- // TODO Deallocate memory in shfc
+ delete shfc;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff