*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, 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 "grompp.h"
+#include <array>
#include <cerrno>
#include <climits>
#include <cmath>
#include <cstring>
#include <algorithm>
+#include <memory>
#include <vector>
#include <sys/types.h>
-#include "gromacs/awh/read-params.h"
+#include "gromacs/applied_forces/awh/read_params.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/compat/make_unique.h"
-#include "gromacs/ewald/ewald-utils.h"
+#include "gromacs/ewald/ewald_utils.h"
#include "gromacs/ewald/pme.h"
#include "gromacs/fft/calcgrid.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/gmxpreprocess/convparm.h"
#include "gromacs/gmxpreprocess/gen_maxwell_velocities.h"
#include "gromacs/gmxpreprocess/gpp_atomtype.h"
-#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp_impl.h"
#include "gromacs/gmxpreprocess/notset.h"
#include "gromacs/gmxpreprocess/readir.h"
#include "gromacs/gmxpreprocess/tomorse.h"
#include "gromacs/mdlib/calc_verletbuf.h"
#include "gromacs/mdlib/compute_io.h"
#include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/md_support.h"
#include "gromacs/mdlib/perf_est.h"
-#include "gromacs/mdlib/sim_util.h"
-#include "gromacs/mdrunutility/mdmodules.h"
+#include "gromacs/mdlib/vsite.h"
+#include "gromacs/mdrun/mdmodules.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/nblist.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/filestream.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/keyvaluetreebuilder.h"
+#include "gromacs/utility/listoflists.h"
+#include "gromacs/utility/logger.h"
+#include "gromacs/utility/loggerbuilder.h"
+#include "gromacs/utility/mdmodulesnotifiers.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/snprintf.h"
-static int rm_interactions(int ifunc, int nrmols, t_molinfo mols[])
+/* TODO The implementation details should move to their own source file. */
+InteractionOfType::InteractionOfType(gmx::ArrayRef<const int> atoms,
+ gmx::ArrayRef<const real> params,
+ const std::string& name) :
+ atoms_(atoms.begin(), atoms.end()), interactionTypeName_(name)
{
- int i, n;
+ GMX_RELEASE_ASSERT(
+ params.size() <= forceParam_.size(),
+ gmx::formatString("Cannot have more parameters than the maximum number possible (%d)", MAXFORCEPARAM)
+ .c_str());
+ std::array<real, MAXFORCEPARAM>::iterator forceParamIt = forceParam_.begin();
+ for (const auto param : params)
+ {
+ *forceParamIt++ = param;
+ }
+ while (forceParamIt != forceParam_.end())
+ {
+ *forceParamIt++ = NOTSET;
+ }
+}
+
+const int& InteractionOfType::ai() const
+{
+ GMX_RELEASE_ASSERT(!atoms_.empty(), "Need to have at least one atom set");
+ return atoms_[0];
+}
+
+const int& InteractionOfType::aj() const
+{
+ GMX_RELEASE_ASSERT(atoms_.size() > 1, "Need to have at least two atoms set");
+ return atoms_[1];
+}
+
+const int& InteractionOfType::ak() const
+{
+ GMX_RELEASE_ASSERT(atoms_.size() > 2, "Need to have at least three atoms set");
+ return atoms_[2];
+}
+
+const int& InteractionOfType::al() const
+{
+ GMX_RELEASE_ASSERT(atoms_.size() > 3, "Need to have at least four atoms set");
+ return atoms_[3];
+}
+
+const int& InteractionOfType::am() const
+{
+ GMX_RELEASE_ASSERT(atoms_.size() > 4, "Need to have at least five atoms set");
+ return atoms_[4];
+}
+
+const real& InteractionOfType::c0() const
+{
+ return forceParam_[0];
+}
+
+const real& InteractionOfType::c1() const
+{
+ return forceParam_[1];
+}
+
+const real& InteractionOfType::c2() const
+{
+ return forceParam_[2];
+}
+
+const std::string& InteractionOfType::interactionTypeName() const
+{
+ return interactionTypeName_;
+}
+
+void InteractionOfType::sortBondAtomIds()
+{
+ if (aj() < ai())
+ {
+ std::swap(atoms_[0], atoms_[1]);
+ }
+}
+
+void InteractionOfType::sortAngleAtomIds()
+{
+ if (ak() < ai())
+ {
+ std::swap(atoms_[0], atoms_[2]);
+ }
+}
+
+void InteractionOfType::sortDihedralAtomIds()
+{
+ if (al() < ai())
+ {
+ std::swap(atoms_[0], atoms_[3]);
+ std::swap(atoms_[1], atoms_[2]);
+ }
+}
- n = 0;
+void InteractionOfType::sortAtomIds()
+{
+ if (isBond())
+ {
+ sortBondAtomIds();
+ }
+ else if (isAngle())
+ {
+ sortAngleAtomIds();
+ }
+ else if (isDihedral())
+ {
+ sortDihedralAtomIds();
+ }
+ else
+ {
+ GMX_THROW(gmx::InternalError(
+ "Can not sort parameters other than bonds, angles or dihedrals"));
+ }
+};
+
+void InteractionOfType::setForceParameter(int pos, real value)
+{
+ GMX_RELEASE_ASSERT(pos < MAXFORCEPARAM,
+ "Can't set parameter beyond the maximum number of parameters");
+ forceParam_[pos] = value;
+}
+
+void MoleculeInformation::initMolInfo()
+{
+ init_block(&mols);
+ excls.clear();
+ init_t_atoms(&atoms, 0, FALSE);
+}
+
+void MoleculeInformation::partialCleanUp()
+{
+ done_block(&mols);
+}
+
+void MoleculeInformation::fullCleanUp()
+{
+ done_atom(&atoms);
+ done_block(&mols);
+}
+
+static int rm_interactions(int ifunc, gmx::ArrayRef<MoleculeInformation> mols)
+{
+ int n = 0;
/* For all the molecule types */
- for (i = 0; i < nrmols; i++)
+ for (auto& mol : mols)
{
- n += mols[i].plist[ifunc].nr;
- mols[i].plist[ifunc].nr = 0;
+ n += mol.interactions[ifunc].size();
+ mol.interactions[ifunc].interactionTypes.clear();
}
return n;
}
-static int check_atom_names(const char *fn1, const char *fn2,
- gmx_mtop_t *mtop, const t_atoms *at)
+static int check_atom_names(const char* fn1,
+ const char* fn2,
+ gmx_mtop_t* mtop,
+ const t_atoms* at,
+ const gmx::MDLogger& logger)
{
int m, i, j, nmismatch;
- t_atoms *tat;
-#define MAXMISMATCH 20
+ t_atoms* tat;
+
+ constexpr int c_maxNumberOfMismatches = 20;
if (mtop->natoms != at->nr)
{
nmismatch = 0;
i = 0;
- for (const gmx_molblock_t &molb : mtop->molblock)
+ for (const gmx_molblock_t& molb : mtop->molblock)
{
tat = &mtop->moltype[molb.type].atoms;
for (m = 0; m < molb.nmol; m++)
{
for (j = 0; j < tat->nr; j++)
{
- if (strcmp( *(tat->atomname[j]), *(at->atomname[i]) ) != 0)
+ if (strcmp(*(tat->atomname[j]), *(at->atomname[i])) != 0)
{
- if (nmismatch < MAXMISMATCH)
+ if (nmismatch < c_maxNumberOfMismatches)
{
- fprintf(stderr,
- "Warning: atom name %d in %s and %s does not match (%s - %s)\n",
- i+1, fn1, fn2, *(tat->atomname[j]), *(at->atomname[i]));
+ GMX_LOG(logger.warning)
+ .asParagraph()
+ .appendTextFormatted(
+ "atom name %d in %s and %s does not match (%s - %s)",
+ i + 1,
+ fn1,
+ fn2,
+ *(tat->atomname[j]),
+ *(at->atomname[i]));
}
- else if (nmismatch == MAXMISMATCH)
+ else if (nmismatch == c_maxNumberOfMismatches)
{
- fprintf(stderr, "(more than %d non-matching atom names)\n", MAXMISMATCH);
+ GMX_LOG(logger.warning)
+ .asParagraph()
+ .appendTextFormatted("(more than %d non-matching atom names)",
+ c_maxNumberOfMismatches);
}
nmismatch++;
}
return nmismatch;
}
-static void check_eg_vs_cg(gmx_mtop_t *mtop)
-{
- int astart, m, cg, j, firstj;
- unsigned char firsteg, eg;
- gmx_moltype_t *molt;
-
- /* Go through all the charge groups and make sure all their
- * atoms are in the same energy group.
- */
-
- astart = 0;
- for (const gmx_molblock_t &molb : mtop->molblock)
- {
- molt = &mtop->moltype[molb.type];
- for (m = 0; m < molb.nmol; m++)
- {
- for (cg = 0; cg < molt->cgs.nr; cg++)
- {
- /* Get the energy group of the first atom in this charge group */
- firstj = astart + molt->cgs.index[cg];
- firsteg = getGroupType(&mtop->groups, egcENER, firstj);
- for (j = molt->cgs.index[cg]+1; j < molt->cgs.index[cg+1]; j++)
- {
- eg = getGroupType(&mtop->groups, egcENER, astart+j);
- if (eg != firsteg)
- {
- gmx_fatal(FARGS, "atoms %d and %d in charge group %d of molecule type '%s' are in different energy groups",
- firstj+1, astart+j+1, cg+1, *molt->name);
- }
- }
- }
- astart += molt->atoms.nr;
- }
- }
-}
-
-static void check_cg_sizes(const char *topfn, const t_block *cgs, warninp_t wi)
-{
- int maxsize, cg;
- char warn_buf[STRLEN];
-
- maxsize = 0;
- for (cg = 0; cg < cgs->nr; cg++)
- {
- maxsize = std::max(maxsize, cgs->index[cg+1]-cgs->index[cg]);
- }
-
- if (maxsize > MAX_CHARGEGROUP_SIZE)
- {
- gmx_fatal(FARGS, "The largest charge group contains %d atoms. The maximum is %d.", maxsize, MAX_CHARGEGROUP_SIZE);
- }
- else if (maxsize > 10)
- {
- set_warning_line(wi, topfn, -1);
- sprintf(warn_buf,
- "The largest charge group contains %d atoms.\n"
- "Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts.\n"
- "For efficiency and accuracy, charge group should consist of a few atoms.\n"
- "For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.",
- maxsize);
- warning_note(wi, warn_buf);
- }
-}
-
-static void check_bonds_timestep(const gmx_mtop_t *mtop, double dt, warninp_t wi)
+static void check_bonds_timestep(const gmx_mtop_t* mtop, double dt, warninp* wi)
{
/* This check is not intended to ensure accurate integration,
* rather it is to signal mistakes in the mdp settings.
* of dt=1 fs without constraints and dt=2 fs with only H-bond constraints
* we set the note limit to 10.
*/
- int min_steps_warn = 5;
- int min_steps_note = 10;
- int ftype;
- int i, a1, a2, w_a1, w_a2, j;
- real twopi2, limit2, fc, re, m1, m2, period2, w_period2;
- bool bFound, bWater, bWarn;
- char warn_buf[STRLEN];
+ int min_steps_warn = 5;
+ int min_steps_note = 10;
+ int ftype;
+ int i, a1, a2, w_a1, w_a2, j;
+ real twopi2, limit2, fc, re, m1, m2, period2, w_period2;
+ bool bFound, bWater, bWarn;
/* Get the interaction parameters */
gmx::ArrayRef<const t_iparams> ip = mtop->ffparams.iparams;
- twopi2 = gmx::square(2*M_PI);
+ twopi2 = gmx::square(2 * M_PI);
- limit2 = gmx::square(min_steps_note*dt);
+ limit2 = gmx::square(min_steps_note * dt);
- w_a1 = w_a2 = -1;
- w_period2 = -1.0;
+ w_a1 = w_a2 = -1;
+ w_period2 = -1.0;
- const gmx_moltype_t *w_moltype = nullptr;
- for (const gmx_moltype_t &moltype : mtop->moltype)
+ const gmx_moltype_t* w_moltype = nullptr;
+ for (const gmx_moltype_t& moltype : mtop->moltype)
{
- const t_atom *atom = moltype.atoms.atom;
- const InteractionLists &ilist = moltype.ilist;
- const InteractionList &ilc = ilist[F_CONSTR];
- const InteractionList &ils = ilist[F_SETTLE];
+ const t_atom* atom = moltype.atoms.atom;
+ const InteractionLists& ilist = moltype.ilist;
+ const InteractionList& ilc = ilist[F_CONSTR];
+ const InteractionList& ils = ilist[F_SETTLE];
for (ftype = 0; ftype < F_NRE; ftype++)
{
if (!(ftype == F_BONDS || ftype == F_G96BONDS || ftype == F_HARMONIC))
continue;
}
- const InteractionList &ilb = ilist[ftype];
+ const InteractionList& ilb = ilist[ftype];
for (i = 0; i < ilb.size(); i += 3)
{
fc = ip[ilb.iatoms[i]].harmonic.krA;
if (ftype == F_G96BONDS)
{
/* Convert squared sqaure fc to harmonic fc */
- fc = 2*fc*re;
+ fc = 2 * fc * re;
}
- a1 = ilb.iatoms[i+1];
- a2 = ilb.iatoms[i+2];
+ a1 = ilb.iatoms[i + 1];
+ a2 = ilb.iatoms[i + 2];
m1 = atom[a1].m;
m2 = atom[a2].m;
if (fc > 0 && m1 > 0 && m2 > 0)
{
- period2 = twopi2*m1*m2/((m1 + m2)*fc);
+ period2 = twopi2 * m1 * m2 / ((m1 + m2) * fc);
}
else
{
}
if (debug)
{
- fprintf(debug, "fc %g m1 %g m2 %g period %g\n",
- fc, m1, m2, std::sqrt(period2));
+ fprintf(debug, "fc %g m1 %g m2 %g period %g\n", fc, m1, m2, std::sqrt(period2));
}
if (period2 < limit2)
{
bFound = false;
for (j = 0; j < ilc.size(); j += 3)
{
- if ((ilc.iatoms[j+1] == a1 && ilc.iatoms[j+2] == a2) ||
- (ilc.iatoms[j+1] == a2 && ilc.iatoms[j+2] == a1))
+ if ((ilc.iatoms[j + 1] == a1 && ilc.iatoms[j + 2] == a2)
+ || (ilc.iatoms[j + 1] == a2 && ilc.iatoms[j + 2] == a1))
{
bFound = true;
}
}
for (j = 0; j < ils.size(); j += 4)
{
- if ((a1 == ils.iatoms[j+1] || a1 == ils.iatoms[j+2] || a1 == ils.iatoms[j+3]) &&
- (a2 == ils.iatoms[j+1] || a2 == ils.iatoms[j+2] || a2 == ils.iatoms[j+3]))
+ if ((a1 == ils.iatoms[j + 1] || a1 == ils.iatoms[j + 2] || a1 == ils.iatoms[j + 3])
+ && (a2 == ils.iatoms[j + 1] || a2 == ils.iatoms[j + 2]
+ || a2 == ils.iatoms[j + 3]))
{
bFound = true;
}
}
- if (!bFound &&
- (w_moltype == nullptr || period2 < w_period2))
+ if (!bFound && (w_moltype == nullptr || period2 < w_period2))
{
w_moltype = &moltype;
w_a1 = a1;
if (w_moltype != nullptr)
{
- bWarn = (w_period2 < gmx::square(min_steps_warn*dt));
+ bWarn = (w_period2 < gmx::square(min_steps_warn * dt));
/* A check that would recognize most water models */
- bWater = ((*w_moltype->atoms.atomname[0])[0] == 'O' &&
- w_moltype->atoms.nr <= 5);
- sprintf(warn_buf, "The bond in molecule-type %s between atoms %d %s and %d %s has an estimated oscillational period of %.1e ps, which is less than %d times the time step of %.1e ps.\n"
+ bWater = ((*w_moltype->atoms.atomname[0])[0] == 'O' && w_moltype->atoms.nr <= 5);
+ std::string warningMessage = gmx::formatString(
+ "The bond in molecule-type %s between atoms %d %s and %d %s has an estimated "
+ "oscillational period of %.1e ps, which is less than %d times the time step of "
+ "%.1e ps.\n"
"%s",
*w_moltype->name,
- w_a1+1, *w_moltype->atoms.atomname[w_a1],
- w_a2+1, *w_moltype->atoms.atomname[w_a2],
- std::sqrt(w_period2), bWarn ? min_steps_warn : min_steps_note, dt,
- bWater ?
- "Maybe you asked for fexible water." :
- "Maybe you forgot to change the constraints mdp option.");
+ w_a1 + 1,
+ *w_moltype->atoms.atomname[w_a1],
+ w_a2 + 1,
+ *w_moltype->atoms.atomname[w_a2],
+ std::sqrt(w_period2),
+ bWarn ? min_steps_warn : min_steps_note,
+ dt,
+ bWater ? "Maybe you asked for fexible water."
+ : "Maybe you forgot to change the constraints mdp option.");
if (bWarn)
{
- warning(wi, warn_buf);
+ warning(wi, warningMessage.c_str());
}
else
{
- warning_note(wi, warn_buf);
+ warning_note(wi, warningMessage.c_str());
}
}
}
-static void check_vel(gmx_mtop_t *mtop, rvec v[])
+static void check_vel(gmx_mtop_t* mtop, rvec v[])
{
- gmx_mtop_atomloop_all_t aloop;
- const t_atom *atom;
- int a;
-
- aloop = gmx_mtop_atomloop_all_init(mtop);
- while (gmx_mtop_atomloop_all_next(aloop, &a, &atom))
+ for (const AtomProxy atomP : AtomRange(*mtop))
{
- if (atom->ptype == eptShell ||
- atom->ptype == eptBond ||
- atom->ptype == eptVSite)
+ const t_atom& local = atomP.atom();
+ int i = atomP.globalAtomNumber();
+ if (local.ptype == ParticleType::Shell || local.ptype == ParticleType::Bond
+ || local.ptype == ParticleType::VSite)
{
- clear_rvec(v[a]);
+ clear_rvec(v[i]);
}
}
}
-static void check_shells_inputrec(gmx_mtop_t *mtop,
- t_inputrec *ir,
- warninp_t wi)
+static void check_shells_inputrec(gmx_mtop_t* mtop, t_inputrec* ir, warninp* wi)
{
- gmx_mtop_atomloop_all_t aloop;
- const t_atom *atom;
- int a, nshells = 0;
- char warn_buf[STRLEN];
+ int nshells = 0;
- aloop = gmx_mtop_atomloop_all_init(mtop);
- while (gmx_mtop_atomloop_all_next(aloop, &a, &atom))
+ for (const AtomProxy atomP : AtomRange(*mtop))
{
- if (atom->ptype == eptShell ||
- atom->ptype == eptBond)
+ const t_atom& local = atomP.atom();
+ if (local.ptype == ParticleType::Shell || local.ptype == ParticleType::Bond)
{
nshells++;
}
if ((nshells > 0) && (ir->nstcalcenergy != 1))
{
set_warning_line(wi, "unknown", -1);
- snprintf(warn_buf, STRLEN,
- "There are %d shells, changing nstcalcenergy from %d to 1",
- nshells, ir->nstcalcenergy);
+ std::string warningMessage = gmx::formatString(
+ "There are %d shells, changing nstcalcenergy from %d to 1", nshells, ir->nstcalcenergy);
ir->nstcalcenergy = 1;
- warning(wi, warn_buf);
+ warning(wi, warningMessage.c_str());
}
}
/* TODO Decide whether this function can be consolidated with
* gmx_mtop_ftype_count */
-static int nint_ftype(gmx_mtop_t *mtop, t_molinfo *mi, int ftype)
+static int nint_ftype(gmx_mtop_t* mtop, gmx::ArrayRef<const MoleculeInformation> mi, int ftype)
{
int nint = 0;
- for (const gmx_molblock_t &molb : mtop->molblock)
+ for (const gmx_molblock_t& molb : mtop->molblock)
{
- nint += molb.nmol*mi[molb.type].plist[ftype].nr;
+ nint += molb.nmol * mi[molb.type].interactions[ftype].size();
}
return nint;
* in the order of use in the molblocks,
* unused molecule types are deleted.
*/
-static void renumber_moltypes(gmx_mtop_t *sys,
- int *nmolinfo, t_molinfo **molinfo)
+static void renumber_moltypes(gmx_mtop_t* sys, std::vector<MoleculeInformation>* molinfo)
{
- int *order, norder;
- t_molinfo *minew;
- snew(order, *nmolinfo);
- norder = 0;
- for (gmx_molblock_t &molblock : sys->molblock)
+ std::vector<int> order;
+ for (gmx_molblock_t& molblock : sys->molblock)
{
- int i;
- for (i = 0; i < norder; i++)
+ const auto found = std::find_if(order.begin(), order.end(), [&molblock](const auto& entry) {
+ return molblock.type == entry;
+ });
+ if (found == order.end())
{
- if (order[i] == molblock.type)
- {
- break;
- }
+ /* This type did not occur yet, add it */
+ order.push_back(molblock.type);
+ molblock.type = order.size() - 1;
}
- if (i == norder)
+ else
{
- /* This type did not occur yet, add it */
- order[norder] = molblock.type;
- /* Renumber the moltype in the topology */
- norder++;
+ molblock.type = std::distance(order.begin(), found);
}
- molblock.type = i;
}
/* We still need to reorder the molinfo structs */
- snew(minew, norder);
- for (int mi = 0; mi < *nmolinfo; mi++)
+ std::vector<MoleculeInformation> minew(order.size());
+ int index = 0;
+ for (auto& mi : *molinfo)
{
- int i;
- for (i = 0; i < norder; i++)
+ const auto found = std::find(order.begin(), order.end(), index);
+ if (found != order.end())
{
- if (order[i] == mi)
- {
- break;
- }
- }
- if (i == norder)
- {
- done_mi(&(*molinfo)[mi]);
+ int pos = std::distance(order.begin(), found);
+ minew[pos] = mi;
}
else
{
- minew[i] = (*molinfo)[mi];
+ // Need to manually clean up memory ....
+ mi.fullCleanUp();
}
+ index++;
}
- sfree(order);
- sfree(*molinfo);
- *nmolinfo = norder;
- *molinfo = minew;
+ *molinfo = minew;
}
-static void molinfo2mtop(int nmi, t_molinfo *mi, gmx_mtop_t *mtop)
+static void molinfo2mtop(gmx::ArrayRef<const MoleculeInformation> mi, gmx_mtop_t* mtop)
{
- mtop->moltype.resize(nmi);
- for (int m = 0; m < nmi; m++)
+ mtop->moltype.resize(mi.size());
+ int pos = 0;
+ for (const auto& mol : mi)
{
- gmx_moltype_t &molt = mtop->moltype[m];
- molt.name = mi[m].name;
- molt.atoms = mi[m].atoms;
+ gmx_moltype_t& molt = mtop->moltype[pos];
+ molt.name = mol.name;
+ molt.atoms = mol.atoms;
/* ilists are copied later */
- molt.cgs = mi[m].cgs;
- molt.excls = mi[m].excls;
+ molt.excls = mol.excls;
+ pos++;
}
}
-static void
-new_status(const char *topfile, const char *topppfile, const char *confin,
- t_gromppopts *opts, t_inputrec *ir, gmx_bool bZero,
- bool bGenVel, bool bVerbose, t_state *state,
- gpp_atomtype_t atype, gmx_mtop_t *sys,
- int *nmi, t_molinfo **mi, t_molinfo **intermolecular_interactions,
- t_params plist[],
- int *comb, double *reppow, real *fudgeQQ,
- gmx_bool bMorse,
- warninp_t wi)
+static void new_status(const char* topfile,
+ const char* topppfile,
+ const char* confin,
+ t_gromppopts* opts,
+ t_inputrec* ir,
+ gmx_bool bZero,
+ bool bGenVel,
+ bool bVerbose,
+ t_state* state,
+ PreprocessingAtomTypes* atypes,
+ gmx_mtop_t* sys,
+ std::vector<MoleculeInformation>* mi,
+ std::unique_ptr<MoleculeInformation>* intermolecular_interactions,
+ gmx::ArrayRef<InteractionsOfType> interactions,
+ CombinationRule* comb,
+ double* reppow,
+ real* fudgeQQ,
+ gmx_bool bMorse,
+ warninp* wi,
+ const gmx::MDLogger& logger)
{
- t_molinfo *molinfo = nullptr;
std::vector<gmx_molblock_t> molblock;
- int i, nrmols, nmismatch;
+ int i, nmismatch;
bool ffParametrizedWithHBondConstraints;
- char buf[STRLEN];
- char warn_buf[STRLEN];
/* TOPOLOGY processing */
- sys->name = do_top(bVerbose, topfile, topppfile, opts, bZero, &(sys->symtab),
- plist, comb, reppow, fudgeQQ,
- atype, &nrmols, &molinfo, intermolecular_interactions,
+ sys->name = do_top(bVerbose,
+ topfile,
+ topppfile,
+ opts,
+ bZero,
+ &(sys->symtab),
+ interactions,
+ comb,
+ reppow,
+ fudgeQQ,
+ atypes,
+ mi,
+ intermolecular_interactions,
ir,
&molblock,
&ffParametrizedWithHBondConstraints,
- wi);
+ wi,
+ logger);
sys->molblock.clear();
sys->natoms = 0;
- for (const gmx_molblock_t &molb : molblock)
+ for (const gmx_molblock_t& molb : molblock)
{
- if (!sys->molblock.empty() &&
- molb.type == sys->molblock.back().type)
+ if (!sys->molblock.empty() && molb.type == sys->molblock.back().type)
{
/* Merge consecutive blocks with the same molecule type */
sys->molblock.back().nmol += molb.nmol;
/* Add a new molblock to the topology */
sys->molblock.push_back(molb);
}
- sys->natoms += molb.nmol*molinfo[sys->molblock.back().type].atoms.nr;
+ sys->natoms += molb.nmol * (*mi)[sys->molblock.back().type].atoms.nr;
}
if (sys->molblock.empty())
{
gmx_fatal(FARGS, "No molecules were defined in the system");
}
- renumber_moltypes(sys, &nrmols, &molinfo);
+ renumber_moltypes(sys, mi);
if (bMorse)
{
- convert_harmonics(nrmols, molinfo, atype);
+ convert_harmonics(*mi, atypes);
}
- if (ir->eDisre == edrNone)
+ if (ir->eDisre == DistanceRestraintRefinement::None)
{
- i = rm_interactions(F_DISRES, nrmols, molinfo);
+ i = rm_interactions(F_DISRES, *mi);
if (i > 0)
{
set_warning_line(wi, "unknown", -1);
- sprintf(warn_buf, "disre = no, removed %d distance restraints", i);
- warning_note(wi, warn_buf);
+ std::string warningMessage =
+ gmx::formatString("disre = no, removed %d distance restraints", i);
+ warning_note(wi, warningMessage.c_str());
}
}
if (!opts->bOrire)
{
- i = rm_interactions(F_ORIRES, nrmols, molinfo);
+ i = rm_interactions(F_ORIRES, *mi);
if (i > 0)
{
set_warning_line(wi, "unknown", -1);
- sprintf(warn_buf, "orire = no, removed %d orientation restraints", i);
- warning_note(wi, warn_buf);
+ std::string warningMessage =
+ gmx::formatString("orire = no, removed %d orientation restraints", i);
+ warning_note(wi, warningMessage.c_str());
}
}
/* Copy structures from msys to sys */
- molinfo2mtop(nrmols, molinfo, sys);
+ molinfo2mtop(*mi, sys);
- gmx_mtop_finalize(sys);
+ sys->finalize();
/* Discourage using the, previously common, setup of applying constraints
* to all bonds with force fields that have been parametrized with H-bond
* constraints only. Do not print note with large timesteps or vsites.
*/
- if (opts->nshake == eshALLBONDS &&
- ffParametrizedWithHBondConstraints &&
- ir->delta_t < 0.0026 &&
- gmx_mtop_ftype_count(sys, F_VSITE3FD) == 0)
+ if (opts->nshake == eshALLBONDS && ffParametrizedWithHBondConstraints && ir->delta_t < 0.0026
+ && gmx_mtop_ftype_count(*sys, F_VSITE3FD) == 0)
{
set_warning_line(wi, "unknown", -1);
- warning_note(wi, "You are using constraints on all bonds, whereas the forcefield "
+ warning_note(wi,
+ "You are using constraints on all bonds, whereas the forcefield "
"has been parametrized only with constraints involving hydrogen atoms. "
- "We suggest using constraints = h-bonds instead, this will also improve performance.");
+ "We suggest using constraints = h-bonds instead, this will also improve "
+ "performance.");
}
/* COORDINATE file processing */
if (bVerbose)
{
- fprintf(stderr, "processing coordinates...\n");
+ GMX_LOG(logger.info).asParagraph().appendTextFormatted("processing coordinates...");
}
- t_topology *conftop;
- rvec *x = nullptr;
- rvec *v = nullptr;
+ t_topology* conftop;
+ rvec* x = nullptr;
+ rvec* v = nullptr;
snew(conftop, 1);
read_tps_conf(confin, conftop, nullptr, &x, &v, state->box, FALSE);
state->natoms = conftop->atoms.nr;
if (state->natoms != sys->natoms)
{
- gmx_fatal(FARGS, "number of coordinates in coordinate file (%s, %d)\n"
+ gmx_fatal(FARGS,
+ "number of coordinates in coordinate file (%s, %d)\n"
" does not match topology (%s, %d)",
- confin, state->natoms, topfile, sys->natoms);
+ confin,
+ state->natoms,
+ topfile,
+ sys->natoms);
}
/* It would be nice to get rid of the copies below, but we don't know
* a priori if the number of atoms in confin matches what we expect.
*/
- state->flags |= (1 << estX);
+ state->flags |= enumValueToBitMask(StateEntry::X);
if (v != nullptr)
{
- state->flags |= (1 << estV);
+ state->flags |= enumValueToBitMask(StateEntry::V);
}
state_change_natoms(state, state->natoms);
- std::copy(x, x+state->natoms, state->x.data());
+ std::copy(x, x + state->natoms, state->x.data());
sfree(x);
if (v != nullptr)
{
- std::copy(v, v+state->natoms, state->v.data());
+ std::copy(v, v + state->natoms, state->v.data());
sfree(v);
}
/* This call fixes the box shape for runs with pressure scaling */
set_box_rel(ir, state);
- nmismatch = check_atom_names(topfile, confin, sys, &conftop->atoms);
+ nmismatch = check_atom_names(topfile, confin, sys, &conftop->atoms, logger);
done_top(conftop);
sfree(conftop);
if (nmismatch)
{
- sprintf(buf, "%d non-matching atom name%s\n"
+ std::string warningMessage = gmx::formatString(
+ "%d non-matching atom name%s\n"
"atom names from %s will be used\n"
"atom names from %s will be ignored\n",
- nmismatch, (nmismatch == 1) ? "" : "s", topfile, confin);
- warning(wi, buf);
- }
-
- /* If using the group scheme, make sure charge groups are made whole to avoid errors
- * in calculating charge group size later on
- */
- if (ir->cutoff_scheme == ecutsGROUP && ir->ePBC != epbcNONE)
- {
- // Need temporary rvec for coordinates
- do_pbc_first_mtop(nullptr, ir->ePBC, state->box, sys, state->x.rvec_array());
+ nmismatch,
+ (nmismatch == 1) ? "" : "s",
+ topfile,
+ confin);
+ warning(wi, warningMessage.c_str());
}
/* Do more checks, mostly related to constraints */
if (bVerbose)
{
- fprintf(stderr, "double-checking input for internal consistency...\n");
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted("double-checking input for internal consistency...");
}
{
- bool bHasNormalConstraints = 0 < (nint_ftype(sys, molinfo, F_CONSTR) +
- nint_ftype(sys, molinfo, F_CONSTRNC));
- bool bHasAnyConstraints = bHasNormalConstraints || 0 < nint_ftype(sys, molinfo, F_SETTLE);
- double_check(ir, state->box,
- bHasNormalConstraints,
- bHasAnyConstraints,
- wi);
+ bool bHasNormalConstraints =
+ 0 < (nint_ftype(sys, *mi, F_CONSTR) + nint_ftype(sys, *mi, F_CONSTRNC));
+ bool bHasAnyConstraints = bHasNormalConstraints || 0 < nint_ftype(sys, *mi, F_SETTLE);
+ double_check(ir, state->box, bHasNormalConstraints, bHasAnyConstraints, wi);
}
if (bGenVel)
{
- real *mass;
- gmx_mtop_atomloop_all_t aloop;
- const t_atom *atom;
+ real* mass;
snew(mass, state->natoms);
- aloop = gmx_mtop_atomloop_all_init(sys);
- while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
+ for (const AtomProxy atomP : AtomRange(*sys))
{
- mass[i] = atom->m;
+ const t_atom& local = atomP.atom();
+ int i = atomP.globalAtomNumber();
+ mass[i] = local.m;
}
if (opts->seed == -1)
{
opts->seed = static_cast<int>(gmx::makeRandomSeed());
- fprintf(stderr, "Setting gen_seed to %d\n", opts->seed);
+ GMX_LOG(logger.info).asParagraph().appendTextFormatted("Setting gen_seed to %d", opts->seed);
}
- state->flags |= (1 << estV);
- maxwell_speed(opts->tempi, opts->seed, sys, state->v.rvec_array());
+ state->flags |= enumValueToBitMask(StateEntry::V);
+ maxwell_speed(opts->tempi, opts->seed, sys, state->v.rvec_array(), logger);
- stop_cm(stdout, state->natoms, mass, state->x.rvec_array(), state->v.rvec_array());
+ stop_cm(logger, state->natoms, mass, state->x.rvec_array(), state->v.rvec_array());
sfree(mass);
}
-
- *nmi = nrmols;
- *mi = molinfo;
}
-static void copy_state(const char *slog, t_trxframe *fr,
- bool bReadVel, t_state *state,
- double *use_time)
+static void copy_state(const char* slog, t_trxframe* fr, bool bReadVel, t_state* state, double* use_time)
{
if (fr->not_ok & FRAME_NOT_OK)
{
}
if (!fr->bX)
{
- gmx_fatal(FARGS, "Did not find a frame with coordinates in file %s",
- slog);
+ gmx_fatal(FARGS, "Did not find a frame with coordinates in file %s", slog);
}
- std::copy(fr->x, fr->x+state->natoms, state->x.data());
+ std::copy(fr->x, fr->x + state->natoms, state->x.data());
if (bReadVel)
{
if (!fr->bV)
{
gmx_incons("Trajecory frame unexpectedly does not contain velocities");
}
- std::copy(fr->v, fr->v+state->natoms, state->v.data());
+ std::copy(fr->v, fr->v + state->natoms, state->v.data());
}
if (fr->bBox)
{
*use_time = fr->time;
}
-static void cont_status(const char *slog, const char *ener,
- bool bNeedVel, bool bGenVel, real fr_time,
- t_inputrec *ir, t_state *state,
- gmx_mtop_t *sys,
- const gmx_output_env_t *oenv)
+static void cont_status(const char* slog,
+ const char* ener,
+ bool bNeedVel,
+ bool bGenVel,
+ real fr_time,
+ t_inputrec* ir,
+ t_state* state,
+ gmx_mtop_t* sys,
+ const gmx_output_env_t* oenv,
+ const gmx::MDLogger& logger)
/* If fr_time == -1 read the last frame available which is complete */
{
bool bReadVel;
t_trxframe fr;
- t_trxstatus *fp;
+ t_trxstatus* fp;
double use_time;
bReadVel = (bNeedVel && !bGenVel);
- fprintf(stderr,
- "Reading Coordinates%s and Box size from old trajectory\n",
- bReadVel ? ", Velocities" : "");
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted("Reading Coordinates%s and Box size from old trajectory",
+ bReadVel ? ", Velocities" : "");
if (fr_time == -1)
{
- fprintf(stderr, "Will read whole trajectory\n");
+ GMX_LOG(logger.info).asParagraph().appendTextFormatted("Will read whole trajectory");
}
else
{
- fprintf(stderr, "Will read till time %g\n", fr_time);
+ GMX_LOG(logger.info).asParagraph().appendTextFormatted("Will read till time %g", fr_time);
}
if (!bReadVel)
{
if (bGenVel)
{
- fprintf(stderr, "Velocities generated: "
- "ignoring velocities in input trajectory\n");
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted(
+ "Velocities generated: "
+ "ignoring velocities in input trajectory");
}
read_first_frame(oenv, &fp, slog, &fr, TRX_NEED_X);
}
if (!fr.bV)
{
- fprintf(stderr,
- "\n"
- "WARNING: Did not find a frame with velocities in file %s,\n"
- " all velocities will be set to zero!\n\n", slog);
- for (auto &vi : makeArrayRef(state->v))
+ GMX_LOG(logger.warning)
+ .asParagraph()
+ .appendTextFormatted(
+ "WARNING: Did not find a frame with velocities in file %s,\n"
+ " all velocities will be set to zero!",
+ slog);
+ for (auto& vi : makeArrayRef(state->v))
{
- vi = {0, 0, 0};
+ vi = { 0, 0, 0 };
}
close_trx(fp);
/* Search for a frame without velocities */
if (sys->natoms != state->natoms)
{
- gmx_fatal(FARGS, "Number of atoms in Topology "
+ gmx_fatal(FARGS,
+ "Number of atoms in Topology "
"is not the same as in Trajectory");
}
copy_state(slog, &fr, bReadVel, state, &use_time);
/* Find the appropriate frame */
- while ((fr_time == -1 || fr.time < fr_time) &&
- read_next_frame(oenv, fp, &fr))
+ while ((fr_time == -1 || fr.time < fr_time) && read_next_frame(oenv, fp, &fr))
{
copy_state(slog, &fr, bReadVel, state, &use_time);
}
*/
set_box_rel(ir, state);
- fprintf(stderr, "Using frame at t = %g ps\n", use_time);
- fprintf(stderr, "Starting time for run is %g ps\n", ir->init_t);
+ GMX_LOG(logger.info).asParagraph().appendTextFormatted("Using frame at t = %g ps", use_time);
+ GMX_LOG(logger.info).asParagraph().appendTextFormatted("Starting time for run is %g ps", ir->init_t);
- if ((ir->epc != epcNO || ir->etc == etcNOSEHOOVER) && ener)
+ if ((ir->epc != PressureCoupling::No || ir->etc == TemperatureCoupling::NoseHoover) && ener)
{
- get_enx_state(ener, use_time, &sys->groups, ir, state);
+ get_enx_state(ener, use_time, sys->groups, ir, state);
preserve_box_shape(ir, state->box_rel, state->boxv);
}
}
-static void read_posres(gmx_mtop_t *mtop, t_molinfo *molinfo, gmx_bool bTopB,
- const char *fn,
- int rc_scaling, int ePBC,
- rvec com,
- warninp_t wi)
+static void read_posres(gmx_mtop_t* mtop,
+ gmx::ArrayRef<const MoleculeInformation> molinfo,
+ gmx_bool bTopB,
+ const char* fn,
+ RefCoordScaling rc_scaling,
+ PbcType pbcType,
+ rvec com,
+ warninp* wi,
+ const gmx::MDLogger& logger)
{
- gmx_bool *hadAtom;
- rvec *x, *v;
- dvec sum;
- double totmass;
- t_topology *top;
- matrix box, invbox;
- int natoms, npbcdim = 0;
- char warn_buf[STRLEN];
- int a, i, ai, j, k, nat_molb;
- t_params *pr, *prfb;
- t_atom *atom;
+ gmx_bool* hadAtom;
+ rvec * x, *v;
+ dvec sum;
+ double totmass;
+ t_topology* top;
+ matrix box, invbox;
+ int natoms, npbcdim = 0;
+ int a, nat_molb;
+ t_atom* atom;
snew(top, 1);
read_tps_conf(fn, top, nullptr, &x, &v, box, FALSE);
sfree(top);
if (natoms != mtop->natoms)
{
- sprintf(warn_buf, "The number of atoms in %s (%d) does not match the number of atoms in the topology (%d). Will assume that the first %d atoms in the topology and %s match.", fn, natoms, mtop->natoms, std::min(mtop->natoms, natoms), fn);
- warning(wi, warn_buf);
+ std::string warningMessage = gmx::formatString(
+ "The number of atoms in %s (%d) does not match the number of atoms in the topology "
+ "(%d). Will assume that the first %d atoms in the topology and %s match.",
+ fn,
+ natoms,
+ mtop->natoms,
+ std::min(mtop->natoms, natoms),
+ fn);
+ warning(wi, warningMessage.c_str());
}
- npbcdim = ePBC2npbcdim(ePBC);
+ npbcdim = numPbcDimensions(pbcType);
+ GMX_RELEASE_ASSERT(npbcdim <= DIM, "Invalid npbcdim");
clear_rvec(com);
- if (rc_scaling != erscNO)
+ if (rc_scaling != RefCoordScaling::No)
{
copy_mat(box, invbox);
- for (j = npbcdim; j < DIM; j++)
+ for (int j = npbcdim; j < DIM; j++)
{
clear_rvec(invbox[j]);
invbox[j][j] = 1;
totmass = 0;
a = 0;
snew(hadAtom, natoms);
- for (gmx_molblock_t &molb : mtop->molblock)
+ for (gmx_molblock_t& molb : mtop->molblock)
{
- nat_molb = molb.nmol*mtop->moltype[molb.type].atoms.nr;
- pr = &(molinfo[molb.type].plist[F_POSRES]);
- prfb = &(molinfo[molb.type].plist[F_FBPOSRES]);
- if (pr->nr > 0 || prfb->nr > 0)
+ nat_molb = molb.nmol * mtop->moltype[molb.type].atoms.nr;
+ const InteractionsOfType* pr = &(molinfo[molb.type].interactions[F_POSRES]);
+ const InteractionsOfType* prfb = &(molinfo[molb.type].interactions[F_FBPOSRES]);
+ if (pr->size() > 0 || prfb->size() > 0)
{
atom = mtop->moltype[molb.type].atoms.atom;
- for (i = 0; (i < pr->nr); i++)
+ for (const auto& restraint : pr->interactionTypes)
{
- ai = pr->param[i].ai();
+ int ai = restraint.ai();
if (ai >= natoms)
{
- gmx_fatal(FARGS, "Position restraint atom index (%d) in moltype '%s' is larger than number of atoms in %s (%d).\n",
- ai+1, *molinfo[molb.type].name, fn, natoms);
+ gmx_fatal(FARGS,
+ "Position restraint atom index (%d) in moltype '%s' is larger than "
+ "number of atoms in %s (%d).\n",
+ ai + 1,
+ *molinfo[molb.type].name,
+ fn,
+ natoms);
}
hadAtom[ai] = TRUE;
- if (rc_scaling == erscCOM)
+ if (rc_scaling == RefCoordScaling::Com)
{
/* Determine the center of mass of the posres reference coordinates */
- for (j = 0; j < npbcdim; j++)
+ for (int j = 0; j < npbcdim; j++)
{
- sum[j] += atom[ai].m*x[a+ai][j];
+ sum[j] += atom[ai].m * x[a + ai][j];
}
- totmass += atom[ai].m;
+ totmass += atom[ai].m;
}
}
/* Same for flat-bottomed posres, but do not count an atom twice for COM */
- for (i = 0; (i < prfb->nr); i++)
+ for (const auto& restraint : prfb->interactionTypes)
{
- ai = prfb->param[i].ai();
+ int ai = restraint.ai();
if (ai >= natoms)
{
- gmx_fatal(FARGS, "Position restraint atom index (%d) in moltype '%s' is larger than number of atoms in %s (%d).\n",
- ai+1, *molinfo[molb.type].name, fn, natoms);
+ gmx_fatal(FARGS,
+ "Position restraint atom index (%d) in moltype '%s' is larger than "
+ "number of atoms in %s (%d).\n",
+ ai + 1,
+ *molinfo[molb.type].name,
+ fn,
+ natoms);
}
- if (rc_scaling == erscCOM && !hadAtom[ai])
+ if (rc_scaling == RefCoordScaling::Com && !hadAtom[ai])
{
/* Determine the center of mass of the posres reference coordinates */
- for (j = 0; j < npbcdim; j++)
+ for (int j = 0; j < npbcdim; j++)
{
- sum[j] += atom[ai].m*x[a+ai][j];
+ sum[j] += atom[ai].m * x[a + ai][j];
}
- totmass += atom[ai].m;
+ totmass += atom[ai].m;
}
}
if (!bTopB)
{
molb.posres_xA.resize(nat_molb);
- for (i = 0; i < nat_molb; i++)
+ for (int i = 0; i < nat_molb; i++)
{
- copy_rvec(x[a+i], molb.posres_xA[i]);
+ copy_rvec(x[a + i], molb.posres_xA[i]);
}
}
else
{
molb.posres_xB.resize(nat_molb);
- for (i = 0; i < nat_molb; i++)
+ for (int i = 0; i < nat_molb; i++)
{
- copy_rvec(x[a+i], molb.posres_xB[i]);
+ copy_rvec(x[a + i], molb.posres_xB[i]);
}
}
}
a += nat_molb;
}
- if (rc_scaling == erscCOM)
+ if (rc_scaling == RefCoordScaling::Com)
{
if (totmass == 0)
{
gmx_fatal(FARGS, "The total mass of the position restraint atoms is 0");
}
- for (j = 0; j < npbcdim; j++)
+ for (int j = 0; j < npbcdim; j++)
{
- com[j] = sum[j]/totmass;
+ com[j] = sum[j] / totmass;
}
- fprintf(stderr, "The center of mass of the position restraint coord's is %6.3f %6.3f %6.3f\n", com[XX], com[YY], com[ZZ]);
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted(
+ "The center of mass of the position restraint coord's is %6.3f %6.3f %6.3f",
+ com[XX],
+ com[YY],
+ com[ZZ]);
}
- if (rc_scaling != erscNO)
+ if (rc_scaling != RefCoordScaling::No)
{
GMX_ASSERT(npbcdim <= DIM, "Only DIM dimensions can have PBC");
- for (gmx_molblock_t &molb : mtop->molblock)
+ for (gmx_molblock_t& molb : mtop->molblock)
{
- nat_molb = molb.nmol*mtop->moltype[molb.type].atoms.nr;
+ nat_molb = molb.nmol * mtop->moltype[molb.type].atoms.nr;
if (!molb.posres_xA.empty() || !molb.posres_xB.empty())
{
- std::vector<gmx::RVec> &xp = (!bTopB ? molb.posres_xA : molb.posres_xB);
- for (i = 0; i < nat_molb; i++)
+ std::vector<gmx::RVec>& xp = (!bTopB ? molb.posres_xA : molb.posres_xB);
+ for (int i = 0; i < nat_molb; i++)
{
- for (j = 0; j < npbcdim; j++)
+ for (int j = 0; j < npbcdim; j++)
{
- if (rc_scaling == erscALL)
+ if (rc_scaling == RefCoordScaling::All)
{
/* Convert from Cartesian to crystal coordinates */
xp[i][j] *= invbox[j][j];
- for (k = j+1; k < npbcdim; k++)
+ for (int k = j + 1; k < npbcdim; k++)
{
- xp[i][j] += invbox[k][j]*xp[i][k];
+ xp[i][j] += invbox[k][j] * xp[i][k];
}
}
- else if (rc_scaling == erscCOM)
+ else if (rc_scaling == RefCoordScaling::Com)
{
/* Subtract the center of mass */
xp[i][j] -= com[j];
}
}
- if (rc_scaling == erscCOM)
+ if (rc_scaling == RefCoordScaling::Com)
{
/* Convert the COM from Cartesian to crystal coordinates */
- for (j = 0; j < npbcdim; j++)
+ for (int j = 0; j < npbcdim; j++)
{
com[j] *= invbox[j][j];
- for (k = j+1; k < npbcdim; k++)
+ for (int k = j + 1; k < npbcdim; k++)
{
- com[j] += invbox[k][j]*com[k];
+ com[j] += invbox[k][j] * com[k];
}
}
}
sfree(hadAtom);
}
-static void gen_posres(gmx_mtop_t *mtop, t_molinfo *mi,
- const char *fnA, const char *fnB,
- int rc_scaling, int ePBC,
- rvec com, rvec comB,
- warninp_t wi)
+static void gen_posres(gmx_mtop_t* mtop,
+ gmx::ArrayRef<const MoleculeInformation> mi,
+ const char* fnA,
+ const char* fnB,
+ RefCoordScaling rc_scaling,
+ PbcType pbcType,
+ rvec com,
+ rvec comB,
+ warninp* wi,
+ const gmx::MDLogger& logger)
{
- read_posres (mtop, mi, FALSE, fnA, rc_scaling, ePBC, com, wi);
+ read_posres(mtop, mi, FALSE, fnA, rc_scaling, pbcType, com, wi, logger);
/* It is safer to simply read the b-state posres rather than trying
* to be smart and copy the positions.
*/
- read_posres(mtop, mi, TRUE, fnB, rc_scaling, ePBC, comB, wi);
+ read_posres(mtop, mi, TRUE, fnB, rc_scaling, pbcType, comB, wi, logger);
}
-static void set_wall_atomtype(gpp_atomtype_t at, t_gromppopts *opts,
- t_inputrec *ir, warninp_t wi)
+static void set_wall_atomtype(PreprocessingAtomTypes* at,
+ t_gromppopts* opts,
+ t_inputrec* ir,
+ warninp* wi,
+ const gmx::MDLogger& logger)
{
- int i;
- char warn_buf[STRLEN];
+ int i;
if (ir->nwall > 0)
{
- fprintf(stderr, "Searching the wall atom type(s)\n");
+ GMX_LOG(logger.info).asParagraph().appendTextFormatted("Searching the wall atom type(s)");
}
for (i = 0; i < ir->nwall; i++)
{
- ir->wall_atomtype[i] = get_atomtype_type(opts->wall_atomtype[i], at);
- if (ir->wall_atomtype[i] == NOTSET)
+ auto atomType = at->atomTypeFromName(opts->wall_atomtype[i]);
+ if (!atomType.has_value())
{
- sprintf(warn_buf, "Specified wall atom type %s is not defined", opts->wall_atomtype[i]);
- warning_error(wi, warn_buf);
+ std::string warningMessage = gmx::formatString(
+ "Specified wall atom type %s is not defined", opts->wall_atomtype[i]);
+ warning_error(wi, warningMessage.c_str());
+ }
+ else
+ {
+ ir->wall_atomtype[i] = *atomType;
}
}
}
-static int nrdf_internal(t_atoms *atoms)
+static int nrdf_internal(const t_atoms* atoms)
{
int i, nmass, nrdf;
for (i = 0; i < atoms->nr; i++)
{
/* Vsite ptype might not be set here yet, so also check the mass */
- if ((atoms->atom[i].ptype == eptAtom ||
- atoms->atom[i].ptype == eptNucleus)
+ if ((atoms->atom[i].ptype == ParticleType::Atom || atoms->atom[i].ptype == ParticleType::Nucleus)
&& atoms->atom[i].m > 0)
{
nmass++;
}
switch (nmass)
{
- case 0: nrdf = 0; break;
- case 1: nrdf = 0; break;
- case 2: nrdf = 1; break;
- default: nrdf = nmass*3 - 6; break;
+ case 0: // Fall through intended
+ case 1: nrdf = 0; break;
+ case 2: nrdf = 1; break;
+ default: nrdf = nmass * 3 - 6; break;
}
return nrdf;
}
-static void
-spline1d( double dx,
- const double * y,
- int n,
- double * u,
- double * y2 )
+static void spline1d(double dx, const double* y, int n, double* u, double* y2)
{
int i;
double p, q;
y2[0] = 0.0;
u[0] = 0.0;
- for (i = 1; i < n-1; i++)
+ for (i = 1; i < n - 1; i++)
{
- p = 0.5*y2[i-1]+2.0;
- y2[i] = -0.5/p;
- q = (y[i+1]-2.0*y[i]+y[i-1])/dx;
- u[i] = (3.0*q/dx-0.5*u[i-1])/p;
+ p = 0.5 * y2[i - 1] + 2.0;
+ y2[i] = -0.5 / p;
+ q = (y[i + 1] - 2.0 * y[i] + y[i - 1]) / dx;
+ u[i] = (3.0 * q / dx - 0.5 * u[i - 1]) / p;
}
- y2[n-1] = 0.0;
+ y2[n - 1] = 0.0;
- for (i = n-2; i >= 0; i--)
+ for (i = n - 2; i >= 0; i--)
{
- y2[i] = y2[i]*y2[i+1]+u[i];
+ y2[i] = y2[i] * y2[i + 1] + u[i];
}
}
static void
-interpolate1d( double xmin,
- double dx,
- const double * ya,
- const double * y2a,
- double x,
- double * y,
- double * y1)
+interpolate1d(double xmin, double dx, const double* ya, const double* y2a, double x, double* y, double* y1)
{
int ix;
double a, b;
- ix = static_cast<int>((x-xmin)/dx);
+ ix = static_cast<int>((x - xmin) / dx);
- a = (xmin+(ix+1)*dx-x)/dx;
- b = (x-xmin-ix*dx)/dx;
+ a = (xmin + (ix + 1) * dx - x) / dx;
+ b = (x - xmin - ix * dx) / dx;
- *y = a*ya[ix]+b*ya[ix+1]+((a*a*a-a)*y2a[ix]+(b*b*b-b)*y2a[ix+1])*(dx*dx)/6.0;
- *y1 = (ya[ix+1]-ya[ix])/dx-(3.0*a*a-1.0)/6.0*dx*y2a[ix]+(3.0*b*b-1.0)/6.0*dx*y2a[ix+1];
+ *y = a * ya[ix] + b * ya[ix + 1]
+ + ((a * a * a - a) * y2a[ix] + (b * b * b - b) * y2a[ix + 1]) * (dx * dx) / 6.0;
+ *y1 = (ya[ix + 1] - ya[ix]) / dx - (3.0 * a * a - 1.0) / 6.0 * dx * y2a[ix]
+ + (3.0 * b * b - 1.0) / 6.0 * dx * y2a[ix + 1];
}
-static void
-setup_cmap (int grid_spacing,
- int nc,
- const real * grid,
- gmx_cmap_t * cmap_grid)
+static void setup_cmap(int grid_spacing, int nc, gmx::ArrayRef<const real> grid, gmx_cmap_t* cmap_grid)
{
- int i, j, k, ii, jj, kk, idx;
- int offset;
- double dx, xmin, v, v1, v2, v12;
- double phi, psi;
+ int i, j, k, ii, jj, kk, idx;
+ int offset;
+ double dx, xmin, v, v1, v2, v12;
+ double phi, psi;
- std::vector<double> tmp_u(2*grid_spacing, 0.0);
- std::vector<double> tmp_u2(2*grid_spacing, 0.0);
- std::vector<double> tmp_yy(2*grid_spacing, 0.0);
- std::vector<double> tmp_y1(2*grid_spacing, 0.0);
- std::vector<double> tmp_t2(2*grid_spacing*2*grid_spacing, 0.0);
- std::vector<double> tmp_grid(2*grid_spacing*2*grid_spacing, 0.0);
+ std::vector<double> tmp_u(2 * grid_spacing, 0.0);
+ std::vector<double> tmp_u2(2 * grid_spacing, 0.0);
+ std::vector<double> tmp_yy(2 * grid_spacing, 0.0);
+ std::vector<double> tmp_y1(2 * grid_spacing, 0.0);
+ std::vector<double> tmp_t2(2 * grid_spacing * 2 * grid_spacing, 0.0);
+ std::vector<double> tmp_grid(2 * grid_spacing * 2 * grid_spacing, 0.0);
- dx = 360.0/grid_spacing;
- xmin = -180.0-dx*grid_spacing/2;
+ dx = 360.0 / grid_spacing;
+ xmin = -180.0 - dx * grid_spacing / 2;
for (kk = 0; kk < nc; kk++)
{
*/
offset = kk * grid_spacing * grid_spacing * 2;
- for (i = 0; i < 2*grid_spacing; i++)
+ for (i = 0; i < 2 * grid_spacing; i++)
{
- ii = (i+grid_spacing-grid_spacing/2)%grid_spacing;
+ ii = (i + grid_spacing - grid_spacing / 2) % grid_spacing;
- for (j = 0; j < 2*grid_spacing; j++)
+ for (j = 0; j < 2 * grid_spacing; j++)
{
- jj = (j+grid_spacing-grid_spacing/2)%grid_spacing;
- tmp_grid[i*grid_spacing*2+j] = grid[offset+ii*grid_spacing+jj];
+ jj = (j + grid_spacing - grid_spacing / 2) % grid_spacing;
+ tmp_grid[i * grid_spacing * 2 + j] = grid[offset + ii * grid_spacing + jj];
}
}
- for (i = 0; i < 2*grid_spacing; i++)
+ for (i = 0; i < 2 * grid_spacing; i++)
{
- spline1d(dx, &(tmp_grid[2*grid_spacing*i]), 2*grid_spacing, tmp_u.data(), &(tmp_t2[2*grid_spacing*i]));
+ spline1d(dx,
+ &(tmp_grid[2 * grid_spacing * i]),
+ 2 * grid_spacing,
+ tmp_u.data(),
+ &(tmp_t2[2 * grid_spacing * i]));
}
- for (i = grid_spacing/2; i < grid_spacing+grid_spacing/2; i++)
+ for (i = grid_spacing / 2; i < grid_spacing + grid_spacing / 2; i++)
{
- ii = i-grid_spacing/2;
- phi = ii*dx-180.0;
+ ii = i - grid_spacing / 2;
+ phi = ii * dx - 180.0;
- for (j = grid_spacing/2; j < grid_spacing+grid_spacing/2; j++)
+ for (j = grid_spacing / 2; j < grid_spacing + grid_spacing / 2; j++)
{
- jj = j-grid_spacing/2;
- psi = jj*dx-180.0;
+ jj = j - grid_spacing / 2;
+ psi = jj * dx - 180.0;
- for (k = 0; k < 2*grid_spacing; k++)
+ for (k = 0; k < 2 * grid_spacing; k++)
{
- interpolate1d(xmin, dx, &(tmp_grid[2*grid_spacing*k]),
- &(tmp_t2[2*grid_spacing*k]), psi, &tmp_yy[k], &tmp_y1[k]);
+ interpolate1d(xmin,
+ dx,
+ &(tmp_grid[2 * grid_spacing * k]),
+ &(tmp_t2[2 * grid_spacing * k]),
+ psi,
+ &tmp_yy[k],
+ &tmp_y1[k]);
}
- spline1d(dx, tmp_yy.data(), 2*grid_spacing, tmp_u.data(), tmp_u2.data());
+ spline1d(dx, tmp_yy.data(), 2 * grid_spacing, tmp_u.data(), tmp_u2.data());
interpolate1d(xmin, dx, tmp_yy.data(), tmp_u2.data(), phi, &v, &v1);
- spline1d(dx, tmp_y1.data(), 2*grid_spacing, tmp_u.data(), tmp_u2.data());
+ spline1d(dx, tmp_y1.data(), 2 * grid_spacing, tmp_u.data(), tmp_u2.data());
interpolate1d(xmin, dx, tmp_y1.data(), tmp_u2.data(), phi, &v2, &v12);
- idx = ii*grid_spacing+jj;
- cmap_grid->cmapdata[kk].cmap[idx*4] = grid[offset+ii*grid_spacing+jj];
- cmap_grid->cmapdata[kk].cmap[idx*4+1] = v1;
- cmap_grid->cmapdata[kk].cmap[idx*4+2] = v2;
- cmap_grid->cmapdata[kk].cmap[idx*4+3] = v12;
+ idx = ii * grid_spacing + jj;
+ cmap_grid->cmapdata[kk].cmap[idx * 4] = grid[offset + ii * grid_spacing + jj];
+ cmap_grid->cmapdata[kk].cmap[idx * 4 + 1] = v1;
+ cmap_grid->cmapdata[kk].cmap[idx * 4 + 2] = v2;
+ cmap_grid->cmapdata[kk].cmap[idx * 4 + 3] = v12;
}
}
}
}
-static void init_cmap_grid(gmx_cmap_t *cmap_grid, int ngrid, int grid_spacing)
+static void init_cmap_grid(gmx_cmap_t* cmap_grid, int ngrid, int grid_spacing)
{
int i, nelem;
cmap_grid->grid_spacing = grid_spacing;
- nelem = cmap_grid->grid_spacing*cmap_grid->grid_spacing;
+ nelem = cmap_grid->grid_spacing * cmap_grid->grid_spacing;
cmap_grid->cmapdata.resize(ngrid);
for (i = 0; i < ngrid; i++)
{
- cmap_grid->cmapdata[i].cmap.resize(4*nelem);
+ cmap_grid->cmapdata[i].cmap.resize(4 * nelem);
}
}
-static int count_constraints(const gmx_mtop_t *mtop, t_molinfo *mi, warninp_t wi)
+static int count_constraints(const gmx_mtop_t* mtop, gmx::ArrayRef<const MoleculeInformation> mi, warninp* wi)
{
- int count, count_mol, i;
- t_params *plist;
- char buf[STRLEN];
+ int count, count_mol;
count = 0;
- for (const gmx_molblock_t &molb : mtop->molblock)
+ for (const gmx_molblock_t& molb : mtop->molblock)
{
- count_mol = 0;
- plist = mi[molb.type].plist;
+ count_mol = 0;
+ gmx::ArrayRef<const InteractionsOfType> interactions = mi[molb.type].interactions;
- for (i = 0; i < F_NRE; i++)
+ for (int i = 0; i < F_NRE; i++)
{
if (i == F_SETTLE)
{
- count_mol += 3*plist[i].nr;
+ count_mol += 3 * interactions[i].size();
}
else if (interaction_function[i].flags & IF_CONSTRAINT)
{
- count_mol += plist[i].nr;
+ count_mol += interactions[i].size();
}
}
if (count_mol > nrdf_internal(&mi[molb.type].atoms))
{
- sprintf(buf,
+ std::string warningMessage = gmx::formatString(
"Molecule type '%s' has %d constraints.\n"
- "For stability and efficiency there should not be more constraints than internal number of degrees of freedom: %d.\n",
- *mi[molb.type].name, count_mol,
+ "For stability and efficiency there should not be more constraints than "
+ "internal number of degrees of freedom: %d.\n",
+ *mi[molb.type].name,
+ count_mol,
nrdf_internal(&mi[molb.type].atoms));
- warning(wi, buf);
+ warning(wi, warningMessage.c_str());
}
- count += molb.nmol*count_mol;
+ count += molb.nmol * count_mol;
}
return count;
}
-static real calc_temp(const gmx_mtop_t *mtop,
- const t_inputrec *ir,
- rvec *v)
+static real calc_temp(const gmx_mtop_t* mtop, const t_inputrec* ir, rvec* v)
{
- gmx_mtop_atomloop_all_t aloop;
- const t_atom *atom;
- int a;
-
- double sum_mv2 = 0;
- aloop = gmx_mtop_atomloop_all_init(mtop);
- while (gmx_mtop_atomloop_all_next(aloop, &a, &atom))
+ double sum_mv2 = 0;
+ for (const AtomProxy atomP : AtomRange(*mtop))
{
- sum_mv2 += atom->m*norm2(v[a]);
+ const t_atom& local = atomP.atom();
+ int i = atomP.globalAtomNumber();
+ sum_mv2 += local.m * norm2(v[i]);
}
double nrdf = 0;
nrdf += ir->opts.nrdf[g];
}
- return sum_mv2/(nrdf*BOLTZ);
+ return sum_mv2 / (nrdf * gmx::c_boltz);
}
-static real get_max_reference_temp(const t_inputrec *ir,
- warninp_t wi)
+static real get_max_reference_temp(const t_inputrec* ir, warninp* wi)
{
- real ref_t;
- int i;
- bool bNoCoupl;
+ real ref_t;
+ int i;
+ bool bNoCoupl;
ref_t = 0;
bNoCoupl = false;
if (bNoCoupl)
{
- char buf[STRLEN];
-
- sprintf(buf, "Some temperature coupling groups do not use temperature coupling. We will assume their temperature is not more than %.3f K. If their temperature is higher, the energy error and the Verlet buffer might be underestimated.",
+ std::string warningMessage = gmx::formatString(
+ "Some temperature coupling groups do not use temperature coupling. We will assume "
+ "their temperature is not more than %.3f K. If their temperature is higher, the "
+ "energy error and the Verlet buffer might be underestimated.",
ref_t);
- warning(wi, buf);
+ warning(wi, warningMessage.c_str());
}
return ref_t;
/* Checks if there are unbound atoms in moleculetype molt.
* Prints a note for each unbound atoms and a warning if any is present.
*/
-static void checkForUnboundAtoms(const gmx_moltype_t *molt,
- gmx_bool bVerbose,
- warninp_t wi)
+static void checkForUnboundAtoms(const gmx_moltype_t* molt, gmx_bool bVerbose, warninp* wi, const gmx::MDLogger& logger)
{
- const t_atoms *atoms = &molt->atoms;
+ const t_atoms* atoms = &molt->atoms;
if (atoms->nr == 1)
{
for (int ftype = 0; ftype < F_NRE; ftype++)
{
- if (((interaction_function[ftype].flags & IF_BOND) && ftype != F_CONNBONDS) ||
- (interaction_function[ftype].flags & IF_CONSTRAINT) ||
- ftype == F_SETTLE)
+ if (((interaction_function[ftype].flags & IF_BOND) && NRAL(ftype) == 2 && ftype != F_CONNBONDS)
+ || (interaction_function[ftype].flags & IF_CONSTRAINT) || ftype == F_SETTLE)
{
- const InteractionList &il = molt->ilist[ftype];
+ const InteractionList& il = molt->ilist[ftype];
const int nral = NRAL(ftype);
for (int i = 0; i < il.size(); i += 1 + nral)
int numDanglingAtoms = 0;
for (int a = 0; a < atoms->nr; a++)
{
- if (atoms->atom[a].ptype != eptVSite &&
- count[a] == 0)
+ if (atoms->atom[a].ptype != ParticleType::VSite && count[a] == 0)
{
if (bVerbose)
{
- fprintf(stderr, "\nAtom %d '%s' in moleculetype '%s' is not bound by a potential or constraint to any other atom in the same moleculetype.\n",
- a + 1, *atoms->atomname[a], *molt->name);
+ GMX_LOG(logger.warning)
+ .asParagraph()
+ .appendTextFormatted(
+ "Atom %d '%s' in moleculetype '%s' is not bound by a potential or "
+ "constraint to any other atom in the same moleculetype.",
+ a + 1,
+ *atoms->atomname[a],
+ *molt->name);
}
numDanglingAtoms++;
}
if (numDanglingAtoms > 0)
{
- char buf[STRLEN];
- sprintf(buf, "In moleculetype '%s' %d atoms are not bound by a potential or constraint to any other atom in the same moleculetype. Although technically this might not cause issues in a simulation, this often means that the user forgot to add a bond/potential/constraint or put multiple molecules in the same moleculetype definition by mistake. Run with -v to get information for each atom.",
- *molt->name, numDanglingAtoms);
- warning_note(wi, buf);
+ std::string warningMessage = gmx::formatString(
+ "In moleculetype '%s' %d atoms are not bound by a potential or constraint to any "
+ "other atom in the same moleculetype. Although technically this might not cause "
+ "issues in a simulation, this often means that the user forgot to add a "
+ "bond/potential/constraint or put multiple molecules in the same moleculetype "
+ "definition by mistake. Run with -v to get information for each atom.",
+ *molt->name,
+ numDanglingAtoms);
+ warning_note(wi, warningMessage.c_str());
}
}
/* Checks all moleculetypes for unbound atoms */
-static void checkForUnboundAtoms(const gmx_mtop_t *mtop,
- gmx_bool bVerbose,
- warninp_t wi)
+static void checkForUnboundAtoms(const gmx_mtop_t* mtop, gmx_bool bVerbose, warninp* wi, const gmx::MDLogger& logger)
{
- for (const gmx_moltype_t &molt : mtop->moltype)
+ for (const gmx_moltype_t& molt : mtop->moltype)
{
- checkForUnboundAtoms(&molt, bVerbose, wi);
+ checkForUnboundAtoms(&molt, bVerbose, wi, logger);
}
}
* involved in a single constraint; the mass of the two atoms needs to
* differ by more than \p massFactorThreshold.
*/
-static bool haveDecoupledModeInMol(const gmx_moltype_t &molt,
- gmx::ArrayRef<const t_iparams> iparams,
- real massFactorThreshold)
+static bool haveDecoupledModeInMol(const gmx_moltype_t& molt,
+ gmx::ArrayRef<const t_iparams> iparams,
+ real massFactorThreshold)
{
- if (molt.ilist[F_CONSTR].size() == 0 &&
- molt.ilist[F_CONSTRNC].size() == 0)
+ if (molt.ilist[F_CONSTR].empty() && molt.ilist[F_CONSTRNC].empty())
{
return false;
}
- const t_atom * atom = molt.atoms.atom;
+ const t_atom* atom = molt.atoms.atom;
- t_blocka atomToConstraints =
- gmx::make_at2con(molt, iparams,
- gmx::FlexibleConstraintTreatment::Exclude);
+ const auto atomToConstraints =
+ gmx::make_at2con(molt, iparams, gmx::FlexibleConstraintTreatment::Exclude);
- bool haveDecoupledMode = false;
+ bool haveDecoupledMode = false;
for (int ftype = 0; ftype < F_NRE; ftype++)
{
if (interaction_function[ftype].flags & IF_ATYPE)
{
const int nral = NRAL(ftype);
- const InteractionList &il = molt.ilist[ftype];
+ const InteractionList& il = molt.ilist[ftype];
for (int i = 0; i < il.size(); i += 1 + nral)
{
/* Here we check for the mass difference between the atoms
int a0 = il.iatoms[1 + i];
int a1 = il.iatoms[1 + i + 1];
int a2 = il.iatoms[1 + i + 2];
- if ((atom[a0].m > atom[a2].m*massFactorThreshold ||
- atom[a2].m > atom[a0].m*massFactorThreshold) &&
- atomToConstraints.index[a0 + 1] - atomToConstraints.index[a0] == 1 &&
- atomToConstraints.index[a2 + 1] - atomToConstraints.index[a2] == 1 &&
- atomToConstraints.index[a1 + 1] - atomToConstraints.index[a1] >= 3)
+ if ((atom[a0].m > atom[a2].m * massFactorThreshold || atom[a2].m > atom[a0].m * massFactorThreshold)
+ && atomToConstraints[a0].ssize() == 1 && atomToConstraints[a2].ssize() == 1
+ && atomToConstraints[a1].ssize() >= 3)
{
- int constraint0 = atomToConstraints.a[atomToConstraints.index[a0]];
- int constraint2 = atomToConstraints.a[atomToConstraints.index[a2]];
+ int constraint0 = atomToConstraints[a0][0];
+ int constraint2 = atomToConstraints[a2][0];
- bool foundAtom0 = false;
- bool foundAtom2 = false;
- for (int conIndex = atomToConstraints.index[a1]; conIndex < atomToConstraints.index[a1 + 1]; conIndex++)
+ bool foundAtom0 = false;
+ bool foundAtom2 = false;
+ for (const int constraint : atomToConstraints[a1])
{
- if (atomToConstraints.a[conIndex] == constraint0)
+ if (constraint == constraint0)
{
foundAtom0 = true;
}
- if (atomToConstraints.a[conIndex] == constraint2)
+ if (constraint == constraint2)
{
foundAtom2 = true;
}
}
}
- done_blocka(&atomToConstraints);
-
return haveDecoupledMode;
}
/*! \brief Checks if the Verlet buffer and constraint accuracy is sufficient for decoupled dynamic modes.
*
- * When decoupled modes are present and the accuray in insufficient,
+ * When decoupled modes are present and the accuracy in insufficient,
* this routine issues a warning if the accuracy is insufficient.
*/
-static void checkDecoupledModeAccuracy(const gmx_mtop_t *mtop,
- const t_inputrec *ir,
- warninp_t wi)
+static void checkDecoupledModeAccuracy(const gmx_mtop_t* mtop, const t_inputrec* ir, warninp* wi)
{
/* We only have issues with decoupled modes with normal MD.
* With stochastic dynamics equipartitioning is enforced strongly.
* energy/time, respectively, so they will "only" work correctly
* for atomistic force fields using MD units.
*/
- const real massFactorThreshold = 13.0;
- const real bufferToleranceThreshold = 1e-4;
- const int lincsIterationThreshold = 2;
- const int lincsOrderThreshold = 4;
- const real shakeToleranceThreshold = 0.005*ir->delta_t;
-
- bool lincsWithSufficientTolerance = (ir->eConstrAlg == econtLINCS && ir->nLincsIter >= lincsIterationThreshold && ir->nProjOrder >= lincsOrderThreshold);
- bool shakeWithSufficientTolerance = (ir->eConstrAlg == econtSHAKE && ir->shake_tol <= 1.1*shakeToleranceThreshold);
- if (ir->cutoff_scheme == ecutsVERLET &&
- ir->verletbuf_tol <= 1.1*bufferToleranceThreshold &&
- (lincsWithSufficientTolerance || shakeWithSufficientTolerance))
+ const real massFactorThreshold = 13.0;
+ const real bufferToleranceThreshold = 1e-4;
+ const int lincsIterationThreshold = 2;
+ const int lincsOrderThreshold = 4;
+ const real shakeToleranceThreshold = 0.005 * ir->delta_t;
+
+ bool lincsWithSufficientTolerance =
+ (ir->eConstrAlg == ConstraintAlgorithm::Lincs
+ && ir->nLincsIter >= lincsIterationThreshold && ir->nProjOrder >= lincsOrderThreshold);
+ bool shakeWithSufficientTolerance = (ir->eConstrAlg == ConstraintAlgorithm::Shake
+ && ir->shake_tol <= 1.1 * shakeToleranceThreshold);
+ if (ir->cutoff_scheme == CutoffScheme::Verlet && ir->verletbuf_tol <= 1.1 * bufferToleranceThreshold
+ && (lincsWithSufficientTolerance || shakeWithSufficientTolerance))
{
return;
}
bool haveDecoupledMode = false;
- for (const gmx_moltype_t &molt : mtop->moltype)
+ for (const gmx_moltype_t& molt : mtop->moltype)
{
- if (haveDecoupledModeInMol(molt, mtop->ffparams.iparams,
- massFactorThreshold))
+ if (haveDecoupledModeInMol(molt, mtop->ffparams.iparams, massFactorThreshold))
{
haveDecoupledMode = true;
}
if (haveDecoupledMode)
{
std::string message = gmx::formatString(
- "There are atoms at both ends of an angle, connected by constraints "
- "and with masses that differ by more than a factor of %g. This means "
- "that there are likely dynamic modes that are only very weakly coupled.",
- massFactorThreshold);
- if (ir->cutoff_scheme == ecutsVERLET)
+ "There are atoms at both ends of an angle, connected by constraints "
+ "and with masses that differ by more than a factor of %g. This means "
+ "that there are likely dynamic modes that are only very weakly coupled.",
+ massFactorThreshold);
+ if (ir->cutoff_scheme == CutoffScheme::Verlet)
{
message += gmx::formatString(
- " To ensure good equipartitioning, you need to either not use "
- "constraints on all bonds (but, if possible, only on bonds involving "
- "hydrogens) or use integrator = %s or decrease one or more tolerances: "
- "verlet-buffer-tolerance <= %g, LINCS iterations >= %d, LINCS order "
- ">= %d or SHAKE tolerance <= %g",
- ei_names[eiSD1],
- bufferToleranceThreshold,
- lincsIterationThreshold, lincsOrderThreshold,
- shakeToleranceThreshold);
+ " To ensure good equipartitioning, you need to either not use "
+ "constraints on all bonds (but, if possible, only on bonds involving "
+ "hydrogens) or use integrator = %s or decrease one or more tolerances: "
+ "verlet-buffer-tolerance <= %g, LINCS iterations >= %d, LINCS order "
+ ">= %d or SHAKE tolerance <= %g",
+ enumValueToString(IntegrationAlgorithm::SD1),
+ bufferToleranceThreshold,
+ lincsIterationThreshold,
+ lincsOrderThreshold,
+ shakeToleranceThreshold);
}
else
{
message += gmx::formatString(
- " To ensure good equipartitioning, we suggest to switch to the %s "
- "cutoff-scheme, since that allows for better control over the Verlet "
- "buffer size and thus over the energy drift.",
- ecutscheme_names[ecutsVERLET]);
+ " To ensure good equipartitioning, we suggest to switch to the %s "
+ "cutoff-scheme, since that allows for better control over the Verlet "
+ "buffer size and thus over the energy drift.",
+ enumValueToString(CutoffScheme::Verlet));
}
warning(wi, message);
}
}
-static void set_verlet_buffer(const gmx_mtop_t *mtop,
- t_inputrec *ir,
- real buffer_temp,
- matrix box,
- warninp_t wi)
+static void set_verlet_buffer(const gmx_mtop_t* mtop,
+ t_inputrec* ir,
+ real buffer_temp,
+ matrix box,
+ warninp* wi,
+ const gmx::MDLogger& logger)
{
- real rlist_1x1;
- int n_nonlin_vsite;
- char warn_buf[STRLEN];
-
- printf("Determining Verlet buffer for a tolerance of %g kJ/mol/ps at %g K\n", ir->verletbuf_tol, buffer_temp);
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted(
+ "Determining Verlet buffer for a tolerance of %g kJ/mol/ps at %g K",
+ ir->verletbuf_tol,
+ buffer_temp);
/* Calculate the buffer size for simple atom vs atoms list */
VerletbufListSetup listSetup1x1;
listSetup1x1.cluster_size_i = 1;
listSetup1x1.cluster_size_j = 1;
- calc_verlet_buffer_size(mtop, det(box), ir, ir->nstlist, ir->nstlist - 1,
- buffer_temp, &listSetup1x1,
- &n_nonlin_vsite, &rlist_1x1);
+ const real rlist_1x1 = calcVerletBufferSize(
+ *mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1, buffer_temp, listSetup1x1);
/* Set the pair-list buffer size in ir */
- VerletbufListSetup listSetup4x4 =
- verletbufGetSafeListSetup(ListSetupType::CpuNoSimd);
- calc_verlet_buffer_size(mtop, det(box), ir, ir->nstlist, ir->nstlist - 1,
- buffer_temp, &listSetup4x4,
- &n_nonlin_vsite, &ir->rlist);
+ VerletbufListSetup listSetup4x4 = verletbufGetSafeListSetup(ListSetupType::CpuNoSimd);
+ ir->rlist = calcVerletBufferSize(
+ *mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1, buffer_temp, listSetup4x4);
+ const int n_nonlin_vsite = gmx::countNonlinearVsites(*mtop);
if (n_nonlin_vsite > 0)
{
- sprintf(warn_buf, "There are %d non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly.", n_nonlin_vsite);
- warning_note(wi, warn_buf);
- }
-
- printf("Calculated rlist for %dx%d atom pair-list as %.3f nm, buffer size %.3f nm\n",
- 1, 1, rlist_1x1, rlist_1x1-std::max(ir->rvdw, ir->rcoulomb));
-
- printf("Set rlist, assuming %dx%d atom pair-list, to %.3f nm, buffer size %.3f nm\n",
- listSetup4x4.cluster_size_i, listSetup4x4.cluster_size_j,
- ir->rlist, ir->rlist-std::max(ir->rvdw, ir->rcoulomb));
-
- printf("Note that mdrun will redetermine rlist based on the actual pair-list setup\n");
-
- if (gmx::square(ir->rlist) >= max_cutoff2(ir->ePBC, box))
- {
- gmx_fatal(FARGS, "The pair-list cut-off (%g nm) is longer than half the shortest box vector or longer than the smallest box diagonal element (%g nm). Increase the box size or decrease nstlist or increase verlet-buffer-tolerance.", ir->rlist, std::sqrt(max_cutoff2(ir->ePBC, box)));
+ std::string warningMessage = gmx::formatString(
+ "There are %d non-linear virtual site constructions. Their contribution to the "
+ "energy error is approximated. In most cases this does not affect the error "
+ "significantly.",
+ n_nonlin_vsite);
+ warning_note(wi, warningMessage);
+ }
+
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted(
+ "Calculated rlist for %dx%d atom pair-list as %.3f nm, buffer size %.3f nm",
+ 1,
+ 1,
+ rlist_1x1,
+ rlist_1x1 - std::max(ir->rvdw, ir->rcoulomb));
+
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted(
+ "Set rlist, assuming %dx%d atom pair-list, to %.3f nm, buffer size %.3f nm",
+ listSetup4x4.cluster_size_i,
+ listSetup4x4.cluster_size_j,
+ ir->rlist,
+ ir->rlist - std::max(ir->rvdw, ir->rcoulomb));
+
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted(
+ "Note that mdrun will redetermine rlist based on the actual pair-list setup");
+
+ if (gmx::square(ir->rlist) >= max_cutoff2(ir->pbcType, box))
+ {
+ gmx_fatal(FARGS,
+ "The pair-list cut-off (%g nm) is longer than half the shortest box vector or "
+ "longer than the smallest box diagonal element (%g nm). Increase the box size or "
+ "decrease nstlist or increase verlet-buffer-tolerance.",
+ ir->rlist,
+ std::sqrt(max_cutoff2(ir->pbcType, box)));
}
}
-int gmx_grompp(int argc, char *argv[])
+int gmx_grompp(int argc, char* argv[])
{
- const char *desc[] = {
+ const char* desc[] = {
"[THISMODULE] (the gromacs preprocessor)",
"reads a molecular topology file, checks the validity of the",
"file, expands the topology from a molecular description to an atomic",
"Then a coordinate file is read and velocities can be generated",
"from a Maxwellian distribution if requested.",
"[THISMODULE] also reads parameters for [gmx-mdrun] ",
- "(eg. number of MD steps, time step, cut-off), and others such as",
- "NEMD parameters, which are corrected so that the net acceleration",
- "is zero.",
+ "(eg. number of MD steps, time step, cut-off).",
"Eventually a binary file is produced that can serve as the sole input",
"file for the MD program.[PAR]",
"interpret the output messages before attempting to bypass them with",
"this option."
};
- t_gromppopts *opts;
- int nmi;
- t_molinfo *mi, *intermolecular_interactions;
- gpp_atomtype_t atype;
- int nvsite, comb;
- t_params *plist;
- real fudgeQQ;
- double reppow;
- const char *mdparin;
- int ntype;
- bool bNeedVel, bGenVel;
- gmx_bool have_atomnumber;
- gmx_output_env_t *oenv;
- gmx_bool bVerbose = FALSE;
- warninp_t wi;
- char warn_buf[STRLEN];
-
- t_filenm fnm[] = {
- { efMDP, nullptr, nullptr, ffREAD },
- { efMDP, "-po", "mdout", ffWRITE },
- { efSTX, "-c", nullptr, ffREAD },
- { efSTX, "-r", "restraint", ffOPTRD },
- { efSTX, "-rb", "restraint", ffOPTRD },
- { efNDX, nullptr, nullptr, ffOPTRD },
- { efTOP, nullptr, nullptr, ffREAD },
- { efTOP, "-pp", "processed", ffOPTWR },
- { efTPR, "-o", nullptr, ffWRITE },
- { efTRN, "-t", nullptr, ffOPTRD },
- { efEDR, "-e", nullptr, ffOPTRD },
- /* This group is needed by the VMD viewer as the start configuration for IMD sessions: */
- { efGRO, "-imd", "imdgroup", ffOPTWR },
- { efTRN, "-ref", "rotref", ffOPTRW }
- };
+ std::vector<MoleculeInformation> mi;
+ std::unique_ptr<MoleculeInformation> intermolecular_interactions;
+ int nvsite;
+ CombinationRule comb;
+ real fudgeQQ;
+ double reppow;
+ const char* mdparin;
+ bool bNeedVel, bGenVel;
+ gmx_output_env_t* oenv;
+ gmx_bool bVerbose = FALSE;
+ warninp* wi;
+
+ t_filenm fnm[] = { { efMDP, nullptr, nullptr, ffREAD },
+ { efMDP, "-po", "mdout", ffWRITE },
+ { efSTX, "-c", nullptr, ffREAD },
+ { efSTX, "-r", "restraint", ffOPTRD },
+ { efSTX, "-rb", "restraint", ffOPTRD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
+ { efTOP, nullptr, nullptr, ffREAD },
+ { efTOP, "-pp", "processed", ffOPTWR },
+ { efTPR, "-o", nullptr, ffWRITE },
+ { efTRN, "-t", nullptr, ffOPTRD },
+ { efEDR, "-e", nullptr, ffOPTRD },
+ /* This group is needed by the VMD viewer as the start configuration for IMD sessions: */
+ { efGRO, "-imd", "imdgroup", ffOPTWR },
+ { efTRN, "-ref", "rotref", ffOPTRW | ffALLOW_MISSING },
+ /* This group is needed by the QMMM MDModule: */
+ { efQMI, "-qmi", nullptr, ffOPTRD } };
#define NFILE asize(fnm)
/* Command line options */
- gmx_bool bRenum = TRUE;
- gmx_bool bRmVSBds = TRUE, bZero = FALSE;
- int i, maxwarn = 0;
- real fr_time = -1;
- t_pargs pa[] = {
- { "-v", FALSE, etBOOL, {&bVerbose},
- "Be loud and noisy" },
- { "-time", FALSE, etREAL, {&fr_time},
- "Take frame at or first after this time." },
- { "-rmvsbds", FALSE, etBOOL, {&bRmVSBds},
+ gmx_bool bRenum = TRUE;
+ gmx_bool bRmVSBds = TRUE, bZero = FALSE;
+ int i, maxwarn = 0;
+ real fr_time = -1;
+ t_pargs pa[] = {
+ { "-v", FALSE, etBOOL, { &bVerbose }, "Be loud and noisy" },
+ { "-time", FALSE, etREAL, { &fr_time }, "Take frame at or first after this time." },
+ { "-rmvsbds",
+ FALSE,
+ etBOOL,
+ { &bRmVSBds },
"Remove constant bonded interactions with virtual sites" },
- { "-maxwarn", FALSE, etINT, {&maxwarn},
- "Number of allowed warnings during input processing. Not for normal use and may generate unstable systems" },
- { "-zero", FALSE, etBOOL, {&bZero},
- "Set parameters for bonded interactions without defaults to zero instead of generating an error" },
- { "-renum", FALSE, etBOOL, {&bRenum},
+ { "-maxwarn",
+ FALSE,
+ etINT,
+ { &maxwarn },
+ "Number of allowed warnings during input processing. Not for normal use and may "
+ "generate unstable systems" },
+ { "-zero",
+ FALSE,
+ etBOOL,
+ { &bZero },
+ "Set parameters for bonded interactions without defaults to zero instead of "
+ "generating an error" },
+ { "-renum",
+ FALSE,
+ etBOOL,
+ { &bRenum },
"Renumber atomtypes and minimize number of atomtypes" }
};
/* Parse the command line */
- if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
/* Initiate some variables */
gmx::MDModules mdModules;
t_inputrec irInstance;
- t_inputrec *ir = &irInstance;
- snew(opts, 1);
+ t_inputrec* ir = &irInstance;
+ t_gromppopts optsInstance;
+ t_gromppopts* opts = &optsInstance;
snew(opts->include, STRLEN);
snew(opts->define, STRLEN);
+ gmx::LoggerBuilder builder;
+ builder.addTargetStream(gmx::MDLogger::LogLevel::Info, &gmx::TextOutputFile::standardOutput());
+ builder.addTargetStream(gmx::MDLogger::LogLevel::Warning, &gmx::TextOutputFile::standardError());
+ gmx::LoggerOwner logOwner(builder.build());
+ const gmx::MDLogger logger(logOwner.logger());
+
+
wi = init_warning(TRUE, maxwarn);
/* PARAMETER file processing */
{
get_ir(mdparin, opt2fn("-po", NFILE, fnm), &mdModules, ir, opts, WriteMdpHeader::yes, wi);
}
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
+
+ // Now that the MDModules have their options assigned from get_ir, subscribe
+ // to eventual notifications during pre-processing their data
+ mdModules.subscribeToPreProcessingNotifications();
+
+ // Notify MDModules of existing logger
+ mdModules.notifiers().preProcessingNotifier_.notify(logger);
+
+ // Notify MDModules of existing warninp
+ mdModules.notifiers().preProcessingNotifier_.notify(wi);
+
+ // Notify QMMM MDModule of external QM input file command-line option
+ {
+ gmx::QMInputFileName qmInputFileName = { ftp2bSet(efQMI, NFILE, fnm), ftp2fn(efQMI, NFILE, fnm) };
+ mdModules.notifiers().preProcessingNotifier_.notify(qmInputFileName);
+ }
if (bVerbose)
{
- fprintf(stderr, "checking input for internal consistency...\n");
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted("checking input for internal consistency...");
}
- check_ir(mdparin, ir, opts, wi);
+ check_ir(mdparin, mdModules.notifiers(), ir, opts, wi);
if (ir->ld_seed == -1)
{
ir->ld_seed = static_cast<int>(gmx::makeRandomSeed());
- fprintf(stderr, "Setting the LD random seed to %" PRId64 "\n", ir->ld_seed);
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted("Setting the LD random seed to %" PRId64 "", ir->ld_seed);
}
if (ir->expandedvals->lmc_seed == -1)
{
ir->expandedvals->lmc_seed = static_cast<int>(gmx::makeRandomSeed());
- fprintf(stderr, "Setting the lambda MC random seed to %d\n", ir->expandedvals->lmc_seed);
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted("Setting the lambda MC random seed to %d", ir->expandedvals->lmc_seed);
}
bNeedVel = EI_STATE_VELOCITY(ir->eI);
bGenVel = (bNeedVel && opts->bGenVel);
if (bGenVel && ir->bContinuation)
{
- sprintf(warn_buf,
+ std::string warningMessage = gmx::formatString(
"Generating velocities is inconsistent with attempting "
"to continue a previous run. Choose only one of "
"gen-vel = yes and continuation = yes.");
- warning_error(wi, warn_buf);
+ warning_error(wi, warningMessage);
}
- snew(plist, F_NRE);
- init_plist(plist);
- gmx_mtop_t sys;
- atype = init_atomtype();
+ std::array<InteractionsOfType, F_NRE> interactions;
+ gmx_mtop_t sys;
+ PreprocessingAtomTypes atypes;
if (debug)
{
pr_symtab(debug, 0, "Just opened", &sys.symtab);
}
- const char *fn = ftp2fn(efTOP, NFILE, fnm);
+ const char* fn = ftp2fn(efTOP, NFILE, fnm);
if (!gmx_fexist(fn))
{
gmx_fatal(FARGS, "%s does not exist", fn);
}
t_state state;
- new_status(fn, opt2fn_null("-pp", NFILE, fnm), opt2fn("-c", NFILE, fnm),
- opts, ir, bZero, bGenVel, bVerbose, &state,
- atype, &sys, &nmi, &mi, &intermolecular_interactions,
- plist, &comb, &reppow, &fudgeQQ,
+ new_status(fn,
+ opt2fn_null("-pp", NFILE, fnm),
+ opt2fn("-c", NFILE, fnm),
+ opts,
+ ir,
+ bZero,
+ bGenVel,
+ bVerbose,
+ &state,
+ &atypes,
+ &sys,
+ &mi,
+ &intermolecular_interactions,
+ interactions,
+ &comb,
+ &reppow,
+ &fudgeQQ,
opts->bMorse,
- wi);
+ wi,
+ logger);
if (debug)
{
/* set parameters for virtual site construction (not for vsiten) */
for (size_t mt = 0; mt < sys.moltype.size(); mt++)
{
- nvsite +=
- set_vsites(bVerbose, &sys.moltype[mt].atoms, atype, mi[mt].plist);
+ nvsite += set_vsites(bVerbose, &sys.moltype[mt].atoms, &atypes, mi[mt].interactions, logger);
}
/* now throw away all obsolete bonds, angles and dihedrals: */
/* note: constraints are ALWAYS removed */
{
for (size_t mt = 0; mt < sys.moltype.size(); mt++)
{
- clean_vsite_bondeds(mi[mt].plist, sys.moltype[mt].atoms.nr, bRmVSBds);
+ clean_vsite_bondeds(mi[mt].interactions, sys.moltype[mt].atoms.nr, bRmVSBds, logger);
}
}
- if (ir->cutoff_scheme == ecutsVERLET)
- {
- fprintf(stderr, "Removing all charge groups because cutoff-scheme=%s\n",
- ecutscheme_names[ir->cutoff_scheme]);
-
- /* Remove all charge groups */
- gmx_mtop_remove_chargegroups(&sys);
- }
-
- if (count_constraints(&sys, mi, wi) && (ir->eConstrAlg == econtSHAKE))
+ if ((count_constraints(&sys, mi, wi) != 0) && (ir->eConstrAlg == ConstraintAlgorithm::Shake))
{
- if (ir->eI == eiCG || ir->eI == eiLBFGS)
+ if (ir->eI == IntegrationAlgorithm::CG || ir->eI == IntegrationAlgorithm::LBFGS)
{
- sprintf(warn_buf, "Can not do %s with %s, use %s",
- EI(ir->eI), econstr_names[econtSHAKE], econstr_names[econtLINCS]);
- warning_error(wi, warn_buf);
+ std::string warningMessage =
+ gmx::formatString("Can not do %s with %s, use %s",
+ enumValueToString(ir->eI),
+ enumValueToString(ConstraintAlgorithm::Shake),
+ enumValueToString(ConstraintAlgorithm::Lincs));
+ warning_error(wi, warningMessage);
}
if (ir->bPeriodicMols)
{
- sprintf(warn_buf, "Can not do periodic molecules with %s, use %s",
- econstr_names[econtSHAKE], econstr_names[econtLINCS]);
- warning_error(wi, warn_buf);
+ std::string warningMessage =
+ gmx::formatString("Can not do periodic molecules with %s, use %s",
+ enumValueToString(ConstraintAlgorithm::Shake),
+ enumValueToString(ConstraintAlgorithm::Lincs));
+ warning_error(wi, warningMessage);
}
}
- if (EI_SD (ir->eI) && ir->etc != etcNO)
+ if (EI_SD(ir->eI) && ir->etc != TemperatureCoupling::No)
{
warning_note(wi, "Temperature coupling is ignored with SD integrators.");
}
- /* If we are doing QM/MM, check that we got the atom numbers */
- have_atomnumber = TRUE;
- for (i = 0; i < get_atomtype_ntypes(atype); i++)
- {
- have_atomnumber = have_atomnumber && (get_atomtype_atomnumber(i, atype) >= 0);
- }
- if (!have_atomnumber && ir->bQMMM)
- {
- warning_error(wi,
- "\n"
- "It appears as if you are trying to run a QM/MM calculation, but the force\n"
- "field you are using does not contain atom numbers fields. This is an\n"
- "optional field (introduced in GROMACS 3.3) for general runs, but mandatory\n"
- "for QM/MM. The good news is that it is easy to add - put the atom number as\n"
- "an integer just before the mass column in ffXXXnb.itp.\n"
- "NB: United atoms have the same atom numbers as normal ones.\n\n");
- }
-
/* Check for errors in the input now, since they might cause problems
* during processing further down.
*/
check_warning_error(wi, FARGS);
- if (nint_ftype(&sys, mi, F_POSRES) > 0 ||
- nint_ftype(&sys, mi, F_FBPOSRES) > 0)
+ if (nint_ftype(&sys, mi, F_POSRES) > 0 || nint_ftype(&sys, mi, F_FBPOSRES) > 0)
{
- if (ir->epc == epcPARRINELLORAHMAN || ir->epc == epcMTTK)
+ if (ir->epc == PressureCoupling::ParrinelloRahman || ir->epc == PressureCoupling::Mttk)
{
- sprintf(warn_buf, "You are combining position restraints with %s pressure coupling, which can lead to instabilities. If you really want to combine position restraints with pressure coupling, we suggest to use %s pressure coupling instead.",
- EPCOUPLTYPE(ir->epc), EPCOUPLTYPE(epcBERENDSEN));
- warning_note(wi, warn_buf);
+ std::string warningMessage = gmx::formatString(
+ "You are combining position restraints with %s pressure coupling, which can "
+ "lead to instabilities. If you really want to combine position restraints with "
+ "pressure coupling, we suggest to use %s pressure coupling instead.",
+ enumValueToString(ir->epc),
+ enumValueToString(PressureCoupling::Berendsen));
+ warning_note(wi, warningMessage);
}
- const char *fn = opt2fn("-r", NFILE, fnm);
- const char *fnB;
+ const char* fn = opt2fn("-r", NFILE, fnm);
+ const char* fnB;
if (!gmx_fexist(fn))
{
"Cannot find position restraint file %s (option -r).\n"
"From GROMACS-2018, you need to specify the position restraint "
"coordinate files explicitly to avoid mistakes, although you can "
- "still use the same file as you specify for the -c option.", fn);
+ "still use the same file as you specify for the -c option.",
+ fn);
}
if (opt2bSet("-rb", NFILE, fnm))
"Cannot find B-state position restraint file %s (option -rb).\n"
"From GROMACS-2018, you need to specify the position restraint "
"coordinate files explicitly to avoid mistakes, although you can "
- "still use the same file as you specify for the -c option.", fn);
+ "still use the same file as you specify for the -c option.",
+ fn);
}
}
else
if (bVerbose)
{
- fprintf(stderr, "Reading position restraint coords from %s", fn);
- if (strcmp(fn, fnB) == 0)
+ std::string message = gmx::formatString("Reading position restraint coords from %s", fn);
+ if (strcmp(fn, fnB) != 0)
{
- fprintf(stderr, "\n");
- }
- else
- {
- fprintf(stderr, " and %s\n", fnB);
+ message += gmx::formatString(" and %s", fnB);
}
+ GMX_LOG(logger.info).asParagraph().appendText(message);
}
- gen_posres(&sys, mi, fn, fnB,
- ir->refcoord_scaling, ir->ePBC,
- ir->posres_com, ir->posres_comB,
- wi);
+ gen_posres(&sys, mi, fn, fnB, ir->refcoord_scaling, ir->pbcType, ir->posres_com, ir->posres_comB, wi, logger);
}
/* If we are using CMAP, setup the pre-interpolation grid */
- if (plist[F_CMAP].ncmap > 0)
+ if (interactions[F_CMAP].ncmap() > 0)
{
- init_cmap_grid(&sys.ffparams.cmap_grid, plist[F_CMAP].nc, plist[F_CMAP].grid_spacing);
- setup_cmap(plist[F_CMAP].grid_spacing, plist[F_CMAP].nc, plist[F_CMAP].cmap, &sys.ffparams.cmap_grid);
+ init_cmap_grid(&sys.ffparams.cmap_grid,
+ interactions[F_CMAP].cmapAngles,
+ interactions[F_CMAP].cmakeGridSpacing);
+ setup_cmap(interactions[F_CMAP].cmakeGridSpacing,
+ interactions[F_CMAP].cmapAngles,
+ interactions[F_CMAP].cmap,
+ &sys.ffparams.cmap_grid);
}
- set_wall_atomtype(atype, opts, ir, wi);
+ set_wall_atomtype(&atypes, opts, ir, wi, logger);
if (bRenum)
{
- renum_atype(plist, &sys, ir->wall_atomtype, atype, bVerbose);
- get_atomtype_ntypes(atype);
+ atypes.renumberTypes(interactions, &sys, ir->wall_atomtype, bVerbose);
}
if (ir->implicit_solvent)
}
/* PELA: Copy the atomtype data to the topology atomtype list */
- copy_atomtype_atomtypes(atype, &(sys.atomtypes));
+ atypes.copyTot_atomtypes(&(sys.atomtypes));
if (debug)
{
- pr_symtab(debug, 0, "After renum_atype", &sys.symtab);
+ pr_symtab(debug, 0, "After atype.renumberTypes", &sys.symtab);
}
if (bVerbose)
{
- fprintf(stderr, "converting bonded parameters...\n");
+ GMX_LOG(logger.info).asParagraph().appendTextFormatted("converting bonded parameters...");
}
- ntype = get_atomtype_ntypes(atype);
- convert_params(ntype, plist, mi, intermolecular_interactions,
- comb, reppow, fudgeQQ, &sys);
+ const int ntype = atypes.size();
+ convertInteractionsOfType(
+ ntype, interactions, mi, intermolecular_interactions.get(), comb, reppow, fudgeQQ, &sys);
if (debug)
{
- pr_symtab(debug, 0, "After convert_params", &sys.symtab);
+ pr_symtab(debug, 0, "After converInteractionsOfType", &sys.symtab);
}
/* set ptype to VSite for virtual sites */
- for (gmx_moltype_t &moltype : sys.moltype)
+ for (gmx_moltype_t& moltype : sys.moltype)
{
- set_vsites_ptype(FALSE, &moltype);
+ set_vsites_ptype(FALSE, &moltype, logger);
}
if (debug)
{
/* check masses */
check_mol(&sys, wi);
- checkForUnboundAtoms(&sys, bVerbose, wi);
-
- for (const gmx_moltype_t &moltype : sys.moltype)
+ if (haveFepPerturbedMassesInSettles(sys))
{
- check_cg_sizes(ftp2fn(efTOP, NFILE, fnm), &moltype.cgs, wi);
+ warning_error(wi,
+ "SETTLE is not implemented for atoms whose mass is perturbed. "
+ "You might instead use normal constraints.");
}
- if (EI_DYNAMICS(ir->eI) && ir->eI != eiBD)
+ checkForUnboundAtoms(&sys, bVerbose, wi, logger);
+
+ if (EI_DYNAMICS(ir->eI) && ir->eI != IntegrationAlgorithm::BD)
{
check_bonds_timestep(&sys, ir->delta_t, wi);
}
if (EI_ENERGY_MINIMIZATION(ir->eI) && 0 == ir->nsteps)
{
- warning_note(wi, "Zero-step energy minimization will alter the coordinates before calculating the energy. If you just want the energy of a single point, try zero-step MD (with unconstrained_start = yes). To do multiple single-point energy evaluations of different configurations of the same topology, use mdrun -rerun.");
+ warning_note(
+ wi,
+ "Zero-step energy minimization will alter the coordinates before calculating the "
+ "energy. If you just want the energy of a single point, try zero-step MD (with "
+ "unconstrained_start = yes). To do multiple single-point energy evaluations of "
+ "different configurations of the same topology, use mdrun -rerun.");
}
check_warning_error(wi, FARGS);
if (bVerbose)
{
- fprintf(stderr, "initialising group options...\n");
+ GMX_LOG(logger.info).asParagraph().appendTextFormatted("initialising group options...");
}
- do_index(mdparin, ftp2fn_null(efNDX, NFILE, fnm),
- &sys, bVerbose, ir,
- wi);
+ do_index(mdparin, ftp2fn_null(efNDX, NFILE, fnm), &sys, bVerbose, mdModules.notifiers(), ir, wi);
- if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0)
+ // Notify topology to MdModules for pre-processing after all indexes were built
+ mdModules.notifiers().preProcessingNotifier_.notify(&sys);
+
+ if (ir->cutoff_scheme == CutoffScheme::Verlet && ir->verletbuf_tol > 0)
{
if (EI_DYNAMICS(ir->eI) && inputrec2nboundeddim(ir) == 3)
{
real buffer_temp;
- if (EI_MD(ir->eI) && ir->etc == etcNO)
+ if (EI_MD(ir->eI) && ir->etc == TemperatureCoupling::No)
{
if (bGenVel)
{
}
if (buffer_temp > 0)
{
- sprintf(warn_buf, "NVE simulation: will use the initial temperature of %.3f K for determining the Verlet buffer size", buffer_temp);
- warning_note(wi, warn_buf);
+ std::string warningMessage = gmx::formatString(
+ "NVE simulation: will use the initial temperature of %.3f K for "
+ "determining the Verlet buffer size",
+ buffer_temp);
+ warning_note(wi, warningMessage);
}
else
{
- sprintf(warn_buf, "NVE simulation with an initial temperature of zero: will use a Verlet buffer of %d%%. Check your energy drift!",
- gmx::roundToInt(verlet_buffer_ratio_NVE_T0*100));
- warning_note(wi, warn_buf);
+ std::string warningMessage = gmx::formatString(
+ "NVE simulation with an initial temperature of zero: will use a Verlet "
+ "buffer of %d%%. Check your energy drift!",
+ gmx::roundToInt(verlet_buffer_ratio_NVE_T0 * 100));
+ warning_note(wi, warningMessage);
}
}
else
buffer_temp = get_max_reference_temp(ir, wi);
}
- if (EI_MD(ir->eI) && ir->etc == etcNO && buffer_temp == 0)
+ if (EI_MD(ir->eI) && ir->etc == TemperatureCoupling::No && buffer_temp == 0)
{
/* NVE with initial T=0: we add a fixed ratio to rlist.
* Since we don't actually use verletbuf_tol, we set it to -1
* so it can't be misused later.
*/
- ir->rlist *= 1.0 + verlet_buffer_ratio_NVE_T0;
- ir->verletbuf_tol = -1;
+ ir->rlist *= 1.0 + verlet_buffer_ratio_NVE_T0;
+ ir->verletbuf_tol = -1;
}
else
{
* Note that we can't warn when nsteps=0, since we don't
* know how many steps the user intends to run.
*/
- if (EI_MD(ir->eI) && ir->etc == etcNO && ir->nstlist > 1 &&
- ir->nsteps > 0)
+ if (EI_MD(ir->eI) && ir->etc == TemperatureCoupling::No && ir->nstlist > 1 && ir->nsteps > 0)
{
const real driftTolerance = 0.01;
/* We use 2 DOF per atom = 2kT pot+kin energy,
* to be on the safe side with constraints.
*/
- const real totalEnergyDriftPerAtomPerPicosecond = 2*BOLTZ*buffer_temp/(ir->nsteps*ir->delta_t);
+ const real totalEnergyDriftPerAtomPerPicosecond =
+ 2 * gmx::c_boltz * buffer_temp / (ir->nsteps * ir->delta_t);
- if (ir->verletbuf_tol > 1.1*driftTolerance*totalEnergyDriftPerAtomPerPicosecond)
+ if (ir->verletbuf_tol > 1.1 * driftTolerance * totalEnergyDriftPerAtomPerPicosecond)
{
- sprintf(warn_buf, "You are using a Verlet buffer tolerance of %g kJ/mol/ps for an NVE simulation of length %g ps, which can give a final drift of %d%%. For conserving energy to %d%% when using constraints, you might need to set verlet-buffer-tolerance to %.1e.",
- ir->verletbuf_tol, ir->nsteps*ir->delta_t,
- gmx::roundToInt(ir->verletbuf_tol/totalEnergyDriftPerAtomPerPicosecond*100),
- gmx::roundToInt(100*driftTolerance),
- driftTolerance*totalEnergyDriftPerAtomPerPicosecond);
- warning_note(wi, warn_buf);
+ std::string warningMessage = gmx::formatString(
+ "You are using a Verlet buffer tolerance of %g kJ/mol/ps for an "
+ "NVE simulation of length %g ps, which can give a final drift of "
+ "%d%%. For conserving energy to %d%% when using constraints, you "
+ "might need to set verlet-buffer-tolerance to %.1e.",
+ ir->verletbuf_tol,
+ ir->nsteps * ir->delta_t,
+ gmx::roundToInt(ir->verletbuf_tol / totalEnergyDriftPerAtomPerPicosecond * 100),
+ gmx::roundToInt(100 * driftTolerance),
+ driftTolerance * totalEnergyDriftPerAtomPerPicosecond);
+ warning_note(wi, warningMessage);
}
}
- set_verlet_buffer(&sys, ir, buffer_temp, state.box, wi);
+ set_verlet_buffer(&sys, ir, buffer_temp, state.box, wi, logger);
}
}
}
/* Init the temperature coupling state */
init_gtc_state(&state, ir->opts.ngtc, 0, ir->opts.nhchainlength); /* need to add nnhpres here? */
- if (bVerbose)
- {
- fprintf(stderr, "Checking consistency between energy and charge groups...\n");
- }
- check_eg_vs_cg(&sys);
-
if (debug)
{
pr_symtab(debug, 0, "After index", &sys.symtab);
pr_symtab(debug, 0, "After close", &sys.symtab);
}
- /* make exclusions between QM atoms */
- if (ir->bQMMM)
+ if (ir->eI == IntegrationAlgorithm::Mimic)
{
- if (ir->QMMMscheme == eQMMMschemenormal && ir->ns_type == ensSIMPLE)
- {
- gmx_fatal(FARGS, "electrostatic embedding only works with grid neighboursearching, use ns-type=grid instead\n");
- }
- else
- {
- generate_qmexcl(&sys, ir, wi, GmxQmmmMode::GMX_QMMM_ORIGINAL);
- }
- }
-
- if (ir->eI == eiMimic)
- {
- generate_qmexcl(&sys, ir, wi, GmxQmmmMode::GMX_QMMM_MIMIC);
+ generate_qmexcl(&sys, ir, logger);
}
if (ftp2bSet(efTRN, NFILE, fnm))
{
if (bVerbose)
{
- fprintf(stderr, "getting data from old trajectory ...\n");
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted("getting data from old trajectory ...");
}
- cont_status(ftp2fn(efTRN, NFILE, fnm), ftp2fn_null(efEDR, NFILE, fnm),
- bNeedVel, bGenVel, fr_time, ir, &state, &sys, oenv);
+ cont_status(ftp2fn(efTRN, NFILE, fnm),
+ ftp2fn_null(efEDR, NFILE, fnm),
+ bNeedVel,
+ bGenVel,
+ fr_time,
+ ir,
+ &state,
+ &sys,
+ oenv,
+ logger);
}
- if (ir->ePBC == epbcXY && ir->nwall != 2)
+ if (ir->pbcType == PbcType::XY && ir->nwall != 2)
{
clear_rvec(state.box[ZZ]);
}
- if (ir->cutoff_scheme != ecutsVERLET && ir->rlist > 0)
- {
- set_warning_line(wi, mdparin, -1);
- check_chargegroup_radii(&sys, ir, state.x.rvec_array(), wi);
- }
-
if (EEL_FULL(ir->coulombtype) || EVDW_PME(ir->vdwtype))
{
/* Calculate the optimal grid dimensions */
matrix scaledBox;
- EwaldBoxZScaler boxScaler(*ir);
+ EwaldBoxZScaler boxScaler(inputrecPbcXY2Walls(ir), ir->wall_ewald_zfac);
boxScaler.scaleBox(state.box, scaledBox);
if (ir->nkx > 0 && ir->nky > 0 && ir->nkz > 0)
else if (ir->nkx != 0 && ir->nky != 0 && ir->nkz != 0)
{
set_warning_line(wi, mdparin, -1);
- warning_error(wi, "Some of the Fourier grid sizes are set, but all of them need to be set.");
+ warning_error(
+ wi, "Some of the Fourier grid sizes are set, but all of them need to be set.");
}
const int minGridSize = minimalPmeGridSize(ir->pme_order);
- calcFftGrid(stdout, scaledBox, ir->fourier_spacing, minGridSize,
- &(ir->nkx), &(ir->nky), &(ir->nkz));
- if (ir->nkx < minGridSize ||
- ir->nky < minGridSize ||
- ir->nkz < minGridSize)
+ calcFftGrid(stdout, scaledBox, ir->fourier_spacing, minGridSize, &(ir->nkx), &(ir->nky), &(ir->nkz));
+ if (ir->nkx < minGridSize || ir->nky < minGridSize || ir->nkz < minGridSize)
{
- warning_error(wi, "The PME grid size should be >= 2*(pme-order - 1); either manually increase the grid size or decrease pme-order");
+ warning_error(wi,
+ "The PME grid size should be >= 2*(pme-order - 1); either manually "
+ "increase the grid size or decrease pme-order");
}
}
/* MRS: eventually figure out better logic for initializing the fep
values that makes declaring the lambda and declaring the state not
potentially conflict if not handled correctly. */
- if (ir->efep != efepNO)
+ if (ir->efep != FreeEnergyPerturbationType::No)
{
state.fep_state = ir->fepvals->init_fep_state;
- for (i = 0; i < efptNR; i++)
+ for (i = 0; i < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); i++)
{
/* init_lambda trumps state definitions*/
if (ir->fepvals->init_lambda >= 0)
}
else
{
- if (ir->fepvals->all_lambda[i] == nullptr)
+ if (ir->fepvals->all_lambda[i].empty())
{
gmx_fatal(FARGS, "Values of lambda not set for a free energy calculation!");
}
}
}
- struct pull_t *pull = nullptr;
+ pull_t* pull = nullptr;
if (ir->bPull)
{
- pull = set_pull_init(ir, &sys, state.x.rvec_array(), state.box, state.lambda[efptMASS], wi);
+ pull = set_pull_init(
+ ir, sys, state.x, state.box, state.lambda[FreeEnergyPerturbationCouplingType::Mass], wi);
}
/* Modules that supply external potential for pull coordinates
if (ir->bDoAwh)
{
tensor compressibility = { { 0 } };
- if (ir->epc != epcNO)
+ if (ir->epc != PressureCoupling::No)
{
copy_mat(ir->compress, compressibility);
}
- setStateDependentAwhParams(ir->awhParams, ir->pull, pull,
- state.box, ir->ePBC, compressibility,
- &ir->opts, wi);
+ setStateDependentAwhParams(
+ ir->awhParams.get(),
+ *ir->pull,
+ pull,
+ state.box,
+ ir->pbcType,
+ compressibility,
+ &ir->opts,
+ ir->efep != FreeEnergyPerturbationType::No ? ir->fepvals->all_lambda[static_cast<int>(
+ FreeEnergyPerturbationCouplingType::Fep)][ir->fepvals->init_fep_state]
+ : 0,
+ sys,
+ wi);
}
if (ir->bPull)
if (ir->bRot)
{
- set_reference_positions(ir->rot, state.x.rvec_array(), state.box,
- opt2fn("-ref", NFILE, fnm), opt2bSet("-ref", NFILE, fnm),
+ set_reference_positions(ir->rot,
+ state.x.rvec_array(),
+ state.box,
+ opt2fn("-ref", NFILE, fnm),
+ opt2bSet("-ref", NFILE, fnm),
wi);
}
if (EEL_PME(ir->coulombtype))
{
- float ratio = pme_load_estimate(&sys, ir, state.box);
- fprintf(stderr, "Estimate for the relative computational load of the PME mesh part: %.2f\n", ratio);
+ float ratio = pme_load_estimate(sys, *ir, state.box);
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted(
+ "Estimate for the relative computational load of the PME mesh part: %.2f", ratio);
/* With free energy we might need to do PME both for the A and B state
* charges. This will double the cost, but the optimal performance will
* then probably be at a slightly larger cut-off and grid spacing.
*/
- if ((ir->efep == efepNO && ratio > 1.0/2.0) ||
- (ir->efep != efepNO && ratio > 2.0/3.0))
+ if ((ir->efep == FreeEnergyPerturbationType::No && ratio > 1.0 / 2.0)
+ || (ir->efep != FreeEnergyPerturbationType::No && ratio > 2.0 / 3.0))
{
- warning_note(wi,
- "The optimal PME mesh load for parallel simulations is below 0.5\n"
- "and for highly parallel simulations between 0.25 and 0.33,\n"
- "for higher performance, increase the cut-off and the PME grid spacing.\n");
- if (ir->efep != efepNO)
+ warning_note(
+ wi,
+ "The optimal PME mesh load for parallel simulations is below 0.5\n"
+ "and for highly parallel simulations between 0.25 and 0.33,\n"
+ "for higher performance, increase the cut-off and the PME grid spacing.\n");
+ if (ir->efep != FreeEnergyPerturbationType::No)
{
warning_note(wi,
- "For free energy simulations, the optimal load limit increases from 0.5 to 0.667\n");
+ "For free energy simulations, the optimal load limit increases from "
+ "0.5 to 0.667\n");
}
}
}
{
- char warn_buf[STRLEN];
- double cio = compute_io(ir, sys.natoms, &sys.groups, F_NRE, 1);
- sprintf(warn_buf, "This run will generate roughly %.0f Mb of data", cio);
+ double cio = compute_io(ir, sys.natoms, sys.groups, F_NRE, 1);
+ std::string warningMessage =
+ gmx::formatString("This run will generate roughly %.0f Mb of data", cio);
if (cio > 2000)
{
set_warning_line(wi, mdparin, -1);
- warning_note(wi, warn_buf);
+ warning_note(wi, warningMessage);
}
else
{
- printf("%s\n", warn_buf);
+ GMX_LOG(logger.info).asParagraph().appendText(warningMessage);
+ }
+ }
+
+ // Hand over box and coordiantes to MdModules before they evaluate their final parameters
+ {
+ gmx::CoordinatesAndBoxPreprocessed coordinatesAndBoxPreprocessed;
+ coordinatesAndBoxPreprocessed.coordinates_ = state.x.arrayRefWithPadding();
+ copy_mat(state.box, coordinatesAndBoxPreprocessed.box_);
+ coordinatesAndBoxPreprocessed.pbc_ = ir->pbcType;
+ mdModules.notifiers().preProcessingNotifier_.notify(coordinatesAndBoxPreprocessed);
+ }
+
+ // Add the md modules internal parameters that are not mdp options
+ // e.g., atom indices
+
+ {
+ gmx::KeyValueTreeBuilder internalParameterBuilder;
+ mdModules.notifiers().preProcessingNotifier_.notify(internalParameterBuilder.rootObject());
+ ir->internalParameters =
+ std::make_unique<gmx::KeyValueTreeObject>(internalParameterBuilder.build());
+ }
+
+ if (ir->comm_mode != ComRemovalAlgorithm::No)
+ {
+ const int nstglobalcomm = computeGlobalCommunicationPeriod(ir);
+ if (ir->nstcomm % nstglobalcomm != 0)
+ {
+ warning_note(
+ wi,
+ gmx::formatString(
+ "COM removal frequency is set to (%d).\n"
+ "Other settings require a global communication frequency of %d.\n"
+ "Note that this will require additional global communication steps,\n"
+ "which will reduce performance when using multiple ranks.\n"
+ "Consider setting nstcomm to a multiple of %d.",
+ ir->nstcomm,
+ nstglobalcomm,
+ nstglobalcomm));
}
}
if (bVerbose)
{
- fprintf(stderr, "writing run input file...\n");
+ GMX_LOG(logger.info).asParagraph().appendTextFormatted("writing run input file...");
}
done_warning(wi, FARGS);
- write_tpx_state(ftp2fn(efTPR, NFILE, fnm), ir, &state, &sys);
+ write_tpx_state(ftp2fn(efTPR, NFILE, fnm), ir, &state, sys);
/* Output IMD group, if bIMD is TRUE */
- write_IMDgroup_to_file(ir->bIMD, ir, &state, &sys, NFILE, fnm);
+ gmx::write_IMDgroup_to_file(ir->bIMD, ir, &state, sys, NFILE, fnm);
sfree(opts->define);
+ sfree(opts->wall_atomtype[0]);
+ sfree(opts->wall_atomtype[1]);
sfree(opts->include);
- sfree(opts);
- done_plist(plist);
- sfree(plist);
- for (int i = 0; i < nmi; i++)
+ sfree(opts->couple_moltype);
+
+ for (auto& mol : mi)
{
// Some of the contents of molinfo have been stolen, so
- // done_mi can't be called.
- done_block(&mi[i].mols);
- done_plist(mi[i].plist);
+ // fullCleanUp can't be called.
+ mol.partialCleanUp();
}
- sfree(mi);
- done_atomtype(atype);
done_inputrec_strings();
output_env_done(oenv);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff