*
* 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, 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 <cmath>
#include <cstring>
-#include "gromacs/compat/make_unique.h"
+#include <memory>
+
#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp_impl.h"
#include "gromacs/gmxpreprocess/topio.h"
#include "gromacs/gmxpreprocess/toputil.h"
#include "gromacs/math/functions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-static int round_check(real r, int limit, int ftype, const char *name)
+static int round_check(real r, int limit, int ftype, const char* name)
{
const int i = gmx::roundToInt(r);
- if (r-i > 0.01 || r-i < -0.01)
+ if (r - i > 0.01 || r - i < -0.01)
{
- gmx_fatal(FARGS, "A non-integer value (%f) was supplied for '%s' in %s",
- r, name, interaction_function[ftype].longname);
+ gmx_fatal(FARGS,
+ "A non-integer value (%f) was supplied for '%s' in %s",
+ r,
+ name,
+ interaction_function[ftype].longname);
}
if (i < limit)
{
- gmx_fatal(FARGS, "Value of '%s' in %s is %d, which is smaller than the minimum of %d",
- name, interaction_function[ftype].longname, i, limit);
+ gmx_fatal(FARGS,
+ "Value of '%s' in %s is %d, which is smaller than the minimum of %d",
+ name,
+ interaction_function[ftype].longname,
+ i,
+ limit);
}
return i;
}
-static void set_ljparams(int comb, double reppow, double v, double w,
- real *c6, real *c12)
+static void set_ljparams(CombinationRule comb, double reppow, double v, double w, real* c6, real* c12)
{
- if (comb == eCOMB_ARITHMETIC || comb == eCOMB_GEOM_SIG_EPS)
+ if (comb == CombinationRule::Arithmetic || comb == CombinationRule::GeomSigEps)
{
if (v >= 0)
{
- *c6 = 4*w*gmx::power6(v);
- *c12 = 4*w*std::pow(v, reppow);
+ *c6 = 4 * w * gmx::power6(v);
+ *c12 = 4 * w * std::pow(v, reppow);
}
else
{
/* Interpret negative sigma as c6=0 and c12 with -sigma */
*c6 = 0;
- *c12 = 4*w*std::pow(-v, reppow);
+ *c12 = 4 * w * std::pow(-v, reppow);
}
}
else
/* A return value of 0 means parameters were assigned successfully,
* returning -1 means this is an all-zero interaction that should not be added.
*/
-static int
-assign_param(t_functype ftype, t_iparams *newparam,
- real old[MAXFORCEPARAM], int comb, double reppow)
+static int assign_param(t_functype ftype,
+ t_iparams* newparam,
+ gmx::ArrayRef<const real> old,
+ CombinationRule comb,
+ double reppow)
{
- int i, j;
- bool all_param_zero = TRUE;
+ bool all_param_zero = true;
/* Set to zero */
- for (j = 0; (j < MAXFORCEPARAM); j++)
+ for (int j = 0; (j < MAXFORCEPARAM); j++)
{
newparam->generic.buf[j] = 0.0;
/* If all parameters are zero we might not add some interaction types (selected below).
if (all_param_zero)
{
- if (IS_ANGLE(ftype) || IS_RESTRAINT_TYPE(ftype) || ftype == F_IDIHS ||
- ftype == F_PDIHS || ftype == F_PIDIHS || ftype == F_RBDIHS || ftype == F_FOURDIHS)
+ if (IS_ANGLE(ftype) || IS_RESTRAINT_TYPE(ftype) || ftype == F_IDIHS || ftype == F_PDIHS
+ || ftype == F_PIDIHS || ftype == F_RBDIHS || ftype == F_FOURDIHS)
{
return -1;
}
{
case F_G96ANGLES:
/* Post processing of input data: store cosine iso angle itself */
- newparam->harmonic.rA = cos(old[0]*DEG2RAD);
+ newparam->harmonic.rA = cos(old[0] * gmx::c_deg2Rad);
newparam->harmonic.krA = old[1];
- newparam->harmonic.rB = cos(old[2]*DEG2RAD);
+ newparam->harmonic.rB = cos(old[2] * gmx::c_deg2Rad);
newparam->harmonic.krB = old[3];
break;
case F_G96BONDS:
break;
case F_QUARTIC_ANGLES:
newparam->qangle.theta = old[0];
- for (i = 0; i < 5; i++)
+ for (int i = 0; i < 5; i++)
{
- newparam->qangle.c[i] = old[i+1];
+ newparam->qangle.c[i] = old[i + 1];
}
break;
case F_LINEAR_ANGLES:
newparam->harmonic.krA = old[1];
break;
case F_MORSE:
- newparam->morse.b0A = old[0];
- newparam->morse.cbA = old[1];
- newparam->morse.betaA = old[2];
- newparam->morse.b0B = old[3];
- newparam->morse.cbB = old[4];
- newparam->morse.betaB = old[5];
+ newparam->morse.b0A = old[0];
+ newparam->morse.cbA = old[1];
+ newparam->morse.betaA = old[2];
+ newparam->morse.b0B = old[3];
+ newparam->morse.cbB = old[4];
+ newparam->morse.betaB = old[5];
break;
case F_CUBICBONDS:
- newparam->cubic.b0 = old[0];
- newparam->cubic.kb = old[1];
- newparam->cubic.kcub = old[2];
- break;
- case F_CONNBONDS:
- break;
- case F_POLARIZATION:
- newparam->polarize.alpha = old[0];
+ newparam->cubic.b0 = old[0];
+ newparam->cubic.kb = old[1];
+ newparam->cubic.kcub = old[2];
break;
+ case F_CONNBONDS: break;
+ case F_POLARIZATION: newparam->polarize.alpha = old[0]; break;
case F_ANHARM_POL:
newparam->anharm_polarize.alpha = old[0];
newparam->anharm_polarize.drcut = old[1];
newparam->anharm_polarize.khyp = old[2];
break;
case F_WATER_POL:
- newparam->wpol.al_x = old[0];
- newparam->wpol.al_y = old[1];
- newparam->wpol.al_z = old[2];
- newparam->wpol.rOH = old[3];
- newparam->wpol.rHH = old[4];
- newparam->wpol.rOD = old[5];
+ newparam->wpol.al_x = old[0];
+ newparam->wpol.al_y = old[1];
+ newparam->wpol.al_z = old[2];
+ newparam->wpol.rOH = old[3];
+ newparam->wpol.rHH = old[4];
+ newparam->wpol.rOD = old[5];
break;
case F_THOLE_POL:
newparam->thole.a = old[0];
newparam->thole.alpha1 = old[1];
newparam->thole.alpha2 = old[2];
- if ((old[1] > 0) && (old[2] > 0))
- {
- newparam->thole.rfac = old[0]*gmx::invsixthroot(old[1]*old[2]);
- }
- else
- {
- newparam->thole.rfac = 1;
- }
break;
case F_BHAM:
newparam->bham.a = old[0];
newparam->posres.pos0B[ZZ] = old[11];
break;
case F_FBPOSRES:
- newparam->fbposres.geom = round_check(old[0], 0, ftype, "geometry");
+ newparam->fbposres.geom = round_check(old[0], 0, ftype, "geometry");
if (!(newparam->fbposres.geom > efbposresZERO && newparam->fbposres.geom < efbposresNR))
{
- gmx_fatal(FARGS, "Invalid geometry for flat-bottomed position restraint.\n"
- "Expected number between 1 and %d. Found %d\n", efbposresNR-1,
+ gmx_fatal(FARGS,
+ "Invalid geometry for flat-bottomed position restraint.\n"
+ "Expected number between 1 and %d. Found %d\n",
+ efbposresNR - 1,
newparam->fbposres.geom);
}
newparam->fbposres.r = old[1];
newparam->orires.kfac = old[5];
break;
case F_DIHRES:
- newparam->dihres.phiA = old[0];
- newparam->dihres.dphiA = old[1];
- newparam->dihres.kfacA = old[2];
- newparam->dihres.phiB = old[3];
- newparam->dihres.dphiB = old[4];
- newparam->dihres.kfacB = old[5];
+ newparam->dihres.phiA = old[0];
+ newparam->dihres.dphiA = old[1];
+ newparam->dihres.kfacA = old[2];
+ newparam->dihres.phiB = old[3];
+ newparam->dihres.dphiB = old[4];
+ newparam->dihres.kfacB = old[5];
break;
case F_RBDIHS:
- for (i = 0; (i < NR_RBDIHS); i++)
+ for (int i = 0; (i < NR_RBDIHS); i++)
{
newparam->rbdihs.rbcA[i] = old[i];
- newparam->rbdihs.rbcB[i] = old[NR_RBDIHS+i];
+ newparam->rbdihs.rbcB[i] = old[NR_RBDIHS + i];
}
break;
case F_CBTDIHS:
- for (i = 0; (i < NR_CBTDIHS); i++)
+ for (int i = 0; (i < NR_CBTDIHS); i++)
{
newparam->cbtdihs.cbtcA[i] = old[i];
}
* Ryckaert-Bellemans form.
*/
/* Use conversion formula for OPLS to Ryckaert-Bellemans: */
- newparam->rbdihs.rbcA[0] = old[1]+0.5*(old[0]+old[2]);
- newparam->rbdihs.rbcA[1] = 0.5*(3.0*old[2]-old[0]);
- newparam->rbdihs.rbcA[2] = 4.0*old[3]-old[1];
- newparam->rbdihs.rbcA[3] = -2.0*old[2];
- newparam->rbdihs.rbcA[4] = -4.0*old[3];
+ newparam->rbdihs.rbcA[0] = old[1] + 0.5 * (old[0] + old[2]);
+ newparam->rbdihs.rbcA[1] = 0.5 * (3.0 * old[2] - old[0]);
+ newparam->rbdihs.rbcA[2] = 4.0 * old[3] - old[1];
+ newparam->rbdihs.rbcA[3] = -2.0 * old[2];
+ newparam->rbdihs.rbcA[4] = -4.0 * old[3];
newparam->rbdihs.rbcA[5] = 0.0;
- newparam->rbdihs.rbcB[0] = old[NR_FOURDIHS+1]+0.5*(old[NR_FOURDIHS+0]+old[NR_FOURDIHS+2]);
- newparam->rbdihs.rbcB[1] = 0.5*(3.0*old[NR_FOURDIHS+2]-old[NR_FOURDIHS+0]);
- newparam->rbdihs.rbcB[2] = 4.0*old[NR_FOURDIHS+3]-old[NR_FOURDIHS+1];
- newparam->rbdihs.rbcB[3] = -2.0*old[NR_FOURDIHS+2];
- newparam->rbdihs.rbcB[4] = -4.0*old[NR_FOURDIHS+3];
+ newparam->rbdihs.rbcB[0] =
+ old[NR_FOURDIHS + 1] + 0.5 * (old[NR_FOURDIHS + 0] + old[NR_FOURDIHS + 2]);
+ newparam->rbdihs.rbcB[1] = 0.5 * (3.0 * old[NR_FOURDIHS + 2] - old[NR_FOURDIHS + 0]);
+ newparam->rbdihs.rbcB[2] = 4.0 * old[NR_FOURDIHS + 3] - old[NR_FOURDIHS + 1];
+ newparam->rbdihs.rbcB[3] = -2.0 * old[NR_FOURDIHS + 2];
+ newparam->rbdihs.rbcB[4] = -4.0 * old[NR_FOURDIHS + 3];
newparam->rbdihs.rbcB[5] = 0.0;
break;
case F_CONSTR:
newparam->settle.doh = old[0];
newparam->settle.dhh = old[1];
break;
+ case F_VSITE1:
case F_VSITE2:
+ case F_VSITE2FD:
case F_VSITE3:
case F_VSITE3FD:
case F_VSITE3OUT:
newparam->vsite.f = old[5];
break;
case F_VSITE3FAD:
- newparam->vsite.a = old[1] * cos(DEG2RAD * old[0]);
- newparam->vsite.b = old[1] * sin(DEG2RAD * old[0]);
+ newparam->vsite.a = old[1] * cos(gmx::c_deg2Rad * old[0]);
+ newparam->vsite.b = old[1] * sin(gmx::c_deg2Rad * old[0]);
newparam->vsite.c = old[2];
newparam->vsite.d = old[3];
newparam->vsite.e = old[4];
break;
case F_GB12_NOLONGERUSED:
case F_GB13_NOLONGERUSED:
- case F_GB14_NOLONGERUSED:
- break;
+ case F_GB14_NOLONGERUSED: break;
default:
- gmx_fatal(FARGS, "unknown function type %d in %s line %d",
- ftype, __FILE__, __LINE__);
+ gmx_fatal(FARGS, "unknown function type %d in %s line %d", ftype, __FILE__, __LINE__);
}
return 0;
}
-static int enter_params(gmx_ffparams_t *ffparams, t_functype ftype,
- real forceparams[MAXFORCEPARAM], int comb, real reppow,
- int start, bool bAppend)
+static int enter_params(gmx_ffparams_t* ffparams,
+ t_functype ftype,
+ gmx::ArrayRef<const real> forceparams,
+ CombinationRule comb,
+ real reppow,
+ int start,
+ bool bAppend)
{
t_iparams newparam;
- int type;
int rc;
- if ( (rc = assign_param(ftype, &newparam, forceparams, comb, reppow)) < 0)
+ if ((rc = assign_param(ftype, &newparam, forceparams, comb, reppow)) < 0)
{
/* -1 means this interaction is all-zero and should not be added */
return rc;
if (!bAppend)
{
- for (type = start; (type < ffparams->numTypes()); type++)
+ if (ftype != F_DISRES)
{
- if (ffparams->functype[type] == ftype)
+ for (int type = start; type < ffparams->numTypes(); type++)
{
- if (memcmp(&newparam, &ffparams->iparams[type], static_cast<size_t>(sizeof(newparam))) == 0)
+ // Note that the first condition is always met by starting the loop at start
+ if (ffparams->functype[type] == ftype
+ && memcmp(&newparam, &ffparams->iparams[type], static_cast<size_t>(sizeof(newparam))) == 0)
{
return type;
}
}
}
- }
- else
- {
- type = ffparams->numTypes();
+ else
+ {
+ // Distance restraints should have unique labels and pairs with the same label
+ // should be consecutive, so we here we only need to check the last type in the list.
+ // This changes the complexity from quadratic to linear in the number of restraints.
+ const int type = ffparams->numTypes() - 1;
+ if (type >= 0 && ffparams->functype[type] == ftype
+ && memcmp(&newparam, &ffparams->iparams[type], static_cast<size_t>(sizeof(newparam))) == 0)
+ {
+ return type;
+ }
+ }
}
+ const int type = ffparams->numTypes();
+
ffparams->iparams.push_back(newparam);
ffparams->functype.push_back(ftype);
- GMX_ASSERT(ffparams->iparams.size() == ffparams->functype.size(),
- "sizes should match");
+ GMX_ASSERT(ffparams->iparams.size() == ffparams->functype.size(), "sizes should match");
return type;
}
-static void append_interaction(InteractionList *ilist,
- int type, int nral, const int a[MAXATOMLIST])
+static void append_interaction(InteractionList* ilist, int type, gmx::ArrayRef<const int> a)
{
ilist->iatoms.push_back(type);
- for (int i = 0; (i < nral); i++)
+ for (const auto& atom : a)
{
- ilist->iatoms.push_back(a[i]);
+ ilist->iatoms.push_back(atom);
}
}
-static void enter_function(t_params *p, t_functype ftype, int comb, real reppow,
- gmx_ffparams_t *ffparams, InteractionList *il,
- bool bNB, bool bAppend)
+static void enter_function(const InteractionsOfType* p,
+ t_functype ftype,
+ CombinationRule comb,
+ real reppow,
+ gmx_ffparams_t* ffparams,
+ InteractionList* il,
+ bool bNB,
+ bool bAppend)
{
- int k, type, nr, nral, start;
-
- start = ffparams->numTypes();
- nr = p->nr;
+ int start = ffparams->numTypes();
- for (k = 0; k < nr; k++)
+ for (const auto& parm : p->interactionTypes)
{
- type = enter_params(ffparams, ftype, p->param[k].c, comb, reppow, start, bAppend);
+ int type = enter_params(ffparams, ftype, parm.forceParam(), comb, reppow, start, bAppend);
/* Type==-1 is used as a signal that this interaction is all-zero and should not be added. */
if (!bNB && type >= 0)
{
- assert(il);
- nral = NRAL(ftype);
- append_interaction(il, type, nral, p->param[k].a);
+ GMX_RELEASE_ASSERT(il, "Need valid interaction list");
+ GMX_RELEASE_ASSERT(parm.atoms().ssize() == NRAL(ftype),
+ "Need to have correct number of atoms for the parameter");
+ append_interaction(il, type, parm.atoms());
}
}
}
-void convert_params(int atnr, t_params nbtypes[],
- t_molinfo *mi, t_molinfo *intermolecular_interactions,
- int comb, double reppow, real fudgeQQ,
- gmx_mtop_t *mtop)
+void convertInteractionsOfType(int atnr,
+ gmx::ArrayRef<const InteractionsOfType> nbtypes,
+ gmx::ArrayRef<const MoleculeInformation> mi,
+ const MoleculeInformation* intermolecular_interactions,
+ CombinationRule comb,
+ double reppow,
+ real fudgeQQ,
+ gmx_mtop_t* mtop)
{
int i;
unsigned long flags;
- gmx_ffparams_t *ffp;
- gmx_moltype_t *molt;
- t_params *plist;
+ gmx_ffparams_t* ffp;
+ gmx_moltype_t* molt;
- ffp = &mtop->ffparams;
- ffp->atnr = atnr;
+ ffp = &mtop->ffparams;
+ ffp->atnr = atnr;
ffp->functype.clear();
ffp->iparams.clear();
- ffp->reppow = reppow;
+ ffp->reppow = reppow;
- enter_function(&(nbtypes[F_LJ]), static_cast<t_functype>(F_LJ), comb, reppow, ffp, nullptr,
- TRUE, TRUE);
- enter_function(&(nbtypes[F_BHAM]), static_cast<t_functype>(F_BHAM), comb, reppow, ffp, nullptr,
- TRUE, TRUE);
+ enter_function(&(nbtypes[F_LJ]), static_cast<t_functype>(F_LJ), comb, reppow, ffp, nullptr, TRUE, TRUE);
+ enter_function(
+ &(nbtypes[F_BHAM]), static_cast<t_functype>(F_BHAM), comb, reppow, ffp, nullptr, TRUE, TRUE);
for (size_t mt = 0; mt < mtop->moltype.size(); mt++)
{
{
molt->ilist[i].iatoms.clear();
- plist = mi[mt].plist;
+ gmx::ArrayRef<const InteractionsOfType> interactions = mi[mt].interactions;
flags = interaction_function[i].flags;
- if ((i != F_LJ) && (i != F_BHAM) && ((flags & IF_BOND) ||
- (flags & IF_VSITE) ||
- (flags & IF_CONSTRAINT)))
+ if ((i != F_LJ) && (i != F_BHAM)
+ && ((flags & IF_BOND) || (flags & IF_VSITE) || (flags & IF_CONSTRAINT)))
{
- enter_function(&(plist[i]), static_cast<t_functype>(i), comb, reppow,
- ffp, &molt->ilist[i],
- FALSE, (i == F_POSRES || i == F_FBPOSRES));
+ enter_function(&(interactions[i]),
+ static_cast<t_functype>(i),
+ comb,
+ reppow,
+ ffp,
+ &molt->ilist[i],
+ FALSE,
+ (i == F_POSRES || i == F_FBPOSRES));
}
}
}
if (intermolecular_interactions != nullptr)
{
/* Process the intermolecular interaction list */
- mtop->intermolecular_ilist = gmx::compat::make_unique<InteractionLists>();
+ mtop->intermolecular_ilist = std::make_unique<InteractionLists>();
for (i = 0; (i < F_NRE); i++)
{
(*mtop->intermolecular_ilist)[i].iatoms.clear();
- plist = intermolecular_interactions->plist;
+ gmx::ArrayRef<const InteractionsOfType> interactions = intermolecular_interactions->interactions;
- if (plist[i].nr > 0)
+ if (!interactions[i].interactionTypes.empty())
{
flags = interaction_function[i].flags;
/* For intermolecular interactions we (currently)
*/
if (!(flags & IF_BOND))
{
- gmx_fatal(FARGS, "The intermolecular_interaction section may only contain bonded potentials");
+ gmx_fatal(FARGS,
+ "The intermolecular_interaction section may only contain bonded "
+ "potentials");
}
else if (NRAL(i) == 1) /* e.g. position restraints */
{
- gmx_fatal(FARGS, "Single atom interactions don't make sense in the intermolecular_interaction section, you can put them in the moleculetype section");
+ gmx_fatal(FARGS,
+ "Single atom interactions don't make sense in the "
+ "intermolecular_interaction section, you can put them in the "
+ "moleculetype section");
}
else if (flags & IF_CHEMBOND)
{
- gmx_fatal(FARGS, "The intermolecular_interaction can not contain chemically bonding interactions");
+ gmx_fatal(FARGS,
+ "The intermolecular_interaction can not contain chemically bonding "
+ "interactions");
}
else
{
- enter_function(&(plist[i]), static_cast<t_functype>(i), comb, reppow,
- ffp, &(*mtop->intermolecular_ilist)[i],
- FALSE, FALSE);
+ enter_function(&(interactions[i]),
+ static_cast<t_functype>(i),
+ comb,
+ reppow,
+ ffp,
+ &(*mtop->intermolecular_ilist)[i],
+ FALSE,
+ FALSE);
mtop->bIntermolecularInteractions = TRUE;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff