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lammps/src/fix_adapt.cpp
Axel Kohlmeyer 17f39d9d2c rename fix STORE/PERATOM to STORE/ATOM
2023-03-13 22:33:47 -04:00

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// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "fix_adapt.h"
#include "angle.h"
#include "atom.h"
#include "bond.h"
#include "domain.h"
#include "error.h"
#include "fix_store_atom.h"
#include "force.h"
#include "group.h"
#include "input.h"
#include "kspace.h"
#include "math_const.h"
#include "memory.h"
#include "modify.h"
#include "pair.h"
#include "pair_hybrid.h"
#include "respa.h"
#include "update.h"
#include "variable.h"
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
enum{PAIR,KSPACE,ATOM,BOND,ANGLE};
enum{DIAMETER,CHARGE};
/* ---------------------------------------------------------------------- */
FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), nadapt(0), anypair(0), anybond(0), anyangle(0),
id_fix_diam(nullptr), id_fix_chg(nullptr), adapt(nullptr)
{
if (narg < 5) error->all(FLERR,"Illegal fix adapt command");
nevery = utils::inumeric(FLERR,arg[3],false,lmp);
if (nevery < 0) error->all(FLERR,"Illegal fix adapt command");
dynamic_group_allow = 1;
create_attribute = 1;
// count # of adaptations
nadapt = 0;
int iarg = 4;
while (iarg < narg) {
if (strcmp(arg[iarg],"pair") == 0) {
if (iarg+6 > narg) error->all(FLERR,"Illegal fix adapt command");
nadapt++;
iarg += 6;
} else if (strcmp(arg[iarg],"kspace") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix adapt command");
nadapt++;
iarg += 2;
} else if (strcmp(arg[iarg],"atom") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix adapt command");
nadapt++;
iarg += 3;
} else if (strcmp(arg[iarg],"bond") == 0) {
if (iarg+5 > narg) error->all(FLERR,"Illegal fix adapt command");
nadapt++;
iarg += 5;
} else if (strcmp(arg[iarg],"angle") == 0) {
if (iarg+5 > narg) error->all(FLERR,"Illegal fix adapt command");
nadapt++;
iarg += 5;
} else break;
}
if (nadapt == 0) error->all(FLERR,"Illegal fix adapt command");
adapt = new Adapt[nadapt];
// parse keywords
nadapt = 0;
diamflag = 0;
chgflag = 0;
iarg = 4;
while (iarg < narg) {
if (strcmp(arg[iarg],"pair") == 0) {
if (iarg+6 > narg) error->all(FLERR,"Illegal fix adapt command");
adapt[nadapt].which = PAIR;
adapt[nadapt].pair = nullptr;
adapt[nadapt].pstyle = utils::strdup(arg[iarg+1]);
adapt[nadapt].pparam = utils::strdup(arg[iarg+2]);
utils::bounds(FLERR,arg[iarg+3],1,atom->ntypes,
adapt[nadapt].ilo,adapt[nadapt].ihi,error);
utils::bounds(FLERR,arg[iarg+4],1,atom->ntypes,
adapt[nadapt].jlo,adapt[nadapt].jhi,error);
if (utils::strmatch(arg[iarg+5],"^v_")) {
adapt[nadapt].var = utils::strdup(arg[iarg+5]+2);
} else error->all(FLERR,"Illegal fix adapt command");
nadapt++;
iarg += 6;
} else if (strcmp(arg[iarg],"bond") == 0) {
if (iarg+5 > narg) error->all(FLERR, "Illegal fix adapt command");
adapt[nadapt].which = BOND;
adapt[nadapt].bond = nullptr;
adapt[nadapt].bstyle = utils::strdup(arg[iarg+1]);
adapt[nadapt].bparam = utils::strdup(arg[iarg+2]);
utils::bounds(FLERR,arg[iarg+3],1,atom->nbondtypes,
adapt[nadapt].ilo,adapt[nadapt].ihi,error);
if (utils::strmatch(arg[iarg+4],"^v_")) {
adapt[nadapt].var = utils::strdup(arg[iarg+4]+2);
} else error->all(FLERR,"Illegal fix adapt command");
nadapt++;
iarg += 5;
} else if (strcmp(arg[iarg],"angle") == 0) {
if (iarg+5 > narg) error->all(FLERR, "Illegal fix adapt command");
adapt[nadapt].which = ANGLE;
adapt[nadapt].angle = nullptr;
adapt[nadapt].astyle = utils::strdup(arg[iarg+1]);
adapt[nadapt].aparam = utils::strdup(arg[iarg+2]);
utils::bounds(FLERR,arg[iarg+3],1,atom->nangletypes,
adapt[nadapt].ilo,adapt[nadapt].ihi,error);
if (utils::strmatch(arg[iarg+4],"^v_")) {
adapt[nadapt].var = utils::strdup(arg[iarg+4]+2);
} else error->all(FLERR,"Illegal fix adapt command");
nadapt++;
iarg += 5;
} else if (strcmp(arg[iarg],"kspace") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix adapt command");
adapt[nadapt].which = KSPACE;
if (utils::strmatch(arg[iarg+1],"^v_")) {
adapt[nadapt].var = utils::strdup(arg[iarg+1]+2);
} else error->all(FLERR,"Illegal fix adapt command");
nadapt++;
iarg += 2;
} else if (strcmp(arg[iarg],"atom") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix adapt command");
adapt[nadapt].which = ATOM;
if (strcmp(arg[iarg+1],"diameter") == 0 ||
strcmp(arg[iarg+1],"diameter/disc") == 0) {
adapt[nadapt].atomparam = DIAMETER;
diamflag = 1;
discflag = 0;
if (strcmp(arg[iarg+1],"diameter/disc") == 0) discflag = 1;
} else if (strcmp(arg[iarg+1],"charge") == 0) {
adapt[nadapt].atomparam = CHARGE;
chgflag = 1;
} else error->all(FLERR,"Illegal fix adapt command");
if (utils::strmatch(arg[iarg+2],"^v_")) {
adapt[nadapt].var = utils::strdup(arg[iarg+2]+2);
} else error->all(FLERR,"Illegal fix adapt command");
nadapt++;
iarg += 3;
} else break;
}
// optional keywords
resetflag = 0;
scaleflag = 0;
massflag = 1;
while (iarg < narg) {
if (strcmp(arg[iarg],"reset") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix adapt command");
resetflag = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"scale") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix adapt command");
scaleflag = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"mass") == 0) {
if (iarg+2 > narg)error->all(FLERR,"Illegal fix adapt command");
massflag = utils::logical(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else error->all(FLERR,"Illegal fix adapt command");
}
// if scaleflag set with diameter or charge adaptation,
// then previous step scale factors are written to restart file
// initialize them here in case one is used and other is never defined
if (scaleflag && (diamflag || chgflag)) restart_global = 1;
previous_diam_scale = previous_chg_scale = 1.0;
// allocate pair style arrays
int n = atom->ntypes;
for (int m = 0; m < nadapt; m++)
if (adapt[m].which == PAIR)
memory->create(adapt[m].array_orig,n+1,n+1,"adapt:array_orig");
// allocate bond style arrays:
n = atom->nbondtypes;
for (int m = 0; m < nadapt; ++m)
if (adapt[m].which == BOND)
memory->create(adapt[m].vector_orig,n+1,"adapt:vector_orig");
// allocate angle style arrays:
n = atom->nbondtypes;
for (int m = 0; m < nadapt; ++m)
if (adapt[m].which == ANGLE)
memory->create(adapt[m].vector_orig,n+1,"adapt:vector_orig");
}
/* ---------------------------------------------------------------------- */
FixAdapt::~FixAdapt()
{
for (int m = 0; m < nadapt; m++) {
delete[] adapt[m].var;
if (adapt[m].which == PAIR) {
delete[] adapt[m].pstyle;
delete[] adapt[m].pparam;
memory->destroy(adapt[m].array_orig);
} else if (adapt[m].which == BOND) {
delete[] adapt[m].bstyle;
delete[] adapt[m].bparam;
memory->destroy(adapt[m].vector_orig);
} else if (adapt[m].which == ANGLE) {
delete[] adapt[m].astyle;
delete[] adapt[m].aparam;
memory->destroy(adapt[m].vector_orig);
}
}
delete[] adapt;
// check nfix in case all fixes have already been deleted
if (id_fix_diam && modify->nfix) modify->delete_fix(id_fix_diam);
if (id_fix_chg && modify->nfix) modify->delete_fix(id_fix_chg);
delete[] id_fix_diam;
delete[] id_fix_chg;
}
/* ---------------------------------------------------------------------- */
int FixAdapt::setmask()
{
int mask = 0;
mask |= PRE_FORCE;
mask |= POST_RUN;
mask |= PRE_FORCE_RESPA;
return mask;
}
/* ----------------------------------------------------------------------
if need to restore per-atom quantities, create new fix STORE styles
------------------------------------------------------------------------- */
void FixAdapt::post_constructor()
{
if (!resetflag) return;
if (!diamflag && !chgflag) return;
// new id = fix-ID + FIX_STORE_ATTRIBUTE
// new fix group = group for this fix
id_fix_diam = nullptr;
id_fix_chg = nullptr;
if (diamflag && atom->radius_flag) {
id_fix_diam = utils::strdup(id + std::string("_FIX_STORE_DIAM"));
fix_diam = dynamic_cast<FixStoreAtom *>(
modify->add_fix(fmt::format("{} {} STORE/ATOM 1 0 0 1", id_fix_diam,group->names[igroup])));
if (fix_diam->restart_reset) fix_diam->restart_reset = 0;
else {
double *vec = fix_diam->vstore;
double *radius = atom->radius;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) vec[i] = radius[i];
else vec[i] = 0.0;
}
}
}
if (chgflag && atom->q_flag) {
id_fix_chg = utils::strdup(id + std::string("_FIX_STORE_CHG"));
fix_chg = dynamic_cast<FixStoreAtom *>(
modify->add_fix(fmt::format("{} {} STORE/ATOM 1 0 0 1",id_fix_chg,group->names[igroup])));
if (fix_chg->restart_reset) fix_chg->restart_reset = 0;
else {
double *vec = fix_chg->vstore;
double *q = atom->q;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) vec[i] = q[i];
else vec[i] = 0.0;
}
}
}
}
/* ---------------------------------------------------------------------- */
void FixAdapt::init()
{
int i,j;
// allow a dynamic group only if ATOM attribute not used
if (group->dynamic[igroup])
for (i = 0; i < nadapt; i++)
if (adapt[i].which == ATOM)
error->all(FLERR,"Cannot use dynamic group with fix adapt atom");
// setup and error checks
anypair = 0;
anybond = 0;
anyangle = 0;
for (int m = 0; m < nadapt; m++) {
Adapt *ad = &adapt[m];
ad->ivar = input->variable->find(ad->var);
if (ad->ivar < 0)
error->all(FLERR,"Variable name for fix adapt does not exist");
if (!input->variable->equalstyle(ad->ivar))
error->all(FLERR,"Variable for fix adapt is invalid style");
if (ad->which == PAIR) {
anypair = 1;
ad->pair = nullptr;
// if ad->pstyle has trailing sub-style annotation ":N",
// strip it for pstyle arg to pair_match() and set nsub = N
// this should work for appended suffixes as well
char *pstyle = utils::strdup(ad->pstyle);
char *cptr;
int nsub = 0;
if ((cptr = strchr(pstyle,':'))) {
*cptr = '\0';
nsub = utils::inumeric(FLERR,cptr+1,false,lmp);
}
if (lmp->suffix_enable) {
if (lmp->suffix)
ad->pair = force->pair_match(fmt::format("{}/{}",pstyle,lmp->suffix),1,nsub);
if ((ad->pair == nullptr) && lmp->suffix2)
ad->pair = force->pair_match(fmt::format("{}/{}",pstyle,lmp->suffix2),1,nsub);
}
if (ad->pair == nullptr) ad->pair = force->pair_match(pstyle,1,nsub);
if (ad->pair == nullptr) error->all(FLERR,"Fix adapt pair style {} not found", pstyle);
void *ptr = ad->pair->extract(ad->pparam,ad->pdim);
if (ptr == nullptr)
error->all(FLERR,"Fix adapt pair style param not supported");
// for pair styles only parameters that are 2-d arrays in atom types or
// scalars are supported
if (ad->pdim != 2 && ad->pdim != 0)
error->all(FLERR,"Fix adapt pair style param is not compatible");
if (ad->pdim == 2) ad->array = (double **) ptr;
if (ad->pdim == 0) ad->scalar = (double *) ptr;
// if pair hybrid, test that ilo,ihi,jlo,jhi are valid for sub-style
if (utils::strmatch(force->pair_style,"^hybrid")) {
auto pair = dynamic_cast<PairHybrid *>(force->pair);
for (i = ad->ilo; i <= ad->ihi; i++)
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
if (!pair->check_ijtype(i,j,pstyle))
error->all(FLERR,"Fix adapt type pair range is not valid "
"for pair hybrid sub-style {}", pstyle);
}
delete[] pstyle;
} else if (ad->which == BOND) {
ad->bond = nullptr;
anybond = 1;
char *bstyle = utils::strdup(ad->bstyle);
if (lmp->suffix_enable)
ad->bond = force->bond_match(fmt::format("{}/{}",bstyle,lmp->suffix));
if (ad->bond == nullptr) ad->bond = force->bond_match(bstyle);
if (ad->bond == nullptr )
error->all(FLERR,"Fix adapt bond style does not exist");
void *ptr = ad->bond->extract(ad->bparam,ad->bdim);
if (ptr == nullptr)
error->all(FLERR,"Fix adapt bond style param not supported");
// for bond styles, use a vector
if (ad->bdim == 1) ad->vector = (double *) ptr;
if (utils::strmatch(force->bond_style,"^hybrid"))
error->all(FLERR,"Fix adapt does not support bond_style hybrid");
delete[] bstyle;
} else if (ad->which == ANGLE) {
ad->angle = nullptr;
anyangle = 1;
char *astyle = utils::strdup(ad->astyle);
if (lmp->suffix_enable)
ad->angle = force->angle_match(fmt::format("{}/{}",astyle,lmp->suffix));
if (ad->angle == nullptr) ad->angle = force->angle_match(astyle);
if (ad->angle == nullptr )
error->all(FLERR,"Fix adapt angle style does not exist");
void *ptr = ad->angle->extract(ad->aparam,ad->adim);
if (ptr == nullptr)
error->all(FLERR,"Fix adapt angle style param not supported");
// for angle styles, use a vector
if (ad->adim == 1) ad->vector = (double *) ptr;
if (utils::strmatch(force->angle_style,"^hybrid"))
error->all(FLERR,"Fix adapt does not support angle_style hybrid");
delete[] astyle;
} else if (ad->which == KSPACE) {
if (force->kspace == nullptr)
error->all(FLERR,"Fix adapt kspace style does not exist");
kspace_scale = (double *) force->kspace->extract("scale");
} else if (ad->which == ATOM) {
if (ad->atomparam == DIAMETER) {
if (!atom->radius_flag)
error->all(FLERR,"Fix adapt requires atom attribute diameter");
if (!atom->rmass_flag)
error->all(FLERR,"Fix adapt requires atom attribute mass");
if (discflag && domain->dimension != 2)
error->all(FLERR,"Fix adapt requires 2d simulation");
if (!restart_reset) previous_diam_scale = 1.0;
}
if (ad->atomparam == CHARGE) {
if (!atom->q_flag)
error->all(FLERR,"Fix adapt requires atom attribute charge");
if (!restart_reset) previous_chg_scale = 1.0;
}
}
}
if (restart_reset) restart_reset = 0;
// make copy of original pair/bond/angle array values
for (int m = 0; m < nadapt; m++) {
Adapt *ad = &adapt[m];
if (ad->which == PAIR && ad->pdim == 2) {
for (i = ad->ilo; i <= ad->ihi; i++)
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
ad->array_orig[i][j] = ad->array[i][j];
} else if (ad->which == PAIR && ad->pdim == 0) {
ad->scalar_orig = *ad->scalar;
} else if (ad->which == BOND && ad->bdim == 1) {
for (i = ad->ilo; i <= ad->ihi; ++i )
ad->vector_orig[i] = ad->vector[i];
} else if (ad->which == ANGLE && ad->adim == 1) {
for (i = ad->ilo; i <= ad->ihi; ++i )
ad->vector_orig[i] = ad->vector[i];
}
}
// fixes that store initial per-atom values
if (id_fix_diam) {
fix_diam = dynamic_cast<FixStoreAtom *>(modify->get_fix_by_id(id_fix_diam));
if (!fix_diam) error->all(FLERR,"Could not find fix adapt storage fix ID {}", id_fix_diam);
}
if (id_fix_chg) {
fix_chg = dynamic_cast<FixStoreAtom *>(modify->get_fix_by_id(id_fix_chg));
if (!fix_chg) error->all(FLERR,"Could not find fix adapt storage fix ID {}", id_fix_chg);
}
if (utils::strmatch(update->integrate_style,"^respa"))
nlevels_respa = (dynamic_cast<Respa *>(update->integrate))->nlevels;
}
/* ---------------------------------------------------------------------- */
void FixAdapt::setup_pre_force(int /*vflag*/)
{
change_settings();
}
/* ---------------------------------------------------------------------- */
void FixAdapt::setup_pre_force_respa(int vflag, int ilevel)
{
if (ilevel < nlevels_respa-1) return;
setup_pre_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixAdapt::pre_force(int /*vflag*/)
{
if (nevery == 0) return;
if (update->ntimestep % nevery) return;
change_settings();
}
/* ---------------------------------------------------------------------- */
void FixAdapt::pre_force_respa(int vflag, int ilevel, int)
{
if (ilevel < nlevels_respa-1) return;
pre_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixAdapt::post_run()
{
if (resetflag) restore_settings();
}
/* ----------------------------------------------------------------------
change pair,bond,angle,kspace,atom parameters based on variable evaluation
------------------------------------------------------------------------- */
void FixAdapt::change_settings()
{
int i,j;
// variable evaluation may invoke computes so wrap with clear/add
modify->clearstep_compute();
for (int m = 0; m < nadapt; m++) {
Adapt *ad = &adapt[m];
double value = input->variable->compute_equal(ad->ivar);
// set global scalar or type pair array values
if (ad->which == PAIR) {
if (ad->pdim == 0) {
if (scaleflag) *ad->scalar = value * ad->scalar_orig;
else *ad->scalar = value;
} else if (ad->pdim == 2) {
if (scaleflag)
for (i = ad->ilo; i <= ad->ihi; i++)
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
ad->array[i][j] = value*ad->array_orig[i][j];
else
for (i = ad->ilo; i <= ad->ihi; i++)
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
ad->array[i][j] = value;
}
// set bond type array values:
} else if (ad->which == BOND) {
if (ad->bdim == 1) {
if (scaleflag)
for (i = ad->ilo; i <= ad->ihi; ++i )
ad->vector[i] = value*ad->vector_orig[i];
else
for (i = ad->ilo; i <= ad->ihi; ++i )
ad->vector[i] = value;
}
// set angle type array values:
} else if (ad->which == ANGLE) {
if (ad->adim == 1) {
if (scaleflag)
for (i = ad->ilo; i <= ad->ihi; ++i )
ad->vector[i] = value*ad->vector_orig[i];
else
for (i = ad->ilo; i <= ad->ihi; ++i )
ad->vector[i] = value;
}
// set kspace scale factor
} else if (ad->which == KSPACE) {
*kspace_scale = value;
// set per atom values, also make changes for ghost atoms
} else if (ad->which == ATOM) {
// reset radius to new value, for both owned and ghost atoms
// also reset rmass to new value assuming density remains constant
// for scaleflag, previous_diam_scale is the scale factor on previous step
if (ad->atomparam == DIAMETER) {
double scale;
double *radius = atom->radius;
double *rmass = atom->rmass;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
if (scaleflag) scale = value / previous_diam_scale;
for (i = 0; i < nall; i++) {
if (mask[i] & groupbit) {
if (massflag) {
if (!scaleflag) scale = 0.5*value / radius[i];
if (discflag) rmass[i] *= scale*scale;
else rmass[i] *= scale*scale*scale;
}
if (scaleflag) radius[i] *= scale;
else radius[i] = 0.5*value;
}
}
if (scaleflag) previous_diam_scale = value;
// reset charge to new value, for both owned and ghost atoms
// for scaleflag, previous_chg_scale is the scale factor on previous step
} else if (ad->atomparam == CHARGE) {
double scale;
double *q = atom->q;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
if (scaleflag) scale = value / previous_chg_scale;
for (i = 0; i < nall; i++) {
if (mask[i] & groupbit) {
if (scaleflag) q[i] *= scale;
else q[i] = value;
}
}
if (scaleflag) previous_chg_scale = value;
}
}
}
modify->addstep_compute(update->ntimestep + nevery);
// re-initialize pair styles if any PAIR settings were changed
// ditto for bond/angle styles if any BOND/ANGLE settings were changed
// this resets other coeffs that may depend on changed values,
// and also offset and tail corrections
// we must call force->pair->reinit() instead of the individual
// adapted pair styles so that also the top-level
// tail correction values are updated for hybrid pair styles.
// same for bond styles
if (anypair) force->pair->reinit();
if (anybond) force->bond->reinit();
if (anyangle) force->angle->reinit();
// reset KSpace charges if charges have changed
if (chgflag && force->kspace) force->kspace->qsum_qsq();
}
/* ----------------------------------------------------------------------
restore pair,kspace,atom parameters to original values
------------------------------------------------------------------------- */
void FixAdapt::restore_settings()
{
for (int m = 0; m < nadapt; m++) {
Adapt *ad = &adapt[m];
if (ad->which == PAIR) {
if (ad->pdim == 0) *ad->scalar = ad->scalar_orig;
else if (ad->pdim == 2) {
for (int i = ad->ilo; i <= ad->ihi; i++)
for (int j = MAX(ad->jlo,i); j <= ad->jhi; j++)
ad->array[i][j] = ad->array_orig[i][j];
}
} else if (ad->which == BOND) {
if (ad->bdim == 1) {
for (int i = ad->ilo; i <= ad->ihi; i++)
ad->vector[i] = ad->vector_orig[i];
}
} else if (ad->which == ANGLE) {
if (ad->adim == 1) {
for (int i = ad->ilo; i <= ad->ihi; i++)
ad->vector[i] = ad->vector_orig[i];
}
} else if (ad->which == KSPACE) {
*kspace_scale = 1.0;
} else if (ad->which == ATOM) {
if (diamflag) {
double scale;
double *vec = fix_diam->vstore;
double *radius = atom->radius;
double *rmass = atom->rmass;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (scaleflag) scale = previous_diam_scale;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (massflag) {
if (!scaleflag) scale = vec[i] / radius[i];
if (discflag) rmass[i] *= scale*scale;
else rmass[i] *= scale*scale*scale;
}
radius[i] = vec[i];
}
}
if (chgflag) {
double *vec = fix_chg->vstore;
double *q = atom->q;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) q[i] = vec[i];
}
}
}
if (anypair) force->pair->reinit();
if (anybond) force->bond->reinit();
if (anyangle) force->angle->reinit();
if (chgflag && force->kspace) force->kspace->qsum_qsq();
}
/* ----------------------------------------------------------------------
initialize one atom's storage values, called when atom is created
------------------------------------------------------------------------- */
void FixAdapt::set_arrays(int i)
{
if (fix_diam) fix_diam->vstore[i] = atom->radius[i];
if (fix_chg) fix_chg->vstore[i] = atom->q[i];
}
/* ----------------------------------------------------------------------
write scale factors for diameter and charge to restart file
------------------------------------------------------------------------- */
void FixAdapt::write_restart(FILE *fp)
{
int size = 2*sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(&previous_diam_scale,sizeof(double),1,fp);
fwrite(&previous_chg_scale,sizeof(double),1,fp);
}
/* ----------------------------------------------------------------------
use scale factors from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixAdapt::restart(char *buf)
{
auto dbuf = (double *) buf;
previous_diam_scale = dbuf[0];
previous_chg_scale = dbuf[1];
}
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