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implement the scale keyword of fix adapt for diameter and charge

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This commit is contained in:
Jibril B. Coulibaly
2020-03-12 11:11:38 -05:00
parent 3be6347ad4
commit 437055f913
1 changed files with 26 additions and 25 deletions
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51
src/fix_adapt.cpp
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@ -235,7 +235,7 @@ int FixAdapt::setmask()
void FixAdapt::post_constructor()
{
if (!resetflag) return;
// Create local Fix Store even when ressetflag == false, to be able to use `scale` keyword for charge and diameter
if (!diamflag && !chgflag) return;
// new id = fix-ID + FIX_STORE_ATTRIBUTE
@ -251,7 +251,7 @@ void FixAdapt::post_constructor()
newarg[4] = (char *) "1";
newarg[5] = (char *) "1";
if (diamflag) {
if (diamflag && atom->radius_flag) {// Previously unsafe! The radius_flag was not checked, could run an atom_style w/o radius attribute and get here without a previous check / error !
int n = strlen(id) + strlen("_FIX_STORE_DIAM") + 1;
id_fix_diam = new char[n];
strcpy(id_fix_diam,id);
@ -274,7 +274,7 @@ void FixAdapt::post_constructor()
}
}
if (chgflag) {
if (chgflag && atom->q_flag) {// Previously unsafe! The q_flag was not checked, could run an atom_style w/o charge attribute and get here without a previous check / error !
int n = strlen(id) + strlen("_FIX_STORE_CHG") + 1;
id_fix_chg = new char[n];
strcpy(id_fix_chg,id);
@ -455,7 +455,7 @@ void FixAdapt::init()
}
// fixes that store initial per-atom values
/* Unnecessary ? `fix_diam` and `fix_chg` seem to be already defined in FixAdapt::post_constructor(), commenting them out does not crash my MWE
if (id_fix_diam) {
int ifix = modify->find_fix(id_fix_diam);
if (ifix < 0) error->all(FLERR,"Could not find fix adapt storage fix ID");
@ -465,7 +465,7 @@ void FixAdapt::init()
int ifix = modify->find_fix(id_fix_chg);
if (ifix < 0) error->all(FLERR,"Could not find fix adapt storage fix ID");
fix_chg = (FixStore *) modify->fix[ifix];
}
}*/
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
@ -568,38 +568,39 @@ void FixAdapt::change_settings()
// also scale rmass to new value
if (ad->aparam == DIAMETER) {
int mflag = 0;
if (atom->rmass_flag) mflag = 1;
/* `mflag` unnecessary ? the test if (!atom->radius_flag) in FixAdapt::init() should perevent `atom->rmass_flag == false`. Unless there can be combinations of atoms with `radius` but without `rmass`
It could also be unsafe since rmass_flag could be added using `fix property/atom` even for an atom_style that does not have radius attributes */
double density;
double *radius = atom->radius;
double *vec = fix_diam->vstore; // Get initial radius to use `scale` keyword
double *radius = atom->radius;
double *rmass = atom->rmass;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
if (mflag == 0) {
for (i = 0; i < nall; i++)
if (mask[i] & groupbit)
radius[i] = 0.5*value;
} else {
for (i = 0; i < nall; i++)
if (mask[i] & groupbit) {
density = rmass[i] / (4.0*MY_PI/3.0 *
radius[i]*radius[i]*radius[i]);
radius[i] = 0.5*value;
rmass[i] = 4.0*MY_PI/3.0 *
radius[i]*radius[i]*radius[i] * density;
}
}
for (i = 0; i < nall; i++)
if (mask[i] & groupbit) {
density = rmass[i] / (4.0*MY_PI/3.0 *
radius[i]*radius[i]*radius[i]);
if (scaleflag) radius[i] = value * vec[i];
else radius[i] = 0.5*value;
rmass[i] = 4.0*MY_PI/3.0 *
radius[i]*radius[i]*radius[i] * density;
}
} else if (ad->aparam == CHARGE) {
double *q = atom->q;
double *vec = fix_chg->vstore; // Get initial charge to use `scale` keyword
double *q = atom->q;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
for (i = 0; i < nall; i++)
if (mask[i] & groupbit) q[i] = value;
if (mask[i] & groupbit) {
if (scaleflag) q[i] = value * vec[i];
else q[i] = value;
}
}
}
}
@ -607,7 +608,7 @@ void FixAdapt::change_settings()
modify->addstep_compute(update->ntimestep + nevery);
// re-initialize pair styles if any PAIR settings were changed
// ditto for bond styles if any BOND setitings were changes
// ditto for bond styles if any BOND settings were changed
// this resets other coeffs that may depend on changed values,
// and also offset and tail corrections