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add rmass_flag and rectify comments and indents

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This commit is contained in:
Jibril B. Coulibaly
2020-04-10 16:04:56 -05:00
parent 8b8f928347
commit e114d814f4
2 changed files with 32 additions and 28 deletions
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58
src/fix_adapt.cpp
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@ -143,8 +143,8 @@ nadapt(0), id_fix_diam(NULL), id_fix_chg(NULL), adapt(NULL)
if (strcmp(arg[iarg+1],"diameter") == 0 || strcmp(arg[iarg+1],"diameter/disc") == 0) {
adapt[nadapt].aparam = DIAMETER;
diamflag = 1;
discflag = 0;
if(strcmp(arg[iarg+1],"diameter/disc") == 0) discflag = 1;
discflag = 0;
if (strcmp(arg[iarg+1],"diameter/disc") == 0) discflag = 1;
} else if (strcmp(arg[iarg+1],"charge") == 0) {
adapt[nadapt].aparam = CHARGE;
chgflag = 1;
@ -238,7 +238,6 @@ int FixAdapt::setmask()
void FixAdapt::post_constructor()
{
// 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
@ -254,7 +253,7 @@ void FixAdapt::post_constructor()
newarg[4] = (char *) "1";
newarg[5] = (char *) "1";
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 !
if (diamflag && atom->radius_flag) {
int n = strlen(id) + strlen("_FIX_STORE_DIAM") + 1;
id_fix_diam = new char[n];
strcpy(id_fix_diam,id);
@ -277,7 +276,7 @@ void FixAdapt::post_constructor()
}
}
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 !
if (chgflag && atom->q_flag) {
int n = strlen(id) + strlen("_FIX_STORE_CHG") + 1;
id_fix_chg = new char[n];
strcpy(id_fix_chg,id);
@ -431,8 +430,10 @@ void FixAdapt::init()
if (ad->aparam == DIAMETER) {
if (!atom->radius_flag)
error->all(FLERR,"Fix adapt requires atom attribute diameter");
if(discflag && domain->dimension!=2)
error->all(FLERR,"Fix adapt requires 2d simulation");
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 (ad->aparam == CHARGE) {
if (!atom->q_flag)
@ -460,7 +461,7 @@ 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");
@ -470,7 +471,7 @@ 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;
@ -573,12 +574,12 @@ void FixAdapt::change_settings()
// also scale rmass to new value
if (ad->aparam == DIAMETER) {
/* `mflag` unnecessary ? the test `if(!atom->radius_flag)` in `FixAdapt::init()` should perevent `atom->rmass_flag == false`. Unless there can be combinations of atom styles 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 attribute, although that possibility should be avoided as well with the test `if(!atom->radius_flag)` in `FixAdapt::init()` */
double density;
double *vec = fix_diam->vstore; // Get initial radius to use `scale` keyword
double *radius = atom->radius;
// Get initial diameter if `scale` keyword is used
double *vec = fix_diam->vstore;
double *radius = atom->radius;
double *rmass = atom->rmass;
int *mask = atom->mask;
int nlocal = atom->nlocal;
@ -586,28 +587,31 @@ void FixAdapt::change_settings()
for (i = 0; i < nall; i++)
if (mask[i] & groupbit) {
if(discflag) density = rmass[i] / (MY_PI * radius[i]*radius[i]);
else density = rmass[i] / (4.0*MY_PI/3.0 *
if (discflag) density = rmass[i] / (MY_PI * radius[i]*radius[i]);
else 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;
if(discflag) rmass[i] = MY_PI * radius[i]*radius[i] * density;
if (scaleflag) radius[i] = value * vec[i];
else radius[i] = 0.5*value;
if (discflag) rmass[i] = MY_PI * radius[i]*radius[i] * density;
else rmass[i] = 4.0*MY_PI/3.0 *
radius[i]*radius[i]*radius[i] * density;
}
} else if (ad->aparam == CHARGE) {
double *vec = fix_chg->vstore; // Get initial charge to use `scale` keyword
double *q = atom->q;
// Get initial charge if `scale` keyword is used
double *vec = fix_chg->vstore;
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) {
if (scaleflag) q[i] = value * vec[i];
else q[i] = value;
}
if (scaleflag) q[i] = value * vec[i];
else q[i] = value;
}
}
}
}
@ -678,13 +682,13 @@ void FixAdapt::restore_settings()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if(discflag) density = rmass[i] / (MY_PI * radius[i]*radius[i]);
else density = rmass[i] / (4.0*MY_PI/3.0 *
if(discflag) density = rmass[i] / (MY_PI * radius[i]*radius[i]);
else density = rmass[i] / (4.0*MY_PI/3.0 *
radius[i]*radius[i]*radius[i]);
radius[i] = vec[i];
if(discflag) rmass[i] = MY_PI * radius[i]*radius[i] * density;
else rmass[i] = 4.0*MY_PI/3.0 *
radius[i]*radius[i]*radius[i] * density;
else rmass[i] = 4.0*MY_PI/3.0 *
radius[i]*radius[i]*radius[i] * density;
}
}
if (chgflag) {

2
src/fix_adapt.h
View File

@ -47,7 +47,7 @@ class FixAdapt : public Fix {
int nlevels_respa;
char *id_fix_diam,*id_fix_chg;
class FixStore *fix_diam,*fix_chg;
int discflag;
int discflag;
struct Adapt {
int which,ivar;