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Merge branch 'develop' into patch-2

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This commit is contained in:
Evangelos Voyiatzis
2025-02-15 17:15:33 +01:00
committed by GitHub
parent c83ae0365e 36e739b734
commit eaf624c0f0
70 changed files with 2090 additions and 507 deletions
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74
src/fix_adapt.cpp
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@ -54,7 +54,7 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) :
{
if (narg < 5) utils::missing_cmd_args(FLERR,"fix adapt", error);
nevery = utils::inumeric(FLERR,arg[3],false,lmp);
if (nevery < 0) error->all(FLERR,"Illegal fix adapt every value {}", nevery);
if (nevery < 0) error->all(FLERR, 3, "Illegal fix adapt every value {}", nevery);
dynamic_group_allow = 1;
create_attribute = 1;
@ -92,7 +92,7 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) :
} else break;
}
if (nadapt == 0) error->all(FLERR,"Nothing to adapt in fix adapt command");
if (nadapt == 0) error->all(FLERR, 3, "Nothing to adapt in fix adapt command");
adapt = new Adapt[nadapt];
// parse keywords
@ -125,7 +125,7 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) :
if (utils::strmatch(arg[iarg+5],"^v_")) {
adapt[nadapt].var = utils::strdup(arg[iarg+5]+2);
} else error->all(FLERR,"Argument #{} must be variable not {}", iarg+6, arg[iarg+5]);
} else error->all(FLERR, iarg+5, "Argument must be variable not {}", arg[iarg+5]);
nadapt++;
iarg += 6;
@ -138,7 +138,7 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) :
adapt[nadapt].ilo, adapt[nadapt].ihi, lmp, Atom::BOND);
if (utils::strmatch(arg[iarg+4],"^v_")) {
adapt[nadapt].var = utils::strdup(arg[iarg+4]+2);
} else error->all(FLERR,"Argument #{} must be variable not {}", iarg+5, arg[iarg+4]);
} else error->all(FLERR, iarg+4, "Argument must be variable not {}", arg[iarg+4]);
nadapt++;
iarg += 5;
@ -151,7 +151,7 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) :
adapt[nadapt].ilo, adapt[nadapt].ihi, lmp, Atom::ANGLE);
if (utils::strmatch(arg[iarg+4],"^v_")) {
adapt[nadapt].var = utils::strdup(arg[iarg+4]+2);
} else error->all(FLERR,"Argument #{} must be variable not {}", iarg+5, arg[iarg+4]);
} else error->all(FLERR,iarg+4, "Argument must be variable not {}", arg[iarg+4]);
nadapt++;
iarg += 5;
@ -172,7 +172,7 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) :
adapt[nadapt].which = KSPACE;
if (utils::strmatch(arg[iarg+1],"^v_")) {
adapt[nadapt].var = utils::strdup(arg[iarg+1]+2);
} else error->all(FLERR,"Argument #{} must be variable not {}", iarg+2, arg[iarg+1]);
} else error->all(FLERR, iarg+1, "Argument must be variable not {}", arg[iarg+1]);
nadapt++;
iarg += 2;
@ -187,10 +187,11 @@ FixAdapt::FixAdapt(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg+1],"charge") == 0) {
adapt[nadapt].atomparam = CHARGE;
chgflag = 1;
} else error->all(FLERR,"Unsupported per-atom property {} for fix adapt", arg[iarg+1]);
} else error->all(FLERR, iarg+1, "Unsupported per-atom property {} for fix adapt",
arg[iarg+1]);
if (utils::strmatch(arg[iarg+2],"^v_")) {
adapt[nadapt].var = utils::strdup(arg[iarg+2]+2);
} else error->all(FLERR,"Argument #{} must be variable not {}", iarg+3, arg[iarg+2]);
} else error->all(FLERR, iarg+2, "Argument must be variable not {}", arg[iarg+2]);
nadapt++;
iarg += 3;
} else break;
@ -359,7 +360,8 @@ void FixAdapt::init()
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", group->names[igroup]);
error->all(FLERR, Error::NOLASTLINE,
"Cannot use dynamic group {} with fix adapt atom", group->names[igroup]);
// setup and error checks
@ -373,9 +375,11 @@ void FixAdapt::init()
ad->ivar = input->variable->find(ad->var);
if (ad->ivar < 0)
error->all(FLERR,"Variable name {} for fix adapt does not exist", ad->var);
error->all(FLERR, Error::NOLASTLINE,
"Variable name {} for fix adapt does not exist", ad->var);
if (!input->variable->equalstyle(ad->ivar))
error->all(FLERR,"Variable {} for fix adapt is invalid style", ad->var);
error->all(FLERR, Error::NOLASTLINE,
"Variable {} for fix adapt is invalid style", ad->var);
if (ad->which == PAIR) {
anypair = 1;
@ -400,17 +404,20 @@ void FixAdapt::init()
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);
if (ad->pair == nullptr)
error->all(FLERR, Error::NOLASTLINE, "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", ad->pstyle, ad->pparam);
error->all(FLERR, Error::NOLASTLINE,
"Fix adapt pair style {} param {} not supported", ad->pstyle, ad->pparam);
// 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,"Pair style parameter {} is not compatible with fix adapt", ad->pparam);
error->all(FLERR, Error::NOLASTLINE,
"Pair style parameter {} is not compatible with fix adapt", ad->pparam);
if (ad->pdim == 2) ad->array = (double **) ptr;
if (ad->pdim == 0) ad->scalar = (double *) ptr;
@ -423,7 +430,7 @@ void FixAdapt::init()
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 "
error->all(FLERR, Error::NOLASTLINE, "Fix adapt type pair range is not valid "
"for pair hybrid sub-style {}", pstyle);
}
}
@ -442,12 +449,13 @@ void FixAdapt::init()
if (ad->bond == nullptr) ad->bond = force->bond_match(bstyle);
if (ad->bond == nullptr )
error->all(FLERR,"Fix adapt bond style {} does not exist", bstyle);
error->all(FLERR, Error::NOLASTLINE,"Fix adapt bond style {} does not exist", bstyle);
void *ptr = ad->bond->extract(ad->bparam,ad->bdim);
if (ptr == nullptr)
error->all(FLERR,"Fix adapt bond style parameter {} not supported", ad->bparam);
error->all(FLERR, Error::NOLASTLINE,
"Fix adapt bond style parameter {} not supported", ad->bparam);
// for bond styles, use a vector
@ -458,8 +466,8 @@ void FixAdapt::init()
if (bond) {
for (i = ad->ilo; i <= ad->ihi; i++) {
if (!bond->check_itype(i,bstyle))
error->all(FLERR,"Fix adapt type bond range is not valid "
"for pair hybrid sub-style {}", bstyle);
error->all(FLERR, Error::NOLASTLINE, "Fix adapt type bond range is not valid "
"for bond hybrid sub-style {}", bstyle);
}
}
}
@ -476,12 +484,13 @@ void FixAdapt::init()
if (ad->angle == nullptr) ad->angle = force->angle_match(astyle);
if (ad->angle == nullptr )
error->all(FLERR,"Fix adapt angle style {} does not exist", astyle);
error->all(FLERR, Error::NOLASTLINE, "Fix adapt angle style {} does not exist", astyle);
void *ptr = ad->angle->extract(ad->aparam,ad->adim);
if (ptr == nullptr)
error->all(FLERR,"Fix adapt angle style parameter {} not supported", ad->aparam);
error->all(FLERR, Error::NOLASTLINE,
"Fix adapt angle style parameter {} not supported", ad->aparam);
// for angle styles, use a vector
@ -492,8 +501,8 @@ void FixAdapt::init()
if (angle) {
for (i = ad->ilo; i <= ad->ihi; i++) {
if (!angle->check_itype(i,astyle))
error->all(FLERR,"Fix adapt type angle range is not valid "
"for pair hybrid sub-style {}", astyle);
error->all(FLERR, Error::NOLASTLINE, "Fix adapt type angle range is not valid "
"for angle hybrid sub-style {}", astyle);
}
}
}
@ -536,22 +545,23 @@ void FixAdapt::init()
} else if (ad->which == KSPACE) {
if (force->kspace == nullptr)
error->all(FLERR,"Fix adapt expected a kspace style but none was defined");
error->all(FLERR, Error::NOLASTLINE,
"Fix adapt expected a kspace style but none was defined");
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");
error->all(FLERR, Error::NOLASTLINE, "Fix adapt requires atom attribute diameter");
if (!atom->rmass_flag)
error->all(FLERR,"Fix adapt requires atom attribute mass");
error->all(FLERR, Error::NOLASTLINE, "Fix adapt requires atom attribute mass");
if (discflag && domain->dimension != 2)
error->all(FLERR,"Fix adapt requires 2d simulation");
error->all(FLERR, Error::NOLASTLINE, "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");
error->all(FLERR, Error::NOLASTLINE, "Fix adapt requires atom attribute charge");
if (!restart_reset) previous_chg_scale = 1.0;
}
}
@ -589,11 +599,15 @@ void FixAdapt::init()
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 (!fix_diam)
error->all(FLERR, Error::NOLASTLINE,
"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 (!fix_chg)
error->all(FLERR, Error::NOLASTLINE,
"Could not find fix adapt storage fix ID {}", id_fix_chg);
}
if (utils::strmatch(update->integrate_style,"^respa"))