ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge pull request #4636 from wapisani/fix_bond_create_inter_intra

Browse Source 
Add support for inter-/intra-molecular bonding to fix bond/create
This commit is contained in:
Axel Kohlmeyer
2025-06-28 09:43:54 -04:00
committed by GitHub
parent 575411c92c e139d935ab
commit 0c68c4d493
3 changed files with 96 additions and 75 deletions
Download Patch File Download Diff File Expand all files Collapse all files

9
doc/src/fix_bond_create.rst
View File

@ -21,7 +21,7 @@ Syntax
* Rmin = two atoms separated by less than Rmin can bond (distance units)
* bondtype = type of created bonds (integer or type label)
* zero or more keyword/value pairs may be appended to args
* keyword = *iparam* or *jparam* or *prob* or *atype* or *dtype* or *itype* or *aconstrain*
* keyword = *iparam* or *jparam* or *prob* or *atype* or *dtype* or *itype* or *aconstrain* or *molecule*
.. parsed-literal::
@ -43,6 +43,10 @@ Syntax
*aconstrain* value = amin amax
amin = minimal angle at which new bonds can be created
amax = maximal angle at which new bonds can be created
*molecule* value = *off* or *inter* or *intra*
*off* = allow both inter- and intramolecular reactions (default)
*inter* = search for reactions between molecules with different IDs
*intra* = search for reactions within the same molecule
Examples
""""""""
@ -52,6 +56,7 @@ Examples
fix 5 all bond/create 10 1 2 0.8 1
fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3
fix 5 all bond/create 1 3 3 0.8 1 prob 0.5 85784 iparam 2 3 atype 1 dtype 2
fix 5 all bond/create 10 13 25 7 28 iparam 1 15 jparam 1 27 prob 0.2 91322 molecule inter
fix 5 all bond/create/angle 10 1 2 1.122 1 aconstrain 120 180 prob 1 4928459 iparam 2 1 jparam 2 2
labelmap atom 1 c1 2 n2
@ -123,6 +128,8 @@ actually created. The *fraction* setting must be a value between 0.0
and 1.0. A uniform random number between 0.0 and 1.0 is generated and
the eligible bond is only created if the random number is less than *fraction*.
The *molecule* keyword can be used to force the reaction to be intermolecular, intramolecular or either. When the value is set to *off*, molecule IDs are not considered when searching for reactions (default). When the value is set to *inter*, atoms must have different molecule IDs in order to be considered for the reaction. When the value is set to *intra*, only atoms with the same molecule ID are considered for the reaction.
The *aconstrain* keyword is only available with the fix
bond/create/angle command. It allows one to specify minimum and maximum
angles *amin* and *amax*, respectively, between the two prospective bonding

160
src/MC/fix_bond_create.cpp
View File

@ -37,6 +37,9 @@ using namespace MathConst;
static constexpr double BIG = 1.0e20;
static constexpr int DELTA = 16;
// values for molecule_keyword, matching fix_bond_react.cpp
enum { OFF, INTER, INTRA };
/* ---------------------------------------------------------------------- */
FixBondCreate::FixBondCreate(LAMMPS *lmp, int narg, char **arg) :
@ -44,12 +47,11 @@ FixBondCreate::FixBondCreate(LAMMPS *lmp, int narg, char **arg) :
bondcount(nullptr), partner(nullptr), finalpartner(nullptr), distsq(nullptr),
probability(nullptr), created(nullptr), copy(nullptr), random(nullptr), list(nullptr)
{
if (narg < 8) error->all(FLERR,"Illegal fix bond/create command");
MPI_Comm_rank(world,&me);
std::string fixname = fmt::format("fix {}", style);
if (narg < 8) utils::missing_cmd_args(FLERR, fixname, error);
nevery = utils::inumeric(FLERR,arg[3],false,lmp);
if (nevery <= 0) error->all(FLERR,"Illegal fix bond/create command");
if (nevery <= 0) error->all(FLERR, 3, "Illegal fix {} nevery value {}", style, nevery);
dynamic_group_allow = 1;
force_reneighbor = 1;
@ -66,10 +68,10 @@ FixBondCreate::FixBondCreate(LAMMPS *lmp, int narg, char **arg) :
if (iatomtype < 1 || iatomtype > atom->ntypes ||
jatomtype < 1 || jatomtype > atom->ntypes)
error->all(FLERR,"Invalid atom type in fix bond/create command");
if (cutoff < 0.0) error->all(FLERR,"Illegal fix bond/create command");
error->all(FLERR,"Invalid atom type in fix {} command", style);
if (cutoff < 0.0) error->all(FLERR, 6, "Illegal fix {} cutoff value {}", style, cutoff);
if (btype < 1 || btype > atom->nbondtypes)
error->all(FLERR,"Invalid bond type in fix bond/create command");
error->all(FLERR, 7, "Invalid bond type {} in fix {} command", style, btype);
cutsq = cutoff*cutoff;
@ -82,7 +84,7 @@ FixBondCreate::FixBondCreate(LAMMPS *lmp, int narg, char **arg) :
fraction = 1.0;
int seed = 12345;
atype = dtype = itype = 0;
molecule_keyword = OFF;
constrainflag = 0;
constrainpass = 0;
amin = 0;
@ -91,75 +93,80 @@ FixBondCreate::FixBondCreate(LAMMPS *lmp, int narg, char **arg) :
int iarg = 8;
while (iarg < narg) {
if (strcmp(arg[iarg],"iparam") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix bond/create command");
if (iarg+3 > narg) utils::missing_cmd_args(FLERR,fixname + " iparam", error);
imaxbond = utils::inumeric(FLERR, arg[iarg+1], false, lmp);
inewtype = utils::expand_type_int(FLERR, arg[iarg+2], Atom::ATOM, lmp);
if (imaxbond < 0) error->all(FLERR,"Illegal fix bond/create command");
if (inewtype < 1 || inewtype > atom->ntypes)
error->all(FLERR,"Invalid atom type in fix bond/create command");
if (imaxbond < 0)
error->all(FLERR, iarg + 1, "Invalid fix {} iparam imaxbond value {}", style, imaxbond);
if ((inewtype < 1) || (inewtype > atom->ntypes))
error->all(FLERR, iarg + 2, "Invalid atom type {} in fix {} iparam command", inewtype, style);
iarg += 3;
} else if (strcmp(arg[iarg],"jparam") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix bond/create command");
if (iarg+3 > narg) utils::missing_cmd_args(FLERR,fixname + " jparam", error);
jmaxbond = utils::inumeric(FLERR, arg[iarg+1], false, lmp);
jnewtype = utils::expand_type_int(FLERR, arg[iarg+2], Atom::ATOM, lmp);
if (jmaxbond < 0) error->all(FLERR,"Illegal fix bond/create command");
if (jnewtype < 1 || jnewtype > atom->ntypes)
error->all(FLERR,"Invalid atom type in fix bond/create command");
if (jmaxbond < 0)
error->all(FLERR, iarg + 1, "Invalid fix {} jparam jmaxbond value {}", style, jmaxbond);
if ((jnewtype < 1) || (jnewtype > atom->ntypes))
error->all(FLERR, iarg + 2, "Invalid atom type {} in fix {} jparam command", jnewtype, style);
iarg += 3;
} else if (strcmp(arg[iarg],"prob") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix bond/create command");
if (iarg+3 > narg) utils::missing_cmd_args(FLERR,fixname + " prob", error);
fraction = utils::numeric(FLERR, arg[iarg+1], false, lmp);
seed = utils::inumeric(FLERR, arg[iarg+2], false, lmp);
if (fraction < 0.0 || fraction > 1.0)
error->all(FLERR,"Illegal fix bond/create command");
if (seed <= 0) error->all(FLERR,"Illegal fix bond/create command");
if ((fraction < 0.0) || (fraction > 1.0))
error->all(FLERR, iarg + 1, "Invalid fix {} prob fraction value {}", style, fraction);
if (seed <= 0) error->all(FLERR,"Invalid fix {} prob seed value {}", style, seed);
iarg += 3;
} else if (strcmp(arg[iarg],"atype") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/create command");
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, fixname + " atype", error);
atype = utils::expand_type_int(FLERR, arg[iarg+1], Atom::ANGLE, lmp);
if (atype < 0) error->all(FLERR,"Illegal fix bond/create command");
if (atype < 0) error->all(FLERR, iarg + 1, "Invalid fix {} atype value {}", style, atype);
iarg += 2;
} else if (strcmp(arg[iarg],"dtype") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/create command");
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, fixname + " dtype", error);
dtype = utils::expand_type_int(FLERR, arg[iarg+1], Atom::DIHEDRAL, lmp);
if (dtype < 0) error->all(FLERR,"Illegal fix bond/create command");
if (dtype < 0) error->all(FLERR, iarg + 1, "Invalid fix {} dtype value {}", style, dtype);
iarg += 2;
} else if (strcmp(arg[iarg],"itype") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/create command");
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, fixname + " itype", error);
itype = utils::expand_type_int(FLERR, arg[iarg+1], Atom::IMPROPER, lmp);
if (itype < 0) error->all(FLERR,"Illegal fix bond/create command");
if (itype < 0) error->all(FLERR, iarg + 1, "Invalid fix {} itype value {}", style, itype);
iarg += 2;
} else if (strcmp(arg[iarg],"molecule") == 0) {
if (iarg+2 > narg) utils::missing_cmd_args(FLERR, fixname + " molecule", error);
if (strcmp(arg[iarg+1],"off") == 0) molecule_keyword = OFF; //default
else if (strcmp(arg[iarg+1],"inter") == 0) molecule_keyword = INTER;
else if (strcmp(arg[iarg+1],"intra") == 0) molecule_keyword = INTRA;
else error->all(FLERR, iarg + 1, "Unknown option {} for fix {} molecule", arg[iarg+1], style);
iarg += 2;
} else if (strcmp(arg[iarg],"aconstrain") == 0 &&
strcmp(style,"bond/create/angle") == 0) {
if (iarg+3 > narg)
error->all(FLERR,"Illegal fix bond/create/angle command");
if (iarg+3 > narg) utils::missing_cmd_args(FLERR,"fix bond/create/angle aconstrain", error);
amin = utils::numeric(FLERR, arg[iarg+1], false, lmp);
amax = utils::inumeric(FLERR, arg[iarg+2], false, lmp);
if (amin >= amax)
error->all(FLERR,"Illegal fix bond/create/angle command");
if (amin < 0 || amin > 180)
error->all(FLERR,"Illegal fix bond/create/angle command");
if (amax < 0 || amax > 180)
error->all(FLERR,"Illegal fix bond/create/angle command");
if (amin >= amax) error->all(FLERR,"Illegal fix bond/create/angle aconstrain command");
if ((amin < 0) || (amin > 180))
error->all(FLERR,"Invalid fix bond/create/angle aconstrain amin value {}", amin);
if ((amax < 0) || (amax > 180))
error->all(FLERR,"Invalid fix bond/create/angle aconstrain amax value {}", amax);
amin = (MY_PI/180.0) * amin;
amax = (MY_PI/180.0) * amax;
constrainflag = 1;
iarg += 3;
} else error->all(FLERR,"Illegal fix bond/create command");
} else error->all(FLERR, iarg, "Unknown fix {} keyword {}", style, arg[iarg]);
}
// error check
if (atom->molecular != Atom::MOLECULAR)
error->all(FLERR,"Cannot use fix bond/create with non-molecular systems");
if (iatomtype == jatomtype &&
((imaxbond != jmaxbond) || (inewtype != jnewtype)))
error->all(FLERR,
"Inconsistent iparam/jparam values in fix bond/create command");
error->all(FLERR, Error::NOLASTLINE, "Cannot use fix {} with non-molecular systems", style);
if ((iatomtype == jatomtype) && ((imaxbond != jmaxbond) || (inewtype != jnewtype)))
error->all(FLERR, Error::NOLASTLINE, "Inconsistent iparam/jparam values in fix {} command", style);
// initialize Marsaglia RNG with processor-unique seed
random = new RanMars(lmp,seed + me);
random = new RanMars(lmp, seed + comm->me);
// perform initial allocation of atom-based arrays
// register with Atom class
@ -239,21 +246,21 @@ void FixBondCreate::init()
// check cutoff for iatomtype,jatomtype
if (force->pair == nullptr || cutsq > force->pair->cutsq[iatomtype][jatomtype])
error->all(FLERR,"Fix bond/create cutoff is longer than pairwise cutoff");
if ((force->pair == nullptr) || (cutsq > force->pair->cutsq[iatomtype][jatomtype]))
error->all(FLERR, Error::NOLASTLINE, "Fix {} cutoff is longer than pairwise cutoff", style);
// warn if more than one fix bond/create or also a fix bond/break
// warn if more than one fix {} or also a fix bond/break
// because this fix stores per-atom state in bondcount
// if other fixes create/break bonds, this fix will not know about it
int count = 0;
for (int i = 0; i < modify->nfix; i++) {
if (strcmp(modify->fix[i]->style,"bond/create") == 0) count++;
if (strcmp(modify->fix[i]->style,"bond/break") == 0) count++;
for (const auto &ifix : modify->get_fix_list()) {
if (utils::strmatch(ifix->style, "^bond/create")) count++;
if (utils::strmatch(ifix->style, "^bond/break")) count++;
}
if (count > 1 && me == 0)
error->warning(FLERR,"Fix bond/create is used multiple times "
" or with fix bond/break - may not work as expected");
if ((count > 1) && (comm->me == 0))
error->warning(FLERR, "Using fix {} multiple times or with fix bond/break "
"may not work as expected", style);
// enable angle/dihedral/improper creation if atype/dtype/itype
// option was used and a force field has been specified
@ -261,25 +268,25 @@ void FixBondCreate::init()
if (atype && force->angle) {
angleflag = 1;
if (atype > atom->nangletypes)
error->all(FLERR,"Fix bond/create angle type is invalid");
error->all(FLERR, Error::NOLASTLINE, "Fix {} angle type is invalid", style);
} else angleflag = 0;
if (dtype && force->dihedral) {
dihedralflag = 1;
if (dtype > atom->ndihedraltypes)
error->all(FLERR,"Fix bond/create dihedral type is invalid");
error->all(FLERR, Error::NOLASTLINE, "Fix {} dihedral type is invalid", style);
} else dihedralflag = 0;
if (itype && force->improper) {
improperflag = 1;
if (itype > atom->nimpropertypes)
error->all(FLERR,"Fix bond/create improper type is invalid");
error->all(FLERR, Error::NOLASTLINE, "Fix {} improper type is invalid", style);
} else improperflag = 0;
if (force->improper) {
if (force->improper_match("class2") || force->improper_match("ring"))
error->all(FLERR,"Cannot yet use fix bond/create with this "
"improper style");
error->all(FLERR,"Cannot yet use fix {} with improper style {} ",
style, force->improper_style);
}
// need a half neighbor list, built every Nevery steps
@ -329,8 +336,8 @@ void FixBondCreate::setup(int /*vflag*/)
if (newton_bond) {
m = atom->map(bond_atom[i][j]);
if (m < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms "
"from further away");
error->one(FLERR, Error::NOLASTLINE,
"Fix {} needs ghost atoms from further away", style);
bondcount[m]++;
}
}
@ -436,6 +443,13 @@ void FixBondCreate::post_integrate()
j = jlist[jj];
j &= NEIGHMASK;
if (!(mask[j] & groupbit)) continue;
// Copied from lines 1169 - 1173 of REACTION/fix_bond_react.cpp
if (molecule_keyword == INTER) {
if (atom->molecule[i] == atom->molecule[j]) continue;
} else if (molecule_keyword == INTRA) {
if (atom->molecule[i] != atom->molecule[j]) continue;
}
jtype = type[j];
possible = 0;
@ -528,7 +542,7 @@ void FixBondCreate::post_integrate()
if (!newton_bond || tag[i] < tag[j]) {
if (num_bond[i] == atom->bond_per_atom)
error->one(FLERR,"New bond exceeded bonds per atom in fix bond/create");
error->one(FLERR, Error::NOLASTLINE, "New bond from fix {} exceeded bonds per atom limit", style);
bond_type[i][num_bond[i]] = btype;
bond_atom[i][num_bond[i]] = tag[j];
num_bond[i]++;
@ -551,8 +565,7 @@ void FixBondCreate::post_integrate()
if (m < n2) n2--;
}
if (n3 == atom->maxspecial)
error->one(FLERR,
"New bond exceeded special list size in fix bond/create");
error->one(FLERR, Error::NOLASTLINE, "New bond from fix {} exceeds special list size limit", style);
for (m = n3; m > n1; m--) slist[m] = slist[m-1];
slist[n1] = tag[j];
nspecial[i][0] = n1+1;
@ -651,7 +664,7 @@ void FixBondCreate::check_ghosts()
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall)
error->all(FLERR,"Fix bond/create needs ghost atoms from further away");
error->all(FLERR, Error::NOLASTLINE, "Fix {} needs ghost atoms from further away", style);
lastcheck = update->ntimestep;
}
@ -716,8 +729,9 @@ void FixBondCreate::update_topology()
int overflowall;
MPI_Allreduce(&overflow,&overflowall,1,MPI_INT,MPI_SUM,world);
if (overflowall) error->all(FLERR,"Fix bond/create induced too many "
"angles/dihedrals/impropers per atom");
if (overflowall)
error->all(FLERR, Error::NOLASTLINE,
"Fix {} induced too many angles/dihedrals/impropers per atom", style);
int newton_bond = force->newton_bond;
@ -770,7 +784,7 @@ void FixBondCreate::rebuild_special_one(int m)
for (i = 0; i < cn1; i++) {
n = atom->map(copy[i]);
if (n < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
error->one(FLERR, Error::NOLASTLINE, "Fix {} needs ghost atoms from further away", style);
slist = special[n];
n1 = nspecial[n][0];
for (j = 0; j < n1; j++)
@ -779,7 +793,7 @@ void FixBondCreate::rebuild_special_one(int m)
cn2 = dedup(cn1,cn2,copy);
if (cn2 > atom->maxspecial)
error->one(FLERR,"Special list size exceeded in fix bond/create");
error->one(FLERR, Error::NOLASTLINE, "Special list size exceeded in fix {}", style);
// new 1-4 neighs of atom M, based on 1-2 neighs of 1-3 neighs
// exclude self
@ -789,7 +803,7 @@ void FixBondCreate::rebuild_special_one(int m)
for (i = cn1; i < cn2; i++) {
n = atom->map(copy[i]);
if (n < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
error->one(FLERR, Error::NOLASTLINE, "Fix {} needs ghost atoms from further away", style);
slist = special[n];
n1 = nspecial[n][0];
for (j = 0; j < n1; j++)
@ -798,7 +812,7 @@ void FixBondCreate::rebuild_special_one(int m)
cn3 = dedup(cn2,cn3,copy);
if (cn3 > atom->maxspecial)
error->one(FLERR,"Special list size exceeded in fix bond/create");
error->one(FLERR, Error::NOLASTLINE, "Special list size exceeded in fix {}", style);
// store new special list with atom M
@ -883,7 +897,7 @@ void FixBondCreate::create_angles(int m)
i2 = s1list[i];
i2local = atom->map(i2);
if (i2local < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
error->one(FLERR, Error::NOLASTLINE, "Fix {} needs ghost atoms from further away", style);
s2list = special[i2local];
n2 = nspecial[i2local][0];
@ -964,7 +978,7 @@ void FixBondCreate::create_dihedrals(int m)
if (force->newton_bond && i2 > i3) continue;
i3local = atom->map(i3);
if (i3local < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
error->one(FLERR, Error::NOLASTLINE, "Fix {} needs ghost atoms from further away", style);
s3list = special[i3local];
n3 = nspecial[i3local][0];
@ -1003,7 +1017,7 @@ void FixBondCreate::create_dihedrals(int m)
if (force->newton_bond && i2 > i1) continue;
i1local = atom->map(i1);
if (i1local < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
error->one(FLERR, Error::NOLASTLINE, "Fix {} needs ghost atoms from further away", style);
s3list = special[i1local];
n3 = nspecial[i1local][0];
@ -1053,7 +1067,7 @@ void FixBondCreate::create_dihedrals(int m)
i2 = s1list[i];
i2local = atom->map(i2);
if (i2local < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
error->one(FLERR, Error::NOLASTLINE, "Fix {} needs ghost atoms from further away", style);
s2list = special[i2local];
n2 = nspecial[i2local][0];
@ -1062,7 +1076,7 @@ void FixBondCreate::create_dihedrals(int m)
if (i3 == i1) continue;
i3local = atom->map(i3);
if (i3local < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
error->one(FLERR, Error::NOLASTLINE, "Fix {} needs ghost atoms from further away", style);
s3list = special[i3local];
n3 = nspecial[i3local][0];
@ -1179,7 +1193,7 @@ void FixBondCreate::create_impropers(int m)
i1 = s2list[i];
i1local = atom->map(i1);
if (i1local < 0)
error->one(FLERR,"Fix bond/create needs ghost atoms from further away");
error->one(FLERR, Error::NOLASTLINE, "Fix {} needs ghost atoms from further away", style);
s1list = special[i1local];
n1 = nspecial[i1local][0];

2
src/MC/fix_bond_create.h
View File

@ -49,7 +49,6 @@ class FixBondCreate : public Fix {
double memory_usage() override;
protected:
int me;
int iatomtype, jatomtype;
int btype, seed;
int imaxbond, jmaxbond;
@ -59,6 +58,7 @@ class FixBondCreate : public Fix {
double cutsq, fraction;
int atype, dtype, itype;
int angleflag, dihedralflag, improperflag;
int molecule_keyword;
int overflow;
tagint lastcheck;