diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp
index 0703171e480d097b419a4230d096d58531875491..33a4b441fda4f9f3eefb3039db46c4ea2724a454 100644
--- a/src/RIGID/fix_rigid.cpp
+++ b/src/RIGID/fix_rigid.cpp
@@ -137,9 +137,10 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
int custom_flag = strcmp(arg[3],"custom") == 0;
if (custom_flag) {
if (narg < 5) error->all(FLERR,"Illegal fix rigid command");
+
// determine whether atom-style variable or atom property is used.
if (strstr(arg[4],"i_") == arg[4]) {
- int is_double;
+ int is_double=0;
int custom_index = atom->find_custom(arg[4]+2,is_double);
if (custom_index == -1)
error->all(FLERR,"Fix rigid custom requires previously defined property/atom");
@@ -153,13 +154,17 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
MPI_Allreduce(&vmin,&minval,1,MPI_INT,MPI_MIN,world);
molecule = new tagint[nlocal];
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) molecule[i] = (tagint)(value[i] - minval + 1);
+ if (mask[i] & groupbit)
+ molecule[i] = (tagint)(value[i] - minval + 1);
+ else
+ molecule[i] = 0;
+
} else if (strstr(arg[4],"v_") == arg[4]) {
int ivariable = input->variable->find(arg[4]+2);
if (ivariable < 0)
error->all(FLERR,"Variable name for fix rigid custom does not exist");
if (input->variable->atomstyle(ivariable) == 0)
- error->all(FLERR,"Fix rigid custom variable is not atom-style variable");
+ error->all(FLERR,"Fix rigid custom variable is no atom-style variable");
double *value = new double[nlocal];
input->variable->compute_atom(ivariable,0,value,1,0);
int minval = INT_MAX;
@@ -169,7 +174,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
MPI_Allreduce(&vmin,&minval,1,MPI_INT,MPI_MIN,world);
molecule = new tagint[nlocal];
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) molecule[i] = (tagint)((int)value[i] - minval + 1);
+ if (mask[i] & groupbit) molecule[i] = (tagint)((tagint)value[i] - minval + 1);
delete[] value;
} else error->all(FLERR,"Unsupported fix rigid custom property");
} else {
diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp
index 1404c3bf58da22f20739dbf521c8aa2adcfea723..13208d4c4c434f4be2602a1447650dced9dca3f2 100644
--- a/src/RIGID/fix_rigid_small.cpp
+++ b/src/RIGID/fix_rigid_small.cpp
@@ -29,7 +29,9 @@
#include "group.h"
#include "comm.h"
#include "force.h"
+#include "input.h"
#include "output.h"
+#include "variable.h"
#include "random_mars.h"
#include "math_const.h"
#include "memory.h"
@@ -64,11 +66,12 @@ enum{FULL_BODY,INITIAL,FINAL,FORCE_TORQUE,VCM_ANGMOM,XCM_MASS,ITENSOR,DOF};
FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), step_respa(NULL),
- infile(NULL), body(NULL), bodyown(NULL), bodytag(NULL), atom2body(NULL),
- xcmimage(NULL), displace(NULL), eflags(NULL), orient(NULL), dorient(NULL),
- avec_ellipsoid(NULL), avec_line(NULL), avec_tri(NULL), counts(NULL),
- itensor(NULL), mass_body(NULL), langextra(NULL), random(NULL), id_dilate(NULL),
- onemols(NULL), hash(NULL), bbox(NULL), ctr(NULL), idclose(NULL), rsqclose(NULL)
+ infile(NULL), body(NULL), bodyown(NULL), bodytag(NULL), atom2body(NULL),
+ xcmimage(NULL), displace(NULL), eflags(NULL), orient(NULL), dorient(NULL),
+ avec_ellipsoid(NULL), avec_line(NULL), avec_tri(NULL), counts(NULL),
+ itensor(NULL), mass_body(NULL), langextra(NULL), random(NULL),
+ id_dilate(NULL), onemols(NULL), hash(NULL), bbox(NULL), ctr(NULL),
+ idclose(NULL), rsqclose(NULL)
{
int i;
@@ -89,7 +92,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
// perform initial allocation of atom-based arrays
// register with Atom class
- extended = orientflag = dorientflag = 0;
+ extended = orientflag = dorientflag = customflag = 0;
bodyown = NULL;
bodytag = NULL;
atom2body = NULL;
@@ -103,24 +106,70 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
// parse args for rigid body specification
+ int *mask = atom->mask;
+ tagint *bodyid = NULL;
+ int nlocal = atom->nlocal;
+
if (narg < 4) error->all(FLERR,"Illegal fix rigid/small command");
- if (strcmp(arg[3],"molecule") != 0)
- error->all(FLERR,"Illegal fix rigid/small command");
+ if (strcmp(arg[3],"molecule") == 0) {
+ if (atom->molecule_flag == 0)
+ error->all(FLERR,"Fix rigid/small requires atom attribute molecule");
+
+ } else if (strcmp(arg[3],"custom") == 0) {
+ if (narg < 5) error->all(FLERR,"Illegal fix rigid/small command");
+ bodyid = new tagint[nlocal];
+ customflag = 1;
+
+ // determine whether atom-style variable or atom property is used.
+ if (strstr(arg[4],"i_") == arg[4]) {
+ int is_double=0;
+ int custom_index = atom->find_custom(arg[4]+2,is_double);
+ if (custom_index == -1)
+ error->all(FLERR,"Fix rigid/small custom requires previously defined property/atom");
+ else if (is_double)
+ error->all(FLERR,"Fix rigid/small custom requires integer-valued property/atom");
+
+ int minval = INT_MAX;
+ int *value = atom->ivector[custom_index];
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) minval = MIN(minval,value[i]);
+ int vmin = minval;
+ MPI_Allreduce(&vmin,&minval,1,MPI_INT,MPI_MIN,world);
+
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit)
+ bodyid[i] = (tagint)(value[i] - minval + 1);
+ else bodyid[i] = 0;
+
+ } else if (strstr(arg[4],"v_") == arg[4]) {
+ int ivariable = input->variable->find(arg[4]+2);
+ if (ivariable < 0)
+ error->all(FLERR,"Variable name for fix rigid/small custom does not exist");
+ if (input->variable->atomstyle(ivariable) == 0)
+ error->all(FLERR,"Fix rigid/small custom variable is no atom-style variable");
+ double *value = new double[nlocal];
+ input->variable->compute_atom(ivariable,0,value,1,0);
+ int minval = INT_MAX;
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) minval = MIN(minval,(int)value[i]);
+ int vmin = minval;
+ MPI_Allreduce(&vmin,&minval,1,MPI_INT,MPI_MIN,world);
+
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit)
+ bodyid[i] = (tagint)((tagint)value[i] - minval + 1);
+ else bodyid[0] = 0;
+ delete[] value;
+ } else error->all(FLERR,"Unsupported fix rigid custom property");
+ } else error->all(FLERR,"Illegal fix rigid/small command");
- if (atom->molecule_flag == 0)
- error->all(FLERR,"Fix rigid/small requires atom attribute molecule");
if (atom->map_style == 0)
error->all(FLERR,"Fix rigid/small requires an atom map, see atom_modify");
- // maxmol = largest molecule #
-
- int *mask = atom->mask;
- tagint *molecule = atom->molecule;
- int nlocal = atom->nlocal;
-
+ // maxmol = largest bodyid #
maxmol = -1;
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) maxmol = MAX(maxmol,molecule[i]);
+ if (mask[i] & groupbit) maxmol = MAX(maxmol,bodyid[i]);
tagint itmp;
MPI_Allreduce(&maxmol,&itmp,1,MPI_LMP_TAGINT,MPI_MAX,world);
@@ -155,6 +204,8 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
}
int iarg = 4;
+ if (customflag) ++iarg;
+
while (iarg < narg) {
if (strcmp(arg[iarg],"langevin") == 0) {
if (iarg+5 > narg) error->all(FLERR,"Illegal fix rigid/small command");
@@ -344,11 +395,12 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
if (pcouple == XYZ || (domain->dimension == 2 && pcouple == XY)) pstyle = ISO;
else pstyle = ANISO;
- // create rigid bodies based on molecule ID
+ // create rigid bodies based on molecule or custom ID
// sets bodytag for owned atoms
// body attributes are computed later by setup_bodies()
- create_bodies();
+ create_bodies(bodyid);
+ if (customflag) delete [] bodyid;
// set nlocal_body and allocate bodies I own
@@ -1424,7 +1476,7 @@ void FixRigidSmall::set_v()
set bodytag for all owned atoms
------------------------------------------------------------------------- */
-void FixRigidSmall::create_bodies()
+void FixRigidSmall::create_bodies(tagint *bodyid)
{
int i,m,n;
double unwrap[3];
@@ -1464,8 +1516,8 @@ void FixRigidSmall::create_bodies()
double *buf;
memory->create(buf,ncount*percount,"rigid/small:buf");
- // create map hash for storing unique molecule IDs of my atoms
- // key = molecule ID
+ // create map hash for storing unique body IDs of my atoms
+ // key = body ID
// value = index into per-body data structure
// n = # of entries in hash
@@ -1477,12 +1529,10 @@ void FixRigidSmall::create_bodies()
// value = index into N-length data structure
// n = count of unique bodies my atoms are part of
- tagint *molecule = atom->molecule;
-
n = 0;
for (i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
- if (hash->find(molecule[i]) == hash->end()) (*hash)[molecule[i]] = n++;
+ if (hash->find(bodyid[i]) == hash->end()) (*hash)[bodyid[i]] = n++;
}
// bbox = bounding box of each rigid body my atoms are part of
@@ -1494,7 +1544,7 @@ void FixRigidSmall::create_bodies()
bbox[i][1] = bbox[i][3] = bbox[i][5] = -BIG;
}
- // pack my atoms into buffer as molecule ID, unwrapped coords
+ // pack my atoms into buffer as body ID, unwrapped coords
double **x = atom->x;
@@ -1502,7 +1552,7 @@ void FixRigidSmall::create_bodies()
for (i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
domain->unmap(x[i],image[i],unwrap);
- buf[m++] = molecule[i];
+ buf[m++] = bodyid[i];
buf[m++] = unwrap[0];
buf[m++] = unwrap[1];
buf[m++] = unwrap[2];
@@ -1542,7 +1592,7 @@ void FixRigidSmall::create_bodies()
for (i = 0; i < n; i++) rsqclose[i] = BIG;
- // pack my atoms into buffer as molecule ID, atom ID, unwrapped coords
+ // pack my atoms into buffer as body ID, atom ID, unwrapped coords
tagint *tag = atom->tag;
@@ -1550,7 +1600,7 @@ void FixRigidSmall::create_bodies()
for (i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
domain->unmap(x[i],image[i],unwrap);
- buf[m++] = molecule[i];
+ buf[m++] = bodyid[i];
buf[m++] = ubuf(tag[i]).d;
buf[m++] = unwrap[0];
buf[m++] = unwrap[1];
@@ -1570,7 +1620,7 @@ void FixRigidSmall::create_bodies()
for (i = 0; i < nlocal; i++) {
bodytag[i] = 0;
if (!(mask[i] & groupbit)) continue;
- m = hash->find(molecule[i])->second;
+ m = hash->find(bodyid[i])->second;
bodytag[i] = idclose[m];
rsqmax = MAX(rsqmax,rsqclose[m]);
}
diff --git a/src/RIGID/fix_rigid_small.h b/src/RIGID/fix_rigid_small.h
index b07dea4f333ea3f27b7919fb74a4b2c52fc9585e..22f9b0c16c31e7ba8910a558dc1802fff6d4b128 100644
--- a/src/RIGID/fix_rigid_small.h
+++ b/src/RIGID/fix_rigid_small.h
@@ -79,6 +79,7 @@ class FixRigidSmall : public Fix {
char *infile; // file to read rigid body attributes from
int setupflag; // 1 if body properties are setup, else 0
int commflag; // various modes of forward/reverse comm
+ int customflag; // 1 if custom property/variable define bodies
int nbody; // total # of rigid bodies
int nlinear; // total # of linear rigid bodies
tagint maxmol; // max mol-ID
@@ -187,7 +188,7 @@ class FixRigidSmall : public Fix {
void image_shift();
void set_xv();
void set_v();
- void create_bodies();
+ void create_bodies(tagint *);
void setup_bodies_static();
void setup_bodies_dynamic();
void readfile(int, double **, int *);