diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt
index 99105e13507249636d2c0b5118450cf9d11da040..a5a631bd382e851c60cda8bfbe17c51eb0b73d18 100644
--- a/doc/src/fix_rigid.txt
+++ b/doc/src/fix_rigid.txt
@@ -26,6 +26,9 @@ style = {rigid} or {rigid/nve} or {rigid/nvt} or {rigid/npt} or {rigid/nph} or {
bodystyle = {single} or {molecule} or {group} :l
{single} args = none
{molecule} args = none
+ {custom} args = {i_propname} or {v_varname}
+ i_propname = an integer property defined via fix property/atom
+ v_varname = an atom-style or atomfile-style variable
{group} args = N groupID1 groupID2 ...
N = # of groups
groupID1, groupID2, ... = list of N group IDs :pre
@@ -80,6 +83,16 @@ fix 1 rods rigid/npt molecule temp 300.0 300.0 100.0 iso 0.5 0.5 10.0
fix 1 particles rigid/npt molecule temp 1.0 1.0 5.0 x 0.5 0.5 1.0 z 0.5 0.5 1.0 couple xz
fix 1 water rigid/nph molecule iso 0.5 0.5 1.0
fix 1 particles rigid/npt/small molecule temp 1.0 1.0 1.0 iso 0.5 0.5 1.0 :pre
+
+variable bodyid atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)
+fix 1 clump rigid custom v_bodyid :pre
+
+variable bodyid atomfile bodies.txt
+fix 1 clump rigid custom v_bodyid :pre
+
+fix 0 all property/atom i_bodyid
+read_restart data.rigid fix 0 NULL Bodies
+fix 1 clump rigid/small custom i_bodyid :pre
[Description:]
@@ -100,7 +113,7 @@ of a biomolecule such as a protein.
Example of small rigid bodies are patchy nanoparticles, such as those
modeled in "this paper"_#Zhang1 by Sharon Glotzer's group, clumps of
-granular particles, lipid molecules consiting of one or more point
+granular particles, lipid molecules consisting of one or more point
dipoles connected to other spheroids or ellipsoids, irregular
particles built from line segments (2d) or triangles (3d), and
coarse-grain models of nano or colloidal particles consisting of a
@@ -203,11 +216,11 @@ most one rigid body. Which atoms are in which bodies can be defined
via several options.
NOTE: With the {rigid/small} styles, which require that {bodystyle} be
-specified as {molecule}, you can define a system that has no rigid
-bodies initially. This is useful when you are using the {mol} keyword
-in conjunction with another fix that is adding rigid bodies on-the-fly
-as molecules, such as "fix deposit"_fix_deposit.html or "fix
-pour"_fix_pour.html.
+specified as {molecule} or {custom}, you can define a system that has
+no rigid bodies initially. This is useful when you are using the {mol}
+keyword in conjunction with another fix that is adding rigid bodies
+on-the-fly as molecules, such as "fix deposit"_fix_deposit.html or
+"fix pour"_fix_pour.html.
For bodystyle {single} the entire fix group of atoms is treated as one
rigid body. This option is only allowed for the {rigid} styles.
@@ -222,6 +235,15 @@ molecule ID = 0) surrounding rigid bodies, this may not be what you
want. Thus you should be careful to use a fix group that only
includes atoms you want to be part of rigid bodies.
+Bodystyle {custom} is similar to bodystyle {molecule}, however some
+custom properties are used to group atoms into rigid bodies. The
+special case for molecule/body ID = 0 is not available. Possible
+custom properties are an integer property associated with atoms through
+"fix property/atom"_fix_property_atom.html or an atom style variable
+or an atomfile style variable. For the latter two, the variable value
+will be rounded to an integer and then rigid bodies defined from
+those values.
+
For bodystyle {group}, each of the listed groups is treated as a
separate rigid body. Only atoms that are also in the fix group are
included in each rigid body. This option is only allowed for the
diff --git a/examples/rigid/bodies.txt b/examples/rigid/bodies.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ddca2c7539b57a1eed2109d954bd5903bc7a765d
--- /dev/null
+++ b/examples/rigid/bodies.txt
@@ -0,0 +1,83 @@
+81
+1 1
+2 1
+3 1
+4 1
+5 1
+6 1
+7 1
+8 1
+9 1
+10 2
+11 2
+12 2
+13 2
+14 2
+15 2
+16 2
+17 2
+18 2
+19 3
+20 3
+21 3
+22 3
+23 3
+24 3
+25 3
+26 3
+27 3
+28 4
+29 4
+30 4
+31 4
+32 4
+33 4
+34 4
+35 4
+36 4
+37 5
+38 5
+39 5
+40 5
+41 5
+42 5
+43 5
+44 5
+45 5
+46 6
+47 6
+48 6
+49 6
+50 6
+51 6
+52 6
+53 6
+54 6
+55 7
+56 7
+57 7
+58 7
+59 7
+60 7
+61 7
+62 7
+63 7
+64 8
+65 8
+66 8
+67 8
+68 8
+69 8
+70 8
+71 8
+72 8
+73 9
+74 9
+75 9
+76 9
+77 9
+78 9
+79 9
+80 9
+81 9
+
diff --git a/examples/rigid/data.rigid-property b/examples/rigid/data.rigid-property
new file mode 100644
index 0000000000000000000000000000000000000000..66fc42d2d2cf6b0e27a1ca0cb4cedbac889b0d75
--- /dev/null
+++ b/examples/rigid/data.rigid-property
@@ -0,0 +1,185 @@
+# LAMMPS data file for rigid bodies
+
+81 atoms
+1 atom types
+
+-12 12 xlo xhi
+-12 12 ylo yhi
+-12 12 zlo zhi
+
+Masses
+
+1 1
+
+Pair Coeffs
+
+1 1 1
+
+Atoms
+
+1 1 0 0 0
+2 1 0 1 0
+3 1 0 0.5 0
+4 1 0.5 0 0
+5 1 0.5 0.5 1
+6 1 1 0.5 0
+7 1 0.5 1 0
+8 1 1 0 0
+9 1 1 1 0
+10 1 2 1 0
+11 1 1 2 0
+12 1 1.5 2 0
+13 1 1.5 1 0
+14 1 1 1.5 0
+15 1 1.5 1.5 1
+16 1 2 1.5 0
+17 1 2 2 0
+18 1 2 3 0
+19 1 2 2.5 0
+20 1 2.5 2 0
+21 1 2.5 2.5 1
+22 1 3 2.5 0
+23 1 2.5 3 0
+24 1 3 2 0
+25 1 3 3 0
+26 1 4 3 0
+27 1 3 4 0
+28 1 3.5 4 0
+29 1 3.5 3 0
+30 1 3 3.5 0
+31 1 3.5 3.5 1
+32 1 4 3.5 0
+33 1 4 4 0
+34 1 4 5 0
+35 1 4 4.5 0
+36 1 4.5 4 0
+37 1 4.5 4.5 1
+38 1 5 4.5 0
+39 1 4.5 5 0
+40 1 5 4 0
+41 1 5 5 0
+42 1 6 5 0
+43 1 5 6 0
+44 1 5.5 6 0
+45 1 5.5 5 0
+46 1 5 5.5 0
+47 1 5.5 5.5 1
+48 1 6 5.5 0
+49 1 6 6 0
+50 1 6 7 0
+51 1 6 6.5 0
+52 1 6.5 6 0
+53 1 6.5 6.5 1
+54 1 7 6.5 0
+55 1 6.5 7 0
+56 1 7 6 0
+57 1 7 7 0
+58 1 8 7 0
+59 1 7 8 0
+60 1 7.5 8 0
+61 1 7.5 7 0
+62 1 7 7.5 0
+63 1 7.5 7.5 1
+64 1 8 7.5 0
+65 1 8 8 0
+66 1 8 9 0
+67 1 8 8.5 0
+68 1 8.5 8 0
+69 1 8.5 8.5 1
+70 1 9 8.5 0
+71 1 8.5 9 0
+72 1 9 8 0
+73 1 9 9 0
+74 1 10 9 0
+75 1 9 10 0
+76 1 9.5 10 0
+77 1 9.5 9 0
+78 1 9 9.5 0
+79 1 9.5 9.5 1
+80 1 10 9.5 0
+81 1 10 10 0
+
+Bodies
+
+1 1
+2 1
+3 1
+4 1
+5 1
+6 1
+7 1
+8 1
+9 1
+10 2
+11 2
+12 2
+13 2
+14 2
+15 2
+16 2
+17 2
+18 2
+19 3
+20 3
+21 3
+22 3
+23 3
+24 3
+25 3
+26 3
+27 3
+28 4
+29 4
+30 4
+31 4
+32 4
+33 4
+34 4
+35 4
+36 4
+37 5
+38 5
+39 5
+40 5
+41 5
+42 5
+43 5
+44 5
+45 5
+46 6
+47 6
+48 6
+49 6
+50 6
+51 6
+52 6
+53 6
+54 6
+55 7
+56 7
+57 7
+58 7
+59 7
+60 7
+61 7
+62 7
+63 7
+64 8
+65 8
+66 8
+67 8
+68 8
+69 8
+70 8
+71 8
+72 8
+73 9
+74 9
+75 9
+76 9
+77 9
+78 9
+79 9
+80 9
+81 9
+
diff --git a/examples/rigid/in.rigid-atomfile b/examples/rigid/in.rigid-atomfile
new file mode 100644
index 0000000000000000000000000000000000000000..8817386c79f7df174b1a538b107b88da5897d5b4
--- /dev/null
+++ b/examples/rigid/in.rigid-atomfile
@@ -0,0 +1,83 @@
+# Simple rigid body system
+
+units lj
+atom_style atomic
+atom_modify map array
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+
+velocity all create 100.0 4928459
+
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+group clump2 id <> 10 18
+group clump3 id <> 19 27
+group clump4 id <> 28 36
+group clump5 id <> 37 45
+group clump6 id <> 46 54
+group clump7 id <> 55 63
+group clump8 id <> 64 72
+group clump9 id <> 73 81
+
+variable bodies atomfile bodies.txt
+fix 1 all rigid custom v_bodies
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
+# clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type &
+# axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type &
+# axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
diff --git a/examples/rigid/in.rigid-atomvar b/examples/rigid/in.rigid-atomvar
new file mode 100644
index 0000000000000000000000000000000000000000..994ab1d28432db3a934cac421f419d6d5adbf127
--- /dev/null
+++ b/examples/rigid/in.rigid-atomvar
@@ -0,0 +1,83 @@
+# Simple rigid body system
+
+units lj
+atom_style atomic
+atom_modify map array
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+
+velocity all create 100.0 4928459
+
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+group clump2 id <> 10 18
+group clump3 id <> 19 27
+group clump4 id <> 28 36
+group clump5 id <> 37 45
+group clump6 id <> 46 54
+group clump7 id <> 55 63
+group clump8 id <> 64 72
+group clump9 id <> 73 81
+
+variable bodies atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)+4.0*gmask(clump4)+5.0*gmask(clump5)+6.0*gmask(clump6)+7.0*gmask(clump7)+8.0*gmask(clump8)+9.0*gmask(clump9)
+fix 1 all rigid custom v_bodies
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
+# clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type &
+# axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type &
+# axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
diff --git a/examples/rigid/in.rigid-property b/examples/rigid/in.rigid-property
new file mode 100644
index 0000000000000000000000000000000000000000..53d62776e6764c4e22573324f4bc69da8cb79d7a
--- /dev/null
+++ b/examples/rigid/in.rigid-property
@@ -0,0 +1,85 @@
+# Simple rigid body system
+
+units lj
+atom_style atomic
+atom_modify map array
+
+pair_style lj/cut 2.5
+
+fix 0 all property/atom i_bodies
+
+read_data data.rigid-property fix 0 NULL Bodies
+
+velocity all create 100.0 4928459
+
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+group clump2 id <> 10 18
+group clump3 id <> 19 27
+group clump4 id <> 28 36
+group clump5 id <> 37 45
+group clump6 id <> 46 54
+group clump7 id <> 55 63
+group clump8 id <> 64 72
+group clump9 id <> 73 81
+
+# assemble bodies from per-atom custom integer property bodies
+fix 1 all rigid custom i_bodies
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
+# clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type &
+# axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type &
+# axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp
index d2a770cc4712db6b48b2f18823a86a23e1b61f82..33a4b441fda4f9f3eefb3039db46c4ea2724a454 100644
--- a/src/RIGID/fix_rigid.cpp
+++ b/src/RIGID/fix_rigid.cpp
@@ -29,6 +29,8 @@
#include "comm.h"
#include "random_mars.h"
#include "force.h"
+#include "input.h"
+#include "variable.h"
#include "output.h"
#include "math_const.h"
#include "memory.h"
@@ -127,15 +129,60 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
// nbody = # of non-zero ncount values
// use nall as incremented ptr to set body[] values for each atom
- } else if (strcmp(arg[3],"molecule") == 0) {
+ } else if (strcmp(arg[3],"molecule") == 0 || strcmp(arg[3],"custom") == 0) {
rstyle = MOLECULE;
- iarg = 4;
- if (atom->molecule_flag == 0)
- error->all(FLERR,"Fix rigid molecule requires atom attribute molecule");
-
+ tagint *molecule;
int *mask = atom->mask;
- tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
+ 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=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");
+ else if (is_double)
+ error->all(FLERR,"Fix rigid 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);
+ molecule = new tagint[nlocal];
+ for (i = 0; i < nlocal; i++)
+ 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 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);
+ molecule = new tagint[nlocal];
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) molecule[i] = (tagint)((tagint)value[i] - minval + 1);
+ delete[] value;
+ } else error->all(FLERR,"Unsupported fix rigid custom property");
+ } else {
+ if (atom->molecule_flag == 0)
+ error->all(FLERR,"Fix rigid molecule requires atom attribute molecule");
+ molecule = atom->molecule;
+ }
+ iarg = 4 + custom_flag;
tagint maxmol_tag = -1;
for (i = 0; i < nlocal; i++)
@@ -174,6 +221,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
}
memory->destroy(ncount);
+ if (custom_flag) delete [] molecule;
// each listed group is a rigid body
// check if all listed groups exist
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 *);