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add flag "reinit" with args "yes" / "no" to fixes rigid & rigid/small

This commit is contained in:
Axel Kohlmeyer 2017-06-05 17:31:43 -04:00
parent 286d4f2743
commit deff6c666e
4 changed files with 45 additions and 17 deletions
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24
src/RIGID/fix_rigid.cpp
View File

@ -267,6 +267,8 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
int seed;
langflag = 0;
reinitflag = 1;
tstat_flag = 0;
pstat_flag = 0;
allremap = 1;
@ -501,6 +503,14 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
infile = new char[n];
strcpy(infile,arg[iarg+1]);
restart_file = 1;
reinitflag = 0;
iarg += 2;
} else if (strcmp(arg[iarg],"reinit") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid/small command");
if (strcmp("yes",arg[iarg+1]) == 0) reinitflag = 1;
else if (strcmp("no",arg[iarg+1]) == 0) reinitflag = 0;
else error->all(FLERR,"Illegal fix rigid command");
iarg += 2;
} else error->all(FLERR,"Illegal fix rigid command");
@ -679,15 +689,15 @@ void FixRigid::init()
if (strstr(update->integrate_style,"respa"))
step_respa = ((Respa *) update->integrate)->step;
// setup rigid bodies, using current atom info
// only do initialization once, b/c properties may not be re-computable
// especially if overlapping particles
// do not do dynamic init if read body properties from infile
// this is b/c the infile defines the static and dynamic properties
// and may not be computable if contain overlapping particles
// setup rigid bodies, using current atom info. if reinitflag is not set,
// do the initialization only once, b/c properties may not be re-computable
// especially if overlapping particles.
// do not do dynamic init if read body properties from infile.
// this is b/c the infile defines the static and dynamic properties and may
// not be computable if contain overlapping particles.
// setup_bodies_static() reads infile itself
if (!setupflag) {
if (reinitflag || !setupflag) {
setup_bodies_static();
if (!infile) setup_bodies_dynamic();
setupflag = 1;

1
src/RIGID/fix_rigid.h
View File

@ -104,6 +104,7 @@ class FixRigid : public Fix {
int extended; // 1 if any particles have extended attributes
int orientflag; // 1 if particles store spatial orientation
int dorientflag; // 1 if particles store dipole orientation
int reinitflag; // 1 if re-initialize rigid bodies between runs
imageint *xcmimage; // internal image flags for atoms in rigid bodies
// set relative to in-box xcm of each body

36
src/RIGID/fix_rigid_small.cpp
View File

@ -138,6 +138,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
langflag = 0;
infile = NULL;
onemols = NULL;
reinitflag = 1;
tstat_flag = 0;
pstat_flag = 0;
@ -173,6 +174,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Fix rigid/small langevin period must be > 0.0");
if (seed <= 0) error->all(FLERR,"Illegal fix rigid/small command");
iarg += 5;
} else if (strcmp(arg[iarg],"infile") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid/small command");
delete [] infile;
@ -180,7 +182,16 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
infile = new char[n];
strcpy(infile,arg[iarg+1]);
restart_file = 1;
reinitflag = 0;
iarg += 2;
} else if (strcmp(arg[iarg],"reinit") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid/small command");
if (strcmp("yes",arg[iarg+1]) == 0) reinitflag = 1;
else if (strcmp("no",arg[iarg+1]) == 0) reinitflag = 0;
else error->all(FLERR,"Illegal fix rigid/small command");
iarg += 2;
} else if (strcmp(arg[iarg],"mol") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid/small command");
int imol = atom->find_molecule(arg[iarg+1]);
@ -520,14 +531,15 @@ void FixRigidSmall::init()
}
/* ----------------------------------------------------------------------
setup static/dynamic properties of rigid bodies, using current atom info
only do initialization once, b/c properties may not be re-computable
especially if overlapping particles or bodies inserted from mol template
do not do dynamic init if read body properties from infile
this is b/c the infile defines the static and dynamic properties
and may not be computable if contain overlapping particles
setup_bodies_static() reads infile itself
cannot do this until now, b/c requires comm->setup() to have setup stencil
setup static/dynamic properties of rigid bodies, using current atom info.
if reinitflag is not set, do the initialization only once, b/c properties
may not be re-computable especially if overlapping particles or bodies
are inserted from mol template.
do not do dynamic init if read body properties from infile. this
is b/c the infile defines the static and dynamic properties and may not
be computable if contain overlapping particles setup_bodies_static()
reads infile itself.
cannot do this until now, b/c requires comm->setup() to have setup stencil
invoke pre_neighbor() to insure body xcmimage flags are reset
needed if Verlet::setup::pbc() has remapped/migrated atoms for 2nd run
setup_bodies_static() invokes pre_neighbor itself
@ -535,9 +547,13 @@ void FixRigidSmall::init()
void FixRigidSmall::setup_pre_neighbor()
{
if (!setupflag) setup_bodies_static();
if (reinitflag || !setupflag)
setup_bodies_static();
else pre_neighbor();
if (!setupflag && !infile) setup_bodies_dynamic();
if ((reinitflag || !setupflag) && !infile)
setup_bodies_dynamic();
setupflag = 1;
}

1
src/RIGID/fix_rigid_small.h
View File

@ -131,6 +131,7 @@ class FixRigidSmall : public Fix {
int extended; // 1 if any particles have extended attributes
int orientflag; // 1 if particles store spatial orientation
int dorientflag; // 1 if particles store dipole orientation
int reinitflag; // 1 if re-initialize rigid bodies between runs
int POINT,SPHERE,ELLIPSOID,LINE,TRIANGLE,DIPOLE; // bitmasks for eflags
int OMEGA,ANGMOM,TORQUE;