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Merge pull request #1801 from lammps/rigid-gravity 

enable fix rigid commands to add gravity to COM of rigid bodies
This commit is contained in:
Axel Kohlmeyer 2020-01-08 14:47:03 -05:00 committed by GitHub
parent 97a798c776 1cd6d302bb
commit c5768acbbc
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GPG Key ID: 4AEE18F83AFDEB23
11 changed files with 325 additions and 22 deletions
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63
examples/rigid/in.rigid.gravity Normal file
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@ -0,0 +1,63 @@
#Pour composite granular particles on flat wall
newton on
atom_style sphere
atom_modify map array sort 0 0
thermo_modify flush yes
units si
variable minrad equal 0.5
variable maxrad equal 1.4
variable skin equal 0.3*${maxrad}
boundary p p f
region reg block 0 20 0 20 0 200 units box
create_box 1 reg
fix prop all property/atom mol ghost yes
variable dumpfreq equal 1000
variable logfreq equal 1000
pair_style gran/hooke/history 4e5 NULL 1e2 NULL 0.5 0
pair_coeff * *
timestep 0.0001
group particles type 1
atom_modify first particles
neighbor ${skin} bin
group rigid type 1
neigh_modify every 1 delay 0 check yes exclude molecule/intra all
thermo ${logfreq}
thermo_style custom step cpu atoms ke
thermo_modify flush yes lost warn
comm_modify vel yes cutoff 3
molecule mymol molecule.data
region pourreg block 5 15 5 15 80 100 side in units box
#Note: in versions prior to 1/2020, the 'disable' keyword to fix/gravity
# and the 'gravity' keyword to fix rigid/small were not available.
# These settings produce undesirable behavior, where gravity can induce
# torque on rigid bodies.
#fix gravfix all gravity 9.8 vector 0 0 -1 #disable
#fix rigidfix all rigid/small molecule mol mymol #gravity gravfix
#The correct behavior is recovered with the following settings:
fix gravfix all gravity 9.8 vector 0 0 -1 disable
fix rigidfix all rigid/small molecule mol mymol gravity gravfix
fix pourfix all pour 5 0 1234 region pourreg mol mymol rigid rigidfix
fix zwall all wall/gran hooke/history 4000.0 NULL 100.0 NULL 0.5 0 zplane 0.1 NULL
#dump 1 all custom 1000 molecule_pour.dump id type mass radius x y z fx fy fz
run 100000

41
examples/rigid/molecule.data Normal file
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@ -0,0 +1,41 @@
LAMMPS data file created for rigid body molecule template
5 atoms
2.3388800000000005 mass
6.002239704473936 4.99 4.989999999999999 com
116.79265620480001 144.26721336320003 144.26721336320006 -70.05220681600004 -70.05220681600002 -58.238345888000005 inertia
Coords
1 5 5 5
2 5.1 5.0 5.0
3 5.2 5.0 5.0
4 6.2 5.0 5.0
5 7.2 5.0 5.0
Types
1 1
2 1
3 1
4 1
5 1
Diameters
1 1.0
2 0.9
3 1.2
4 1.2
5 1.0
Masses
1 0.5235987755982988
2 0.3817035074111599
3 0.9047786842338602
4 0.9047786842338602
5 0.5235987755982988

79
src/RIGID/fix_rigid.cpp
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@ -52,8 +52,8 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
torque(NULL), quat(NULL), imagebody(NULL), fflag(NULL),
tflag(NULL), langextra(NULL), sum(NULL), all(NULL),
remapflag(NULL), xcmimage(NULL), eflags(NULL), orient(NULL),
dorient(NULL), id_dilate(NULL), random(NULL), avec_ellipsoid(NULL),
avec_line(NULL), avec_tri(NULL)
dorient(NULL), id_dilate(NULL), id_gravity(NULL), random(NULL),
avec_ellipsoid(NULL), avec_line(NULL), avec_tri(NULL)
{
int i,ibody;
@ -124,14 +124,17 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
if (custom_flag) {
if (narg < 5) error->all(FLERR,"Illegal fix rigid command");
// determine whether atom-style variable or atom property is used.
// 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");
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");
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++)
@ -163,12 +166,15 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
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;
@ -297,6 +303,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
}
// number of linear rigid bodies is counted later
nlinear = 0;
// parse optional args
@ -308,12 +315,14 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
tstat_flag = 0;
pstat_flag = 0;
allremap = 1;
id_dilate = NULL;
t_chain = 10;
t_iter = 1;
t_order = 3;
p_chain = 10;
inpfile = NULL;
id_gravity = NULL;
id_dilate = NULL;
pcouple = NONE;
pstyle = ANISO;
@ -543,12 +552,20 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
iarg += 2;
} else if (strcmp(arg[iarg],"reinit") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid/small command");
if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid 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 if (strcmp(arg[iarg],"gravity") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid command");
delete [] id_gravity;
int n = strlen(arg[iarg+1]) + 1;
id_gravity = new char[n];
strcpy(id_gravity,arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal fix rigid command");
}
@ -621,6 +638,9 @@ FixRigid::~FixRigid()
delete random;
delete [] inpfile;
delete [] id_dilate;
delete [] id_gravity;
memory->destroy(mol2body);
memory->destroy(body2mol);
@ -687,7 +707,7 @@ void FixRigid::init()
avec_tri = (AtomVecTri *) atom->style_match("tri");
// warn if more than one rigid fix
// if earlyflag, warn if any post-force fixes come after POEMS fix
// if earlyflag, warn if any post-force fixes come after a rigid fix
int count = 0;
for (i = 0; i < modify->nfix; i++)
@ -701,24 +721,54 @@ void FixRigid::init()
if (rflag && (modify->fmask[i] & POST_FORCE) &&
!modify->fix[i]->rigid_flag) {
char str[128];
snprintf(str,128,"Fix %s alters forces after fix rigid",modify->fix[i]->id);
snprintf(str,128,"Fix %s alters forces after fix rigid",
modify->fix[i]->id);
error->warning(FLERR,str);
}
}
}
// warn if body properties are read from inpfile
// and the gravity keyword is not set and a gravity fix exists
// this could mean body particles are overlapped
// and gravity is not applied correctly
if (inpfile && !id_gravity) {
for (i = 0; i < modify->nfix; i++) {
if (strcmp(modify->fix[i]->style,"gravity") == 0) {
if (comm->me == 0)
error->warning(FLERR,"Gravity may not be correctly applied "
"to rigid bodies if they consist of "
"overlapped particles");
break;
}
}
}
// error if npt,nph fix comes before rigid fix
for (i = 0; i < modify->nfix; i++) {
if (strcmp(modify->fix[i]->style,"npt") == 0) break;
if (strcmp(modify->fix[i]->style,"nph") == 0) break;
}
if (i < modify->nfix) {
for (int j = i; j < modify->nfix; j++)
if (strcmp(modify->fix[j]->style,"rigid") == 0)
error->all(FLERR,"Rigid fix must come before NPT/NPH fix");
}
// add gravity forces based on gravity vector from fix
if (id_gravity) {
int ifix = modify->find_fix(id_gravity);
if (ifix < 0) error->all(FLERR,"Fix rigid cannot find fix gravity ID");
if (strcmp(modify->fix[ifix]->style,"gravity") != 0)
error->all(FLERR,"Fix rigid gravity fix is invalid");
int tmp;
gvec = (double *) modify->fix[ifix]->extract("gvec",tmp);
}
// timestep info
dtv = update->dt;
@ -1061,8 +1111,17 @@ void FixRigid::compute_forces_and_torques()
torque[ibody][1] = all[ibody][4] + langextra[ibody][4];
torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
}
}
// add gravity force to COM of each body
if (id_gravity) {
for (ibody = 0; ibody < nbody; ibody++) {
fcm[ibody][0] += gvec[0]*masstotal[ibody];
fcm[ibody][1] += gvec[1]*masstotal[ibody];
fcm[ibody][2] += gvec[2]*masstotal[ibody];
}
}
}
/* ---------------------------------------------------------------------- */

6
src/RIGID/fix_rigid.h
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@ -66,7 +66,8 @@ class FixRigid : public Fix {
double *step_respa;
int triclinic;
char *inpfile; // file to read rigid body attributes from
char *inpfile; // file to read rigid body attributes from
int rstyle; // SINGLE,MOLECULE,GROUP
int setupflag; // 1 if body properties are setup, else 0
int earlyflag; // 1 if forces/torques computed at post_force()
@ -131,6 +132,9 @@ class FixRigid : public Fix {
int dilate_group_bit; // mask for dilation group
char *id_dilate; // group name to dilate
char *id_gravity; // ID of fix gravity command to add gravity forces
double *gvec; // ptr to gravity vector inside the fix
class RanMars *random;
class AtomVecEllipsoid *avec_ellipsoid;
class AtomVecLine *avec_line;

57
src/RIGID/fix_rigid_small.cpp
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@ -57,7 +57,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
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)
id_dilate(NULL), id_gravity(NULL), onemols(NULL)
{
int i;
@ -107,7 +107,8 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
bodyID = new tagint[nlocal];
customflag = 1;
// determine whether atom-style variable or atom property is used.
// 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);
@ -356,6 +357,13 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
p_chain = force->numeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"gravity") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid/small command");
delete [] id_gravity;
int n = strlen(arg[iarg+1]) + 1;
id_gravity = new char[n];
strcpy(id_gravity,arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal fix rigid/small command");
}
@ -515,6 +523,8 @@ FixRigidSmall::~FixRigidSmall()
delete random;
delete [] inpfile;
delete [] id_dilate;
delete [] id_gravity;
memory->destroy(langextra);
memory->destroy(mass_body);
@ -543,6 +553,7 @@ void FixRigidSmall::init()
triclinic = domain->triclinic;
// warn if more than one rigid fix
// if earlyflag, warn if any post-force fixes come after a rigid fix
int count = 0;
for (i = 0; i < modify->nfix; i++)
@ -563,6 +574,23 @@ void FixRigidSmall::init()
}
}
// warn if body properties are read from inpfile or a mol template file
// and the gravity keyword is not set and a gravity fix exists
// this could mean body particles are overlapped
// and gravity is not applied correctly
if ((inpfile || onemols) && !id_gravity) {
for (i = 0; i < modify->nfix; i++) {
if (strcmp(modify->fix[i]->style,"gravity") == 0) {
if (comm->me == 0)
error->warning(FLERR,"Gravity may not be correctly applied "
"to rigid bodies if they consist of "
"overlapped particles");
break;
}
}
}
// error if npt,nph fix comes before rigid fix
for (i = 0; i < modify->nfix; i++) {
@ -575,6 +603,17 @@ void FixRigidSmall::init()
error->all(FLERR,"Rigid fix must come before NPT/NPH fix");
}
// add gravity forces based on gravity vector from fix
if (id_gravity) {
int ifix = modify->find_fix(id_gravity);
if (ifix < 0) error->all(FLERR,"Fix rigid/small cannot find fix gravity ID");
if (strcmp(modify->fix[ifix]->style,"gravity") != 0)
error->all(FLERR,"Fix rigid/small gravity fix is invalid");
int tmp;
gvec = (double *) modify->fix[ifix]->extract("gvec",tmp);
}
// timestep info
dtv = update->dt;
@ -954,8 +993,20 @@ void FixRigidSmall::compute_forces_and_torques()
tcm[2] += langextra[ibody][5];
}
}
}
// add gravity force to COM of each body
if (id_gravity) {
double mass;
for (ibody = 0; ibody < nlocal_body; ibody++) {
mass = body[ibody].mass;
fcm = body[ibody].fcm;
fcm[0] += gvec[0]*mass;
fcm[1] += gvec[1]*mass;
fcm[2] += gvec[2]*mass;
}
}
}
/* ---------------------------------------------------------------------- */

3
src/RIGID/fix_rigid_small.h
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@ -164,6 +164,9 @@ class FixRigidSmall : public Fix {
int dilate_group_bit; // mask for dilation group
char *id_dilate; // group name to dilate
char *id_gravity; // ID of fix gravity command to add gravity forces
double *gvec; // ptr to gravity vector inside the fix
double p_current[3],p_target[3];
// molecules added on-the-fly as rigid bodies

13
src/USER-OMP/fix_rigid_nh_omp.cpp
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@ -383,6 +383,19 @@ void FixRigidNHOMP::compute_forces_and_torques()
torque[ibody][1] = all[ibody][4] + langextra[ibody][4];
torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
}
// add gravity force to COM of each body
if (id_gravity) {
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(ibody) schedule(static)
#endif
for (ibody = 0; ibody < nbody; ibody++) {
fcm[ibody][0] += gvec[0]*masstotal[ibody];
fcm[ibody][1] += gvec[1]*masstotal[ibody];
fcm[ibody][2] += gvec[2]*masstotal[ibody];
}
}
}
/* ---------------------------------------------------------------------- */

13
src/USER-OMP/fix_rigid_omp.cpp
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@ -256,6 +256,19 @@ void FixRigidOMP::compute_forces_and_torques()
torque[ibody][1] = all[ibody][4] + langextra[ibody][4];
torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
}
// add gravity force to COM of each body
if (id_gravity) {
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(ibody) schedule(static)
#endif
for (int ibody = 0; ibody < nbody; ibody++) {
fcm[ibody][0] += gvec[0]*masstotal[ibody];
fcm[ibody][1] += gvec[1]*masstotal[ibody];
fcm[ibody][2] += gvec[2]*masstotal[ibody];
}
}
}
/* ---------------------------------------------------------------------- */

15
src/USER-OMP/fix_rigid_small_omp.cpp
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@ -196,6 +196,21 @@ void FixRigidSmallOMP::compute_forces_and_torques()
tcm[2] += langextra[ibody][5];
}
}
// add gravity force to COM of each body
if (id_gravity) {
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(ibody) schedule(static)
#endif
for (int ibody = 0; ibody < nbody; ibody++) {
double * _noalias const fcm = body[ibody].fcm;
const double mass = body[ibody].mass;
fcm[0] += gvec[0]*mass;
fcm[1] += gvec[1]*mass;
fcm[2] += gvec[2]*mass;
}
}
}
/* ---------------------------------------------------------------------- */

52
src/fix_gravity.cpp
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@ -37,7 +37,8 @@ enum{CONSTANT,EQUAL};
FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
mstr(NULL), vstr(NULL), pstr(NULL), tstr(NULL), xstr(NULL), ystr(NULL), zstr(NULL)
mstr(NULL), vstr(NULL), pstr(NULL), tstr(NULL),
xstr(NULL), ystr(NULL), zstr(NULL)
{
if (narg < 5) error->all(FLERR,"Illegal fix gravity command");
@ -61,8 +62,10 @@ FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) :
mstyle = CONSTANT;
}
int iarg;
if (strcmp(arg[4],"chute") == 0) {
if (narg != 6) error->all(FLERR,"Illegal fix gravity command");
if (narg < 6) error->all(FLERR,"Illegal fix gravity command");
style = CHUTE;
if (strstr(arg[5],"v_") == arg[5]) {
int n = strlen(&arg[5][2]) + 1;
@ -73,9 +76,10 @@ FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) :
vert = force->numeric(FLERR,arg[5]);
vstyle = CONSTANT;
}
iarg = 6;
} else if (strcmp(arg[4],"spherical") == 0) {
if (narg != 7) error->all(FLERR,"Illegal fix gravity command");
if (narg < 7) error->all(FLERR,"Illegal fix gravity command");
style = SPHERICAL;
if (strstr(arg[5],"v_") == arg[5]) {
int n = strlen(&arg[5][2]) + 1;
@ -95,9 +99,10 @@ FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) :
theta = force->numeric(FLERR,arg[6]);
tstyle = CONSTANT;
}
iarg = 7;
} else if (strcmp(arg[4],"vector") == 0) {
if (narg != 8) error->all(FLERR,"Illegal fix gravity command");
if (narg < 8) error->all(FLERR,"Illegal fix gravity command");
style = VECTOR;
if (strstr(arg[5],"v_") == arg[5]) {
int n = strlen(&arg[5][2]) + 1;
@ -126,9 +131,23 @@ FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) :
zdir = force->numeric(FLERR,arg[7]);
zstyle = CONSTANT;
}
iarg = 8;
} else error->all(FLERR,"Illegal fix gravity command");
// optional keywords
disable = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"disable") == 0) {
disable = 1;
iarg++;
} else error->all(FLERR,"Illegal fix gravity command");
}
// initializations
degree2rad = MY_PI/180.0;
time_origin = update->ntimestep;
@ -266,6 +285,12 @@ void FixGravity::post_force(int /*vflag*/)
set_acceleration();
}
// just exit if application of force is disabled
if (disable) return;
// apply gravity force to each particle
double **x = atom->x;
double **f = atom->f;
double *rmass = atom->rmass;
@ -338,9 +363,9 @@ void FixGravity::set_acceleration()
}
}
xacc = magnitude*xgrav;
yacc = magnitude*ygrav;
zacc = magnitude*zgrav;
gvec[0] = xacc = magnitude*xgrav;
gvec[1] = yacc = magnitude*ygrav;
gvec[2] = zacc = magnitude*zgrav;
}
/* ----------------------------------------------------------------------
@ -357,3 +382,16 @@ double FixGravity::compute_scalar()
}
return egrav_all;
}
/* ----------------------------------------------------------------------
extract current gravity direction vector
------------------------------------------------------------------------- */
void *FixGravity::extract(const char *name, int &dim)
{
if (strcmp(name,"gvec") == 0) {
dim = 1;
return (void *) gvec;
}
return NULL;
}

5
src/fix_gravity.h
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@ -36,9 +36,10 @@ class FixGravity : public Fix {
virtual void post_force(int);
virtual void post_force_respa(int, int, int);
double compute_scalar();
void *extract(const char *, int &);
protected:
int style;
int style,disable;
double magnitude;
double vert,phi,theta;
double xdir,ydir,zdir;
@ -46,6 +47,8 @@ class FixGravity : public Fix {
double degree2rad;
int ilevel_respa;
int time_origin;
double gvec[3];
int eflag;
double egrav,egrav_all;