Merge pull request #1801 from lammps/rigid-gravity (c5768acb) · Commits · 郑智淋 / lammps

examples/rigid/in.rigid.gravity

0 → 100644

+63 −0

Original line number	Diff line number	Diff line
		#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

examples/rigid/molecule.data

0 → 100644

+41 −0

Original line number	Diff line number	Diff line
		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

src/RIGID/fix_rigid.cpp

+69 −10

Original line number	Diff line number	Diff line
		@@ -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];
		}
		}
		}

		/* ---------------------------------------------------------------------- */

src/RIGID/fix_rigid.h

+5 −1

Original line number	Diff line number	Diff line
		@@ -67,6 +67,7 @@ class FixRigid : public Fix {
		int triclinic;

		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;

src/RIGID/fix_rigid_small.cpp

+54 −3

Original line number	Diff line number	Diff line
		@@ -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;
		}
		}
		}

		/* ---------------------------------------------------------------------- */

Admin message