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Restarting limit_damping, other minor simplifications/cleanups

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This commit is contained in:
jtclemm
2022-11-16 16:36:22 -07:00
parent 5f0fff58ac
commit f51ab2c440
15 changed files with 72 additions and 93 deletions
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2
examples/granular/in.pour.drum
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@ -44,7 +44,7 @@ change_box all boundary p p f
pair_style granular
pair_coeff 1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
pair_coeff 2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
pair_coeff 2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall
variable theta equal 0

32
src/GRANULAR/fix_wall_gran.cpp
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@ -67,11 +67,9 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
model = new GranularModel(lmp);
model->contact_type = WALL;
if (strcmp(arg[3],"granular") == 0) classic_flag = 0;
else classic_flag = 1;
limit_damping = 0;
heat_flag = 0;
int Twall_defined = 0;
int classic_flag = 1;
if (strcmp(arg[3],"granular") == 0) classic_flag = 0;
// wall/particle coefficients
@ -117,10 +115,9 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
}
}
// Define default damping model if unspecified, takes no args
// Define default damping submodel if unspecified, takes no args
if (!model->damping_model)
model->construct_submodel("viscoelastic", DAMPING);
model->init();
size_history = model->size_history;
@ -177,6 +174,7 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
wiggle = 0;
wshear = 0;
peratom_flag = 0;
int Twall_defined = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"wiggle") == 0) {
@ -216,7 +214,7 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
}
if (heat_flag != Twall_defined)
error->all(FLERR, "To model conduction, must define both heat model and wall temperature");
error->all(FLERR, "Must define wall temperature with heat model");
if (wallstyle == NOSTYLE)
error->all(FLERR,"No wall style defined");
@ -376,6 +374,7 @@ void FixWallGran::post_force(int /*vflag*/)
history_update = 1;
if (update->setupflag) history_update = 0;
model->history_update = history_update;
// if just reneighbored:
// update rigid body masses for owned atoms if using FixRigid
@ -407,10 +406,10 @@ void FixWallGran::post_force(int /*vflag*/)
if (wiggle) {
double arg = omega * (update->ntimestep - time_origin) * dt;
if (wallstyle == axis) {
wlo = lo + amplitude - amplitude*cos(arg);
whi = hi + amplitude - amplitude*cos(arg);
wlo = lo + amplitude - amplitude * cos(arg);
whi = hi + amplitude - amplitude * cos(arg);
}
vwall[axis] = amplitude*omega*sin(arg);
vwall[axis] = amplitude * omega * sin(arg);
} else if (wshear) vwall[axis] = vshear;
// loop over all my atoms
@ -473,19 +472,19 @@ void FixWallGran::post_force(int /*vflag*/)
if (del1 < del2) dz = del1;
else dz = -del2;
} else if (wallstyle == ZCYLINDER) {
delxy = sqrt(x[i][0]*x[i][0] + x[i][1]*x[i][1]);
delxy = sqrt(x[i][0] * x[i][0] + x[i][1] * x[i][1]);
delr = cylradius - delxy;
if (delr > radius[i]) {
dz = cylradius;
rwall = 0.0;
} else {
dx = -delr/delxy * x[i][0];
dy = -delr/delxy * x[i][1];
dx = -delr / delxy * x[i][0];
dy = -delr / delxy * x[i][1];
// rwall = -2r_c if inside cylinder, 2r_c outside
rwall = (delxy < cylradius) ? -2*cylradius : 2*cylradius;
rwall = (delxy < cylradius) ? -2 * cylradius : 2 * cylradius;
if (wshear && axis != 2) {
vwall[0] += vshear * x[i][1]/delxy;
vwall[1] += -vshear * x[i][0]/delxy;
vwall[0] += vshear * x[i][1] / delxy;
vwall[1] += -vshear * x[i][0] / delxy;
vwall[2] = 0.0;
}
}
@ -521,7 +520,6 @@ void FixWallGran::post_force(int /*vflag*/)
model->meff = meff;
model->vi = v[i];
model->omegai = omega[i];
model->history_update = history_update;
if (use_history) model->history = history_one[i];
if (heat_flag) model->Ti = temperature[i];

3
src/GRANULAR/fix_wall_gran.h
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@ -53,7 +53,7 @@ class FixWallGran : public Fix {
protected:
int wallstyle, wiggle, wshear, axis;
int classic_flag, nlevels_respa;
int nlevels_respa;
bigint time_origin;
// for granular model choices
@ -69,7 +69,6 @@ class FixWallGran : public Fix {
int history_update; // flag for whether shear history is updated
int size_history; // # of shear history values per contact
int heat_flag;
int limit_damping;
int tvar;
char *tstr;

2
src/GRANULAR/fix_wall_gran_region.cpp
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@ -135,6 +135,7 @@ void FixWallGranRegion::post_force(int /*vflag*/)
history_update = 1;
if (update->setupflag) history_update = 0;
model->history_update = history_update;
// if just reneighbored:
// update rigid body masses for owned atoms if using FixRigid
@ -262,7 +263,6 @@ void FixWallGranRegion::post_force(int /*vflag*/)
model->meff = meff;
model->vi = v[i];
model->omegai = omega[i];
model->history_update = history_update;
if (use_history) model->history = history_many[i][c2r[ic]];
if (heat_flag) model->Ti = temperature[i];

4
src/GRANULAR/gran_sub_mod.h
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@ -29,8 +29,8 @@ class GranSubMod : protected Pointers {
double *coeffs;
void read_restart();
virtual void mix_coeffs(double*, double*);
virtual void coeffs_to_local() = 0;
virtual void init() = 0; // called after all submodel coeffs defined
virtual void coeffs_to_local() {};
virtual void init() {}; // called after all submodels + coeffs defined
void allocate_coeffs();
std::string name;

2
src/GRANULAR/gran_sub_mod_damping.cpp
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@ -108,7 +108,7 @@ void GranSubModDampingTsuji::init()
{
double tmp = gm->normal_model->damp;
damp = 1.2728 - 4.2783 * tmp + 11.087 * square(tmp);
damp += -22.348 * cube(tmp)+ 27.467 * powint(tmp, 4);
damp += -22.348 * cube(tmp) + 27.467 * powint(tmp, 4);
damp += -18.022 * powint(tmp, 5) + 4.8218 * powint(tmp,6);
}

2
src/GRANULAR/gran_sub_mod_damping.h
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@ -48,8 +48,6 @@ class GranSubModDamping : public GranSubMod {
public:
GranSubModDamping(class GranularModel *, class LAMMPS *);
~GranSubModDamping() {};
virtual void coeffs_to_local() {};
virtual void mix_coeffs(double*, double*) {};
virtual void init();
virtual double calculate_forces() = 0;
double damp_prefactor; // Used by tangential models

2
src/GRANULAR/gran_sub_mod_heat.h
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@ -35,8 +35,6 @@ class GranSubModHeat : public GranSubMod {
public:
GranSubModHeat(class GranularModel *, class LAMMPS *);
~GranSubModHeat() {};
virtual void coeffs_to_local() {};
virtual void init() {};
virtual double calculate_heat() = 0;
};

4
src/GRANULAR/gran_sub_mod_normal.h
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@ -51,8 +51,6 @@ class GranSubModNormal : public GranSubMod {
public:
GranSubModNormal(class GranularModel *, class LAMMPS *);
~GranSubModNormal() {};
virtual void coeffs_to_local() {};
virtual void init() {};
virtual bool touch();
virtual double pulloff_distance(double, double);
virtual double calculate_area();
@ -60,7 +58,7 @@ class GranSubModNormal : public GranSubMod {
virtual void set_fncrit();
double damp; // argument historically needed by damping
double Emod, poiss;
double Fncrit, knfac;
double Fncrit;
int material_properties, cohesive_flag;
};

2
src/GRANULAR/gran_sub_mod_rolling.h
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@ -35,8 +35,6 @@ class GranSubModRolling : public GranSubMod {
public:
GranSubModRolling(class GranularModel *, class LAMMPS *);
~GranSubModRolling() {};
virtual void coeffs_to_local() {};
virtual void init() {};
virtual void calculate_forces() = 0;
};

4
src/GRANULAR/gran_sub_mod_tangential.h
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@ -63,8 +63,6 @@ class GranSubModTangential : public GranSubMod {
public:
GranSubModTangential(class GranularModel *, class LAMMPS *);
virtual ~GranSubModTangential() {};
virtual void coeffs_to_local() {};
virtual void init() {};
virtual void calculate_forces() = 0;
double k, damp, mu; // Used by Marshall twisting model
};
@ -105,8 +103,6 @@ class GranSubModTangentialLinearHistoryClassic : public GranSubModTangentialLine
public:
GranSubModTangentialLinearHistoryClassic(class GranularModel *, class LAMMPS *);
void calculate_forces();
protected:
double xt;
};
/* ---------------------------------------------------------------------- */

4
src/GRANULAR/gran_sub_mod_twisting.h
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@ -39,8 +39,6 @@ class GranSubModTwisting : public GranSubMod {
public:
GranSubModTwisting(class GranularModel *, class LAMMPS *);
virtual ~GranSubModTwisting() {};
virtual void coeffs_to_local() {};
virtual void init() {};
virtual void calculate_forces() = 0;
};
@ -57,8 +55,8 @@ class GranSubModTwistingNone : public GranSubModTwisting {
class GranSubModTwistingMarshall : public GranSubModTwisting {
public:
GranSubModTwistingMarshall(class GranularModel *, class LAMMPS *);
void init() override;
void calculate_forces();
void init();
protected:
double k_tang, mu_tang;
};

44
src/GRANULAR/granular_model.cpp
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@ -148,12 +148,13 @@ void GranularModel::construct_submodel(std::string model_name, SubmodelType mode
sub_models[model_type]->name.assign(model_name);
sub_models[model_type]->allocate_coeffs();
if (model_type == NORMAL) normal_model = dynamic_cast<GranSubModNormal *> (sub_models[NORMAL]);
if (model_type == DAMPING) damping_model = dynamic_cast<GranSubModDamping *> (sub_models[DAMPING]);
if (model_type == TANGENTIAL) tangential_model = dynamic_cast<GranSubModTangential *> (sub_models[TANGENTIAL]);
if (model_type == ROLLING) rolling_model = dynamic_cast<GranSubModRolling *> (sub_models[ROLLING]);
if (model_type == TWISTING) twisting_model = dynamic_cast<GranSubModTwisting *> (sub_models[TWISTING]);
if (model_type == HEAT) heat_model = dynamic_cast<GranSubModHeat *> (sub_models[HEAT]);
// Assign specific submodel pointer
if (model_type == NORMAL) normal_model = dynamic_cast<GranSubModNormal *> (sub_models[model_type]);
if (model_type == DAMPING) damping_model = dynamic_cast<GranSubModDamping *> (sub_models[model_type]);
if (model_type == TANGENTIAL) tangential_model = dynamic_cast<GranSubModTangential *> (sub_models[model_type]);
if (model_type == ROLLING) rolling_model = dynamic_cast<GranSubModRolling *> (sub_models[model_type]);
if (model_type == TWISTING) twisting_model = dynamic_cast<GranSubModTwisting *> (sub_models[model_type]);
if (model_type == HEAT) heat_model = dynamic_cast<GranSubModHeat *> (sub_models[model_type]);
}
/* ---------------------------------------------------------------------- */
@ -248,7 +249,8 @@ void GranularModel::init()
beyond_contact = 1;
size_history += sub_models[i]->size_history;
if (!sub_models[i]->allow_cohesion && normal_model->cohesive_flag)
error->all(FLERR,"Cannot use {} model with a cohesive normal model, {}", sub_models[i]->name, normal_model->name);
error->all(FLERR,"Cannot use {} model with a cohesive normal model, {}",
sub_models[i]->name, normal_model->name);
if (sub_models[i]->area_flag) area_flag = 1;
}
@ -260,14 +262,14 @@ void GranularModel::init()
int j;
for (int i = 0; i < size_history; i++) {
// Find which model owns this history value
// Find which submodel owns this history value
size_cumulative = 0;
for (j = 0; j < NSUBMODELS; j++) {
if ((size_cumulative + sub_models[j]->size_history) > i) break;
size_cumulative += sub_models[j]->size_history;
}
// Check if model has nondefault transfers, if so copy its array
// Check if submodel has nondefault transfers, if so copy its array
transfer_history_factor[i] = -1;
if (j != NSUBMODELS) {
if (sub_models[j]->nondefault_history_transfer) {
@ -284,8 +286,7 @@ void GranularModel::init()
int GranularModel::mix_coeffs(GranularModel *g1, GranularModel *g2)
{
int i;
for (i = 0; i < NSUBMODELS; i++) {
for (int i = 0; i < NSUBMODELS; i++) {
if (g1->sub_models[i]->name != g2->sub_models[i]->name) return i;
construct_submodel(g1->sub_models[i]->name, (SubmodelType) i);
@ -311,6 +312,8 @@ void GranularModel::write_restart(FILE *fp)
fwrite(&num_coeffs, sizeof(int), 1, fp);
fwrite(sub_models[i]->coeffs, sizeof(double), num_coeffs, fp);
}
fwrite(&limit_damping, sizeof(int), 1, fp);
}
/* ---------------------------------------------------------------------- */
@ -328,22 +331,23 @@ void GranularModel::read_restart(FILE *fp)
if (comm->me == 0)
utils::sfread(FLERR, const_cast<char*>(model_name.data()), sizeof(char),num_char, fp, nullptr, error);
MPI_Bcast(const_cast<char*>(model_name.data()), num_char, MPI_CHAR, 0, world);
construct_submodel(model_name, (SubmodelType) i);
if (comm->me == 0) {
if (comm->me == 0)
utils::sfread(FLERR, &num_coeff, sizeof(int), 1, fp, nullptr, error);
if (num_coeff != sub_models[i]->num_coeffs)
error->one(FLERR, "Invalid granular model written to restart file");
}
MPI_Bcast(&num_coeff, 1, MPI_INT, 0, world);
if (num_coeff != sub_models[i]->num_coeffs)
error->all(FLERR, "Invalid granular model written to restart file");
if (comm->me == 0) {
if (comm->me == 0)
utils::sfread(FLERR, sub_models[i]->coeffs, sizeof(double), num_coeff, fp, nullptr, error);
}
MPI_Bcast(sub_models[i]->coeffs, num_coeff, MPI_DOUBLE, 0, world);
sub_models[i]->coeffs_to_local();
}
if (comm->me == 0)
utils::sfread(FLERR, &limit_damping, sizeof(int), 1, fp, nullptr, error);
MPI_Bcast(&limit_damping, 1, MPI_INT, 0, world);
}
/* ---------------------------------------------------------------------- */
@ -393,7 +397,7 @@ void GranularModel::calculate_forces()
sub3(vi, vj, vr);
// normal component
vnnr = dot3(vr, nx); //v_R . n
vnnr = dot3(vr, nx);
scale3(vnnr, nx, vn);
// tangential component
@ -433,7 +437,7 @@ void GranularModel::calculate_forces()
if (contact_type == PAIR) {
copy3(torquesi, torquesj);
// Classic pair styles wouldn't scale, but classic option is only used by walls
// Classic pair styles don't scale, but classic option is currently only used by walls
dist_to_contact = radi - 0.5 * delta;
scale3(dist_to_contact, torquesi);
dist_to_contact = radj - 0.5 * delta;

8
src/GRANULAR/granular_model.h
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@ -68,7 +68,7 @@ class GranularModel : protected Pointers {
GranSubModRolling *rolling_model;
GranSubModTwisting *twisting_model;
GranSubModHeat *heat_model;
GranSubMod *sub_models[NSUBMODELS]; // Need to resize if we add more model flavors
GranSubMod *sub_models[NSUBMODELS];
// Extra options
int beyond_contact, limit_damping, history_update;
@ -94,9 +94,9 @@ class GranularModel : protected Pointers {
bool touch;
protected:
int rolling_defined, twisting_defined, heat_defined; // Used to quickly skip undefined submodels
int classic_model;
int area_flag;
int rolling_defined, twisting_defined, heat_defined; // Flag optional submodels
int classic_model; // Flag original pair/gran calculations
int area_flag; // Flag whether area is needed
int nclass;

50
src/GRANULAR/pair_granular.cpp
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@ -57,8 +57,6 @@ PairGranular::PairGranular(LAMMPS *lmp) : Pair(lmp)
svector = new double[single_extra];
neighprev = 0;
nmodels = 0;
maxmodels = 0;
nmax = 0;
mass_rigid = nullptr;
@ -302,6 +300,7 @@ void PairGranular::allocate()
maxmodels = n * n + 1; // should never need any more space
models_list = (GranularModel **) memory->smalloc(maxmodels * sizeof(GranularModel *), "pair:models_list");
for (int i = 0; i < maxmodels; i++) models_list[i] = nullptr;
nmodels = 0;
onerad_dynamic = new double[n+1];
onerad_frozen = new double[n+1];
@ -339,7 +338,6 @@ void PairGranular::coeff(int narg, char **arg)
utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error);
// Construct new model
models_list[nmodels] = new GranularModel(lmp);
class GranularModel* model = models_list[nmodels];
@ -374,9 +372,10 @@ void PairGranular::coeff(int narg, char **arg)
} else error->all(FLERR, "Illegal pair_coeff command {}", arg[iarg]);
}
// Define default damping model if unspecified, has no coeffs
// Define default damping submodel if unspecified, has no coeffs
if (!model->damping_model)
model->construct_submodel("viscoelastic", DAMPING);
model->init();
int count = 0;
for (int i = ilo; i <= ihi; i++) {
@ -388,7 +387,7 @@ void PairGranular::coeff(int narg, char **arg)
}
}
// If there are > ntype^2 models, delete unused ones
// If there are > ntype^2 models, delete unused models
if (nmodels == maxmodels) prune_models();
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
@ -419,7 +418,6 @@ void PairGranular::init_style()
int size_max[NSUBMODELS] = {0};
for (int n = 0; n < nmodels; n++) {
model = models_list[n];
model->init();
if (model->beyond_contact) {
beyond_contact = 1;
@ -559,7 +557,6 @@ double PairGranular::init_one(int i, int j)
model1->sub_models[error_code]->name,
model2->sub_models[error_code]->name);
// Initialize new model, init_one() occurs after init_style
model->init();
for (int k = 0; k < NSUBMODELS; k++)
@ -657,8 +654,10 @@ void PairGranular::read_restart(FILE *fp)
MPI_Bcast(&nmodels,1,MPI_INT,0,world);
for (i = 0; i < nmodels; i++) {
delete models_list[i];
models_list[i] = new GranularModel(lmp);
models_list[i]->read_restart(fp);
models_list[i]->init();
}
for (i = 1; i <= atom->ntypes; i++) {
@ -690,28 +689,22 @@ double PairGranular::single(int i, int j, int itype, int jtype,
double rsq, double /* factor_coul */,
double factor_lj, double &fforce)
{
if (factor_lj == 0) {
fforce = 0.0;
for (int m = 0; m < single_extra; m++) svector[m] = 0.0;
return 0.0;
}
int jnum;
int *jlist;
double *history,*allhistory;
int nall = atom->nlocal + atom->nghost;
if ((i >= nall) || (j >= nall))
error->all(FLERR,"Not enough atoms for pair granular single function");
int touchflag;
double **x = atom->x;
double *radius = atom->radius;
class GranularModel* model = models_list[types_indices[itype][jtype]];
// Reset model and copy initial geometric data
double **x = atom->x;
double *radius = atom->radius;
model->xi = x[i];
model->xj = x[j];
model->radi = radius[i];
@ -719,8 +712,9 @@ double PairGranular::single(int i, int j, int itype, int jtype,
model->history_update = 0; // Don't update history
// If history is needed
jnum = list->numneigh[i];
jlist = list->firstneigh[i];
double *history,*allhistory;
int jnum = list->numneigh[i];
int *jlist = list->firstneigh[i];
if (use_history) {
if ((fix_history == nullptr) || (fix_history->firstvalue == nullptr))
error->one(FLERR,"Pair granular single computation needs history");
@ -730,11 +724,11 @@ double PairGranular::single(int i, int j, int itype, int jtype,
if (neighprev >= jnum) neighprev = 0;
if (jlist[neighprev] == j) break;
}
history = &allhistory[size_history*neighprev];
history = &allhistory[size_history * neighprev];
model->touch = fix_history->firstflag[i][neighprev];
}
touchflag = model->check_contact();
int touchflag = model->check_contact();
if (!touchflag) {
fforce = 0.0;
@ -745,17 +739,16 @@ double PairGranular::single(int i, int j, int itype, int jtype,
// meff = effective mass of pair of particles
// if I or J part of rigid body, use body mass
// if I or J is frozen, meff is other particle
double mi, mj, meff;
double *rmass = atom->rmass;
int *mask = atom->mask;
mi = rmass[i];
mj = rmass[j];
double mi = rmass[i];
double mj = rmass[j];
if (fix_rigid) {
if (mass_rigid[i] > 0.0) mi = mass_rigid[i];
if (mass_rigid[j] > 0.0) mj = mass_rigid[j];
}
meff = mi * mj / (mi + mj);
double meff = mi * mj / (mi + mj);
if (mask[i] & freeze_group_bit) meff = mj;
if (mask[j] & freeze_group_bit) meff = mi;
@ -770,11 +763,10 @@ double PairGranular::single(int i, int j, int itype, int jtype,
model->omegaj = omega[j];
model->history = history;
double *forces, *torquesi, *torquesj;
model->calculate_forces();
forces = model->forces;
torquesi = model->torquesi;
torquesj = model->torquesj;
double *forces = model->forces;
double *torquesi = model->torquesi;
double *torquesj = model->torquesj;
// apply forces & torques
fforce = MathExtra::len3(forces);
@ -843,7 +835,7 @@ void PairGranular::transfer_history(double* source, double* target, int itype, i
class GranularModel* model = models_list[types_indices[itype][jtype]];
if (model->nondefault_history_transfer) {
for (int i = 0; i < size_history; i++) {
target[i] = model->transfer_history_factor[i] * source [i];
target[i] = model->transfer_history_factor[i] * source[i];
}
} else {
for (int i = 0; i < size_history; i++) {