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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14515 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2016-01-28 21:24:58 +00:00
parent bc15585acd
commit f86a9f4283
6 changed files with 60 additions and 11 deletions
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19
src/atom.cpp
View File

@ -93,6 +93,12 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
rho = drho = e = de = cv = NULL;
vest = NULL;
// USER-DPD
uCond = uMech = uChem = uCG = uCGnew = NULL;
duCond = duMech = duChem = NULL;
dpdTheta = NULL;
// USER-SMD
contact_radius = NULL;
@ -157,6 +163,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
cs_flag = csforce_flag = vforce_flag = etag_flag = 0;
rho_flag = e_flag = cv_flag = vest_flag = 0;
dpd_flag = 0;
// USER-SMD
@ -273,6 +280,16 @@ Atom::~Atom()
memory->destroy(eff_plastic_strain_rate);
memory->destroy(damage);
memory->destroy(dpdTheta);
memory->destroy(uCond);
memory->destroy(uMech);
memory->destroy(uChem);
memory->destroy(uCG);
memory->destroy(uCGnew);
memory->destroy(duCond);
memory->destroy(duMech);
memory->destroy(duChem);
memory->destroy(nspecial);
memory->destroy(special);
@ -2105,6 +2122,8 @@ void *Atom::extract(char *name)
return (void *) eff_plastic_strain_rate;
if (strcmp(name, "damage") == 0) return (void *) damage;
if (strcmp(name,"dpdTheta") == 0) return (void *) dpdTheta;
return NULL;
}

7
src/atom.h
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@ -85,6 +85,12 @@ class Atom : protected Pointers {
double *eff_plastic_strain_rate;
double *damage;
// USER-DPD package
double *uCond, *uMech, *uChem, *uCGnew, *uCG;
double *duCond, *duMech, *duChem;
double *dpdTheta;
// molecular info
int **nspecial; // 0,1,2 = cummulative # of 1-2,1-3,1-4 neighs
@ -133,6 +139,7 @@ class Atom : protected Pointers {
int vfrac_flag,spin_flag,eradius_flag,ervel_flag,erforce_flag;
int cs_flag,csforce_flag,vforce_flag,ervelforce_flag,etag_flag;
int rho_flag,e_flag,cv_flag,vest_flag;
int dpd_flag;
// USER-SMD package

2
src/library.cpp
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@ -150,6 +150,8 @@ void *lammps_extract_global(void *ptr, char *name)
if (strcmp(name,"yz") == 0) return (void *) &lmp->domain->yz;
if (strcmp(name,"natoms") == 0) return (void *) &lmp->atom->natoms;
if (strcmp(name,"nlocal") == 0) return (void *) &lmp->atom->nlocal;
if (strcmp(name,"ntimestep") == 0) return (void *) &lmp->update->ntimestep;
return NULL;
}

5
src/neigh_request.cpp
View File

@ -48,6 +48,7 @@ NeighRequest::NeighRequest(LAMMPS *lmp) : Pointers(lmp)
// default is no CUDA neighbor list build
// default is no multi-threaded neighbor list build
// default is no Kokkos neighbor list build
// default is no Shardlow Splitting Algorithm (SSA) neighbor list build
occasional = 0;
newton = 0;
@ -58,6 +59,7 @@ NeighRequest::NeighRequest(LAMMPS *lmp) : Pointers(lmp)
omp = 0;
intel = 0;
kokkos_host = kokkos_device = 0;
ssa = 0;
// default is no copy or skip
@ -133,6 +135,7 @@ int NeighRequest::identical(NeighRequest *other)
if (cudable != other->cudable) same = 0;
if (omp != other->omp) same = 0;
if (intel != other->intel) same = 0;
if (ssa != other->ssa) same = 0;
if (copy != other->copy_original) same = 0;
if (same_skip(other) == 0) same = 0;
@ -163,6 +166,7 @@ int NeighRequest::same_kind(NeighRequest *other)
if (cudable != other->cudable) same = 0;
if (omp != other->omp) same = 0;
if (intel != other->intel) same = 0;
if (ssa != other->ssa) same = 0;
return same;
}
@ -214,4 +218,5 @@ void NeighRequest::copy_request(NeighRequest *other)
cudable = other->cudable;
omp = other->omp;
intel = other->intel;
ssa = other->ssa;
}

4
src/neigh_request.h
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@ -90,6 +90,10 @@ class NeighRequest : protected Pointers {
int kokkos_host;
int kokkos_device;
// 1 if using Shardlow Splitting Algorithm (SSA) neighbor list build
int ssa;
// set by neighbor and pair_hybrid after all requests are made
// these settings do not change kind value

34
src/set.cpp
View File

@ -44,7 +44,8 @@ enum{ATOM_SELECT,MOL_SELECT,TYPE_SELECT,GROUP_SELECT,REGION_SELECT};
enum{TYPE,TYPE_FRACTION,MOLECULE,X,Y,Z,CHARGE,MASS,SHAPE,LENGTH,TRI,
DIPOLE,DIPOLE_RANDOM,QUAT,QUAT_RANDOM,THETA,THETA_RANDOM,ANGMOM,OMEGA,
DIAMETER,DENSITY,VOLUME,IMAGE,BOND,ANGLE,DIHEDRAL,IMPROPER,
MESO_E,MESO_CV,MESO_RHO,SMD_MASS_DENSITY,SMD_CONTACT_RADIUS,INAME,DNAME};
MESO_E,MESO_CV,MESO_RHO,SMD_MASS_DENSITY,SMD_CONTACT_RADIUS,DPDTHETA,
INAME,DNAME};
#define BIG INT_MAX
@ -381,51 +382,61 @@ void Set::command(int narg, char **arg)
topology(IMPROPER);
iarg += 2;
} else if (strcmp(arg[iarg],"meso_e") == 0) {
} else if (strcmp(arg[iarg],"meso/e") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
else dvalue = force->numeric(FLERR,arg[iarg+1]);
if (!atom->e_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
error->all(FLERR,"Cannot set meso/e for this atom style");
set(MESO_E);
iarg += 2;
} else if (strcmp(arg[iarg],"meso_cv") == 0) {
} else if (strcmp(arg[iarg],"meso/cv") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
else dvalue = force->numeric(FLERR,arg[iarg+1]);
if (!atom->cv_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
error->all(FLERR,"Cannot set meso/cv for this atom style");
set(MESO_CV);
iarg += 2;
} else if (strcmp(arg[iarg],"meso_rho") == 0) {
} else if (strcmp(arg[iarg],"meso/rho") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
else dvalue = force->numeric(FLERR,arg[iarg+1]);
if (!atom->rho_flag)
error->all(FLERR,"Cannot set meso_rho for this atom style");
error->all(FLERR,"Cannot set meso/rho for this atom style");
set(MESO_RHO);
iarg += 2;
} else if (strcmp(arg[iarg],"smd_mass_density") == 0) {
} else if (strcmp(arg[iarg],"smd/mass/density") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
else dvalue = force->numeric(FLERR,arg[iarg+1]);
if (!atom->smd_flag)
error->all(FLERR,"Cannot set smd_mass_density for this atom style");
error->all(FLERR,"Cannot set smd/mass/density for this atom style");
set(SMD_MASS_DENSITY);
iarg += 2;
} else if (strcmp(arg[iarg],"smd_contact_radius") == 0) {
} else if (strcmp(arg[iarg],"smd/contact/radius") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
else dvalue = force->numeric(FLERR,arg[iarg+1]);
if (!atom->smd_flag)
error->all(FLERR,"Cannot set smd_contact_radius for this atom style");
error->all(FLERR,"Cannot set smd/contact/radius "
"for this atom style");
set(SMD_CONTACT_RADIUS);
iarg += 2;
} else if (strcmp(arg[iarg],"dpd/theta") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
else dvalue = force->numeric(FLERR,arg[iarg+1]);
if (!atom->dpd_flag)
error->all(FLERR,"Cannot set dpd/theta for this atom style");
set(DPDTHETA);
iarg += 2;
} else if (strstr(arg[iarg],"i_") == arg[iarg]) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
@ -621,6 +632,7 @@ void Set::set(int keyword)
atom->rmass[i] = atom->vfrac[i] * dvalue;
}
else if (keyword == SMD_CONTACT_RADIUS) atom->contact_radius[i] = dvalue;
else if (keyword == DPDTHETA) atom->dpdTheta[i] = dvalue;
// set shape of ellipsoidal particle