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enable per-atom custom arrays in addition to vectors

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This commit is contained in:
Steve Plimpton
2020-09-04 11:33:49 -06:00
parent d00807ee9a
commit d1442b0538
23 changed files with 1390 additions and 722 deletions
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88
src/set.cpp
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@ -45,12 +45,12 @@ using namespace MathConst;
enum{ATOM_SELECT,MOL_SELECT,TYPE_SELECT,GROUP_SELECT,REGION_SELECT};
enum{TYPE,TYPE_FRACTION,TYPE_RATIO,TYPE_SUBSET,
MOLECULE,X,Y,Z,CHARGE,MASS,SHAPE,LENGTH,TRI,
MOLECULE,X,Y,Z,VX,VY,VZ,CHARGE,MASS,SHAPE,LENGTH,TRI,
DIPOLE,DIPOLE_RANDOM,SPIN,SPIN_RANDOM,QUAT,QUAT_RANDOM,
THETA,THETA_RANDOM,ANGMOM,OMEGA,
DIAMETER,DENSITY,VOLUME,IMAGE,BOND,ANGLE,DIHEDRAL,IMPROPER,
SPH_E,SPH_CV,SPH_RHO,EDPD_TEMP,EDPD_CV,CC,SMD_MASS_DENSITY,
SMD_CONTACT_RADIUS,DPDTHETA,INAME,DNAME,VX,VY,VZ};
SMD_CONTACT_RADIUS,DPDTHETA,IVEC,DVEC,IARRAY,DARRAY};
#define BIG INT_MAX
@ -573,28 +573,63 @@ void Set::command(int narg, char **arg)
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);
else ivalue = force->inumeric(FLERR,arg[iarg+1]);
int flag;
index_custom = atom->find_custom(&arg[iarg][2],flag);
if (index_custom < 0 || flag != 0)
error->all(FLERR,"Set command integer vector does not exist");
set(INAME);
iarg += 2;
} else if (strstr(arg[iarg],"d_") == arg[iarg]) {
// custom per-atom vector
} else if (strstr(arg[iarg],"i_") == arg[iarg] ||
strstr(arg[iarg],"d_") == arg[iarg]) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
int which = 0;
if (arg[iarg][0] == 'd') which = 1;
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
else if (!which) ivalue = force->inumeric(FLERR,arg[iarg+1]);
else dvalue = force->numeric(FLERR,arg[iarg+1]);
int flag;
index_custom = atom->find_custom(&arg[iarg][2],flag);
if (index_custom < 0 || flag != 1)
error->all(FLERR,"Set command floating point vector does not exist");
set(DNAME);
int flag,cols;
index_custom = atom->find_custom(&arg[iarg][2],flag,cols);
if ((!which && (index_custom < 0 || flag || cols)) ||
(which && (index_custom < 0 || !flag || cols)))
error->all(FLERR,"Set command per-atom custom vector does not exist");
if (!which) set(IVEC);
else set(DVEC);
iarg += 2;
// custom per-atom array, must include bracketed index
} else if (strstr(arg[iarg],"i2_") == arg[iarg] ||
strstr(arg[iarg],"d2_") == arg[iarg]) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
int which = 0;
if (arg[iarg][0] == 'd') which = 1;
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
else if (!which) ivalue = force->inumeric(FLERR,arg[iarg+1]);
else dvalue = force->numeric(FLERR,arg[iarg+1]);
int n = strlen(arg[iarg]);
char *suffix = new char[n];
strcpy(suffix,&arg[iarg][3]);
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all(FLERR,"Invalid attribute in set command");
icol_custom = atoi(ptr+1);
*ptr = '\0';
} else error->all(FLERR,"Set command per-atom custom array is not indexed");
int flag,cols;
index_custom = atom->find_custom(suffix,flag,cols);
delete [] suffix;
if ((!which && (index_custom < 0 || flag || !cols)) ||
(which && (index_custom < 0 || !flag || !cols)))
error->all(FLERR,"Set command per-atom custom array does not exist");
if (icol_custom <= 0 || icol_custom > cols)
error->all(FLERR,"Set command per-atom custom array is accessed out-of-range");
if (!which) set(IARRAY);
else set(DARRAY);
iarg += 2;
} else error->all(FLERR,"Illegal set command");
// statistics
@ -970,20 +1005,29 @@ void Set::set(int keyword)
(((imageint) (zbox + IMGMAX) & IMGMASK) << IMG2BITS);
}
// set value for custom integer or double vector
// set value for custom vector or array
else if (keyword == INAME) {
else if (keyword == IVEC) {
atom->ivector[index_custom][i] = ivalue;
}
else if (keyword == DNAME) {
else if (keyword == DVEC) {
atom->dvector[index_custom][i] = dvalue;
}
else if (keyword == IARRAY) {
atom->iarray[index_custom][i][icol_custom-1] = ivalue;
}
else if (keyword == DARRAY) {
atom->darray[index_custom][i][icol_custom-1] = dvalue;
}
count++;
}
// update bonus data numbers
if (keyword == SHAPE) {
bigint nlocal_bonus = avec_ellipsoid->nlocal_bonus;
MPI_Allreduce(&nlocal_bonus,&atom->nellipsoids,1,