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new USER-MESO package

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This commit is contained in:
Steve Plimpton
2017-08-18 17:33:42 -06:00
parent b11fe2eddb
commit f945d4567d
81 changed files with 8358 additions and 66 deletions
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72
src/set.cpp
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@ -41,11 +41,12 @@ using namespace LAMMPS_NS;
using namespace MathConst;
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,DPDTHETA,
INAME,DNAME};
MESO_E,MESO_CV,MESO_RHO,EDPD_TEMP,EDPD_CV,CC,SMD_MASS_DENSITY,
SMD_CONTACT_RADIUS,DPDTHETA,INAME,DNAME};
#define BIG INT_MAX
@ -419,6 +420,46 @@ void Set::command(int narg, char **arg)
set(MESO_RHO);
iarg += 2;
} else if (strcmp(arg[iarg],"edpd/temp") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
if (strcmp(arg[iarg+1],"NULL") == 0) dvalue = -1.0;
else if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
else {
dvalue = force->numeric(FLERR,arg[iarg+1]);
if (dvalue < 0.0) error->all(FLERR,"Illegal set command");
}
if (!atom->edpd_flag)
error->all(FLERR,"Cannot set edpd/temp for this atom style");
set(EDPD_TEMP);
iarg += 2;
} else if (strcmp(arg[iarg],"edpd/cv") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
if (strcmp(arg[iarg+1],"NULL") == 0) dvalue = -1.0;
else if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
else {
dvalue = force->numeric(FLERR,arg[iarg+1]);
if (dvalue < 0.0) error->all(FLERR,"Illegal set command");
}
if (!atom->edpd_flag)
error->all(FLERR,"Cannot set edpd/cv for this atom style");
set(EDPD_CV);
iarg += 2;
} else if (strcmp(arg[iarg],"cc") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal set command");
if (strcmp(arg[iarg+1],"NULL") == 0) dvalue = -1.0;
else if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
else {
cc_index = force->inumeric(FLERR,arg[iarg+1]);
dvalue = force->numeric(FLERR,arg[iarg+2]);
if (cc_index < 1) error->all(FLERR,"Illegal set command");
}
if (!atom->tdpd_flag)
error->all(FLERR,"Cannot set cc for this atom style");
set(CC);
iarg += 3;
} 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);
@ -476,14 +517,28 @@ void Set::command(int narg, char **arg)
} else error->all(FLERR,"Illegal set command");
// statistics
// for CC option, include species index
MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world);
if (comm->me == 0) {
if (screen) fprintf(screen," %d settings made for %s\n",
allcount,arg[origarg]);
if (logfile) fprintf(logfile," %d settings made for %s\n",
allcount,arg[origarg]);
if (screen) {
if (strcmp(arg[origarg],"cc") == 0)
fprintf(screen," %d settings made for %s index %s\n",
allcount,arg[origarg],arg[origarg+1]);
else
fprintf(screen," %d settings made for %s\n",
allcount,arg[origarg]);
}
if (logfile) {
if (strcmp(arg[origarg],"cc") == 0)
fprintf(logfile," %d settings made for %s index %s\n",
allcount,arg[origarg],arg[origarg+1]);
else
fprintf(logfile," %d settings made for %s\n",
allcount,arg[origarg]);
}
}
}
@ -663,6 +718,11 @@ void Set::set(int keyword)
else if (keyword == MESO_E) atom->e[i] = dvalue;
else if (keyword == MESO_CV) atom->cv[i] = dvalue;
else if (keyword == MESO_RHO) atom->rho[i] = dvalue;
else if (keyword == EDPD_TEMP) atom->edpd_temp[i] = dvalue;
else if (keyword == EDPD_CV) atom->edpd_cv[i] = dvalue;
else if (keyword == CC) atom->cc[i][cc_index-1] = dvalue;
else if (keyword == SMD_MASS_DENSITY) {
// set mass from volume and supplied mass density
atom->rmass[i] = atom->vfrac[i] * dvalue;