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set.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, [email protected]
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include <mpi.h>
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "set.h"
#include "atom.h"
#include "atom_vec.h"
#include "atom_vec_ellipsoid.h"
#include "atom_vec_line.h"
#include "atom_vec_tri.h"
#include "atom_vec_body.h"
#include "domain.h"
#include "region.h"
#include "group.h"
#include "comm.h"
#include "neighbor.h"
#include "force.h"
#include "pair.h"
#include "input.h"
#include "variable.h"
#include "random_park.h"
#include "math_extra.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
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,LAMBDA,TEMPERATURE,CHEMPOTENTIAL,CONCENTRATION};
#define BIG INT_MAX
/* ---------------------------------------------------------------------- */
void Set::command(int narg, char **arg)
{
if (domain->box_exist == 0)
error->all(FLERR,"Set command before simulation box is defined");
if (atom->natoms == 0)
error->all(FLERR,"Set command with no atoms existing");
if (narg < 3) error->all(FLERR,"Illegal set command");
// style and ID info
if (strcmp(arg[0],"atom") == 0) style = ATOM_SELECT;
else if (strcmp(arg[0],"mol") == 0) style = MOL_SELECT;
else if (strcmp(arg[0],"type") == 0) style = TYPE_SELECT;
else if (strcmp(arg[0],"group") == 0) style = GROUP_SELECT;
else if (strcmp(arg[0],"region") == 0) style = REGION_SELECT;
else error->all(FLERR,"Illegal set command");
int n = strlen(arg[1]) + 1;
id = new char[n];
strcpy(id,arg[1]);
select = NULL;
selection(atom->nlocal);
// loop over keyword/value pairs
// call appropriate routine to reset attributes
if (comm->me == 0 && screen) fprintf(screen,"Setting atom values ...\n");
int allcount,origarg;
int iarg = 2;
while (iarg < narg) {
varflag = varflag1 = varflag2 = varflag3 = varflag4 = 0;
count = 0;
origarg = iarg;
if (strcmp(arg[iarg],"type") == 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 ivalue = force->inumeric(FLERR,arg[iarg+1]);
set(TYPE);
iarg += 2;
} else if (strcmp(arg[iarg],"type/fraction") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal set command");
newtype = force->inumeric(FLERR,arg[iarg+1]);
fraction = force->numeric(FLERR,arg[iarg+2]);
ivalue = force->inumeric(FLERR,arg[iarg+3]);
if (newtype <= 0 || newtype > atom->ntypes)
error->all(FLERR,"Invalid value in set command");
if (fraction < 0.0 || fraction > 1.0)
error->all(FLERR,"Invalid value in set command");
if (ivalue <= 0)
error->all(FLERR,"Invalid random number seed in set command");
setrandom(TYPE_FRACTION);
iarg += 4;
} else if (strcmp(arg[iarg],"mol") == 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 ivalue = force->inumeric(FLERR,arg[iarg+1]);
if (!atom->molecule_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(MOLECULE);
iarg += 2;
} else if (strcmp(arg[iarg],"x") == 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]);
set(X);
iarg += 2;
} else if (strcmp(arg[iarg],"y") == 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]);
set(Y);
iarg += 2;
} else if (strcmp(arg[iarg],"z") == 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]);
set(Z);
iarg += 2;
} else if (strcmp(arg[iarg],"charge") == 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->q_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(CHARGE);
iarg += 2;
} else if (strcmp(arg[iarg],"mass") == 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->rmass_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(MASS);
iarg += 2;
} else if (strcmp(arg[iarg],"shape") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal set command");
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
else xvalue = force->numeric(FLERR,arg[iarg+1]);
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) varparse(arg[iarg+2],2);
else yvalue = force->numeric(FLERR,arg[iarg+2]);
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) varparse(arg[iarg+3],3);
else zvalue = force->numeric(FLERR,arg[iarg+3]);
if (!atom->ellipsoid_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(SHAPE);
iarg += 4;
} else if (strcmp(arg[iarg],"length") == 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->line_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(LENGTH);
iarg += 2;
} else if (strcmp(arg[iarg],"tri") == 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->tri_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(TRI);
iarg += 2;
} else if (strcmp(arg[iarg],"dipole") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal set command");
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
else xvalue = force->numeric(FLERR,arg[iarg+1]);
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) varparse(arg[iarg+2],2);
else yvalue = force->numeric(FLERR,arg[iarg+2]);
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) varparse(arg[iarg+3],3);
else zvalue = force->numeric(FLERR,arg[iarg+3]);
if (!atom->mu_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(DIPOLE);
iarg += 4;
} else if (strcmp(arg[iarg],"dipole/random") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal set command");
ivalue = force->inumeric(FLERR,arg[iarg+1]);
dvalue = force->numeric(FLERR,arg[iarg+2]);
if (!atom->mu_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
if (ivalue <= 0)
error->all(FLERR,"Invalid random number seed in set command");
if (dvalue <= 0.0)
error->all(FLERR,"Invalid dipole length in set command");
setrandom(DIPOLE_RANDOM);
iarg += 3;
} else if (strcmp(arg[iarg],"quat") == 0) {
if (iarg+5 > narg) error->all(FLERR,"Illegal set command");
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
else xvalue = force->numeric(FLERR,arg[iarg+1]);
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) varparse(arg[iarg+2],2);
else yvalue = force->numeric(FLERR,arg[iarg+2]);
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) varparse(arg[iarg+3],3);
else zvalue = force->numeric(FLERR,arg[iarg+3]);
if (strstr(arg[iarg+4],"v_") == arg[iarg+4]) varparse(arg[iarg+4],4);
else wvalue = force->numeric(FLERR,arg[iarg+4]);
if (!atom->ellipsoid_flag && !atom->tri_flag && !atom->body_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(QUAT);
iarg += 5;
} else if (strcmp(arg[iarg],"quat/random") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
ivalue = force->inumeric(FLERR,arg[iarg+1]);
if (!atom->ellipsoid_flag && !atom->tri_flag && !atom->body_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
if (ivalue <= 0)
error->all(FLERR,"Invalid random number seed in set command");
setrandom(QUAT_RANDOM);
iarg += 2;
} else if (strcmp(arg[iarg],"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]);
dvalue *= MY_PI/180.0;
}
if (!atom->line_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(THETA);
iarg += 2;
} else if (strcmp(arg[iarg],"theta/random") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
ivalue = force->inumeric(FLERR,arg[iarg+1]);
if (!atom->line_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
if (ivalue <= 0)
error->all(FLERR,"Invalid random number seed in set command");
set(THETA_RANDOM);
iarg += 2;
} else if (strcmp(arg[iarg],"angmom") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal set command");
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
else xvalue = force->numeric(FLERR,arg[iarg+1]);
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) varparse(arg[iarg+2],2);
else yvalue = force->numeric(FLERR,arg[iarg+2]);
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) varparse(arg[iarg+3],3);
else zvalue = force->numeric(FLERR,arg[iarg+3]);
if (!atom->angmom_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(ANGMOM);
iarg += 4;
} else if (strcmp(arg[iarg],"omega") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal set command");
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
else xvalue = force->numeric(FLERR,arg[iarg+1]);
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) varparse(arg[iarg+2],2);
else yvalue = force->numeric(FLERR,arg[iarg+2]);
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) varparse(arg[iarg+3],3);
else zvalue = force->numeric(FLERR,arg[iarg+3]);
if (!atom->omega_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(OMEGA);
iarg += 4;
} else if (strcmp(arg[iarg],"diameter") == 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->radius_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(DIAMETER);
iarg += 2;
} else if (strcmp(arg[iarg],"density") == 0 ||
(strcmp(arg[iarg],"density/disc") == 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->rmass_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
if (dvalue <= 0.0) error->all(FLERR,"Invalid density in set command");
discflag = 0;
if (strcmp(arg[iarg],"density/disc") == 0) {
discflag = 1;
if (domain->dimension != 2)
error->all(FLERR,"Density/disc option requires 2d simulation");
}
set(DENSITY);
iarg += 2;
} else if (strcmp(arg[iarg],"volume") == 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->vfrac_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
if (dvalue <= 0.0) error->all(FLERR,"Invalid volume in set command");
set(VOLUME);
iarg += 2;
} else if (strcmp(arg[iarg],"image") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal set command");
ximageflag = yimageflag = zimageflag = 0;
if (strcmp(arg[iarg+1],"NULL") != 0) {
ximageflag = 1;
ximage = force->inumeric(FLERR,arg[iarg+1]);
}
if (strcmp(arg[iarg+2],"NULL") != 0) {
yimageflag = 1;
yimage = force->inumeric(FLERR,arg[iarg+2]);
}
if (strcmp(arg[iarg+3],"NULL") != 0) {
zimageflag = 1;
zimage = force->inumeric(FLERR,arg[iarg+3]);
}
if (ximageflag && ximage && !domain->xperiodic)
error->all(FLERR,
"Cannot set non-zero image flag for non-periodic dimension");
if (yimageflag && yimage && !domain->yperiodic)
error->all(FLERR,
"Cannot set non-zero image flag for non-periodic dimension");
if (zimageflag && zimage && !domain->zperiodic)
error->all(FLERR,
"Cannot set non-zero image flag for non-periodic dimension");
set(IMAGE);
iarg += 4;
} else if (strcmp(arg[iarg],"bond") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
ivalue = force->inumeric(FLERR,arg[iarg+1]);
if (atom->avec->bonds_allow == 0)
error->all(FLERR,"Cannot set this attribute for this atom style");
if (ivalue <= 0 || ivalue > atom->nbondtypes)
error->all(FLERR,"Invalid value in set command");
topology(BOND);
iarg += 2;
} else if (strcmp(arg[iarg],"angle") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
ivalue = force->inumeric(FLERR,arg[iarg+1]);
if (atom->avec->angles_allow == 0)
error->all(FLERR,"Cannot set this attribute for this atom style");
if (ivalue <= 0 || ivalue > atom->nangletypes)
error->all(FLERR,"Invalid value in set command");
topology(ANGLE);
iarg += 2;
} else if (strcmp(arg[iarg],"dihedral") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
ivalue = force->inumeric(FLERR,arg[iarg+1]);
if (atom->avec->dihedrals_allow == 0)
error->all(FLERR,"Cannot set this attribute for this atom style");
if (ivalue <= 0 || ivalue > atom->ndihedraltypes)
error->all(FLERR,"Invalid value in set command");
topology(DIHEDRAL);
iarg += 2;
} else if (strcmp(arg[iarg],"improper") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
ivalue = force->inumeric(FLERR,arg[iarg+1]);
if (atom->avec->impropers_allow == 0)
error->all(FLERR,"Cannot set this attribute for this atom style");
if (ivalue <= 0 || ivalue > atom->nimpropertypes)
error->all(FLERR,"Invalid value in set command");
topology(IMPROPER);
iarg += 2;
} 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 meso/e for this atom style");
set(MESO_E);
iarg += 2;
} 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 meso/cv for this atom style");
set(MESO_CV);
iarg += 2;
} 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");
set(MESO_RHO);
iarg += 2;
} 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");
set(SMD_MASS_DENSITY);
iarg += 2;
} 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");
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 (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->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);
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]) {
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]);
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);
iarg += 2;
} else if (strcmp(arg[iarg],"lambda") == 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->vfrac_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
if (dvalue < 0.0 && dvalue > 1.0) error->all(FLERR,"Invalid lambda in set command");
set(LAMBDA);
iarg += 2;
} else if (strcmp(arg[iarg],"temperature") == 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->vfrac_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
if (dvalue < 0.0) error->all(FLERR,"Invalid temperature in set command");
set(TEMPERATURE);
iarg += 2;
} else if (strcmp(arg[iarg],"chemPotential") == 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->vfrac_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
if (dvalue < 0.0) error->all(FLERR,"Invalid chemPotential in set command");
set(CHEMPOTENTIAL);
iarg += 2;
} else if (strcmp(arg[iarg],"concentration") == 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->vfrac_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
if (dvalue < 0.0) error->all(FLERR,"Invalid concentration in set command");
set(CONCENTRATION);
iarg += 2;
} else error->all(FLERR,"Illegal set command");
// statistics
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]);
}
}
// free local memory
delete [] id;
delete [] select;
}
/* ----------------------------------------------------------------------
select atoms according to ATOM, MOLECULE, TYPE, GROUP, REGION style
n = nlocal or nlocal+nghost depending on keyword
------------------------------------------------------------------------- */
void Set::selection(int n)
{
delete [] select;
select = new int[n];
int nlo,nhi;
if (style == ATOM_SELECT) {
if (atom->tag_enable == 0)
error->all(FLERR,"Cannot use set atom with no atom IDs defined");
bigint nlobig,nhibig;
force->boundsbig(FLERR,id,MAXTAGINT,nlobig,nhibig);
tagint *tag = atom->tag;
for (int i = 0; i < n; i++)
if (tag[i] >= nlobig && tag[i] <= nhibig) select[i] = 1;
else select[i] = 0;
} else if (style == MOL_SELECT) {
if (atom->molecule_flag == 0)
error->all(FLERR,"Cannot use set mol with no molecule IDs defined");
bigint nlobig,nhibig;
force->boundsbig(FLERR,id,MAXTAGINT,nlobig,nhibig);
tagint *molecule = atom->molecule;
for (int i = 0; i < n; i++)
if (molecule[i] >= nlobig && molecule[i] <= nhibig) select[i] = 1;
else select[i] = 0;
} else if (style == TYPE_SELECT) {
force->bounds(FLERR,id,atom->ntypes,nlo,nhi);
int *type = atom->type;
for (int i = 0; i < n; i++)
if (type[i] >= nlo && type[i] <= nhi) select[i] = 1;
else select[i] = 0;
} else if (style == GROUP_SELECT) {
int igroup = group->find(id);
if (igroup == -1) error->all(FLERR,"Could not find set group ID");
int groupbit = group->bitmask[igroup];
int *mask = atom->mask;
for (int i = 0; i < n; i++)
if (mask[i] & groupbit) select[i] = 1;
else select[i] = 0;
} else if (style == REGION_SELECT) {
int iregion = domain->find_region(id);
if (iregion == -1) error->all(FLERR,"Set region ID does not exist");
domain->regions[iregion]->prematch();
double **x = atom->x;
for (int i = 0; i < n; i++)
if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
select[i] = 1;
else select[i] = 0;
}
}
/* ----------------------------------------------------------------------
set owned atom properties directly
either scalar or per-atom values from atom-style variable(s)
------------------------------------------------------------------------- */
void Set::set(int keyword)
{
// evaluate atom-style variable(s) if necessary
vec1 = vec2 = vec3 = vec4 = NULL;
if (varflag) {
int nlocal = atom->nlocal;
if (varflag1) {
memory->create(vec1,nlocal,"set:vec1");
input->variable->compute_atom(ivar1,0,vec1,1,0);
}
if (varflag2) {
memory->create(vec2,nlocal,"set:vec2");
input->variable->compute_atom(ivar2,0,vec2,1,0);
}
if (varflag3) {
memory->create(vec3,nlocal,"set:vec3");
input->variable->compute_atom(ivar3,0,vec3,1,0);
}
if (varflag4) {
memory->create(vec4,nlocal,"set:vec4");
input->variable->compute_atom(ivar4,0,vec4,1,0);
}
}
// loop over selected atoms
AtomVecEllipsoid *avec_ellipsoid =
(AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecLine *avec_line = (AtomVecLine *) atom->style_match("line");
AtomVecTri *avec_tri = (AtomVecTri *) atom->style_match("tri");
AtomVecBody *avec_body = (AtomVecBody *) atom->style_match("body");
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
if (!select[i]) continue;
// overwrite dvalue, ivalue, xyzw value if variables defined
// else the input script scalar value remains in place
if (varflag) {
if (varflag1) {
dvalue = xvalue = vec1[i];
ivalue = static_cast<int> (dvalue);
}
if (varflag2) yvalue = vec2[i];
if (varflag3) zvalue = vec3[i];
if (varflag4) wvalue = vec4[i];
}
// set values in per-atom arrays
// error check here in case atom-style variables generated bogus value
if (keyword == TYPE) {
// atom->ntypes = 10;
if (ivalue <= 0 || ivalue > atom->ntypes)
error->one(FLERR,"Invalid value in set command");
atom->type[i] = ivalue;
}
else if (keyword == MOLECULE) atom->molecule[i] = ivalue;
else if (keyword == X) atom->x[i][0] = dvalue;
else if (keyword == Y) atom->x[i][1] = dvalue;
else if (keyword == Z) atom->x[i][2] = dvalue;
else if (keyword == CHARGE) atom->q[i] = dvalue;
else if (keyword == MASS) {
if (dvalue <= 0.0) error->one(FLERR,"Invalid mass in set command");
atom->rmass[i] = dvalue;
}
else if (keyword == DIAMETER) {
if (dvalue < 0.0) error->one(FLERR,"Invalid diameter in set command");
atom->radius[i] = 0.5 * dvalue;
}
else if (keyword == VOLUME) {
if (dvalue <= 0.0) error->one(FLERR,"Invalid volume in set command");
atom->vfrac[i] = dvalue;
}
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 == SMD_MASS_DENSITY) {
// set mass from volume and supplied mass density
atom->rmass[i] = atom->vfrac[i] * dvalue;
}
else if (keyword == SMD_CONTACT_RADIUS) atom->contact_radius[i] = dvalue;
else if (keyword == DPDTHETA) {
if (dvalue >= 0.0) atom->dpdTheta[i] = dvalue;
else {
double onemass;
if (atom->rmass) onemass = atom->rmass[i];
else onemass = atom->mass[atom->type[i]];
double vx = atom->v[i][0];
double vy = atom->v[i][1];
double vz = atom->v[i][2];
double tfactor = force->mvv2e / (domain->dimension * force->boltz);
atom->dpdTheta[i] = tfactor * onemass * (vx*vx + vy*vy + vz*vz);
}
}
// set shape of ellipsoidal particle
else if (keyword == SHAPE) {
if (xvalue < 0.0 || yvalue < 0.0 || zvalue < 0.0)
error->one(FLERR,"Invalid shape in set command");
if (xvalue > 0.0 || yvalue > 0.0 || zvalue > 0.0) {
if (xvalue == 0.0 || yvalue == 0.0 || zvalue == 0.0)
error->one(FLERR,"Invalid shape in set command");
}
avec_ellipsoid->set_shape(i,0.5*xvalue,0.5*yvalue,0.5*zvalue);
}
// set length of line particle
else if (keyword == LENGTH) {
if (dvalue < 0.0) error->one(FLERR,"Invalid length in set command");
avec_line->set_length(i,dvalue);
}
// set corners of tri particle
else if (keyword == TRI) {
if (dvalue < 0.0) error->one(FLERR,"Invalid length in set command");
avec_tri->set_equilateral(i,dvalue);
}
// set rmass via density
// if radius > 0.0, treat as sphere or disc
// if shape > 0.0, treat as ellipsoid (or ellipse, when uncomment below)
// if length > 0.0, treat as line
// if area > 0.0, treat as tri
// else set rmass to density directly
else if (keyword == DENSITY) {
if (dvalue <= 0.0) error->one(FLERR,"Invalid density in set command");
if (atom->radius_flag && atom->radius[i] > 0.0)
if (discflag)
atom->rmass[i] = MY_PI*atom->radius[i]*atom->radius[i] * dvalue;
else
atom->rmass[i] = 4.0*MY_PI/3.0 *
atom->radius[i]*atom->radius[i]*atom->radius[i] * dvalue;
else if (atom->ellipsoid_flag && atom->ellipsoid[i] >= 0) {
double *shape = avec_ellipsoid->bonus[atom->ellipsoid[i]].shape;
// enable 2d ellipse (versus 3d ellipsoid) when time integration
// options (fix nve/asphere, fix nh/asphere) are also implemented
// if (discflag)
// atom->rmass[i] = MY_PI*shape[0]*shape[1] * dvalue;
// else
atom->rmass[i] = 4.0*MY_PI/3.0 * shape[0]*shape[1]*shape[2] * dvalue;
} else if (atom->line_flag && atom->line[i] >= 0) {
double length = avec_line->bonus[atom->line[i]].length;
atom->rmass[i] = length * dvalue;
} else if (atom->tri_flag && atom->tri[i] >= 0) {
double *c1 = avec_tri->bonus[atom->tri[i]].c1;
double *c2 = avec_tri->bonus[atom->tri[i]].c2;
double *c3 = avec_tri->bonus[atom->tri[i]].c3;
double c2mc1[3],c3mc1[3];
MathExtra::sub3(c2,c1,c2mc1);
MathExtra::sub3(c3,c1,c3mc1);
double norm[3];
MathExtra::cross3(c2mc1,c3mc1,norm);
double area = 0.5 * MathExtra::len3(norm);
atom->rmass[i] = area * dvalue;
} else atom->rmass[i] = dvalue;
}
// set dipole moment
else if (keyword == DIPOLE) {
double **mu = atom->mu;
mu[i][0] = xvalue;
mu[i][1] = yvalue;
mu[i][2] = zvalue;
mu[i][3] = sqrt(mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1] +
mu[i][2]*mu[i][2]);
}
// set quaternion orientation of ellipsoid or tri or body particle
// enforce quat rotation vector in z dir for 2d systems
else if (keyword == QUAT) {
double *quat;
if (avec_ellipsoid && atom->ellipsoid[i] >= 0)
quat = avec_ellipsoid->bonus[atom->ellipsoid[i]].quat;
else if (avec_tri && atom->tri[i] >= 0)
quat = avec_tri->bonus[atom->tri[i]].quat;
else if (avec_body && atom->body[i] >= 0)
quat = avec_body->bonus[atom->body[i]].quat;
else
error->one(FLERR,"Cannot set quaternion for atom that has none");
if (domain->dimension == 2 && (xvalue != 0.0 || yvalue != 0.0))
error->one(FLERR,"Cannot set quaternion with xy components "
"for 2d system");
double theta2 = MY_PI2 * wvalue/180.0;
double sintheta2 = sin(theta2);
quat[0] = cos(theta2);
quat[1] = xvalue * sintheta2;
quat[2] = yvalue * sintheta2;
quat[3] = zvalue * sintheta2;
MathExtra::qnormalize(quat);
}
// set theta of line particle
else if (keyword == THETA) {
if (atom->line[i] < 0)
error->one(FLERR,"Cannot set theta for atom that is not a line");
avec_line->bonus[atom->line[i]].theta = dvalue;
}
// set angmom or omega of particle
else if (keyword == ANGMOM) {
atom->angmom[i][0] = xvalue;
atom->angmom[i][1] = yvalue;
atom->angmom[i][2] = zvalue;
}
else if (keyword == OMEGA) {
atom->omega[i][0] = xvalue;
atom->omega[i][1] = yvalue;
atom->omega[i][2] = zvalue;
}
// reset any or all of 3 image flags
else if (keyword == IMAGE) {
int xbox = (atom->image[i] & IMGMASK) - IMGMAX;
int ybox = (atom->image[i] >> IMGBITS & IMGMASK) - IMGMAX;
int zbox = (atom->image[i] >> IMG2BITS) - IMGMAX;
if (ximageflag) xbox = ximage;
if (yimageflag) ybox = yimage;
if (zimageflag) zbox = zimage;
atom->image[i] = ((imageint) (xbox + IMGMAX) & IMGMASK) |
(((imageint) (ybox + IMGMAX) & IMGMASK) << IMGBITS) |
(((imageint) (zbox + IMGMAX) & IMGMASK) << IMG2BITS);
}
// set value for custom integer or double vector
else if (keyword == INAME) {
atom->ivector[index_custom][i] = ivalue;
}
else if (keyword == DNAME) {
atom->dvector[index_custom][i] = dvalue;
}
else if (keyword == LAMBDA) {
if (dvalue < 0.0 && dvalue > 1.0) error->one(FLERR,"Invalid lambda in set command");
atom->lambda[i] = dvalue;
}
else if (keyword == TEMPERATURE) {
if (dvalue < 0.0) error->one(FLERR,"Invalid temperature in set command");
atom->temperature[i] = dvalue;
}
else if (keyword == CHEMPOTENTIAL) {
if (dvalue < 0.0) error->one(FLERR,"Invalid chemPotential in set command");
atom->chemPotential[i] = dvalue;
}
else if (keyword == CONCENTRATION) {
if (dvalue < 0.0) error->one(FLERR,"Invalid concentration in set command");
atom->concentration[i] = dvalue;
}
count++;
}
// clear up per-atom memory if allocated
memory->destroy(vec1);
memory->destroy(vec2);
memory->destroy(vec3);
memory->destroy(vec4);
}
/* ----------------------------------------------------------------------
set an owned atom property randomly
set seed based on atom coordinates
make atom result independent of what proc owns it
------------------------------------------------------------------------- */
void Set::setrandom(int keyword)
{
int i;
AtomVecEllipsoid *avec_ellipsoid =
(AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecLine *avec_line = (AtomVecLine *) atom->style_match("line");
AtomVecTri *avec_tri = (AtomVecTri *) atom->style_match("tri");
AtomVecBody *avec_body = (AtomVecBody *) atom->style_match("body");
RanPark *random = new RanPark(lmp,1);
double **x = atom->x;
int seed = ivalue;
// set fraction of atom types to newtype
if (keyword == TYPE_FRACTION) {
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
if (select[i]) {
random->reset(seed,x[i]);
if (random->uniform() > fraction) continue;
atom->type[i] = newtype;
count++;
}
// set dipole moments to random orientations in 3d or 2d
// dipole length is determined by dipole type array
} else if (keyword == DIPOLE_RANDOM) {
double **mu = atom->mu;
int nlocal = atom->nlocal;
double msq,scale;
if (domain->dimension == 3) {
for (i = 0; i < nlocal; i++)
if (select[i]) {
random->reset(seed,x[i]);
mu[i][0] = random->uniform() - 0.5;
mu[i][1] = random->uniform() - 0.5;
mu[i][2] = random->uniform() - 0.5;
msq = mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1] + mu[i][2]*mu[i][2];
scale = dvalue/sqrt(msq);
mu[i][0] *= scale;
mu[i][1] *= scale;
mu[i][2] *= scale;
mu[i][3] = dvalue;
count++;
}
} else {
for (i = 0; i < nlocal; i++)
if (select[i]) {
random->reset(seed,x[i]);
mu[i][0] = random->uniform() - 0.5;
mu[i][1] = random->uniform() - 0.5;
mu[i][2] = 0.0;
msq = mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1];
scale = dvalue/sqrt(msq);
mu[i][0] *= scale;
mu[i][1] *= scale;
mu[i][3] = dvalue;
count++;
}
}
// set quaternions to random orientations in 3d and 2d
} else if (keyword == QUAT_RANDOM) {
int nlocal = atom->nlocal;
double *quat;
if (domain->dimension == 3) {
double s,t1,t2,theta1,theta2;
for (i = 0; i < nlocal; i++)
if (select[i]) {
if (avec_ellipsoid && atom->ellipsoid[i] >= 0)
quat = avec_ellipsoid->bonus[atom->ellipsoid[i]].quat;
else if (avec_tri && atom->tri[i] >= 0)
quat = avec_tri->bonus[atom->tri[i]].quat;
else if (avec_body && atom->body[i] >= 0)
quat = avec_body->bonus[atom->body[i]].quat;
else
error->one(FLERR,"Cannot set quaternion for atom that has none");
random->reset(seed,x[i]);
s = random->uniform();
t1 = sqrt(1.0-s);
t2 = sqrt(s);
theta1 = 2.0*MY_PI*random->uniform();
theta2 = 2.0*MY_PI*random->uniform();
quat[0] = cos(theta2)*t2;
quat[1] = sin(theta1)*t1;
quat[2] = cos(theta1)*t1;
quat[3] = sin(theta2)*t2;
count++;
}
} else {
double theta2;
for (i = 0; i < nlocal; i++)
if (select[i]) {
if (avec_ellipsoid && atom->ellipsoid[i] >= 0)
quat = avec_ellipsoid->bonus[atom->ellipsoid[i]].quat;
else if (avec_body && atom->body[i] >= 0)
quat = avec_body->bonus[atom->body[i]].quat;
else
error->one(FLERR,"Cannot set quaternion for atom that has none");
random->reset(seed,x[i]);
theta2 = MY_PI*random->uniform();