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This commit is contained in:
Steve Plimpton
2021-01-11 16:13:33 -07:00
parent 64257393b9 102a6eba79
commit 0b14770468
3275 changed files with 181008 additions and 818336 deletions
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197
src/set.cpp
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@ -1,6 +1,6 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
https://lammps.sandia.gov/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
@ -12,32 +12,30 @@
------------------------------------------------------------------------- */
#include "set.h"
#include <mpi.h>
#include <cmath>
#include <cstring>
#include <climits>
#include "atom.h"
#include "atom_vec.h"
#include "atom_vec_body.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 "force.h"
#include "input.h"
#include "variable.h"
#include "random_park.h"
#include "random_mars.h"
#include "math_extra.h"
#include "math_const.h"
#include "memory.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "group.h"
#include "input.h"
#include "math_const.h"
#include "math_extra.h"
#include "memory.h"
#include "modify.h"
#include "utils.h"
#include "fmt/format.h"
#include "random_mars.h"
#include "random_park.h"
#include "region.h"
#include "variable.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;
@ -76,7 +74,7 @@ void Set::command(int narg, char **arg)
int n = strlen(arg[1]) + 1;
id = new char[n];
strcpy(id,arg[1]);
select = NULL;
select = nullptr;
selection(atom->nlocal);
// loop over keyword/value pairs
@ -95,15 +93,15 @@ void Set::command(int narg, char **arg)
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]);
else ivalue = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
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]);
newtype = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
fraction = utils::numeric(FLERR,arg[iarg+2],false,lmp);
ivalue = utils::inumeric(FLERR,arg[iarg+3],false,lmp);
if (newtype <= 0 || newtype > atom->ntypes)
error->all(FLERR,"Invalid value in set command");
if (fraction < 0.0 || fraction > 1.0)
@ -115,9 +113,9 @@ void Set::command(int narg, char **arg)
} else if (strcmp(arg[iarg],"type/ratio") == 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]);
newtype = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
fraction = utils::numeric(FLERR,arg[iarg+2],false,lmp);
ivalue = utils::inumeric(FLERR,arg[iarg+3],false,lmp);
if (newtype <= 0 || newtype > atom->ntypes)
error->all(FLERR,"Invalid value in set command");
if (fraction < 0.0 || fraction > 1.0)
@ -129,9 +127,9 @@ void Set::command(int narg, char **arg)
} else if (strcmp(arg[iarg],"type/subset") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal set command");
newtype = force->inumeric(FLERR,arg[iarg+1]);
nsubset = force->bnumeric(FLERR,arg[iarg+2]);
ivalue = force->inumeric(FLERR,arg[iarg+3]);
newtype = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
nsubset = utils::bnumeric(FLERR,arg[iarg+2],false,lmp);
ivalue = utils::inumeric(FLERR,arg[iarg+3],false,lmp);
if (newtype <= 0 || newtype > atom->ntypes)
error->all(FLERR,"Invalid value in set command");
if (nsubset < 0)
@ -144,7 +142,7 @@ void Set::command(int narg, char **arg)
} 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]);
else ivalue = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (!atom->molecule_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(MOLECULE);
@ -153,49 +151,49 @@ void Set::command(int narg, char **arg)
} 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]);
else dvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
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]);
else dvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
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]);
else dvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
set(Z);
iarg += 2;
} else if (strcmp(arg[iarg],"vx") == 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]);
else dvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
set(VX);
iarg += 2;
} else if (strcmp(arg[iarg],"vy") == 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]);
else dvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
set(VY);
iarg += 2;
} else if (strcmp(arg[iarg],"vz") == 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]);
else dvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
set(VZ);
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]);
else dvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
if (!atom->q_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(CHARGE);
@ -204,7 +202,7 @@ void Set::command(int narg, char **arg)
} 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]);
else dvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
if (!atom->rmass_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(MASS);
@ -213,11 +211,11 @@ void Set::command(int narg, char **arg)
} 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]);
else xvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) varparse(arg[iarg+2],2);
else yvalue = force->numeric(FLERR,arg[iarg+2]);
else yvalue = utils::numeric(FLERR,arg[iarg+2],false,lmp);
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) varparse(arg[iarg+3],3);
else zvalue = force->numeric(FLERR,arg[iarg+3]);
else zvalue = utils::numeric(FLERR,arg[iarg+3],false,lmp);
if (!atom->ellipsoid_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(SHAPE);
@ -226,7 +224,7 @@ void Set::command(int narg, char **arg)
} 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]);
else dvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
if (!atom->line_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(LENGTH);
@ -235,7 +233,7 @@ void Set::command(int narg, char **arg)
} 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]);
else dvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
if (!atom->tri_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(TRI);
@ -244,11 +242,11 @@ void Set::command(int narg, char **arg)
} 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]);
else xvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) varparse(arg[iarg+2],2);
else yvalue = force->numeric(FLERR,arg[iarg+2]);
else yvalue = utils::numeric(FLERR,arg[iarg+2],false,lmp);
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) varparse(arg[iarg+3],3);
else zvalue = force->numeric(FLERR,arg[iarg+3]);
else zvalue = utils::numeric(FLERR,arg[iarg+3],false,lmp);
if (!atom->mu_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(DIPOLE);
@ -256,8 +254,8 @@ void Set::command(int narg, char **arg)
} 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]);
ivalue = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
dvalue = utils::numeric(FLERR,arg[iarg+2],false,lmp);
if (!atom->mu_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
if (ivalue <= 0)
@ -270,13 +268,13 @@ void Set::command(int narg, char **arg)
} else if (strcmp(arg[iarg],"spin") == 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 dvalue = force->numeric(FLERR,arg[iarg+1]);
else dvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) varparse(arg[iarg+2],2);
else xvalue = force->numeric(FLERR,arg[iarg+2]);
else xvalue = utils::numeric(FLERR,arg[iarg+2],false,lmp);
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) varparse(arg[iarg+3],3);
else yvalue = force->numeric(FLERR,arg[iarg+3]);
else yvalue = utils::numeric(FLERR,arg[iarg+3],false,lmp);
if (strstr(arg[iarg+4],"v_") == arg[iarg+4]) varparse(arg[iarg+4],4);
else zvalue = force->numeric(FLERR,arg[iarg+4]);
else zvalue = utils::numeric(FLERR,arg[iarg+4],false,lmp);
if (!atom->sp_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(SPIN);
@ -284,8 +282,8 @@ void Set::command(int narg, char **arg)
} else if (strcmp(arg[iarg],"spin/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]);
ivalue = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
dvalue = utils::numeric(FLERR,arg[iarg+2],false,lmp);
if (!atom->sp_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
if (ivalue <= 0)
@ -298,13 +296,13 @@ void Set::command(int narg, char **arg)
} 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]);
else xvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) varparse(arg[iarg+2],2);
else yvalue = force->numeric(FLERR,arg[iarg+2]);
else yvalue = utils::numeric(FLERR,arg[iarg+2],false,lmp);
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) varparse(arg[iarg+3],3);
else zvalue = force->numeric(FLERR,arg[iarg+3]);
else zvalue = utils::numeric(FLERR,arg[iarg+3],false,lmp);
if (strstr(arg[iarg+4],"v_") == arg[iarg+4]) varparse(arg[iarg+4],4);
else wvalue = force->numeric(FLERR,arg[iarg+4]);
else wvalue = utils::numeric(FLERR,arg[iarg+4],false,lmp);
if (!atom->ellipsoid_flag && !atom->tri_flag && !atom->body_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(QUAT);
@ -312,7 +310,7 @@ void Set::command(int narg, char **arg)
} 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]);
ivalue = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (!atom->ellipsoid_flag && !atom->tri_flag && !atom->body_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
if (ivalue <= 0)
@ -324,7 +322,7 @@ void Set::command(int narg, char **arg)
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 = utils::numeric(FLERR,arg[iarg+1],false,lmp);
dvalue *= MY_PI/180.0;
}
if (!atom->line_flag)
@ -334,7 +332,7 @@ void Set::command(int narg, char **arg)
} 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]);
ivalue = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (!atom->line_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
if (ivalue <= 0)
@ -345,11 +343,11 @@ void Set::command(int narg, char **arg)
} 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]);
else xvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) varparse(arg[iarg+2],2);
else yvalue = force->numeric(FLERR,arg[iarg+2]);
else yvalue = utils::numeric(FLERR,arg[iarg+2],false,lmp);
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) varparse(arg[iarg+3],3);
else zvalue = force->numeric(FLERR,arg[iarg+3]);
else zvalue = utils::numeric(FLERR,arg[iarg+3],false,lmp);
if (!atom->angmom_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(ANGMOM);
@ -358,11 +356,11 @@ void Set::command(int narg, char **arg)
} 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]);
else xvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) varparse(arg[iarg+2],2);
else yvalue = force->numeric(FLERR,arg[iarg+2]);
else yvalue = utils::numeric(FLERR,arg[iarg+2],false,lmp);
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) varparse(arg[iarg+3],3);
else zvalue = force->numeric(FLERR,arg[iarg+3]);
else zvalue = utils::numeric(FLERR,arg[iarg+3],false,lmp);
if (!atom->omega_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(OMEGA);
@ -371,7 +369,7 @@ void Set::command(int narg, char **arg)
} 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]);
else dvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
if (!atom->radius_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
set(DIAMETER);
@ -381,7 +379,7 @@ void Set::command(int narg, char **arg)
(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]);
else dvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
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");
@ -397,7 +395,7 @@ void Set::command(int narg, char **arg)
} 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]);
else dvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
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");
@ -410,17 +408,17 @@ void Set::command(int narg, char **arg)
if (strcmp(arg[iarg+1],"NULL") != 0) {
ximageflag = 1;
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
else ximage = force->inumeric(FLERR,arg[iarg+1]);
else ximage = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
}
if (strcmp(arg[iarg+2],"NULL") != 0) {
yimageflag = 1;
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) varparse(arg[iarg+2],2);
else yimage = force->inumeric(FLERR,arg[iarg+2]);
else yimage = utils::inumeric(FLERR,arg[iarg+2],false,lmp);
}
if (strcmp(arg[iarg+3],"NULL") != 0) {
zimageflag = 1;
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) varparse(arg[iarg+3],3);
else zimage = force->inumeric(FLERR,arg[iarg+3]);
else zimage = utils::inumeric(FLERR,arg[iarg+3],false,lmp);
}
if (ximageflag && ximage && !domain->xperiodic)
error->all(FLERR,
@ -436,7 +434,7 @@ void Set::command(int narg, char **arg)
} else if (strcmp(arg[iarg],"bond") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
ivalue = force->inumeric(FLERR,arg[iarg+1]);
ivalue = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (atom->avec->bonds_allow == 0)
error->all(FLERR,"Cannot set this attribute for this atom style");
if (ivalue <= 0 || ivalue > atom->nbondtypes)
@ -446,7 +444,7 @@ void Set::command(int narg, char **arg)
} else if (strcmp(arg[iarg],"angle") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
ivalue = force->inumeric(FLERR,arg[iarg+1]);
ivalue = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (atom->avec->angles_allow == 0)
error->all(FLERR,"Cannot set this attribute for this atom style");
if (ivalue <= 0 || ivalue > atom->nangletypes)
@ -456,7 +454,7 @@ void Set::command(int narg, char **arg)
} else if (strcmp(arg[iarg],"dihedral") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
ivalue = force->inumeric(FLERR,arg[iarg+1]);
ivalue = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (atom->avec->dihedrals_allow == 0)
error->all(FLERR,"Cannot set this attribute for this atom style");
if (ivalue <= 0 || ivalue > atom->ndihedraltypes)
@ -466,7 +464,7 @@ void Set::command(int narg, char **arg)
} else if (strcmp(arg[iarg],"improper") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
ivalue = force->inumeric(FLERR,arg[iarg+1]);
ivalue = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
if (atom->avec->impropers_allow == 0)
error->all(FLERR,"Cannot set this attribute for this atom style");
if (ivalue <= 0 || ivalue > atom->nimpropertypes)
@ -477,7 +475,7 @@ void Set::command(int narg, char **arg)
} else if (strcmp(arg[iarg],"sph/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]);
else dvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
if (!atom->esph_flag)
error->all(FLERR,"Cannot set meso/e for this atom style");
set(SPH_E);
@ -486,7 +484,7 @@ void Set::command(int narg, char **arg)
} else if (strcmp(arg[iarg],"sph/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]);
else dvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
if (!atom->cv_flag)
error->all(FLERR,"Cannot set meso/cv for this atom style");
set(SPH_CV);
@ -495,7 +493,7 @@ void Set::command(int narg, char **arg)
} else if (strcmp(arg[iarg],"sph/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]);
else dvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
if (!atom->rho_flag)
error->all(FLERR,"Cannot set meso/rho for this atom style");
set(SPH_RHO);
@ -506,7 +504,7 @@ void Set::command(int narg, char **arg)
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]);
dvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
if (dvalue < 0.0) error->all(FLERR,"Illegal set command");
}
if (!atom->edpd_flag)
@ -519,7 +517,7 @@ void Set::command(int narg, char **arg)
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]);
dvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
if (dvalue < 0.0) error->all(FLERR,"Illegal set command");
}
if (!atom->edpd_flag)
@ -532,8 +530,8 @@ void Set::command(int narg, char **arg)
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]);
cc_index = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
dvalue = utils::numeric(FLERR,arg[iarg+2],false,lmp);
if (cc_index < 1) error->all(FLERR,"Illegal set command");
}
if (!atom->tdpd_flag)
@ -544,7 +542,7 @@ void Set::command(int narg, char **arg)
} 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]);
else dvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
if (!atom->smd_flag)
error->all(FLERR,"Cannot set smd/mass/density for this atom style");
set(SMD_MASS_DENSITY);
@ -553,7 +551,7 @@ void Set::command(int narg, char **arg)
} 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]);
else dvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
if (!atom->smd_flag)
error->all(FLERR,"Cannot set smd/contact/radius "
"for this atom style");
@ -565,7 +563,7 @@ void Set::command(int narg, char **arg)
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]);
dvalue = utils::numeric(FLERR,arg[iarg+1],false,lmp);
if (dvalue < 0.0) error->all(FLERR,"Illegal set command");
}
if (!atom->dpd_flag)
@ -668,7 +666,7 @@ void Set::selection(int n)
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);
utils::bounds(FLERR,id,1,MAXTAGINT,nlobig,nhibig,error);
tagint *tag = atom->tag;
for (int i = 0; i < n; i++)
@ -679,7 +677,7 @@ void Set::selection(int n)
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);
utils::bounds(FLERR,id,1,MAXTAGINT,nlobig,nhibig,error);
tagint *molecule = atom->molecule;
for (int i = 0; i < n; i++)
@ -687,7 +685,7 @@ void Set::selection(int n)
else select[i] = 0;
} else if (style == TYPE_SELECT) {
force->bounds(FLERR,id,atom->ntypes,nlo,nhi);
utils::bounds(FLERR,id,1,atom->ntypes,nlo,nhi,error);
int *type = atom->type;
for (int i = 0; i < n; i++)
@ -726,7 +724,7 @@ void Set::set(int keyword)
{
// evaluate atom-style variable(s) if necessary
vec1 = vec2 = vec3 = vec4 = NULL;
vec1 = vec2 = vec3 = vec4 = nullptr;
if (varflag) {
int nlocal = atom->nlocal;
@ -944,7 +942,7 @@ void Set::set(int keyword)
// enforce quat rotation vector in z dir for 2d systems
else if (keyword == QUAT) {
double *quat = NULL;
double *quat = nullptr;
if (avec_ellipsoid && atom->ellipsoid[i] >= 0)
quat = avec_ellipsoid->bonus[atom->ellipsoid[i]].quat;
else if (avec_tri && atom->tri[i] >= 0)
@ -1300,7 +1298,7 @@ void Set::topology(int keyword)
// error check
if (atom->molecular == 2)
if (atom->molecular == Atom::TEMPLATE)
error->all(FLERR,"Cannot set bond topology types for atom style template");
// border swap to acquire ghost atom info
@ -1397,17 +1395,10 @@ void Set::topology(int keyword)
/* ---------------------------------------------------------------------- */
void Set::varparse(char *name, int m)
void Set::varparse(const char *name, int m)
{
varflag = 1;
name = &name[2];
int n = strlen(name) + 1;
char *str = new char[n];
strcpy(str,name);
int ivar = input->variable->find(str);
delete [] str;
int ivar = input->variable->find(name+2);
if (ivar < 0)
error->all(FLERR,"Variable name for set command does not exist");