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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2012-06-06 22:47:51 +00:00
parent f46eb9dedb
commit ef9e700545
1408 changed files with 58053 additions and 57983 deletions
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362
src/set.cpp
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@ -5,7 +5,7 @@
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
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.
@ -79,12 +79,12 @@ void Set::command(int narg, char **arg)
while (iarg < narg) {
count = 0;
origarg = iarg;
if (strcmp(arg[iarg],"type") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (ivalue <= 0 || ivalue > atom->ntypes)
error->all(FLERR,"Invalid value in set command");
error->all(FLERR,"Invalid value in set command");
set(TYPE);
iarg += 2;
} else if (strcmp(arg[iarg],"type/fraction") == 0) {
@ -93,18 +93,18 @@ void Set::command(int narg, char **arg)
fraction = atof(arg[iarg+2]);
ivalue = atoi(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");
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");
ivalue = atoi(arg[iarg+1]);
if (!atom->molecule_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
error->all(FLERR,"Cannot set this attribute for this atom style");
set(MOLECULE);
iarg += 2;
} else if (strcmp(arg[iarg],"x") == 0) {
@ -126,14 +126,14 @@ void Set::command(int narg, char **arg)
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
dvalue = atof(arg[iarg+1]);
if (!atom->q_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
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");
dvalue = atof(arg[iarg+1]);
if (!atom->rmass_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
error->all(FLERR,"Cannot set this attribute for this atom style");
if (dvalue <= 0.0) error->all(FLERR,"Invalid mass in set command");
set(MASS);
iarg += 2;
@ -143,12 +143,12 @@ void Set::command(int narg, char **arg)
yvalue = atof(arg[iarg+2]);
zvalue = atof(arg[iarg+3]);
if (!atom->ellipsoid_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
error->all(FLERR,"Cannot set this attribute for this atom style");
if (xvalue < 0.0 || yvalue < 0.0 || zvalue < 0.0)
error->all(FLERR,"Invalid shape in set command");
error->all(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");
if (xvalue == 0.0 || yvalue == 0.0 || zvalue == 0.0)
error->one(FLERR,"Invalid shape in set command");
}
set(SHAPE);
iarg += 4;
@ -174,7 +174,7 @@ void Set::command(int narg, char **arg)
yvalue = atof(arg[iarg+2]);
zvalue = atof(arg[iarg+3]);
if (!atom->mu_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
error->all(FLERR,"Cannot set this attribute for this atom style");
set(DIPOLE);
iarg += 4;
} else if (strcmp(arg[iarg],"dipole/random") == 0) {
@ -182,11 +182,11 @@ void Set::command(int narg, char **arg)
ivalue = atoi(arg[iarg+1]);
dvalue = atof(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");
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) {
@ -196,16 +196,16 @@ void Set::command(int narg, char **arg)
zvalue = atof(arg[iarg+3]);
wvalue = atof(arg[iarg+4]);
if (!atom->ellipsoid_flag && !atom->tri_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
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 = atoi(arg[iarg+1]);
if (!atom->ellipsoid_flag && !atom->tri_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");
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) {
@ -251,96 +251,96 @@ void Set::command(int narg, char **arg)
if (iarg+4 > narg) error->all(FLERR,"Illegal set command");
ximageflag = yimageflag = zimageflag = 0;
if (strcmp(arg[iarg+1],"NULL") != 0) {
ximageflag = 1;
ximage = atoi(arg[iarg+1]);
ximageflag = 1;
ximage = atoi(arg[iarg+1]);
}
if (strcmp(arg[iarg+2],"NULL") != 0) {
yimageflag = 1;
yimage = atoi(arg[iarg+2]);
yimageflag = 1;
yimage = atoi(arg[iarg+2]);
}
if (strcmp(arg[iarg+3],"NULL") != 0) {
zimageflag = 1;
zimage = atoi(arg[iarg+3]);
zimageflag = 1;
zimage = atoi(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");
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 = atoi(arg[iarg+1]);
if (atom->avec->bonds_allow == 0)
error->all(FLERR,"Cannot set this attribute for this atom style");
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");
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 = atoi(arg[iarg+1]);
if (atom->avec->angles_allow == 0)
error->all(FLERR,"Cannot set this attribute for this atom style");
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");
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 = atoi(arg[iarg+1]);
if (atom->avec->dihedrals_allow == 0)
error->all(FLERR,"Cannot set this attribute for this atom style");
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");
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 = atoi(arg[iarg+1]);
if (atom->avec->impropers_allow == 0)
error->all(FLERR,"Cannot set this attribute for this atom style");
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");
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");
dvalue = atof(arg[iarg+1]);
if (!atom->e_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
error->all(FLERR,"Cannot set this attribute 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");
dvalue = atof(arg[iarg+1]);
if (!atom->cv_flag)
error->all(FLERR,"Cannot set this attribute for this atom style");
error->all(FLERR,"Cannot set this attribute 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");
dvalue = atof(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 error->all(FLERR,"Illegal set command");
} 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]);
allcount,arg[origarg]);
if (logfile) fprintf(logfile," %d settings made for %s\n",
allcount,arg[origarg]);
allcount,arg[origarg]);
}
}
@ -407,7 +407,7 @@ void Set::selection(int n)
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;
select[i] = 1;
else select[i] = 0;
}
}
@ -418,7 +418,7 @@ void Set::selection(int n)
void Set::set(int keyword)
{
AtomVecEllipsoid *avec_ellipsoid =
AtomVecEllipsoid *avec_ellipsoid =
(AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecLine *avec_line = (AtomVecLine *) atom->style_match("line");
AtomVecTri *avec_tri = (AtomVecTri *) atom->style_match("tri");
@ -466,29 +466,29 @@ void Set::set(int keyword)
else if (keyword == DENSITY) {
if (atom->radius_flag && atom->radius[i] > 0.0)
atom->rmass[i] = 4.0*MY_PI/3.0 *
atom->radius[i]*atom->radius[i]*atom->radius[i] * dvalue;
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;
atom->rmass[i] = 4.0*MY_PI/3.0 * shape[0]*shape[1]*shape[2] * dvalue;
double *shape = avec_ellipsoid->bonus[atom->ellipsoid[i]].shape;
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;
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[2],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;
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[2],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;
// reset any or all of 3 image flags
} else if (keyword == IMAGE) {
int xbox = (atom->image[i] & 1023) - 512;
int ybox = (atom->image[i] >> 10 & 1023) - 512;
@ -497,28 +497,28 @@ void Set::set(int keyword)
if (yimageflag) ybox = yimage;
if (zimageflag) zbox = zimage;
atom->image[i] = ((zbox + 512 & 1023) << 20) |
((ybox + 512 & 1023) << 10) | (xbox + 512 & 1023);
((ybox + 512 & 1023) << 10) | (xbox + 512 & 1023);
// 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]);
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 particle
} else if (keyword == QUAT) {
double *quat;
if (avec_ellipsoid && atom->ellipsoid[i] >= 0)
quat = avec_ellipsoid->bonus[atom->ellipsoid[i]].quat;
quat = avec_ellipsoid->bonus[atom->ellipsoid[i]].quat;
else if (avec_tri && atom->tri[i] >= 0)
quat = avec_tri->bonus[atom->tri[i]].quat;
quat = avec_tri->bonus[atom->tri[i]].quat;
else
error->one(FLERR,"Cannot set quaternion for atom that has none");
error->one(FLERR,"Cannot set quaternion for atom that has none");
double theta2 = MY_PI2 * wvalue/180.0;
double sintheta2 = sin(theta2);
@ -532,7 +532,7 @@ void Set::set(int keyword)
} else if (keyword == THETA) {
if (atom->line[i] < 0)
error->one(FLERR,"Cannot set theta for atom that is not a line");
error->one(FLERR,"Cannot set theta for atom that is not a line");
avec_line->bonus[atom->line[i]].theta = dvalue;
// set angmom of ellipsoidal or tri particle
@ -557,7 +557,7 @@ void Set::setrandom(int keyword)
{
int i;
AtomVecEllipsoid *avec_ellipsoid =
AtomVecEllipsoid *avec_ellipsoid =
(AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecLine *avec_line = (AtomVecLine *) atom->style_match("line");
AtomVecTri *avec_tri = (AtomVecTri *) atom->style_match("tri");
@ -574,9 +574,9 @@ void Set::setrandom(int keyword)
for (i = 0; i < nlocal; i++)
if (select[i]) {
random->reset(seed,x[i]);
if (random->uniform() > fraction) continue;
atom->type[i] = newtype;
random->reset(seed,x[i]);
if (random->uniform() > fraction) continue;
atom->type[i] = newtype;
count++;
}
@ -591,34 +591,34 @@ void Set::setrandom(int keyword)
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++;
}
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++;
}
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 or 2d
@ -632,44 +632,44 @@ void Set::setrandom(int keyword)
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
error->one(FLERR,"Cannot set quaternion for atom that has none");
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
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++;
}
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
error->one(FLERR,"Cannot set quaternion for atom that has none");
if (select[i]) {
if (avec_ellipsoid && atom->ellipsoid[i] >= 0)
quat = avec_ellipsoid->bonus[atom->ellipsoid[i]].quat;
else
error->one(FLERR,"Cannot set quaternion for atom that has none");
random->reset(seed,x[i]);
theta2 = MY_PI*random->uniform();
quat[0] = cos(theta2);
quat[1] = 0.0;
quat[2] = 0.0;
quat[3] = sin(theta2);
count++;
}
random->reset(seed,x[i]);
theta2 = MY_PI*random->uniform();
quat[0] = cos(theta2);
quat[1] = 0.0;
quat[2] = 0.0;
quat[3] = sin(theta2);
count++;
}
}
}
@ -686,7 +686,7 @@ void Set::topology(int keyword)
// enforce PBC before in case atoms are outside box
// init entire system since comm->exchange is done
// comm::init needs neighbor::init needs pair::init needs kspace::init, etc
if (comm->me == 0 && screen) fprintf(screen," system init for set ...\n");
lmp->init();
@ -708,12 +708,12 @@ void Set::topology(int keyword)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
for (m = 0; m < atom->num_bond[i]; m++) {
atom1 = atom->map(atom->bond_atom[i][m]);
if (atom1 == -1) error->one(FLERR,"Bond atom missing in set command");
if (select[i] && select[atom1]) {
atom->bond_type[i][m] = ivalue;
count++;
}
atom1 = atom->map(atom->bond_atom[i][m]);
if (atom1 == -1) error->one(FLERR,"Bond atom missing in set command");
if (select[i] && select[atom1]) {
atom->bond_type[i][m] = ivalue;
count++;
}
}
}
@ -723,15 +723,15 @@ void Set::topology(int keyword)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
for (m = 0; m < atom->num_angle[i]; m++) {
atom1 = atom->map(atom->angle_atom1[i][m]);
atom2 = atom->map(atom->angle_atom2[i][m]);
atom3 = atom->map(atom->angle_atom3[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1)
error->one(FLERR,"Angle atom missing in set command");
if (select[atom1] && select[atom2] && select[atom3]) {
atom->angle_type[i][m] = ivalue;
count++;
}
atom1 = atom->map(atom->angle_atom1[i][m]);
atom2 = atom->map(atom->angle_atom2[i][m]);
atom3 = atom->map(atom->angle_atom3[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1)
error->one(FLERR,"Angle atom missing in set command");
if (select[atom1] && select[atom2] && select[atom3]) {
atom->angle_type[i][m] = ivalue;
count++;
}
}
}
@ -741,16 +741,16 @@ void Set::topology(int keyword)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
for (m = 0; m < atom->num_dihedral[i]; m++) {
atom1 = atom->map(atom->dihedral_atom1[i][m]);
atom2 = atom->map(atom->dihedral_atom2[i][m]);
atom3 = atom->map(atom->dihedral_atom3[i][m]);
atom4 = atom->map(atom->dihedral_atom4[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1)
error->one(FLERR,"Dihedral atom missing in set command");
if (select[atom1] && select[atom2] && select[atom3] && select[atom4]) {
atom->dihedral_type[i][m] = ivalue;
count++;
}
atom1 = atom->map(atom->dihedral_atom1[i][m]);
atom2 = atom->map(atom->dihedral_atom2[i][m]);
atom3 = atom->map(atom->dihedral_atom3[i][m]);
atom4 = atom->map(atom->dihedral_atom4[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1)
error->one(FLERR,"Dihedral atom missing in set command");
if (select[atom1] && select[atom2] && select[atom3] && select[atom4]) {
atom->dihedral_type[i][m] = ivalue;
count++;
}
}
}
@ -760,16 +760,16 @@ void Set::topology(int keyword)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
for (m = 0; m < atom->num_improper[i]; m++) {
atom1 = atom->map(atom->improper_atom1[i][m]);
atom2 = atom->map(atom->improper_atom2[i][m]);
atom3 = atom->map(atom->improper_atom3[i][m]);
atom4 = atom->map(atom->improper_atom4[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1)
error->one(FLERR,"Improper atom missing in set command");
if (select[atom1] && select[atom2] && select[atom3] && select[atom4]) {
atom->improper_type[i][m] = ivalue;
count++;
}
atom1 = atom->map(atom->improper_atom1[i][m]);
atom2 = atom->map(atom->improper_atom2[i][m]);
atom3 = atom->map(atom->improper_atom3[i][m]);
atom4 = atom->map(atom->improper_atom4[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1)
error->one(FLERR,"Improper atom missing in set command");
if (select[atom1] && select[atom2] && select[atom3] && select[atom4]) {
atom->improper_type[i][m] = ivalue;
count++;
}
}
}
}