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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7003 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2011-09-23 18:06:55 +00:00
parent 2d99de131d
commit 19e8c92a90
468 changed files with 4628 additions and 5204 deletions
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152
src/set.cpp
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@ -52,10 +52,10 @@ Set::Set(LAMMPS *lmp) : Pointers(lmp)
void Set::command(int narg, char **arg)
{
if (domain->box_exist == 0)
error->all("Set command before simulation box is defined");
error->all(FLERR,"Set command before simulation box is defined");
if (atom->natoms == 0)
error->all("Set command with no atoms existing");
if (narg < 3) error->all("Illegal set command");
error->all(FLERR,"Set command with no atoms existing");
if (narg < 3) error->all(FLERR,"Illegal set command");
// style and ID info
@ -64,7 +64,7 @@ void Set::command(int narg, char **arg)
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("Illegal set command");
else error->all(FLERR,"Illegal set command");
int n = strlen(arg[1]) + 1;
id = new char[n];
@ -84,137 +84,137 @@ void Set::command(int narg, char **arg)
origarg = iarg;
if (strcmp(arg[iarg],"type") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (ivalue <= 0 || ivalue > atom->ntypes)
error->all("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) {
if (iarg+4 > narg) error->all("Illegal set command");
if (iarg+4 > narg) error->all(FLERR,"Illegal set command");
newtype = atoi(arg[iarg+1]);
fraction = atof(arg[iarg+2]);
ivalue = atoi(arg[iarg+3]);
if (newtype <= 0 || newtype > atom->ntypes)
error->all("Invalid value in set command");
error->all(FLERR,"Invalid value in set command");
if (fraction < 0.0 || fraction > 1.0)
error->all("Invalid value in set command");
if (ivalue <= 0) error->all("Invalid random number seed in set command");
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("Illegal set command");
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (!atom->molecule_flag)
error->all("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) {
if (iarg+2 > narg) error->all("Illegal set command");
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
dvalue = atof(arg[iarg+1]);
set(X);
iarg += 2;
} else if (strcmp(arg[iarg],"y") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
dvalue = atof(arg[iarg+1]);
set(Y);
iarg += 2;
} else if (strcmp(arg[iarg],"z") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
dvalue = atof(arg[iarg+1]);
set(Z);
iarg += 2;
} else if (strcmp(arg[iarg],"charge") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
dvalue = atof(arg[iarg+1]);
if (!atom->q_flag)
error->all("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("Illegal set command");
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
dvalue = atof(arg[iarg+1]);
if (!atom->rmass_flag)
error->all("Cannot set this attribute for this atom style");
if (dvalue <= 0.0) error->all("Invalid mass in set command");
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;
} else if (strcmp(arg[iarg],"shape") == 0) {
if (iarg+4 > narg) error->all("Illegal set command");
if (iarg+4 > narg) error->all(FLERR,"Illegal set command");
xvalue = atof(arg[iarg+1]);
yvalue = atof(arg[iarg+2]);
zvalue = atof(arg[iarg+3]);
if (!atom->ellipsoid_flag)
error->all("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("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("Invalid shape in set command");
error->one(FLERR,"Invalid shape in set command");
}
set(SHAPE);
iarg += 4;
} else if (strcmp(arg[iarg],"dipole") == 0) {
if (iarg+4 > narg) error->all("Illegal set command");
if (iarg+4 > narg) error->all(FLERR,"Illegal set command");
xvalue = atof(arg[iarg+1]);
yvalue = atof(arg[iarg+2]);
zvalue = atof(arg[iarg+3]);
if (!atom->mu_flag)
error->all("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) {
if (iarg+3 > narg) error->all("Illegal set command");
if (iarg+3 > narg) error->all(FLERR,"Illegal set command");
ivalue = atoi(arg[iarg+1]);
dvalue = atof(arg[iarg+2]);
if (!atom->mu_flag)
error->all("Cannot set this attribute for this atom style");
if (ivalue <= 0) error->all("Invalid random number seed in set command");
if (dvalue <= 0.0) error->all("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) {
if (iarg+5 > narg) error->all("Illegal set command");
if (iarg+5 > narg) error->all(FLERR,"Illegal set command");
xvalue = atof(arg[iarg+1]);
yvalue = atof(arg[iarg+2]);
zvalue = atof(arg[iarg+3]);
wvalue = atof(arg[iarg+4]);
if (!atom->ellipsoid_flag)
error->all("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("Illegal set command");
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (!atom->ellipsoid_flag)
error->all("Cannot set this attribute for this atom style");
if (ivalue <= 0) error->all("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],"diameter") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
dvalue = atof(arg[iarg+1]);
if (!atom->radius_flag)
error->all("Cannot set this attribute for this atom style");
if (dvalue < 0.0) error->all("Invalid diameter in set command");
error->all(FLERR,"Cannot set this attribute for this atom style");
if (dvalue < 0.0) error->all(FLERR,"Invalid diameter in set command");
set(DIAMETER);
iarg += 2;
} else if (strcmp(arg[iarg],"density") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
dvalue = atof(arg[iarg+1]);
if (!atom->rmass_flag)
error->all("Cannot set this attribute for this atom style");
error->all(FLERR,"Cannot set this attribute for this atom style");
set(DENSITY);
iarg += 2;
} else if (strcmp(arg[iarg],"volume") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
dvalue = atof(arg[iarg+1]);
if (!atom->vfrac_flag)
error->all("Cannot set this attribute for this atom style");
error->all(FLERR,"Cannot set this attribute for this atom style");
set(VOLUME);
iarg += 2;
} else if (strcmp(arg[iarg],"image") == 0) {
if (iarg+4 > narg) error->all("Illegal set command");
if (iarg+4 > narg) error->all(FLERR,"Illegal set command");
ximageflag = yimageflag = zimageflag = 0;
if (strcmp(arg[iarg+1],"NULL") != 0) {
ximageflag = 1;
@ -229,71 +229,71 @@ void Set::command(int narg, char **arg)
zimage = atoi(arg[iarg+3]);
}
if (ximageflag && ximage && !domain->xperiodic)
error->all("Cannot set non-zero image flag for non-periodic dimension");
error->all(FLERR,"Cannot set non-zero image flag for non-periodic dimension");
if (yimageflag && yimage && !domain->yperiodic)
error->all("Cannot set non-zero image flag for non-periodic dimension");
error->all(FLERR,"Cannot set non-zero image flag for non-periodic dimension");
if (zimageflag && zimage && !domain->zperiodic)
error->all("Cannot set non-zero image flag for non-periodic dimension");
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("Illegal set command");
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (atom->avec->bonds_allow == 0)
error->all("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("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("Illegal set command");
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (atom->avec->angles_allow == 0)
error->all("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("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("Illegal set command");
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (atom->avec->dihedrals_allow == 0)
error->all("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("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("Illegal set command");
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (atom->avec->impropers_allow == 0)
error->all("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("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("Illegal set command");
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
dvalue = atof(arg[iarg+1]);
if (!atom->e_flag)
error->all("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("Illegal set command");
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
dvalue = atof(arg[iarg+1]);
if (!atom->cv_flag)
error->all("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("Illegal set command");
if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
dvalue = atof(arg[iarg+1]);
if (!atom->rho_flag)
error->all("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("Illegal set command");
} else error->all(FLERR,"Illegal set command");
// statistics
@ -326,7 +326,7 @@ void Set::selection(int n)
if (style == ATOM_SELECT) {
if (atom->tag_enable == 0)
error->all("Cannot use set atom with no atom IDs defined");
error->all(FLERR,"Cannot use set atom with no atom IDs defined");
force->bounds(id,BIG,nlo,nhi);
int *tag = atom->tag;
@ -336,7 +336,7 @@ void Set::selection(int n)
} else if (style == MOL_SELECT) {
if (atom->molecule_flag == 0)
error->all("Cannot use set mol with no molecule IDs defined");
error->all(FLERR,"Cannot use set mol with no molecule IDs defined");
if (strcmp(id,"0") == 0) nlo = nhi = 0;
else force->bounds(id,BIG,nlo,nhi);
@ -355,7 +355,7 @@ void Set::selection(int n)
} else if (style == GROUP_SELECT) {
int igroup = group->find(id);
if (igroup == -1) error->all("Could not find set group ID");
if (igroup == -1) error->all(FLERR,"Could not find set group ID");
int groupbit = group->bitmask[igroup];
int *mask = atom->mask;
@ -365,7 +365,7 @@ void Set::selection(int n)
} else if (style == REGION_SELECT) {
int iregion = domain->find_region(id);
if (iregion == -1) error->all("Set region ID does not exist");
if (iregion == -1) error->all(FLERR,"Set region ID does not exist");
double **x = atom->x;
for (int i = 0; i < n; i++)
@ -448,7 +448,7 @@ void Set::set(int keyword)
} else if (keyword == QUAT) {
if (atom->ellipsoid[i] < 0)
error->one("Cannot set quaternion for atom that is not an ellipsoid");
error->one(FLERR,"Cannot set quaternion for atom that is not an ellipsoid");
double *quat = avec_ellipsoid->bonus[atom->ellipsoid[i]].quat;
double theta2 = 0.5 * PI * wvalue/180.0;
double sintheta2 = sin(theta2);
@ -547,7 +547,7 @@ void Set::setrandom(int keyword)
for (i = 0; i < nlocal; i++)
if (select[i]) {
if (ellipsoid[i] < 0)
error->one("Cannot set quaternion for atom "
error->one(FLERR,"Cannot set quaternion for atom "
"that is not an ellipsoid");
quat = bonus[ellipsoid[i]].quat;
random->reset(seed,x[i]);
@ -568,7 +568,7 @@ void Set::setrandom(int keyword)
for (i = 0; i < nlocal; i++)
if (select[i]) {
if (ellipsoid[i] < 0)
error->one("Cannot set quaternion for atom "
error->one(FLERR,"Cannot set quaternion for atom "
"that is not an ellipsoid");
quat = bonus[ellipsoid[i]].quat;
random->reset(seed,x[i]);
@ -618,7 +618,7 @@ void Set::topology(int keyword)
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("Bond atom missing in set command");
if (atom1 == -1) error->one(FLERR,"Bond atom missing in set command");
if (select[i] && select[atom1]) {
atom->bond_type[i][m] = ivalue;
count++;
@ -636,7 +636,7 @@ void Set::topology(int keyword)
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("Angle atom missing in set command");
error->one(FLERR,"Angle atom missing in set command");
if (select[atom1] && select[atom2] && select[atom3]) {
atom->angle_type[i][m] = ivalue;
count++;
@ -655,7 +655,7 @@ void Set::topology(int keyword)
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("Dihedral atom missing in set command");
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++;
@ -674,7 +674,7 @@ void Set::topology(int keyword)
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("Improper atom missing in set command");
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++;