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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5932 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2011-04-13 21:40:14 +00:00
parent e45fbd89d1
commit 819524ebd6
71 changed files with 1167 additions and 2718 deletions
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275
src/set.cpp
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@ -31,12 +31,12 @@
using namespace LAMMPS_NS;
enum{ATOM,GROUP,REGION};
enum{TYPE,TYPE_FRACTION,MOLECULE,
X,Y,Z,CHARGE,
DIPOLE,DIPOLE_RANDOM,QUAT,QUAT_RANDOM,
DIAMETER,DENSITY,VOLUME,IMAGE,
BOND,ANGLE,DIHEDRAL,IMPROPER};
enum{ATOM_SELECT,MOL_SELECT,TYPE_SELECT,GROUP_SELECT,REGION_SELECT};
enum{TYPE,TYPE_FRACTION,MOLECULE,X,Y,Z,CHARGE,MASS,SHAPE,
DIPOLE,DIPOLE_RANDOM,QUAT,QUAT_RANDOM,
DIAMETER,DENSITY,VOLUME,IMAGE,BOND,ANGLE,DIHEDRAL,IMPROPER};
#define BIG INT_MAX
/* ---------------------------------------------------------------------- */
@ -55,11 +55,13 @@ void Set::command(int narg, char **arg)
error->all("Set command with no atoms existing");
if (narg < 3) error->all("Illegal set command");
// style and ID
// style and ID info
if (strcmp(arg[0],"atom") == 0) style = ATOM;
else if (strcmp(arg[0],"group") == 0) style = GROUP;
else if (strcmp(arg[0],"region") == 0) style = REGION;
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("Illegal set command");
int n = strlen(arg[1]) + 1;
@ -91,6 +93,8 @@ void Set::command(int narg, char **arg)
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");
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");
@ -125,23 +129,48 @@ void Set::command(int narg, char **arg)
error->all("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");
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");
set(MASS);
iarg += 2;
} else if (strcmp(arg[iarg],"shape") == 0) {
if (iarg+4 > narg) error->all("Illegal set command");
xvalue = atof(arg[iarg+1]);
yvalue = atof(arg[iarg+2]);
zvalue = atof(arg[iarg+3]);
if (!atom->shape_flag)
error->all("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");
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");
}
set(SHAPE);
iarg += 4;
} else if (strcmp(arg[iarg],"dipole") == 0) {
if (iarg+4 > narg) error->all("Illegal set command");
xvalue = atof(arg[iarg+1]);
yvalue = atof(arg[iarg+2]);
zvalue = atof(arg[iarg+3]);
if (!atom->mu_flag || atom->dipole == NULL)
if (!atom->mu_flag)
error->all("Cannot set this attribute for this atom style");
set(DIPOLE);
iarg += 4;
} else if (strcmp(arg[iarg],"dipole/random") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
if (iarg+3 > narg) error->all("Illegal set command");
ivalue = atoi(arg[iarg+1]);
if (!atom->mu_flag || atom->shape == NULL)
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");
setrandom(DIPOLE_RANDOM);
iarg += 2;
iarg += 3;
} else if (strcmp(arg[iarg],"quat") == 0) {
if (iarg+5 > narg) error->all("Illegal set command");
xvalue = atof(arg[iarg+1]);
@ -165,12 +194,13 @@ void Set::command(int narg, char **arg)
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");
set(DIAMETER);
iarg += 2;
} else if (strcmp(arg[iarg],"density") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
dvalue = atof(arg[iarg+1]);
if (!atom->density_flag)
if (!atom->rmass_flag)
error->all("Cannot set this attribute for this atom style");
set(DENSITY);
iarg += 2;
@ -261,7 +291,7 @@ void Set::command(int narg, char **arg)
}
/* ----------------------------------------------------------------------
select atoms according to ATOM, GROUP, REGION style
select atoms according to ATOM, MOLECULE, TYPE, GROUP, REGION style
n = nlocal or nlocal+nghost depending on keyword
------------------------------------------------------------------------- */
@ -269,18 +299,38 @@ void Set::selection(int n)
{
delete [] select;
select = new int[n];
int nlo,nhi;
if (style == ATOM) {
if (style == ATOM_SELECT) {
if (atom->tag_enable == 0)
error->all("Cannot use set atom with no atom IDs defined");
int idatom = atoi(id);
force->bounds(id,BIG,nlo,nhi);
int *tag = atom->tag;
for (int i = 0; i < n; i++)
if (idatom == tag[i]) select[i] = 1;
if (tag[i] >= nlo && tag[i] <= nhi) select[i] = 1;
else select[i] = 0;
} else if (style == GROUP) {
} else if (style == MOL_SELECT) {
if (atom->molecule_flag == 0)
error->all("Cannot use set mol with no molecule IDs defined");
if (strcmp(id,"0") == 0) nlo = nhi = 0;
else force->bounds(id,BIG,nlo,nhi);
int *molecule = atom->molecule;
for (int i = 0; i < n; i++)
if (molecule[i] >= nlo && molecule[i] <= nhi) select[i] = 1;
else select[i] = 0;
} else if (style == TYPE_SELECT) {
force->bounds(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("Could not find set group ID");
int groupbit = group->bitmask[igroup];
@ -290,7 +340,7 @@ void Set::selection(int n)
if (mask[i] & groupbit) select[i] = 1;
else select[i] = 0;
} else {
} else if (style == REGION_SELECT) {
int iregion = domain->find_region(id);
if (iregion == -1) error->all("Set region ID does not exist");
@ -308,83 +358,81 @@ void Set::selection(int n)
void Set::set(int keyword)
{
if (keyword == DIPOLE) atom->check_dipole();
selection(atom->nlocal);
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (select[i]) {
if (keyword == TYPE) 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;
for (int i = 0; i < nlocal; i++) {
if (!select[i]) continue;
// set radius from diameter
// set rmass if both rmass and density are defined
if (keyword == TYPE) 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) atom->rmass[i] = dvalue;
else if (keyword == DIAMETER) atom->radius[i] = 0.5 * dvalue;
else if (keyword == VOLUME) atom->vfrac[i] = dvalue;
// set shape
else if (keyword == DIAMETER) {
atom->radius[i] = 0.5 * dvalue;
if (atom->rmass_flag && atom->density_flag)
atom->rmass[i] = 4.0*PI/3.0 *
atom->radius[i]*atom->radius[i]*atom->radius[i] * atom->density[i];
else if (keyword == SHAPE) {
double **shape = atom->shape;
shape[i][0] = 0.5 * xvalue;
shape[i][1] = 0.5 * yvalue;
shape[i][2] = 0.5 * zvalue;
// set rmass via density
// if radius > 0.0, assume sphere
// if shape > 0.0, assume ellipsoid
// else set rmass to density directly
// set density
// set rmass (granular) if both rmass and radius are defined
// set rmass (peri) if both rmass and vfrac are defined
} else if (keyword == DENSITY) {
atom->density[i] = dvalue;
if (atom->rmass_flag && atom->radius_flag)
atom->rmass[i] = 4.0*PI/3.0 *
atom->radius[i]*atom->radius[i]*atom->radius[i] *
atom->density[i];
else if (atom->rmass_flag && atom->vfrac_flag)
atom->rmass[i] = dvalue;
} else if (keyword == DENSITY) {
if (atom->radius_flag && atom->radius[i] > 0.0)
atom->rmass[i] = 4.0*PI/3.0 *
atom->radius[i]*atom->radius[i]*atom->radius[i] * dvalue;
else if (atom->shape_flag && atom->shape[i][0] > 0.0)
atom->rmass[i] = 4.0*PI/3.0 *
atom->shape[i][0]*atom->shape[i][1]*atom->shape[i][2] * dvalue;
else atom->rmass[i] = dvalue;
} else if (keyword == VOLUME) atom->vfrac[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;
int zbox = (atom->image[i] >> 20) - 512;
if (ximageflag) xbox = ximage;
if (yimageflag) ybox = yimage;
if (zimageflag) zbox = zimage;
atom->image[i] = ((zbox + 512 & 1023) << 20) |
((ybox + 512 & 1023) << 10) | (xbox + 512 & 1023);
} else if (keyword == DIPOLE) {
if (atom->dipole[atom->type[i]] > 0.0) {
double **mu = atom->mu;
mu[i][0] = xvalue;
mu[i][1] = yvalue;
mu[i][2] = zvalue;
double lensq =
mu[i][0]*mu[i][0] + mu[i][1]*mu[i][1] + mu[i][2]*mu[i][2];
double scale = atom->dipole[atom->type[i]]/sqrt(lensq);
mu[i][0] *= scale;
mu[i][1] *= scale;
mu[i][2] *= scale;
}
} else if (keyword == QUAT) {
double PI = 4.0*atan(1.0);
double theta2 = 0.5 * PI * wvalue/180.0;
double sintheta2 = sin(theta2);
double **quat = atom->quat;
quat[i][0] = cos(theta2);
quat[i][1] = xvalue * sintheta2;
quat[i][2] = yvalue * sintheta2;
quat[i][3] = zvalue * sintheta2;
MathExtra::normalize4(quat[i]);
}
count++;
// 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;
int zbox = (atom->image[i] >> 20) - 512;
if (ximageflag) xbox = ximage;
if (yimageflag) ybox = yimage;
if (zimageflag) zbox = zimage;
atom->image[i] = ((zbox + 512 & 1023) << 20) |
((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]);
// set quaternion orientation
} else if (keyword == QUAT) {
double PI = 4.0*atan(1.0);
double theta2 = 0.5 * PI * wvalue/180.0;
double sintheta2 = sin(theta2);
double **quat = atom->quat;
quat[i][0] = cos(theta2);
quat[i][1] = xvalue * sintheta2;
quat[i][2] = yvalue * sintheta2;
quat[i][3] = zvalue * sintheta2;
MathExtra::normalize4(quat[i]);
}
count++;
}
}
/* ----------------------------------------------------------------------
@ -397,8 +445,6 @@ void Set::setrandom(int keyword)
{
int i;
if (keyword == DIPOLE_RANDOM) atom->check_dipole();
selection(atom->nlocal);
RanPark *random = new RanPark(lmp,1);
double **x = atom->x;
@ -422,7 +468,6 @@ void Set::setrandom(int keyword)
} else if (keyword == DIPOLE_RANDOM) {
int *type = atom->type;
double *dipole = atom->dipole;
double **mu = atom->mu;
int nlocal = atom->nlocal;
@ -431,34 +476,32 @@ void Set::setrandom(int keyword)
if (domain->dimension == 3) {
for (i = 0; i < nlocal; i++)
if (select[i]) {
if (dipole[type[i]] > 0.0) {
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 = dipole[type[i]]/sqrt(msq);
mu[i][0] *= scale;
mu[i][1] *= scale;
mu[i][2] *= scale;
count++;
}
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]) {
if (dipole[type[i]] > 0.0) {
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 = dipole[type[i]]/sqrt(msq);
mu[i][0] *= scale;
mu[i][1] *= scale;
count++;
}
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++;
}
}