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modified versions of creating atoms on subset of lattice, ditto for set type/fraction

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This commit is contained in:
Steve Plimpton
2020-01-21 13:31:47 -07:00
parent 4ea679dd54
commit 90ff2eb6c9
13 changed files with 486 additions and 238 deletions
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136
src/set.cpp
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@ -30,6 +30,7 @@
#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"
@ -41,7 +42,8 @@ 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,
enum{TYPE,TYPE_FRACTION,TYPE_RATIO,TYPE_SUBSET,
MOLECULE,X,Y,Z,CHARGE,MASS,SHAPE,LENGTH,TRI,
DIPOLE,DIPOLE_RANDOM,SPIN,SPIN_RANDOM,QUAT,QUAT_RANDOM,
THETA,THETA_RANDOM,ANGMOM,OMEGA,
DIAMETER,DENSITY,VOLUME,IMAGE,BOND,ANGLE,DIHEDRAL,IMPROPER,
@ -109,6 +111,34 @@ void Set::command(int narg, char **arg)
setrandom(TYPE_FRACTION);
iarg += 4;
} 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]);
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_RATIO);
iarg += 4;
} 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]);
if (newtype <= 0 || newtype > atom->ntypes)
error->all(FLERR,"Invalid value in set command");
if (nsubset < 0)
error->all(FLERR,"Invalid value in set command");
if (ivalue <= 0)
error->all(FLERR,"Invalid random number seed in set command");
setrandom(TYPE_SUBSET);
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);
@ -1001,23 +1031,72 @@ void Set::setrandom(int keyword)
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
RanPark *ranpark = new RanPark(lmp,1);
RanMars *ranmars = new RanMars(lmp,seed + comm->me);
// set approx 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;
ranpark->reset(seed,x[i]);
if (ranpark->uniform() > fraction) continue;
atom->type[i] = newtype;
count++;
}
// set exact count of atom types to newtype
// for TYPE_RATIO, exact = fraction out of total eligible
// for TYPE_SUBSET, exact = nsubset out of total eligible
} else if (keyword == TYPE_RATIO || keyword == TYPE_SUBSET) {
int nlocal = atom->nlocal;
// count = number of eligible atoms I own
count = 0;
for (i = 0; i < nlocal; i++)
if (select[i]) count++;
// convert specified fraction to nsubset
bigint bcount = count;
bigint allcount;
MPI_Allreduce(&bcount,&allcount,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (keyword == TYPE_RATIO) {
nsubset = static_cast<bigint> (fraction * allcount);
} else if (keyword == TYPE_SUBSET) {
if (nsubset > allcount)
error->all(FLERR,"Set type/subset value exceeds eligible atoms");
}
// make selection
int *flag = memory->create(flag,count,"set:flag");
int *work = memory->create(work,count,"set:work");
ranmars->select_subset(nsubset,count,flag,work);
// change types of selected atoms
count = 0;
for (i = 0; i < nlocal; i++)
if (select[i] && flag[i]) {
atom->type[i] = newtype;
count++;
}
// clean up
memory->destroy(flag);
memory->destroy(work);
// set dipole moments to random orientations in 3d or 2d
// dipole length is determined by dipole type array
@ -1030,10 +1109,10 @@ 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;
ranpark->reset(seed,x[i]);
mu[i][0] = ranpark->uniform() - 0.5;
mu[i][1] = ranpark->uniform() - 0.5;
mu[i][2] = ranpark->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;
@ -1046,9 +1125,9 @@ void Set::setrandom(int keyword)
} 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;
ranpark->reset(seed,x[i]);
mu[i][0] = ranpark->uniform() - 0.5;
mu[i][1] = ranpark->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);
@ -1072,10 +1151,10 @@ void Set::setrandom(int keyword)
if (domain->dimension == 3) {
for (i = 0; i < nlocal; i++)
if (select[i]) {
random->reset(seed,x[i]);
sp[i][0] = random->uniform() - 0.5;
sp[i][1] = random->uniform() - 0.5;
sp[i][2] = random->uniform() - 0.5;
ranpark->reset(seed,x[i]);
sp[i][0] = ranpark->uniform() - 0.5;
sp[i][1] = ranpark->uniform() - 0.5;
sp[i][2] = ranpark->uniform() - 0.5;
sp_sq = sp[i][0]*sp[i][0] + sp[i][1]*sp[i][1] + sp[i][2]*sp[i][2];
scale = 1.0/sqrt(sp_sq);
sp[i][0] *= scale;
@ -1088,9 +1167,9 @@ void Set::setrandom(int keyword)
} else {
for (i = 0; i < nlocal; i++)
if (select[i]) {
random->reset(seed,x[i]);
sp[i][0] = random->uniform() - 0.5;
sp[i][1] = random->uniform() - 0.5;
ranpark->reset(seed,x[i]);
sp[i][0] = ranpark->uniform() - 0.5;
sp[i][1] = ranpark->uniform() - 0.5;
sp[i][2] = 0.0;
sp_sq = sp[i][0]*sp[i][0] + sp[i][1]*sp[i][1];
scale = 1.0/sqrt(sp_sq);
@ -1120,12 +1199,12 @@ void Set::setrandom(int keyword)
else
error->one(FLERR,"Cannot set quaternion for atom that has none");
random->reset(seed,x[i]);
s = random->uniform();
ranpark->reset(seed,x[i]);
s = ranpark->uniform();
t1 = sqrt(1.0-s);
t2 = sqrt(s);
theta1 = 2.0*MY_PI*random->uniform();
theta2 = 2.0*MY_PI*random->uniform();
theta1 = 2.0*MY_PI*ranpark->uniform();
theta2 = 2.0*MY_PI*ranpark->uniform();
quat[0] = cos(theta2)*t2;
quat[1] = sin(theta1)*t1;
quat[2] = cos(theta1)*t1;
@ -1144,8 +1223,8 @@ void Set::setrandom(int keyword)
else
error->one(FLERR,"Cannot set quaternion for atom that has none");
random->reset(seed,x[i]);
theta2 = MY_PI*random->uniform();
ranpark->reset(seed,x[i]);
theta2 = MY_PI*ranpark->uniform();
quat[0] = cos(theta2);
quat[1] = 0.0;
quat[2] = 0.0;
@ -1162,14 +1241,15 @@ void Set::setrandom(int keyword)
if (select[i]) {
if (atom->line[i] < 0)
error->one(FLERR,"Cannot set theta for atom that is not a line");
random->reset(seed,x[i]);
avec_line->bonus[atom->line[i]].theta = MY_2PI*random->uniform();
ranpark->reset(seed,x[i]);
avec_line->bonus[atom->line[i]].theta = MY_2PI*ranpark->uniform();
count++;
}
}
}
delete random;
delete ranpark;
delete ranmars;
}
/* ---------------------------------------------------------------------- */