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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12200 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2014-07-28 18:46:50 +00:00
parent 16dc820a58
commit cf005551ea
2 changed files with 138 additions and 12 deletions
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145
src/create_atoms.cpp
View File

@ -27,6 +27,8 @@
#include "domain.h"
#include "lattice.h"
#include "region.h"
#include "input.h"
#include "variable.h"
#include "random_park.h"
#include "random_mars.h"
#include "math_extra.h"
@ -41,6 +43,7 @@ using namespace MathConst;
enum{BOX,REGION,SINGLE,RANDOM};
enum{ATOM,MOLECULE};
enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files
/* ---------------------------------------------------------------------- */
@ -103,6 +106,8 @@ void CreateAtoms::command(int narg, char **arg)
remapflag = 0;
mode = ATOM;
int molseed;
varflag = 0;
vstr = xstr = ystr = zstr = NULL;
nbasis = domain->lattice->nbasis;
basistype = new int[nbasis];
@ -141,6 +146,33 @@ void CreateAtoms::command(int narg, char **arg)
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
else error->all(FLERR,"Illegal create_atoms command");
iarg += 2;
} else if (strcmp(arg[iarg],"var") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal create_atoms command");
delete [] vstr;
int n = strlen(arg[iarg+1]) + 1;
vstr = new char[n];
strcpy(vstr,arg[iarg+1]);
varflag = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"set") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal create_atoms command");
if (strcmp(arg[iarg+1],"x") == 0) {
delete [] xstr;
int n = strlen(arg[iarg+2]) + 1;
xstr = new char[n];
strcpy(xstr,arg[iarg+2]);
} else if (strcmp(arg[iarg+1],"y") == 0) {
delete [] ystr;
int n = strlen(arg[iarg+2]) + 1;
ystr = new char[n];
strcpy(ystr,arg[iarg+2]);
} else if (strcmp(arg[iarg+1],"z") == 0) {
delete [] zstr;
int n = strlen(arg[iarg+2]) + 1;
zstr = new char[n];
strcpy(zstr,arg[iarg+2]);
} else error->all(FLERR,"Illegal create_atoms command");
iarg += 3;
} else error->all(FLERR,"Illegal create_atoms command");
}
@ -178,6 +210,47 @@ void CreateAtoms::command(int narg, char **arg)
ranmol = new RanMars(lmp,molseed+comm->me);
}
// error check and further setup for variable test
// save local copy of each equal variable string so can restore at end
if (!vstr && (xstr || ystr || zstr))
error->all(FLERR,"Incomplete use of variables in create_atoms command");
if (vstr && (!xstr && !ystr && !zstr))
error->all(FLERR,"Incomplete use of variables in create_atoms command");
if (varflag) {
vvar = input->variable->find(vstr);
if (vvar < 0)
error->all(FLERR,"Variable name for create_atoms does not exist");
if (!input->variable->equalstyle(vvar))
error->all(FLERR,"Variable for create_atoms is invalid style");
if (xstr) {
xvar = input->variable->find(xstr);
if (xvar < 0)
error->all(FLERR,"Variable name for create_atoms does not exist");
if (!input->variable->equalstyle(xvar))
error->all(FLERR,"Variable for create_atoms is invalid style");
input->variable->equal_save(xvar,xstr_copy);
}
if (ystr) {
yvar = input->variable->find(ystr);
if (yvar < 0)
error->all(FLERR,"Variable name for create_atoms does not exist");
if (!input->variable->equalstyle(yvar))
error->all(FLERR,"Variable for create_atoms is invalid style");
input->variable->equal_save(yvar,ystr_copy);
}
if (zstr) {
zvar = input->variable->find(zstr);
if (zvar < 0)
error->all(FLERR,"Variable name for create_atoms does not exist");
if (!input->variable->equalstyle(zvar))
error->all(FLERR,"Variable for create_atoms is invalid style");
input->variable->equal_save(zvar,zstr_copy);
}
}
// demand non-none lattice be defined for BOX and REGION
// else setup scaling for SINGLE and RANDOM
// could use domain->lattice->lattice2box() to do conversion of
@ -226,17 +299,32 @@ void CreateAtoms::command(int narg, char **arg)
}
if (style == BOX || style == REGION) {
if (domain->xperiodic) {
if (comm->myloc[0] == 0) sublo[0] -= epsilon[0];
if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] -= 2.0*epsilon[0];
}
if (domain->yperiodic) {
if (comm->myloc[1] == 0) sublo[1] -= epsilon[1];
if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] -= 2.0*epsilon[1];
}
if (domain->zperiodic) {
if (comm->myloc[2] == 0) sublo[2] -= epsilon[2];
if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] -= 2.0*epsilon[2];
if (comm->layout != LAYOUT_TILED) {
if (domain->xperiodic) {
if (comm->myloc[0] == 0) sublo[0] -= epsilon[0];
if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] -= 2.0*epsilon[0];
}
if (domain->yperiodic) {
if (comm->myloc[1] == 0) sublo[1] -= epsilon[1];
if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] -= 2.0*epsilon[1];
}
if (domain->zperiodic) {
if (comm->myloc[2] == 0) sublo[2] -= epsilon[2];
if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] -= 2.0*epsilon[2];
}
} else {
if (domain->xperiodic) {
if (comm->mysplit[0][0] == 0.0) sublo[0] -= epsilon[0];
if (comm->mysplit[0][1] == 1.0) subhi[0] -= 2.0*epsilon[0];
}
if (domain->yperiodic) {
if (comm->mysplit[1][0] == 0.0) sublo[1] -= epsilon[1];
if (comm->mysplit[1][1] == 1.0) subhi[1] -= 2.0*epsilon[1];
}
if (domain->zperiodic) {
if (comm->mysplit[2][0] == 0.0) sublo[2] -= epsilon[2];
if (comm->mysplit[2][1] == 1.0) subhi[2] -= 2.0*epsilon[2];
}
}
}
@ -259,6 +347,14 @@ void CreateAtoms::command(int narg, char **arg)
fix->set_arrays(i);
}
// restore each equal variable string previously saved
if (varflag) {
if (xstr) input->variable->equal_restore(xvar,xstr_copy);
if (ystr) input->variable->equal_restore(yvar,ystr_copy);
if (zstr) input->variable->equal_restore(zvar,zstr_copy);
}
// set new total # of atoms and error check
bigint nblocal = atom->nlocal;
@ -409,6 +505,10 @@ void CreateAtoms::command(int narg, char **arg)
delete ranmol;
if (domain->lattice) delete [] basistype;
delete [] vstr;
delete [] xstr;
delete [] ystr;
delete [] zstr;
// print status
@ -509,7 +609,7 @@ void CreateAtoms::add_random()
}
// generate random positions for each new atom/molecule within bounding box
// iterate until atom is within region and triclinic simulation box
// iterate until atom is within region, variable, and triclinic simulation box
// if final atom position is in my subbox, create it
if (xlo > xhi || ylo > yhi || zlo > zhi)
@ -527,6 +627,7 @@ void CreateAtoms::add_random()
if (nregion >= 0 &&
domain->regions[nregion]->match(xone[0],xone[1],xone[2]) == 0)
valid = 0;
if (varflag && vartest(xone) == 0) valid = 0;
if (triclinic) {
domain->x2lamda(xone,lamda);
coord = lamda;
@ -642,6 +743,10 @@ void CreateAtoms::add_lattice()
if (style == REGION)
if (!domain->regions[nregion]->match(x[0],x[1],x[2])) continue;
// if variable test specified, eval variable
if (varflag && vartest(x) == 0) continue;
// test if atom/molecule position is in my subbox
if (triclinic) {
@ -696,3 +801,19 @@ void CreateAtoms::add_molecule(double *center)
atom->add_molecule_atom(onemol,m,n,0);
}
}
/* ----------------------------------------------------------------------
test a generated atom position against variable evaluation
first plug in x,y,z values as requested
------------------------------------------------------------------------- */
int CreateAtoms::vartest(double *x)
{
if (xstr) input->variable->equal_override(xvar,x[0]);
if (ystr) input->variable->equal_override(yvar,x[1]);
if (zstr) input->variable->equal_override(zvar,x[2]);
double value = input->variable->compute_equal(vvar);
if (value == 0.0) return 0;
return 1;
}

5
src/create_atoms.h
View File

@ -35,6 +35,10 @@ class CreateAtoms : protected Pointers {
double xone[3];
int remapflag;
int varflag,vvar,xvar,yvar,zvar;
char *vstr,*xstr,*ystr,*zstr;
char *xstr_copy,*ystr_copy,*zstr_copy;
class Molecule *onemol;
class RanMars *ranmol;
@ -45,6 +49,7 @@ class CreateAtoms : protected Pointers {
void add_random();
void add_lattice();
void add_molecule(double *);
int vartest(double *); // evaluate a variable with new atom position
};
}