ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

add support for building rigid bodies from custom atom properties or atom style variables

Browse Source
This commit is contained in:
Axel Kohlmeyer
2017-10-04 01:14:57 -04:00
parent f2c1172741
commit f12031f84d
1 changed files with 49 additions and 6 deletions
Download Patch File Download Diff File Expand all files Collapse all files

55
src/RIGID/fix_rigid.cpp
View File

@ -29,6 +29,8 @@
#include "comm.h"
#include "random_mars.h"
#include "force.h"
#include "input.h"
#include "variable.h"
#include "output.h"
#include "math_const.h"
#include "memory.h"
@ -127,15 +129,55 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
// nbody = # of non-zero ncount values
// use nall as incremented ptr to set body[] values for each atom
} else if (strcmp(arg[3],"molecule") == 0) {
} else if (strcmp(arg[3],"molecule") == 0 || strcmp(arg[3],"custom") == 0) {
rstyle = MOLECULE;
iarg = 4;
if (atom->molecule_flag == 0)
error->all(FLERR,"Fix rigid molecule requires atom attribute molecule");
tagint *molecule;
int *mask = atom->mask;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
int custom_flag = strcmp(arg[3],"custom") == 0;
if (custom_flag) {
if (narg < 5) error->all(FLERR,"Illegal fix rigid command");
// determine whether atom-style variable or atom property is used.
if (strstr(arg[4],"i_") == arg[4]) {
int is_double;
int custom_index = atom->find_custom(arg[4]+2,is_double);
if (custom_index == -1)
error->all(FLERR,"Fix rigid custom requires previously defined property/atom");
else if (is_double)
error->all(FLERR,"Fix rigid custom requires integer-valued property/atom");
int minval = INT_MAX;
int *value = atom->ivector[custom_index];
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) minval = MIN(minval,value[i]);
int vmin = minval;
MPI_Allreduce(&vmin,&minval,1,MPI_INT,MPI_MIN,world);
molecule = new tagint[nlocal];
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) molecule[i] = (tagint)(value[i] - minval + 1);
} else if (strstr(arg[4],"v_") == arg[4]) {
int ivariable = input->variable->find(arg[4]+2);
if (ivariable < 0)
error->all(FLERR,"Variable name for fix rigid custom does not exist");
if (input->variable->atomstyle(ivariable) == 0)
error->all(FLERR,"Fix rigid custom variable is not atom-style variable");
double *value = new double[nlocal];
input->variable->compute_atom(ivariable,0,value,1,0);
int minval = INT_MAX;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) minval = MIN(minval,(int)value[i]);
int vmin = minval;
MPI_Allreduce(&vmin,&minval,1,MPI_INT,MPI_MIN,world);
molecule = new tagint[nlocal];
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) molecule[i] = (tagint)((int)value[i] - minval + 1);
delete[] value;
} else error->all(FLERR,"Unsupported fix rigid custom property");
} else {
if (atom->molecule_flag == 0)
error->all(FLERR,"Fix rigid molecule requires atom attribute molecule");
molecule = atom->molecule;
}
iarg = 4 + custom_flag;
tagint maxmol_tag = -1;
for (i = 0; i < nlocal; i++)
@ -174,6 +216,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
}
memory->destroy(ncount);
if (custom_flag) delete [] molecule;
// each listed group is a rigid body
// check if all listed groups exist