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fix elstop: Inline kinetic energy computation

This commit is contained in:
Risto Toijala 2019-04-01 12:59:25 +03:00
parent 053bdea234
commit a8e5af3cb4
2 changed files with 5 additions and 34 deletions
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33
src/USER-MISC/fix_elstop.cpp
View File

@ -54,20 +54,6 @@ FixElstop::FixElstop(LAMMPS *lmp, int narg, char **arg) :
nevery = 1; // Run fix every step
// Make sure the id for the kinetic energy compute is unique
// by prepending the ID of this fix.
int n = strlen(id) + strlen("_ke_atom") + 1;
id_ke_atom = new char[n];
strcpy(id_ke_atom, id);
strcat(id_ke_atom, "_ke_atom");
char *newarg[3];
newarg[0] = id_ke_atom;
newarg[1] = group->names[igroup];
newarg[2] = (char *) "ke/atom";
modify->add_compute(3, newarg);
// args: 0 = fix ID, 1 = group ID, 2 = "elstop"
// 3 = Ecut, 4 = file path
// optional rest: "region" <region name>
@ -133,8 +119,6 @@ FixElstop::FixElstop(LAMMPS *lmp, int narg, char **arg) :
FixElstop::~FixElstop()
{
memory->destroy(elstop_ranges);
modify->delete_compute(id_ke_atom);
delete id_ke_atom;
}
/* ---------------------------------------------------------------------- */
@ -153,12 +137,6 @@ void FixElstop::init()
SeLoss_sync_flag = 0;
SeLoss = 0.0;
int ikeatom = modify->find_compute(id_ke_atom);
if (ikeatom < 0)
error->all(FLERR, "KE compute ID for fix elstop does not exist");
c_ke = modify->compute[ikeatom];
// need an occasional full neighbor list
int irequest = neighbor->request(this, instance_me);
neighbor->requests[irequest]->pair = 0;
@ -193,9 +171,6 @@ void FixElstop::post_force(int /*vflag*/)
neighbor->build_one(list);
int *numneigh = list->numneigh;
c_ke->compute_peratom();
double *ke = c_ke->vector_atom;
for (int i = 0; i < nlocal; ++i) {
// Do fast checks first, only then the region check
@ -204,7 +179,11 @@ void FixElstop::post_force(int /*vflag*/)
// Avoid atoms outside bulk material
if (numneigh[i] < minneigh) continue;
double energy = ke[i];
int itype = type[i];
double massone = (atom->rmass) ? atom->rmass[i] : atom->mass[itype];
double v2 = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
double energy = 0.5 * force->mvv2e * massone * v2;
if (energy < Ecut) continue;
if (energy < elstop_ranges[0][0]) continue;
if (energy > elstop_ranges[0][table_entries - 1])
@ -226,7 +205,6 @@ void FixElstop::post_force(int /*vflag*/)
else iup = ihalf;
}
int itype = type[i];
double Se_lo = elstop_ranges[itype][idown];
double Se_hi = elstop_ranges[itype][iup];
double E_lo = elstop_ranges[0][idown];
@ -235,7 +213,6 @@ void FixElstop::post_force(int /*vflag*/)
// Get elstop with a simple linear interpolation
double Se = (Se_hi - Se_lo) / (E_hi - E_lo) * (energy - E_lo) + Se_lo;
double v2 = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
double vabs = sqrt(v2);
double factor = -Se / vabs;

6
src/USER-MISC/fix_elstop.h
View File

@ -53,12 +53,10 @@ class FixElstop : public Fix {
double **elstop_ranges; // [ 0][i]: energies
// [>0][i]: stopping powers per type
char *id_ke_atom; // name of kinetic energy compute
int iregion; // region index if used, else -1
int minneigh; // minimum number of neighbors
class NeighList *list;
class Compute *c_ke;
};
}
@ -78,10 +76,6 @@ E: Region ID for fix elstop does not exist
Self-explanatory.
E: KE compute ID for fix elstop does not exist
Internal error. Should not happen.
E: Atom kinetic energy too high for fix elstop
The group given in the fix elstop command includes an atom that has