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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5648 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2011-02-15 19:32:19 +00:00
parent d40626d7a7
commit 68faba233a
2 changed files with 37 additions and 9 deletions
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39
src/fix_orient_fcc.cpp
View File

@ -28,6 +28,7 @@
#include "neigh_request.h"
#include "comm.h"
#include "output.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
@ -49,6 +50,10 @@ FixOrientFCC::FixOrientFCC(LAMMPS *lmp, int narg, char **arg) :
scalar_flag = 1;
global_freq = 1;
extscalar = 1;
peratom_flag = 1;
size_peratom_cols = 2;
peratom_freq = 1;
nstats = atoi(arg[3]);
direction_of_motion = atoi(arg[4]);
@ -151,6 +156,16 @@ FixOrientFCC::FixOrientFCC(LAMMPS *lmp, int narg, char **arg) :
else comm_forward = 50;
added_energy = 0.0;
nmax = atom->nmax;
nbr = (Nbr *) memory->smalloc(nmax*sizeof(Nbr),"orient/fcc:nbr");
order = memory->create_2d_double_array(nmax,2,"orient/fcc:order");
array_atom = order;
// zero the array since a variable may access it before first run
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) order[i][0] = order[i][1] = 0.0;
}
/* ---------------------------------------------------------------------- */
@ -159,7 +174,8 @@ FixOrientFCC::~FixOrientFCC()
{
delete [] xifilename;
delete [] chifilename;
if (nmax) delete [] nbr;
memory->sfree(nbr);
memory->destroy_2d_double_array(order);
}
/* ---------------------------------------------------------------------- */
@ -235,12 +251,15 @@ void FixOrientFCC::post_force(int vflag)
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// insure nbr data structure is adequate size
// insure nbr and order data structures are adequate size
if (nall > nmax) {
if (nmax) delete [] nbr;
nbr = new Nbr[nall];
nmax = nall;
memory->sfree(nbr);
memory->destroy_2d_double_array(order);
nbr = (Nbr *) memory->smalloc(nmax*sizeof(Nbr),"orient/fcc:nbr");
order = memory->create_2d_double_array(nmax,2,"orient/fcc:order");
array_atom = order;
}
// loop over owned atoms and build Nbr data structure of neighbors
@ -314,19 +333,23 @@ void FixOrientFCC::post_force(int vflag)
if (use_xismooth) nbr[i].xismooth[j] = sort[j].xismooth;
}
xi_total /= n;
order[i][0] = xi_total;
// compute potential derivative to xi
if (xi_total < xi0) {
nbr[i].duxi = 0.0;
edelta = 0.0;
order[i][1] = 0.0;
} else if (xi_total > xi1) {
nbr[i].duxi = 0.0;
edelta = Vxi;
order[i][1] = 1.0;
} else {
omega = (0.5*PI)*(xi_total-xi0) / (xi1-xi0);
nbr[i].duxi = PI*Vxi*sin(2.0*omega) / (2.0*(xi1-xi0));
edelta = Vxi*(1 - cos(2.0*omega)) / 2.0;
order[i][1] = omega / (0.5*PI);
}
added_energy += edelta;
}
@ -432,8 +455,9 @@ void FixOrientFCC::post_force_respa(int vflag, int ilevel, int iloop)
double FixOrientFCC::compute_scalar()
{
MPI_Allreduce(&added_energy,&total_added_e,1,MPI_DOUBLE,MPI_SUM,world);
return total_added_e;
double added_energy_total;
MPI_Allreduce(&added_energy,&added_energy_total,1,MPI_DOUBLE,MPI_SUM,world);
return added_energy_total;
}
/* ---------------------------------------------------------------------- */
@ -562,6 +586,7 @@ int FixOrientFCC::compare(const void *pi, const void *pj)
double FixOrientFCC::memory_usage()
{
double bytes = atom->nmax * sizeof(Nbr);
double bytes = nmax * sizeof(Nbr);
bytes += 2*nmax * sizeof(double);
return bytes;
}

7
src/fix_orient_fcc.h
View File

@ -71,8 +71,11 @@ class FixOrientFCC : public Fix {
bool use_xismooth;
double Rxi[12][3],Rchi[12][3],half_xi_chi_vec[2][6][3];
double xiid,xi0,xi1,xicutoffsq,cutsq,added_energy,total_added_e;
int half_fcc_nn,nmax;
double xiid,xi0,xi1,xicutoffsq,cutsq,added_energy;
int half_fcc_nn;
int nmax; // expose 2 per-atom quantities
double **order; // order param and normalized order param
Nbr *nbr;
Sort *sort;