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Commit 0bdf6303 authored by sjplimp's avatar sjplimp
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src/USER-MISC/README
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......@@ -27,6 +27,7 @@ angle_style quartic, Loukas Peristeras, loukas.peristeras at scienomics.com, 27
bond_style harmonic/shift, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
bond_style harmonic/shift/cut, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
compute ackland/atom, Gerolf Ziegenhain, gerolf at ziegenhain.com, 4 Oct 2007
compute basal/atom, Christopher Barrett, cdb333 at cavs.msstate.edu, 3 Mar 2013
compute temp/rotate, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
dihedral_style cosine/shift/exp, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
dihedral_style fourier, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12
......
src/USER-MISC/compute_basal_atom.cpp 0 → 100644
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: C.D. Barrett, cdb333@cavs.msstate.edu
Copyright (C) 2013
------------------------------------------------------------------------- */
#include "string.h"
#include "compute_basal_atom.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "force.h"
#include "pair.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include <math.h>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeBasalAtom::ComputeBasalAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3) error->all(FLERR,"Illegal compute basal/atom command");
peratom_flag = 1;
size_peratom_cols = 3;
nmax = 0;
BPV = NULL;
maxneigh = 0;
distsq = NULL;
nearest = NULL;
nearest_n0 = NULL;
nearest_n1 = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeBasalAtom::~ComputeBasalAtom()
{
memory->destroy(BPV);
memory->destroy(distsq);
memory->destroy(nearest);
memory->destroy(nearest_n0);
memory->destroy(nearest_n1);
}
/* ---------------------------------------------------------------------- */
void ComputeBasalAtom::init()
{
// need an occasional full neighbor list
int irequest = neighbor->request((void *) this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->occasional = 1;
int count1 = 0;
for (int i = 0; i < modify->ncompute; i++)
if (strcmp(modify->compute[i]->style,"basal/atom") == 0) count1++;
if (count1 > 1 && comm->me == 0)
error->warning(FLERR,"More than one compute basal/atom");
}
/* ---------------------------------------------------------------------- */
void ComputeBasalAtom::init_list(int id, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
void ComputeBasalAtom::compute_peratom()
{
int i,j,ii,jj,k,n,inum,jnum;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq,var5,var6,var7;
int *ilist,*jlist,*numneigh,**firstneigh;
int chi[8];
int value;
int count;
int k2[3];
int j1[3];
double x4[3],y4[3],z4[3],x5[3],y5[3],z5[3],x6[3],y6[3],z6[3];
double x7[3],y7[3],z7[3];
invoked_peratom = update->ntimestep;
// grow structure array if necessary
if (atom->nlocal > nmax) {
memory->destroy(BPV);
nmax = atom->nmax;
memory->create(BPV,nmax,3,"basal/atom:basal");
array_atom = BPV;
}
// invoke full neighbor list (will copy or build if necessary)
neighbor->build_one(list->index);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// compute structure parameter for each atom in group
// use full neighbor list
double **x = atom->x;
int *mask = atom->mask;
double cutsq = force->pair->cutforce * force->pair->cutforce;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (mask[i] & groupbit) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
jlist = firstneigh[i];
jnum = numneigh[i];
// ensure distsq and nearest arrays are long enough
if (jnum > maxneigh) {
memory->destroy(distsq);
memory->destroy(nearest);
memory->destroy(nearest_n0);
memory->destroy(nearest_n1);
maxneigh = jnum;
memory->create(distsq,maxneigh,"compute/basal/atom:distsq");
memory->create(nearest,maxneigh,"compute/basal/atom:nearest");
memory->create(nearest_n0,maxneigh,"compute/basal/atom:nearest_n0");
memory->create(nearest_n1,maxneigh,"compute/basal/atom:nearest_n1");
}
// neighbor selection is identical to ackland/atom algorithm
// loop over list of all neighbors within force cutoff
// distsq[] = distance sq to each
// nearest[] = atom indices of neighbors
n = 0;
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cutsq) {
distsq[n] = rsq;
nearest[n++] = j;
}
}
// Select 6 nearest neighbors
select2(6,n,distsq,nearest);
// Mean squared separation
double r0_sq = 0.0;
for (j = 0; j < 6; j++) r0_sq += distsq[j];
r0_sq /= 6.0;
// n0 near neighbors with: distsq<1.45*r0_sq
// n1 near neighbors with: distsq<1.55*r0_sq
double n0_dist_sq = 1.45*r0_sq,
n1_dist_sq = 1.55*r0_sq;
int n0 = 0, n1 = 0;
for (j = 0; j < n; j++) {
if (distsq[j] < n1_dist_sq) {
nearest_n1[n1++] = nearest[j];
if (distsq[j] < n0_dist_sq) {
nearest_n0[n0++] = nearest[j];
}
}
}
// Evaluate all angles <(r_ij,rik) forall n0 particles with: distsq<1.45*r0_sq
double bond_angle;
double norm_j, norm_k;
chi[0] = chi[1] = chi[2] = chi[3] = chi[4] = chi[5] = chi[6] = chi[7] = 0;
double x_ij, y_ij, z_ij, x_ik, y_ik, z_ik,x3[n0],y3[n0],z3[n0],
xmean5, ymean5, zmean5, xmean6, ymean6, zmean6, xmean7, ymean7, zmean7;
for (j = 0; j < n0; j++) {
x_ij = x[i][0]-x[nearest_n0[j]][0];
y_ij = x[i][1]-x[nearest_n0[j]][1];
z_ij = x[i][2]-x[nearest_n0[j]][2];
norm_j = sqrt (x_ij*x_ij + y_ij*y_ij + z_ij*z_ij);
if (norm_j <= 0.) {continue;}
for (k = j+1; k < n0; k++) {
x_ik = x[i][0]-x[nearest_n0[k]][0];
y_ik = x[i][1]-x[nearest_n0[k]][1];
z_ik = x[i][2]-x[nearest_n0[k]][2];
norm_k = sqrt (x_ik*x_ik + y_ik*y_ik + z_ik*z_ik);
if (norm_k <= 0.) {continue;}
bond_angle = (x_ij*x_ik + y_ij*y_ik + z_ij*z_ik) / (norm_j*norm_k);
//find all bond angles that are about 180 degrees
if (-1. <= bond_angle && bond_angle < -0.945) {
x3[chi[0]] = x_ik - x_ij;
y3[chi[0]] = y_ik - y_ij;
z3[chi[0]] = z_ik - z_ij;
chi[0]++;
}
}
}
// for atoms that have 2 or 3 ~180 bond angles:
if (2 == chi[0] || 3 == chi[0]) {
count = value = 0;
if (chi[0] == 2) {
k2[0] = 0;
j1[0] = 1;
}
else {
k2[0] = 0;
k2[1] = 0;
k2[2] = 1;
j1[0]=1;
j1[1]=2;
j1[2]=2;
}
xmean5 = ymean5 = zmean5 = xmean6 = ymean6 = zmean6 = xmean7 = ymean7 = zmean7 = 0;
for (j = 0; j < chi[0]; j++) {
for (k = j+1; k < chi[0]; k++) {
//get cross products
x4[count] = y3[j1[count]]*z3[k2[count]]-y3[k2[count]]*z3[j1[count]];
y4[count] = z3[j1[count]]*x3[k2[count]]-z3[k2[count]]*x3[j1[count]];
z4[count] = x3[j1[count]]*y3[k2[count]]-x3[k2[count]]*y3[j1[count]];
//get all sign combinations of cross products
x5[count] = x4[count]*copysign(1.0,x4[count]);
y5[count] = y4[count]*copysign(1.0,x4[count]);
z5[count] = z4[count]*copysign(1.0,x4[count]);
x6[count] = x4[count]*copysign(1.0,y4[count]);
y6[count] = y4[count]*copysign(1.0,y4[count]);
z6[count] = z4[count]*copysign(1.0,y4[count]);
x7[count] = x4[count]*copysign(1.0,z4[count]);
y7[count] = y4[count]*copysign(1.0,z4[count]);
z7[count] = z4[count]*copysign(1.0,z4[count]);
//get average cross products
xmean5 = xmean5 + x5[count];
ymean5 = ymean5 + y5[count];
zmean5 = zmean5 + z5[count];
xmean6 = xmean6 + x6[count];
ymean6 = ymean6 + y6[count];
zmean6 = zmean6 + z6[count];
xmean7 = xmean7 + x7[count];
ymean7 = ymean7 + y7[count];
zmean6 = zmean6 + z7[count];
count++;
}
}
xmean5 = xmean5/count;
xmean6 = xmean6/count;
xmean7 = xmean7/count;
ymean5 = ymean5/count;
ymean6 = ymean6/count;
ymean7 = ymean7/count;
zmean5 = zmean5/count;
zmean6 = zmean6/count;
zmean7 = zmean7/count;
var5 = var6 = var7 = 0.0;
//find standard deviations
for (j=0;j<count;j++){
var5 = var5 + x5[j]*x5[j]-2*x5[j]*xmean5+xmean5*xmean5+y5[j]*y5[j]-2*y5[j]*ymean5+ymean5*ymean5+z5[j]*z5[j]-2*z5[j]*zmean5+zmean5*zmean5;
var6 = var6 + x6[j]*x6[j]-2*x6[j]*xmean6+xmean6*xmean6+y6[j]*y6[j]-2*y6[j]*ymean6+ymean6*ymean6+z6[j]*z6[j]-2*z6[j]*zmean6+zmean6*zmean6;
var7 = var7 + x7[j]*x7[j]-2*x7[j]*xmean7+xmean7*xmean7+y7[j]*y7[j]-2*y7[j]*ymean7+ymean7*ymean7+z7[j]*z7[j]-2*z7[j]*zmean7+zmean7*zmean7;
}
//select sign combination with minimum standard deviation
if (var5 < var6) {
if (var5 < var7) { value = 0;}
else {value = 2;}
}
else if (var6 < var7) {value = 1;}
else {value = 2;}
//BPV is average of cross products of all neighbor vectors which are part of 180 degree angles
BPV[i][0] = 0;
BPV[i][1] = 0;
BPV[i][2] = 0;
for (k=0;k<count;k++) {
if (value == 0){
BPV[i][0] = BPV[i][0]+x5[k];
BPV[i][1] = BPV[i][1]+y5[k];
BPV[i][2] = BPV[i][2]+z5[k];
}
else if (value == 1) {
BPV[i][0] = BPV[i][0]+x6[k];
BPV[i][1] = BPV[i][1]+y6[k];
BPV[i][2] = BPV[i][2]+z6[k];
}
else {
BPV[i][0] = BPV[i][0]+x7[k];
BPV[i][1] = BPV[i][1]+y7[k];
BPV[i][2] = BPV[i][2]+z7[k];
}
}
}
//for atoms with more than three 180 degree bond angles:
else if (chi[0] > 3) {
double x44[3], y44[3], z44[3], S0;
int l, m;
count = value = 0;
S0 = 100000;
k2[0] = 0;
k2[1] = 0;
k2[2] = 1;
j1[0]=1;
j1[1]=2;
j1[2]=2;
//algorithm is as above, but now all combinations of three 180 degree angles are compared, and the combination with minimum standard deviation is chosen
for (j=0; j<chi[0]; j++) {
for (k=j+1; k<chi[0]; k++) {
for (l=k+1; l<chi[0]; l++) {
if (k >= chi[0] || l >= chi[0]) continue;
//get unique combination of three neighbor vectors
x4[0] = x3[j];
x4[1] = x3[k];
x4[2] = x3[l];
y4[0] = y3[j];
y4[1] = y3[k];
y4[2] = y3[l];
z4[0] = z3[j];
z4[1] = z3[k];
z4[2] = z3[l];
xmean5 = ymean5 = zmean5 = xmean6 = ymean6 = zmean6 = xmean7 = ymean7 = zmean7 = 0;
for (m=0;m<3;m++) {
//get cross products
x44[m] = y4[j1[m]]*z4[k2[m]]-y4[k2[m]]*z4[j1[m]];
y44[m] = z4[j1[m]]*x4[k2[m]]-z4[k2[m]]*x4[j1[m]];
z44[m] = x4[j1[m]]*y4[k2[m]]-x4[k2[m]]*y4[j1[m]];
x5[m] = x44[m]*copysign(1.0,x44[m]);
y5[m] = y44[m]*copysign(1.0,x44[m]);
z5[m] = z44[m]*copysign(1.0,x44[m]);
x6[m] = x44[m]*copysign(1.0,y44[m]);
y6[m] = y44[m]*copysign(1.0,y44[m]);
z6[m] = z44[m]*copysign(1.0,y44[m]);
x7[m] = x44[m]*copysign(1.0,z44[m]);
y7[m] = y44[m]*copysign(1.0,z44[m]);
z7[m] = z44[m]*copysign(1.0,z44[m]);
//get average cross products
xmean5 = xmean5 + x5[m];
ymean5 = ymean5 + y5[m];
zmean5 = zmean5 + z5[m];
xmean6 = xmean6 + x6[m];
ymean6 = ymean6 + y6[m];
zmean6 = zmean6 + z6[m];
xmean7 = xmean7 + x7[m];
ymean7 = ymean7 + y7[m];
zmean6 = zmean6 + z7[m];
}
xmean5 = xmean5/3;
xmean6 = xmean6/3;
xmean7 = xmean7/3;
ymean5 = ymean5/3;
ymean6 = ymean6/3;
ymean7 = ymean7/3;
zmean5 = zmean5/3;
zmean6 = zmean6/3;
zmean7 = zmean7/3;
var5 = var6 = var7 = 0;
//get standard deviations
for (m=0;m<3;m++){
var5 = var5 + x5[m]*x5[m]-2*x5[m]*xmean5+xmean5*xmean5+y5[m]*y5[m]-2*y5[m]*ymean5+ymean5*ymean5+z5[m]*z5[m]-2*z5[m]*zmean5+zmean5*zmean5;
var6 = var6 + x6[m]*x6[m]-2*x6[m]*xmean6+xmean6*xmean6+y6[m]*y6[m]-2*y6[m]*ymean6+ymean6*ymean6+z6[m]*z6[m]-2*z6[m]*zmean6+zmean6*zmean6;
var7 = var7 + x7[m]*x7[m]-2*x7[m]*xmean7+xmean7*xmean7+y7[m]*y7[m]-2*y7[m]*ymean7+ymean7*ymean7+z7[m]*z7[m]-2*z7[m]*zmean7+zmean7*zmean7;
}
//choose minimum standard deviation
if (var5 < S0) {
S0 = var5;
BPV[i][0] = (x5[0]+x5[1]+x5[2])/3;
BPV[i][1] = (y5[0]+y5[1]+x5[2])/3;
BPV[i][2] = (z5[0]+z5[1]+z5[2])/3;
}
if (var6 < S0) {
S0 = var6;
BPV[i][0] = (x6[0]+x6[1]+x6[2])/3;
BPV[i][1] = (y6[0]+y6[1]+x6[2])/3;
BPV[i][2] = (z6[0]+z6[1]+z6[2])/3;
}
if (var7 < S0) {
S0 = var7;
BPV[i][0] = (x7[0]+x7[1]+x7[2])/3;
BPV[i][1] = (y7[0]+y7[1]+x7[2])/3;
BPV[i][2] = (z7[0]+z7[1]+z7[2])/3;
}
}
}
}
}
//if there are less than two ~180 degree bond angles, the algorithm returns null
else {
BPV[i][0] = 0.0;
BPV[i][1] = 0.0;
BPV[i][2] = 0.0;
}
//normalize BPV:
double Mag = sqrt(BPV[i][0]*BPV[i][0] +
BPV[i][1]*BPV[i][1] + BPV[i][2]*BPV[i][2]);
if (Mag > 0){
BPV[i][0] = BPV[i][0]/Mag;
BPV[i][1] = BPV[i][1]/Mag;
BPV[i][2] = BPV[i][2]/Mag;
}
}
}
}
/* ----------------------------------------------------------------------
2 select routines from Numerical Recipes (slightly modified)
find k smallest values in array of length n
2nd routine sorts auxiliary array at same time
------------------------------------------------------------------------- */
#define SWAP(a,b) tmp = a; a = b; b = tmp;
#define ISWAP(a,b) itmp = a; a = b; b = itmp;
void ComputeBasalAtom::select(int k, int n, double *arr)
{
int i,ir,j,l,mid;
double a,tmp;
arr--;
l = 1;
ir = n;
for (;;) {
if (ir <= l+1) {
if (ir == l+1 && arr[ir] < arr[l]) {
SWAP(arr[l],arr[ir])
}
return;
} else {
mid=(l+ir) >> 1;
SWAP(arr[mid],arr[l+1])
if (arr[l] > arr[ir]) {
SWAP(arr[l],arr[ir])
}
if (arr[l+1] > arr[ir]) {
SWAP(arr[l+1],arr[ir])
}
if (arr[l] > arr[l+1]) {
SWAP(arr[l],arr[l+1])
}
i = l+1;
j = ir;
a = arr[l+1];
for (;;) {
do i++; while (arr[i] < a);
do j--; while (arr[j] > a);
if (j < i) break;
SWAP(arr[i],arr[j])
}
arr[l+1] = arr[j];
arr[j] = a;
if (j >= k) ir = j-1;
if (j <= k) l = i;
}
}
}
/* ---------------------------------------------------------------------- */
void ComputeBasalAtom::select2(int k, int n, double *arr, int *iarr)
{
int i,ir,j,l,mid,ia,itmp;
double a,tmp;
arr--;
iarr--;
l = 1;
ir = n;
for (;;) {
if (ir <= l+1) {
if (ir == l+1 && arr[ir] < arr[l]) {
SWAP(arr[l],arr[ir])
ISWAP(iarr[l],iarr[ir])
}
return;
} else {
mid=(l+ir) >> 1;
SWAP(arr[mid],arr[l+1])
ISWAP(iarr[mid],iarr[l+1])
if (arr[l] > arr[ir]) {
SWAP(arr[l],arr[ir])
ISWAP(iarr[l],iarr[ir])
}
if (arr[l+1] > arr[ir]) {
SWAP(arr[l+1],arr[ir])
ISWAP(iarr[l+1],iarr[ir])
}
if (arr[l] > arr[l+1]) {
SWAP(arr[l],arr[l+1])
ISWAP(iarr[l],iarr[l+1])
}
i = l+1;
j = ir;
a = arr[l+1];
ia = iarr[l+1];
for (;;) {
do i++; while (arr[i] < a);
do j--; while (arr[j] > a);
if (j < i) break;
SWAP(arr[i],arr[j])
ISWAP(iarr[i],iarr[j])
}
arr[l+1] = arr[j];
arr[j] = a;
iarr[l+1] = iarr[j];
iarr[j] = ia;
if (j >= k) ir = j-1;
if (j <= k) l = i;
}
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double ComputeBasalAtom::memory_usage()
{
double bytes = 3*nmax * sizeof(double);
return bytes;
}
src/USER-MISC/compute_basal_atom.h 0 → 100644
+ 50
− 0
View file @ 0bdf6303
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef COMPUTE_CLASS
ComputeStyle(basal/atom,ComputeBasalAtom)
#else
#ifndef LMP_COMPUTE_BASAL_ATOM_H
#define LMP_COMPUTE_BASAL_ATOM_H
#include "compute.h"
namespace LAMMPS_NS {
class ComputeBasalAtom : public Compute {
public:
ComputeBasalAtom(class LAMMPS *, int, char **);
~ComputeBasalAtom();
void init();
void init_list(int, class NeighList *);
void compute_peratom();
double memory_usage();
private:
int nmax,maxneigh;
double *distsq;
int *nearest, *nearest_n0, *nearest_n1;
double **BPV;
class NeighList *list;
void select(int, int, double *);
void select2(int, int, double *, int *);
};
}
#endif
#endif
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