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atom.cpp
453 lines (365 loc) · 10.4 KB
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atom.cpp
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#include "atom.h"
#include <iostream>
#include <iomanip>
#include <algorithm>
#include <stdio.h>
#include "string.h"
#include <chrono>
#include <pybind11/stl.h>
#include <complex>
//-------------------------------------------------------
// Constructor, Destructor
//-------------------------------------------------------
Atom::Atom( vector<double> pos, int idd, int typ){
posx = pos[0];
posy = pos[1];
posz = pos[2];
id = idd;
type = typ;
ghost = 0;
//assign other values - the default ones
belongsto = -1;
issolid = 0;
issurface = 0;
loc = 0;
isneighborset = 0;
n_neighbors = 0;
lcluster = 0;
head = -1;
entropy = 0;
avg_entropy = 0;
energy = 0;
avg_energy = 0;
for (int tn = 0; tn<MAXNUMBEROFNEIGHBORS; tn++){
neighbors[tn] = -1;
neighbordist[tn] = -1.0;
neighborweight[tn] = -1.0;
facevertices[tn] = -1;
faceverticenumbers[tn] = -1;
faceperimeters[tn] = -1.0;
sij[tn] = -1.0;
masks[tn] = -1;
//edgelengths[tn] = -1.0;
}
for (int tn = 0; tn<11; tn++){
q[tn] = -1;
aq[tn] = -1;
for (int tnn =0; tnn<25; tnn++){
realq[tn][tnn] = -1;
imgq[tn][tnn] = -1;
arealq[tn][tnn] = -1;
aimgq[tn][tnn] = -1;
}
}
}
Atom::~Atom(){ }
//-------------------------------------------------------
// Basic Atom properties
//-------------------------------------------------------
//aceesss funcs
vector<double> Atom::gx(){
vector<double> pos;
pos.emplace_back(posx);
pos.emplace_back(posy);
pos.emplace_back(posz);
return pos;
}
void Atom::sx(vector<double> rls){
posx = rls[0];
posy = rls[1];
posz = rls[2];
}
//-------------------------------------------------------
// Neighbor related properties
//-------------------------------------------------------
vector<int> Atom::gneighbors(){
vector<int> nn;
nn.reserve(n_neighbors);
for(int i=0;i<n_neighbors;i++){
nn.emplace_back(neighbors[i]);
}
return nn;
}
void Atom::sneighdist(vector<double> dd){
}
vector<double> Atom::gneighdist(){
vector<double> neighdist;
for(int i=0; i<n_neighbors; i++){
neighdist.emplace_back(neighbordist[i]);
}
return neighdist;
}
void Atom::sneighbors(vector<int> nns){
//first reset all neighbors
for (int i = 0;i<MAXNUMBEROFNEIGHBORS;i++){
neighbors[i] = NILVALUE;
neighbordist[i] = -1.0;
}
//now assign the neighbors
for(int i=0; i<nns.size(); i++){
neighbors[i] = nns[i];
//auto assign weight to 1
neighborweight[i] = 1.00;
}
n_neighbors = nns.size();
isneighborset = 1;
}
void Atom::sneighborweights(vector<double> nss){
for(int i=0; i<nss.size(); i++){
neighborweight[i] = nss[i];
}
}
vector<double> Atom::gneighborweights(){
vector <double> rqlms;
for(int i=0; i<n_neighbors; i++){
rqlms.emplace_back(neighborweight[i]);
}
return rqlms;
}
void Atom::sdistvecs(vector<vector<double>> nss){
}
vector<vector<double>> Atom::gdistvecs(){
vector<vector<double>> m1;
vector <double> m2;
for(int i=0; i<n_neighbors; i++){
m2.clear();
m2.emplace_back(n_diffx[i]);
m2.emplace_back(n_diffy[i]);
m2.emplace_back(n_diffz[i]);
m1.emplace_back(m2);
}
return m1;
}
void Atom::slocalangles(vector<vector<double>> nss){
}
vector<vector<double>> Atom::glocalangles(){
vector<vector<double>> m1;
vector <double> m2;
for(int i=0; i<n_neighbors; i++){
m2.clear();
m2.emplace_back(n_phi[i]);
m2.emplace_back(n_theta[i]);
m1.emplace_back(m2);
}
return m1;
}
//-------------------------------------------------------
// Q parameter properties
//-------------------------------------------------------
void Atom::ssij(vector<double> dd){
}
vector<double> Atom::gsij(){
vector<double> ss;
for(int i=0; i<n_neighbors; i++){
ss.emplace_back(sij[i]);
}
return ss;
}
vector<double> Atom::gallq(){
vector<double> allq;
for(int i=0; i<11; i++){
allq.emplace_back(q[i]);
}
return allq;
}
vector<double> Atom::gallaq(){
vector<double> allq;
for(int i=0; i<11; i++){
allq.emplace_back(aq[i]);
}
return allq;
}
void Atom::sallq(vector<double> allq){
for(int i=0; i<11; i++){
q[i] = allq[i];
}
}
void Atom::sallaq(vector<double> allaq){
for(int i=0; i<11; i++){
aq[i] = allaq[i];
}
}
double Atom::gq(int qq){ return q[qq-2]; }
void Atom::sq(int qq, double qval){ q[qq-2] = qval; }
double Atom::gaq(int qq){ return aq[qq-2]; }
void Atom::saq(int qq, double qval){ aq[qq-2] = qval; }
double Atom::gq_big(int qval, bool averaged){
if ((qval < 2) || (qval > 12)){
throw invalid_argument("q value should be between 2-12");
}
if(averaged == true) { return gaq(qval);}
else {return gq(qval);}
}
void Atom::sq_big(int qval, double val, bool averaged){
if ((qval < 2) || (qval > 12)){
throw invalid_argument("q value should be between 2-12");
}
if(averaged == true) { saq(qval, val);}
else { sq(qval, val);}
}
//overloaded version which takes a vector
vector<double> Atom::gq_big(vector<int> qval, bool averaged ){
int d;
if(averaged == true) {
vector<double> retvals;
for(int i=0; i<qval.size(); i++){
if ((qval[i] < 2) || (qval[i] > 12)){
throw invalid_argument("q value should be between 2-12");
}
retvals.push_back(gaq(qval[i]));
}
return retvals;
}
else {
vector<double> retvals;
for(int i=0; i<qval.size(); i++){
if ((qval[i] < 2) || (qval[i] > 12)){
throw invalid_argument("q value should be between 2-12");
}
retvals.push_back(gq(qval[i]));
}
return retvals;
}
}
//overloaded version which takes a vector
void Atom::sq_big(vector<int> qval, vector<double> setvals, bool averaged){
if(averaged == true) {
for(int i=0; i<qval.size(); i++){
if ((qval[i] < 2) || (qval[i] > 12)){
throw invalid_argument("q value should be between 2-12");
}
saq(qval[i], setvals[i]);
}
}
else {
for(int i=0; i<qval.size(); i++){
if ((qval[i] < 2) || (qval[i] > 12)){
throw invalid_argument("q value should be between 2-12");
}
sq(qval[i], setvals[i]);
}
}
}
vector<complex<double>> Atom::get_qcomps(int qq, bool averaged){
vector<complex<double>> qlms;
qlms.reserve(2*qq+1);
if (!averaged){
for(int i=0;i<(2*qq+1);i++){
complex<double> lmval(realq[qq-2][i], imgq[qq-2][i]);
qlms.emplace_back(lmval);
}
}
else{
for(int i=0;i<(2*qq+1);i++){
complex<double> lmval(arealq[qq-2][i], aimgq[qq-2][i]);
qlms.emplace_back(lmval);
}
}
return qlms;
}
//-------------------------------------------------------
// Solid related properties
//-------------------------------------------------------
//-------------------------------------------------------
// Voronoi related properties
//-------------------------------------------------------
void Atom::sfacevertices(vector<int> nss){
for(int i=0; i<nss.size(); i++){
facevertices[i] = nss[i];
}
}
vector<int> Atom::gfacevertices(){
vector <int> rqlms;
for(int i=0; i<n_neighbors; i++){
rqlms.emplace_back(facevertices[i]);
}
return rqlms;
}
void Atom::sfaceperimeters(vector<double> nss){
for(int i=0; i<nss.size(); i++){
faceperimeters[i] = nss[i];
}
}
vector<double> Atom::gfaceperimeters(){
vector <double> rqlms;
for(int i=0; i<n_neighbors; i++){
rqlms.emplace_back(faceperimeters[i]);
}
return rqlms;
}
void Atom::sedgelengths(vector<vector<double>> nss){
edgelengths.clear();
edgelengths = nss;
}
vector<vector<double>> Atom::gedgelengths(){
return edgelengths;
}
void Atom::svertexpositions(vector<vector<double>> nss){
vertex_positions.clear();
vertex_positions = nss;
}
vector<vector<double>> Atom::gvertexpositions(){
return vertex_positions;
}
vector<int> Atom::gvorovector(){
vector<int> voro;
voro.emplace_back(n3);
voro.emplace_back(n4);
voro.emplace_back(n5);
voro.emplace_back(n6);
return voro;
}
void Atom::svorovector(vector<int> voro){
n3 = voro[0];
n4 = voro[1];
n5 = voro[2];
n6 = voro[3];
}
//-------------------------------------------------------
// Angle related properties
//-------------------------------------------------------
//-------------------------------------------------------
// Other order parameters
//-------------------------------------------------------
double Atom::gmr(double r)
{
double g = 0.00;
double rij,r2;
double sigma2 = sigma*sigma;
double frho = 4.00*PI*rho*r*r;
double fsigma = sqrt(2.00*PI*sigma2);
double factor = (1.00/frho)*(1.00/fsigma);
for(int i=0; i<n_neighbors; i++)
{
rij = neighbordist[i];
r2 = (r-rij)*(r-rij);
g+=exp((-1.00*r2)/(2.00*sigma2));
}
return factor*g;
}
//function which is to be integrated
double Atom::entropy_integrand(double r)
{
double g = gmr(r);
return ((g*log(g)-g +1.00)*r*r);
}
void Atom::trapezoid_integration()
{
int nsteps = (rstop - rstart)/h;
double summ;
double xstart, xend;
summ=0.00;
double rloop;
double integral;
xstart = entropy_integrand(rstart);
for(int j=1; j<nsteps-1; j++)
{
rloop = rstart + j*h;
summ += entropy_integrand(rloop);
}
xend = entropy_integrand(rstart + nsteps*h);
integral = (h/2.00)*(xstart + 2.00*summ + xend);
//cout<<xstart<<endl;
integral = -1.*rho*kb*integral;
entropy = integral;
}