Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/tools/phonon/green.cpp
ae3e0a6678e9efficient_neuronet

Last Change
Raw File

green.cpp
View Options

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include "green.h"
#include <complex>
#define MAXLINE 256
/*******************************************************************************
* The class of Green is designed to evaluate the LDOS via the Green's Function
* method. The meaning of input/output parameters are as follows:
*
* ntm (input, value) total number of atoms in system
* sdim (input, value) dimension of the system; usually 3
* niter (input, value) maximum iterations during Lanczos diagonalization
* min (input, value) minimum value for the angular frequency
* max (input, value) maximum value for the angular frequency
* ndos (input, value) total number of points in LDOS
* eps (input, value) epson that govens the width of delta-function
* Hessian (input, pointer of pointer) mass-weighted force constant matrix, of
* dimension [natom*sysdim][natm*sysdim]; it is actually
* the dynamical matrix at gamma point
* itm (input, value) index of the atom to evaluate local phonon DOS, from 0
* lpdos (output, array) double array of size (ndos, sdim)
*******************************************************************************
* References:
* 1. Z. Tang and N. R. Aluru, Phys. Rev. B 74, 235441 (2006).
* 2. C. Hudon, R. Meyer, and L.J. Lewis, Phys. Rev. B 76, 045409 (2007).
* 3. L.T. Kong and L.J. Lewis, Phys. Rev. B 77, 165422 (2008).
*
* NOTE: The real-space Green's function method is not expected to work accurately
* for small systems, say, system (unit cell) less than 500 atoms.
*******************************************************************************/
/*------------------------------------------------------------------------------
* Constructor is used as the main driver
*----------------------------------------------------------------------------*/
Green::Green(const int ntm, const int sdim, const int niter, const double min, const double max,
const int ndos, const double eps, double **Hessian, const int itm, double **lpdos)
{
const double tpi = 8.*atan(1.);
natom = ntm; sysdim = sdim; nit = niter; epson = eps;
wmin = min*tpi; wmax = max*tpi; nw = ndos + (ndos+1)%2;
H = Hessian; iatom = itm;
ldos = lpdos;
memory = new Memory;
if (natom < 1 || iatom < 0 || iatom >= natom){
printf("\nError: Wrong number of total atoms or wrong index of interested atom!\n");
return;
}
ndim = natom * sysdim;
if (nit < 1){printf("\nError: Wrong input of maximum iterations!\n"); return;}
if (nit > ndim){printf("\nError: # Lanczos iterations is not expected to exceed the degree of freedom!\n"); return;}
if (nw < 1){printf("\nError: Wrong input of points in LDOS!\n"); return;}
// initialize variables and allocate local memories
dw = (wmax - wmin)/double(nw-1);
alpha = memory->create(alpha, sysdim,nit, "Green_Green:alpha");
beta = memory->create(beta, sysdim,nit+1,"Green_Green:beta");
//ldos = memory->create(ldos, nw,sysdim, "Green_Green:ldos");
// use Lanczos algorithm to diagonalize the Hessian
Lanczos();
// Get the inverser of the treated hessian by continued fractional method
Recursion();
return;
}
/*------------------------------------------------------------------------------
* Deconstructor is used to free memory
*----------------------------------------------------------------------------*/
Green::~Green()
{
H = NULL;
ldos = NULL;
memory->destroy(alpha);
memory->destroy(beta);
delete memory;
return;
}
/*------------------------------------------------------------------------------
* Private method to diagonalize a matrix by the Lanczos algorithm
*----------------------------------------------------------------------------*/
void Green::Lanczos()
{
double *vp, *v, *w, *ptr;
vp = new double [ndim];
v = new double [ndim];
w = new double [ndim];
int ipos = iatom*sysdim;
// Loop over dimension
for (int idim=0; idim<sysdim; idim++){
beta[idim][0] = 0.;
for (int i=0; i<ndim; i++){vp[i] = v[i] = 0.;}
v[ipos+idim] = 1.;
// Loop on fraction levels
for (int i=0; i<nit; i++){
double sum_a = 0.;
for (int j=0; j<ndim; j++){
double sumHv = 0.;
for (int k=0; k<ndim; k++) sumHv += H[j][k]*v[k];
w[j] = sumHv - beta[idim][i]*vp[j];
sum_a += w[j]*v[j];
}
alpha[idim][i] = sum_a;
for (int k=0; k<ndim; k++) w[k] -= alpha[idim][i]*v[k];
double gamma = 0.;
for (int k=0; k<ndim; k++) gamma += w[k]*v[k];
for (int k=0; k<ndim; k++) w[k] -= gamma*v[k];
double sum_b = 0.;
for (int k=0; k<ndim; k++) sum_b += w[k]*w[k];
beta[idim][i+1] = sqrt(sum_b);
ptr = vp; vp = v; v = ptr;
double tmp = 1./beta[idim][i+1];
for (int k=0; k<ndim; k++) v[k] = w[k]*tmp;
}
}
ptr = NULL;
delete []vp;
delete []v;
delete []w;
return;
}
/*------------------------------------------------------------------------------
* Private method to compute the LDOS via the recusive method for system with
* many atoms
*----------------------------------------------------------------------------*/
void Green::Recursion()
{
// local variables
double *alpha_inf, *beta_inf, *xmin, *xmax;
alpha_inf = new double [sysdim];
beta_inf = new double [sysdim];
xmin = new double [sysdim];
xmax = new double [sysdim];
int nave = nit/4;
for (int idim=0; idim<sysdim; idim++){
alpha_inf[idim] = beta_inf[idim] = 0.;
for (int i= nit-nave; i<nit; i++){
alpha_inf[idim] += alpha[idim][i];
beta_inf[idim] += beta[idim][i+1];
}
alpha_inf[idim] /= double(nave);
beta_inf[idim] /= double(nave);
xmin[idim] = alpha_inf[idim] - 2.*beta_inf[idim];
xmax[idim] = alpha_inf[idim] + 2.*beta_inf[idim];
}
std::complex<double> Z, z_m_a, r_x, rec_x, rec_x_inv;
double sr, si;
double w = wmin;
for (int i=0; i<nw; i++){
double a = w*w, ax, bx;
Z = std::complex<double>(w*w, epson);
for (int idim=0; idim<sysdim; idim++){
double two_b = 2.*beta_inf[idim]*beta_inf[idim];
double rtwob = 1./two_b;
z_m_a = Z - alpha_inf[idim]*alpha_inf[idim];
if ( a < xmin[idim] ){
r_x = sqrt(-2.*two_b + z_m_a);
ax = std::real(r_x) * rtwob;
bx = std::imag(r_x) * rtwob;
} else if (a > xmax[idim]) {
r_x = sqrt(-2.*two_b + z_m_a);
ax = -std::real(r_x) * rtwob;
bx = -std::imag(r_x) * rtwob;
} else {
r_x = sqrt(2.*two_b - z_m_a);
ax = std::imag(r_x) * rtwob;
bx = -std::real(r_x) * rtwob;
}
sr = (a - alpha_inf[idim])*rtwob + ax;
si = epson * rtwob + bx;
rec_x = std::complex<double> (sr, si);
for (int j=0; j<nit; j++){
rec_x_inv = Z - alpha[idim][nit-j-1] - beta[idim][nit-j]*beta[idim][nit-j]*rec_x;
rec_x = 1./rec_x_inv;
}
ldos[i][idim] = std::imag(rec_x)*w;
}
w += dw;
}
delete []alpha_inf;
delete []beta_inf;
delete []xmin;
delete []xmax;
return;
}
/*------------------------------------------------------------------------------
* Private method to compute the LDOS via the recusive method for system with
* a few atoms (less than NMAX)
*----------------------------------------------------------------------------*/
void Green::recursion()
{
// local variables
std::complex<double> Z, rec_x, rec_x_inv;
std::complex<double> cunit = std::complex<double>(0.,1.);
double w = wmin;
for (int i=0; i<nw; i++){
Z = std::complex<double>(w*w, epson);
for (int idim=0; idim<sysdim; idim++){
rec_x = std::complex<double>(0.,0.);
for (int j=0; j<nit; j++){
rec_x_inv = Z - alpha[idim][nit-j-1] - beta[idim][nit-j]*beta[idim][nit-j]*rec_x;
rec_x = 1./rec_x_inv;
}
ldos[i][idim] = std::imag(rec_x)*w;
}
w += dw;
}
return;
}
/*------------------------------------------------------------------------------*/
c4science · Help