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Move material properties-related stuff to materials.[ch] 

Former-commit-id: 0039b167488c5aca55ea1912e43ec3ab8b289c1e
This commit is contained in:
Marek Nečada 2019-08-08 15:33:06 +03:00
parent b9c72cf333
commit 8158cef41c
8 changed files with 227 additions and 200 deletions
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2
qpms/CMakeLists.txt
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@ -12,7 +12,7 @@ include_directories(${DIRS})
add_library (qpms translations.c tmatrices.c vecprint.c vswf.c wigner.c
lattices2d.c gaunt.c error.c legendre.c symmetries.c vecprint.c
bessel.c own_zgemm.c parsing.c scatsystem.c)
bessel.c own_zgemm.c parsing.c scatsystem.c materials.c)
use_c99()
set(LIBS ${LIBS} ${GSL_LIBRARIES} ${GSLCBLAS_LIBRARIES})

142
qpms/materials.c Normal file
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@ -0,0 +1,142 @@
#define _POSIX_C_SOURCE 200809L // for getline()
#include <stdio.h>
#include <stddef.h>
#include <unistd.h>
#include <string.h>
#include "materials.h"
#include "qpms_error.h"
#define SPEED_OF_LIGHT (2.99792458e8)
qpms_permittivity_interpolator_t *qpms_permittivity_interpolator_create(
const size_t incount, const double *wavelen_m, const double *n, const double *k,
const gsl_interp_type *iptype)
{
if (incount <= 0) return NULL;
qpms_permittivity_interpolator_t *ip;
QPMS_CRASHING_MALLOC(ip, sizeof(qpms_permittivity_interpolator_t));
ip->size = incount;
QPMS_CRASHING_MALLOC(ip->wavelength_m, incount * sizeof(double));
QPMS_CRASHING_MALLOC(ip->n, incount * sizeof(double));
QPMS_CRASHING_MALLOC(ip->k, incount * sizeof(double));
memcpy(ip->wavelength_m, wavelen_m, incount*sizeof(double));
memcpy(ip->k, k, incount*sizeof(double));
memcpy(ip->n, n, incount*sizeof(double));
ip->interp_n = gsl_interp_alloc(iptype, incount);
ip->interp_k = gsl_interp_alloc(iptype, incount);
QPMS_ENSURE_SUCCESS(gsl_interp_init(ip->interp_n, ip->wavelength_m, ip->n, incount));
QPMS_ENSURE_SUCCESS(gsl_interp_init(ip->interp_k, ip->wavelength_m, ip->k, incount));
return ip;
}
void qpms_permittivity_interpolator_free(qpms_permittivity_interpolator_t *interp)
{
if(interp) {
gsl_interp_free(interp->interp_n);
gsl_interp_free(interp->interp_k);
free(interp->n);
free(interp->k);
free(interp->wavelength_m);
}
free(interp);
}
qpms_errno_t qpms_read_refractiveindex_yml(
FILE *f, ///< file handle
size_t *const count, ///< Number of successfully loaded triples.
double* *const lambdas_m, ///< Vacuum wavelengths in metres.
double* *const n, ///< Read refraction indices.
double* *const k ///< Read attenuation coeffs.
)
{
QPMS_ENSURE(f && lambdas_m && n && k,"f, lambdas_m, n, k are mandatory arguments and must not be NULL.");
int count_alloc = 128; // First chunk to allocate
*count = 0;
QPMS_CRASHING_MALLOC(*lambdas_m, count_alloc * sizeof(double));
QPMS_CRASHING_MALLOC(*n, count_alloc * sizeof(double));
QPMS_CRASHING_MALLOC(*k, count_alloc * sizeof(double));
size_t linebufsz = 256;
char *linebuf;
QPMS_CRASHING_MALLOC(linebuf, linebufsz);
ssize_t readchars;
bool data_started = false;
while((readchars = getline(&linebuf, &linebufsz, f)) != -1) {
if (linebuf[0] == '#') continue;
// We need to find the beginning of the tabulated data; everything before that is ignored.
if (!data_started) {
char *test = strstr(linebuf, "data: |");
if(test) data_started = true;
continue;
}
if (3 == sscanf(linebuf, "%lf %lf %lf", *lambdas_m + *count, *n + *count , *k + *count)) {
(*lambdas_m)[*count] *= 1e-6; // The original data is in micrometres.
++*count;
if (*count > count_alloc) {
count_alloc *= 2;
QPMS_CRASHING_REALLOC(*lambdas_m, count_alloc * sizeof(double));
QPMS_CRASHING_REALLOC(*n, count_alloc * sizeof(double));
QPMS_CRASHING_REALLOC(*k, count_alloc * sizeof(double));
}
} else break;
}
QPMS_ENSURE(*count > 0, "Could not read any refractive index data; the format must be wrong!");
free(linebuf);
return QPMS_SUCCESS;
}
qpms_errno_t qpms_load_refractiveindex_yml(
const char *path,
size_t *const count, ///< Number of successfully loaded triples.
double* *const lambdas_m, ///< Vacuum wavelengths in metres.
double* *const n, ///< Read refraction indices.
double* *const k ///< Read attenuation coeffs.
)
{
FILE *f = fopen(path, "r");
QPMS_ENSURE(f, "Could not open refractive index file %s", path);
qpms_errno_t retval =
qpms_read_refractiveindex_yml(f, count, lambdas_m, n, k);
QPMS_ENSURE_SUCCESS(fclose(f));
return retval;
}
qpms_permittivity_interpolator_t *qpms_permittivity_interpolator_from_yml(
const char *path, ///< Path to the yml file.
const gsl_interp_type *iptype ///< GSL interpolator type
)
{
size_t count;
double *lambdas_m, *n, *k;
QPMS_ENSURE_SUCCESS(qpms_load_refractiveindex_yml(path, &count, &lambdas_m, &n, &k));
qpms_permittivity_interpolator_t *ip = qpms_permittivity_interpolator_create(
count, lambdas_m, n, k, iptype);
free(lambdas_m);
free(n);
free(k);
return ip;
}
complex double qpms_permittivity_interpolator_eps_at_omega(
const qpms_permittivity_interpolator_t *ip, double omega_SI)
{
double lambda, n, k;
lambda = 2*M_PI*SPEED_OF_LIGHT/omega_SI;
n = gsl_interp_eval(ip->interp_n, ip->wavelength_m, ip->n, lambda, NULL);
k = gsl_interp_eval(ip->interp_k, ip->wavelength_m, ip->k, lambda, NULL);
complex double epsilon = n*n - k*k + 2*n*k*I;
return epsilon;
}
double qpms_permittivity_interpolator_omega_max(
const qpms_permittivity_interpolator_t *ip)
{
return 2*M_PI*SPEED_OF_LIGHT / ip->wavelength_m[0];
}
double qpms_permittivity_interpolator_omega_min(
const qpms_permittivity_interpolator_t *ip)
{
return 2*M_PI*SPEED_OF_LIGHT / ip->wavelength_m[ip->size-1];
}

61
qpms/materials.h Normal file
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@ -0,0 +1,61 @@
/* \file materials.h
* \brief Optical properties of materials.
*/
#ifndef QPMS_MATERIALS_H
#define QPMS_MATERIALS_H
#include "qpms_types.h"
#include <gsl/gsl_spline.h>
/// Interpolator of tabulated optical properties.
// TODO use gsl_interp instead of gsl_spline.
typedef struct qpms_permittivity_interpolator_t {
double *wavelength_m; ///< Wavelength array (in meters).
double *n; ///< Refraction index array.
double *k; ///< Attenuation coefficient array.
gsl_interp *interp_n; ///< Refraction index interpolator object.
gsl_interp *interp_k; ///< Attenuation coeff interpolator object.
size_t size; ///< Size of n[], k[], and wavelength_m[].
// I could add gsl_interp_accel, but that is not necessary.
} qpms_permittivity_interpolator_t;
/// Creates a permittivity interpolator from tabulated wavelengths, refraction indices and extinction coeffs.
qpms_permittivity_interpolator_t *qpms_permittivity_interpolator_create(const size_t incount,
const double *wavelength_m, ///< Tabulated vacuum wavelength in metres, in strictly increasing order.
const double *n, ///< Tabulated refraction indices at omega.
const double *k, ///< Tabulated extinction coefficients.
const gsl_interp_type *iptype ///< GSL interpolator type
);
/// Creates a permittivity interpolator from an yml file downloaded from refractiveindex.info website.
qpms_permittivity_interpolator_t *qpms_permittivity_interpolator_from_yml(
const char *path, ///< Path to the yml file.
const gsl_interp_type *iptype ///< GSL interpolator type
);
/// Evaluates interpolated material permittivity at a given angular frequency.
complex double qpms_permittivity_interpolator_eps_at_omega(
const qpms_permittivity_interpolator_t *interp, double omega_SI);
/// Returns the minimum angular frequency supported by the interpolator.
double qpms_permittivity_interpolator_omega_min(
const qpms_permittivity_interpolator_t *ip);
/// Returns the minimum angular frequency supported by the interpolator.
double qpms_permittivity_interpolator_omega_max(
const qpms_permittivity_interpolator_t *ip);
/// Destroy a permittivity interpolator.
void qpms_permittivity_interpolator_free(qpms_permittivity_interpolator_t *interp);
/// Relative permittivity from the Drude model.
static inline complex double qpms_drude_epsilon(
complex double eps_inf, ///< Relative permittivity "at infinity".
complex double omega_p, ///< Plasma frequency \f$ \omega_p \f$ of the material.
complex double gamma_p, ///< Decay constant \f$ \gamma_p \f$ of the material.
complex double omega ///< Frequency \f$ \omega \f$ at which the permittivity is evaluated.
) {
return eps_inf - omega_p*omega_p/(omega*(omega+I*gamma_p));
}
#endif //QPMS_MATERIALS_H

3
qpms/qpms_cdefs.pxd
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@ -366,6 +366,8 @@ cdef extern from "tmatrices.h":
cdouble epsilon_fg, cdouble epsilon_bg)
qpms_tmatrix_t *qpms_tmatrix_spherical_mu0(const qpms_vswf_set_spec_t *bspec, double a,
double omega, cdouble epsilon_fg, cdouble epsilon_bg)
cdef extern from "materials.h":
qpms_permittivity_interpolator_t *qpms_permittivity_interpolator_create(const size_t incount,
cdouble *wavelength_m, cdouble *n, cdouble *k, const gsl_interp_type *iptype)
qpms_permittivity_interpolator_t *qpms_permittivity_interpolator_from_yml(const char *path,
@ -375,6 +377,7 @@ cdef extern from "tmatrices.h":
double qpms_permittivity_interpolator_omega_min(const qpms_permittivity_interpolator_t *interp)
void qpms_permittivity_interpolator_free(qpms_permittivity_interpolator_t *interp)
cdef extern from "pointgroups.h":
bint qpms_pg_is_finite_axial(qpms_pointgroup_class cls)
double qpms_pg_quat_cmp_atol

6
qpms/qpms_types.h
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@ -399,6 +399,12 @@ typedef struct qpms_abstract_tmatrix_t {
} qpms_abstract_tmatrix_t;
/// A type holding electric permittivity and magnetic permeability of a material.
typedef struct qpms_epsmu_t {
complex double eps; ///< Relative permittivity.
complex double mu; ///< Relative permeability.
} qpms_epsmu_t;
#define lmcheck(l,m) assert((l) >= 1 && abs(m) <= (l))
#endif // QPMS_TYPES

133
qpms/tmatrices.c
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@ -8,7 +8,6 @@
#include "vswf.h"
#include "groups.h"
#include "symmetries.h"
#include <gsl/gsl_spline.h>
#include <assert.h>
#include <unistd.h>
#include "vectors.h"
@ -557,138 +556,6 @@ qpms_errno_t qpms_tmatrix_spherical_fill(qpms_tmatrix_t *t, ///< T-matrix whose
return QPMS_SUCCESS;
}
qpms_permittivity_interpolator_t *qpms_permittivity_interpolator_create(
const size_t incount, const double *wavelen_m, const double *n, const double *k,
const gsl_interp_type *iptype)
{
if (incount <= 0) return NULL;
qpms_permittivity_interpolator_t *ip;
QPMS_CRASHING_MALLOC(ip, sizeof(qpms_permittivity_interpolator_t));
ip->size = incount;
QPMS_CRASHING_MALLOC(ip->wavelength_m, incount * sizeof(double));
QPMS_CRASHING_MALLOC(ip->n, incount * sizeof(double));
QPMS_CRASHING_MALLOC(ip->k, incount * sizeof(double));
memcpy(ip->wavelength_m, wavelen_m, incount*sizeof(double));
memcpy(ip->k, k, incount*sizeof(double));
memcpy(ip->n, n, incount*sizeof(double));
ip->interp_n = gsl_interp_alloc(iptype, incount);
ip->interp_k = gsl_interp_alloc(iptype, incount);
QPMS_ENSURE_SUCCESS(gsl_interp_init(ip->interp_n, ip->wavelength_m, ip->n, incount));
QPMS_ENSURE_SUCCESS(gsl_interp_init(ip->interp_k, ip->wavelength_m, ip->k, incount));
return ip;
}
void qpms_permittivity_interpolator_free(qpms_permittivity_interpolator_t *interp)
{
if(interp) {
gsl_interp_free(interp->interp_n);
gsl_interp_free(interp->interp_k);
free(interp->n);
free(interp->k);
free(interp->wavelength_m);
}
free(interp);
}
qpms_errno_t qpms_read_refractiveindex_yml(
FILE *f, ///< file handle
size_t *const count, ///< Number of successfully loaded triples.
double* *const lambdas_m, ///< Vacuum wavelengths in metres.
double* *const n, ///< Read refraction indices.
double* *const k ///< Read attenuation coeffs.
)
{
QPMS_ENSURE(f && lambdas_m && n && k,"f, lambdas_m, n, k are mandatory arguments and must not be NULL.");
int count_alloc = 128; // First chunk to allocate
*count = 0;
QPMS_CRASHING_MALLOC(*lambdas_m, count_alloc * sizeof(double));
QPMS_CRASHING_MALLOC(*n, count_alloc * sizeof(double));
QPMS_CRASHING_MALLOC(*k, count_alloc * sizeof(double));
size_t linebufsz = 256;
char *linebuf;
QPMS_CRASHING_MALLOC(linebuf, linebufsz);
ssize_t readchars;
bool data_started = false;
while((readchars = getline(&linebuf, &linebufsz, f)) != -1) {
if (linebuf[0] == '#') continue;
// We need to find the beginning of the tabulated data; everything before that is ignored.
if (!data_started) {
char *test = strstr(linebuf, "data: |");
if(test) data_started = true;
continue;
}
if (3 == sscanf(linebuf, "%lf %lf %lf", *lambdas_m + *count, *n + *count , *k + *count)) {
(*lambdas_m)[*count] *= 1e-6; // The original data is in micrometres.
++*count;
if (*count > count_alloc) {
count_alloc *= 2;
QPMS_CRASHING_REALLOC(*lambdas_m, count_alloc * sizeof(double));
QPMS_CRASHING_REALLOC(*n, count_alloc * sizeof(double));
QPMS_CRASHING_REALLOC(*k, count_alloc * sizeof(double));
}
} else break;
}
QPMS_ENSURE(*count > 0, "Could not read any refractive index data; the format must be wrong!");
free(linebuf);
return QPMS_SUCCESS;
}
qpms_errno_t qpms_load_refractiveindex_yml(
const char *path,
size_t *const count, ///< Number of successfully loaded triples.
double* *const lambdas_m, ///< Vacuum wavelengths in metres.
double* *const n, ///< Read refraction indices.
double* *const k ///< Read attenuation coeffs.
)
{
FILE *f = fopen(path, "r");
QPMS_ENSURE(f, "Could not open refractive index file %s", path);
qpms_errno_t retval =
qpms_read_refractiveindex_yml(f, count, lambdas_m, n, k);
QPMS_ENSURE_SUCCESS(fclose(f));
return retval;
}
qpms_permittivity_interpolator_t *qpms_permittivity_interpolator_from_yml(
const char *path, ///< Path to the yml file.
const gsl_interp_type *iptype ///< GSL interpolator type
)
{
size_t count;
double *lambdas_m, *n, *k;
QPMS_ENSURE_SUCCESS(qpms_load_refractiveindex_yml(path, &count, &lambdas_m, &n, &k));
qpms_permittivity_interpolator_t *ip = qpms_permittivity_interpolator_create(
count, lambdas_m, n, k, iptype);
free(lambdas_m);
free(n);
free(k);
return ip;
}
complex double qpms_permittivity_interpolator_eps_at_omega(
const qpms_permittivity_interpolator_t *ip, double omega_SI)
{
double lambda, n, k;
lambda = 2*M_PI*SPEED_OF_LIGHT/omega_SI;
n = gsl_interp_eval(ip->interp_n, ip->wavelength_m, ip->n, lambda, NULL);
k = gsl_interp_eval(ip->interp_k, ip->wavelength_m, ip->k, lambda, NULL);
complex double epsilon = n*n - k*k + 2*n*k*I;
return epsilon;
}
double qpms_permittivity_interpolator_omega_max(
const qpms_permittivity_interpolator_t *ip)
{
return 2*M_PI*SPEED_OF_LIGHT / ip->wavelength_m[0];
}
double qpms_permittivity_interpolator_omega_min(
const qpms_permittivity_interpolator_t *ip)
{
return 2*M_PI*SPEED_OF_LIGHT / ip->wavelength_m[ip->size-1];
}
/// Convenience function to calculate T-matrix of a non-magnetic spherical \
particle using the permittivity values, replacing existing T-matrix data.
qpms_errno_t qpms_tmatrix_spherical_mu0_fill(

79
qpms/tmatrices.h
View File

@ -3,8 +3,9 @@
*/
#ifndef TMATRICES_H
#define TMATRICES_H
#include "qpms_types.h"
#include <gsl/gsl_spline.h>
// #include "qpms_types.h" // included via materials.h
// #include <gsl/gsl_spline.h> // included via materials.h
#include "materials.h"
#include <stdio.h>
struct qpms_finite_group_t;
@ -276,48 +277,6 @@ qpms_tmatrix_interpolator_t *qpms_tmatrix_interpolator_create(size_t n, ///< Num
//, bool copy_bspec ///< if true, copies its own copy of basis spec from the first T-matrix.
/*, ...? */);
/// Interpolator of tabulated optical properties.
// TODO use gsl_interp instead of gsl_spline.
typedef struct qpms_permittivity_interpolator_t {
double *wavelength_m; ///< Wavelength array (in meters).
double *n; ///< Refraction index array.
double *k; ///< Attenuation coefficient array.
gsl_interp *interp_n; ///< Refraction index interpolator object.
gsl_interp *interp_k; ///< Attenuation coeff interpolator object.
size_t size; ///< Size of n[], k[], and wavelength_m[].
// I could add gsl_interp_accel, but that is not necessary.
} qpms_permittivity_interpolator_t;
/// Creates a permittivity interpolator from tabulated wavelengths, refraction indices and extinction coeffs.
qpms_permittivity_interpolator_t *qpms_permittivity_interpolator_create(const size_t incount,
const double *wavelength_m, ///< Tabulated vacuum wavelength in metres, in strictly increasing order.
const double *n, ///< Tabulated refraction indices at omega.
const double *k, ///< Tabulated extinction coefficients.
const gsl_interp_type *iptype ///< GSL interpolator type
);
/// Creates a permittivity interpolator from an yml file downloaded from refractiveindex.info website.
qpms_permittivity_interpolator_t *qpms_permittivity_interpolator_from_yml(
const char *path, ///< Path to the yml file.
const gsl_interp_type *iptype ///< GSL interpolator type
);
/// Evaluates interpolated material permittivity at a given angular frequency.
complex double qpms_permittivity_interpolator_eps_at_omega(
const qpms_permittivity_interpolator_t *interp, double omega_SI);
/// Returns the minimum angular frequency supported by the interpolator.
double qpms_permittivity_interpolator_omega_min(
const qpms_permittivity_interpolator_t *ip);
/// Returns the minimum angular frequency supported by the interpolator.
double qpms_permittivity_interpolator_omega_max(
const qpms_permittivity_interpolator_t *ip);
/// Destroy a permittivity interpolator.
void qpms_permittivity_interpolator_free(qpms_permittivity_interpolator_t *interp);
/// Calculates the reflection Mie-Lorentz coefficients for a spherical particle.
/**
* This function is based on the previous python implementation mie_coefficients() from qpms_p.py,
@ -332,16 +291,16 @@ void qpms_permittivity_interpolator_free(qpms_permittivity_interpolator_t *inter
* TODO better doc.
*/
complex double *qpms_mie_coefficients_reflection(
complex double *target, ///< Target array of length bspec->n. If NULL, a new one will be allocated.
const qpms_vswf_set_spec_t *bspec, ///< Defines which of the coefficients are calculated.
double a, ///< Radius of the sphere.
complex double k_i, ///< Wave number of the internal material of the sphere.
complex double k_e, ///< Wave number of the surrounding medium.
complex double mu_i, ///< Relative permeability of the sphere material.
complex double mu_e, ///< Relative permeability of the surrounding medium.
qpms_bessel_t J_ext, ///< Kind of the "incoming" waves. Most likely QPMS_BESSEL_REGULAR.
qpms_bessel_t J_scat ///< Kind of the "scattered" waves. Most likely QPMS_HANKEL_PLUS.
);
complex double *target, ///< Target array of length bspec->n. If NULL, a new one will be allocated.
const qpms_vswf_set_spec_t *bspec, ///< Defines which of the coefficients are calculated.
double a, ///< Radius of the sphere.
complex double k_i, ///< Wave number of the internal material of the sphere.
complex double k_e, ///< Wave number of the surrounding medium.
complex double mu_i, ///< Relative permeability of the sphere material.
complex double mu_e, ///< Relative permeability of the surrounding medium.
qpms_bessel_t J_ext, ///< Kind of the "incoming" waves. Most likely QPMS_BESSEL_REGULAR.
qpms_bessel_t J_scat ///< Kind of the "scattered" waves. Most likely QPMS_HANKEL_PLUS.
);
/// Replaces the contents of an existing T-matrix with that of a spherical nanoparticle calculated using the Lorentz-mie theory.
qpms_errno_t qpms_tmatrix_spherical_fill(qpms_tmatrix_t *t, ///< T-matrix whose contents are to be replaced. Not NULL.
@ -366,16 +325,6 @@ static inline qpms_tmatrix_t *qpms_tmatrix_spherical(
return t;
}
/// Relative permittivity from the Drude model.
static inline complex double qpms_drude_epsilon(
complex double eps_inf, ///< Relative permittivity "at infinity".
complex double omega_p, ///< Plasma frequency \f$ \omega_p \f$ of the material.
complex double gamma_p, ///< Decay constant \f$ \gamma_p \f$ of the material.
complex double omega ///< Frequency \f$ \omega \f$ at which the permittivity is evaluated.
) {
return eps_inf - omega_p*omega_p/(omega*(omega+I*gamma_p));
}
/// Convenience function to calculate T-matrix of a non-magnetic spherical \
particle using the permittivity values, replacing existing T-matrix data.
qpms_errno_t qpms_tmatrix_spherical_mu0_fill(
@ -399,8 +348,6 @@ static inline qpms_tmatrix_t *qpms_tmatrix_spherical_mu0(
};
#if 0
// Abstract types that describe T-matrix/particle/scatsystem symmetries
// To be implemented later. See also the thoughts in the beginning of groups.h.

1
setup.py
View File

@ -72,6 +72,7 @@ qpms_c = Extension('qpms_c',
'qpms/vswf.c', # FIXME many things from vswf.c are not required by this module, but they have many dependencies (following in this list); maybe I want to move all the "basespec stuff"
'qpms/legendre.c',
'qpms/tmatrices.c',
'qpms/materials.c',
'qpms/error.c',
'qpms/bessel.c',
'qpms/own_zgemm.c',