mirror of https://github.com/phonopy/phonopy.git
Minor refactoring for born and dielectric in C
This commit is contained in:
Atsushi Togo
parent
0028e15007
commit
236ba5a882
47
c/_phonopy.c
47
c/_phonopy.c
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@ -587,7 +587,7 @@ static PyObject * py_get_nac_dynamical_matrix(PyObject *self, PyObject *args)
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PyArrayObject* mass;
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PyArrayObject* super2prim_map;
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PyArrayObject* prim2super_map;
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PyArrayObject* born;
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PyArrayObject* py_born;
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double factor;
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double* dm;
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@ -596,7 +596,7 @@ static PyObject * py_get_nac_dynamical_matrix(PyObject *self, PyObject *args)
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double* q;
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double (*svecs)[27][3];
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double* m;
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double* z;
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double (*born)[3][3];
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int* multi;
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int* s2p_map;
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int* p2s_map;
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@ -604,7 +604,7 @@ static PyObject * py_get_nac_dynamical_matrix(PyObject *self, PyObject *args)
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int num_satom;
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int n;
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double *charge_sum;
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double (*charge_sum)[3][3];
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if (!PyArg_ParseTuple(args, "OOOOOOOOOOd",
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&dynamical_matrix,
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@ -616,7 +616,7 @@ static PyObject * py_get_nac_dynamical_matrix(PyObject *self, PyObject *args)
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&super2prim_map,
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&prim2super_map,
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&py_q_cart,
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&born,
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&py_born,
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&factor))
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return NULL;
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@ -626,17 +626,18 @@ static PyObject * py_get_nac_dynamical_matrix(PyObject *self, PyObject *args)
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q = (double*)PyArray_DATA(py_q);
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svecs = (double(*)[27][3])PyArray_DATA(py_shortest_vectors);
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m = (double*)PyArray_DATA(mass);
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z = (double*)PyArray_DATA(born);
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born = (double(*)[3][3])PyArray_DATA(py_born);
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multi = (int*)PyArray_DATA(multiplicity);
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s2p_map = (int*)PyArray_DATA(super2prim_map);
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p2s_map = (int*)PyArray_DATA(prim2super_map);
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num_patom = PyArray_DIMS(prim2super_map)[0];
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num_satom = PyArray_DIMS(super2prim_map)[0];
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charge_sum = (double*) malloc(sizeof(double) * num_patom * num_patom * 9);
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charge_sum = (double(*)[3][3])
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malloc(sizeof(double[3][3]) * num_patom * num_patom);
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n = num_satom / num_patom;
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dym_get_charge_sum(charge_sum, num_patom, factor / n, q_cart, z);
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dym_get_charge_sum(charge_sum, num_patom, factor / n, q_cart, born);
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dym_get_dynamical_matrix_at_q(dm,
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num_patom,
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num_satom,
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@ -662,8 +663,8 @@ static PyObject * py_get_dipole_dipole(PyObject *self, PyObject *args)
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PyArrayObject* G_list_py;
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PyArrayObject* q_vector_py;
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PyArrayObject* q_direction_py;
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PyArrayObject* born_py;
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PyArrayObject* dielectric_py;
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PyArrayObject* py_born;
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PyArrayObject* py_dielectric;
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PyArrayObject* pos_py;
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double factor;
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double lambda;
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@ -674,8 +675,8 @@ static PyObject * py_get_dipole_dipole(PyObject *self, PyObject *args)
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double* G_list;
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double* q_vector;
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double* q_direction;
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double* born;
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double* dielectric;
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double (*born)[3][3];
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double (*dielectric)[3];
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double *pos;
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int num_patom, num_G;
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@ -685,8 +686,8 @@ static PyObject * py_get_dipole_dipole(PyObject *self, PyObject *args)
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&G_list_py,
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&q_vector_py,
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&q_direction_py,
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&born_py,
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&dielectric_py,
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&py_born,
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&py_dielectric,
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&pos_py,
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&factor,
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&lambda,
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@ -703,8 +704,8 @@ static PyObject * py_get_dipole_dipole(PyObject *self, PyObject *args)
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q_direction = (double*)PyArray_DATA(q_direction_py);
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}
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q_vector = (double*)PyArray_DATA(q_vector_py);
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born = (double*)PyArray_DATA(born_py);
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dielectric = (double*)PyArray_DATA(dielectric_py);
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born = (double*)PyArray_DATA(py_born);
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dielectric = (double(*)[3])PyArray_DATA(py_dielectric);
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pos = (double*)PyArray_DATA(pos_py);
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num_G = PyArray_DIMS(G_list_py)[0];
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num_patom = PyArray_DIMS(pos_py)[0];
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@ -730,21 +731,21 @@ static PyObject * py_get_dipole_dipole_q0(PyObject *self, PyObject *args)
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{
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PyArrayObject* dd_q0_py;
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PyArrayObject* G_list_py;
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PyArrayObject* dielectric_py;
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PyArrayObject* py_dielectric;
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PyArrayObject* pos_py;
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double lambda;
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double tolerance;
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double* dd_q0;
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double* G_list;
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double* dielectric;
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double (*dielectric)[3];
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double *pos;
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int num_patom, num_G;
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if (!PyArg_ParseTuple(args, "OOOOdd",
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&dd_q0_py,
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&G_list_py,
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&dielectric_py,
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&py_dielectric,
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&pos_py,
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&lambda,
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&tolerance))
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@ -753,7 +754,7 @@ static PyObject * py_get_dipole_dipole_q0(PyObject *self, PyObject *args)
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dd_q0 = (double*)PyArray_DATA(dd_q0_py);
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G_list = (double*)PyArray_DATA(G_list_py);
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dielectric = (double*)PyArray_DATA(dielectric_py);
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dielectric = (double(*)[3])PyArray_DATA(py_dielectric);
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pos = (double*)PyArray_DATA(pos_py);
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num_G = PyArray_DIMS(G_list_py)[0];
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num_patom = PyArray_DIMS(pos_py)[0];
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@ -781,7 +782,7 @@ static PyObject * py_get_derivative_dynmat(PyObject *self, PyObject *args)
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PyArrayObject* mass;
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PyArrayObject* super2prim_map;
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PyArrayObject* prim2super_map;
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PyArrayObject* born;
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PyArrayObject* py_born;
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PyArrayObject* dielectric;
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PyArrayObject* q_direction;
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double nac_factor;
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@ -813,7 +814,7 @@ static PyObject * py_get_derivative_dynmat(PyObject *self, PyObject *args)
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&super2prim_map,
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&prim2super_map,
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&nac_factor,
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&born,
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&py_born,
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&dielectric,
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&q_direction)) {
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return NULL;
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@ -831,10 +832,10 @@ static PyObject * py_get_derivative_dynmat(PyObject *self, PyObject *args)
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num_patom = PyArray_DIMS(prim2super_map)[0];
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num_satom = PyArray_DIMS(super2prim_map)[0];
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if ((PyObject*)born == Py_None) {
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if ((PyObject*)py_born == Py_None) {
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z = NULL;
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} else {
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z = (double*)PyArray_DATA(born);
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z = (double*)PyArray_DATA(py_born);
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}
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if ((PyObject*)dielectric == Py_None) {
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epsilon = NULL;
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@ -42,12 +42,12 @@ static void get_dynmat_ij(double *dynamical_matrix,
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const int num_satom,
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const double *fc,
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const double q[3],
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const double (*svecs)[27][3],
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PHPYCONST double (*svecs)[27][3],
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const int *multi,
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const double *mass,
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const int *s2p_map,
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const int *p2s_map,
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const double *charge_sum,
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PHPYCONST double (*charge_sum)[3][3],
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const int i,
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const int j);
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static void get_dm(double dm_real[3][3],
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@ -60,19 +60,19 @@ static void get_dm(double dm_real[3][3],
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const int *multi,
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const double mass_sqrt,
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const int *p2s_map,
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const double *charge_sum,
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PHPYCONST double (*charge_sum)[3][3],
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const int i,
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const int j,
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const int k);
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static double get_dielectric_part(const double q_cart[3],
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const double *dielectric);
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PHPYCONST double dielectric[3][3]);
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static void get_KK(double *dd_part, /* [natom, 3, natom, 3, (real, imag)] */
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const double *G_list, /* [num_G, 3] */
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const int num_G,
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const int num_patom,
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const double q_cart[3],
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const double q_direction[3],
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const double *dielectric,
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PHPYCONST double dielectric[3][3],
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const double *pos, /* [natom, 3] */
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const double lambda,
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const double tolerance);
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@ -87,7 +87,7 @@ int dym_get_dynamical_matrix_at_q(double *dynamical_matrix,
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const double *mass,
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const int *s2p_map,
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const int *p2s_map,
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const double *charge_sum,
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PHPYCONST double (*charge_sum)[3][3],
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const int with_openmp)
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{
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int i, j, ij, adrs, adrsT;
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@ -151,10 +151,10 @@ void dym_get_dipole_dipole(double *dd, /* [natom, 3, natom, 3, (real, imag)] */
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const double *G_list, /* [num_G, 3] */
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const int num_G,
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const int num_patom,
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const double *q_cart,
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const double *q_direction,
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const double *born,
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const double *dielectric,
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const double q_cart[3],
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const double q_direction[3],
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PHPYCONST double (*born)[3][3],
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PHPYCONST double dielectric[3][3],
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const double *pos, /* [natom, 3] */
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const double factor, /* 4pi/V*unit-conv */
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const double lambda,
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@ -206,7 +206,7 @@ void dym_get_dipole_dipole(double *dd, /* [natom, 3, natom, 3, (real, imag)] */
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for (m = 0; m < 3; m++) { /* alpha' */
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for (n = 0; n < 3; n++) { /* beta' */
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adrs_tmp = i * num_patom * 18 + m * num_patom * 6 + j * 6 + n * 2;
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zz = born[i * 9 + k * 3 + m] * born[j * 9 + l * 3 + n];
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zz = born[i][k][m] * born[j][l][n];
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dd[adrs] += dd_tmp[adrs_tmp] * zz;
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dd[adrs + 1] += dd_tmp[adrs_tmp + 1] * zz;
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}
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@ -224,7 +224,7 @@ void dym_get_dipole_dipole_q0(double *dd_q0, /* [natom, 3, 3, (real, imag)] */
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const double *G_list, /* [num_G, 3] */
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const int num_G,
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const int num_patom,
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const double *dielectric,
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PHPYCONST double dielectric[3][3],
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const double *pos, /* [natom, 3] */
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const double lambda,
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const double tolerance)
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@ -278,11 +278,11 @@ void dym_get_dipole_dipole_q0(double *dd_q0, /* [natom, 3, 3, (real, imag)] */
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}
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void dym_get_charge_sum(double *charge_sum,
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void dym_get_charge_sum(double (*charge_sum)[3][3],
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const int num_patom,
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const double factor, /* 4pi/V*unit-conv and denominator */
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const double q_cart[3],
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const double *born)
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PHPYCONST double (*born)[3][3])
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{
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int i, j, k, a, b;
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double (*q_born)[3];
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@ -297,7 +297,7 @@ void dym_get_charge_sum(double *charge_sum,
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for (i = 0; i < num_patom; i++) {
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for (j = 0; j < 3; j++) {
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for (k = 0; k < 3; k++) {
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q_born[i][j] += q_cart[k] * born[i * 9 + k * 3 + j];
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q_born[i][j] += q_cart[k] * born[i][k][j];
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}
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}
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}
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@ -306,7 +306,7 @@ void dym_get_charge_sum(double *charge_sum,
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for (j = 0; j < num_patom; j++) {
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for (a = 0; a < 3; a++) {
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for (b = 0; b < 3; b++) {
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charge_sum[i * 9 * num_patom + j * 9 + a * 3 + b] =
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charge_sum[i * num_patom + j][a][b] =
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q_born[i][a] * q_born[j][b] * factor;
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}
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}
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@ -377,12 +377,12 @@ static void get_dynmat_ij(double *dynamical_matrix,
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const int num_satom,
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const double *fc,
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const double q[3],
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const double (*svecs)[27][3],
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PHPYCONST double (*svecs)[27][3],
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const int *multi,
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const double *mass,
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const int *s2p_map,
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const int *p2s_map,
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const double *charge_sum,
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PHPYCONST double (*charge_sum)[3][3],
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const int i,
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const int j)
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{
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@ -438,7 +438,7 @@ static void get_dm(double dm_real[3][3],
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const int *multi,
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const double mass_sqrt,
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const int *p2s_map,
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const double *charge_sum,
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PHPYCONST double (*charge_sum)[3][3],
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const int i,
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const int j,
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const int k)
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@ -462,8 +462,7 @@ static void get_dm(double dm_real[3][3],
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for (m = 0; m < 3; m++) {
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if (charge_sum) {
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fc_elem = (fc[p2s_map[i] * num_satom * 9 + k * 9 + l * 3 + m] +
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charge_sum[i * num_patom * 9 +
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j * 9 + l * 3 + m]) / mass_sqrt;
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charge_sum[i * num_patom + j][l][m]) / mass_sqrt;
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} else {
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fc_elem = fc[p2s_map[i] * num_satom * 9 +
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k * 9 + l * 3 + m] / mass_sqrt;
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@ -475,7 +474,7 @@ static void get_dm(double dm_real[3][3],
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}
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static double get_dielectric_part(const double q_cart[3],
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const double *dielectric)
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PHPYCONST double dielectric[3][3])
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{
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int i, j;
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double x[3];
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@ -484,7 +483,7 @@ static double get_dielectric_part(const double q_cart[3],
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for (i = 0; i < 3; i++) {
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x[i] = 0;
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for (j = 0; j < 3; j++) {
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x[i] += dielectric[i * 3 + j] * q_cart[j];
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x[i] += dielectric[i][j] * q_cart[j];
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}
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}
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@ -502,7 +501,7 @@ static void get_KK(double *dd_part, /* [natom, 3, natom, 3, (real, imag)] */
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const int num_patom,
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const double q_cart[3],
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const double q_direction[3],
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const double *dielectric,
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PHPYCONST double dielectric[3][3],
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const double *pos, /* [natom, 3] */
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const double lambda,
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const double tolerance)
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@ -47,17 +47,17 @@ int dym_get_dynamical_matrix_at_q(double *dynamical_matrix,
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const double *mass,
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const int *s2p_map,
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const int *p2s_map,
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const double *charge_sum,
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PHPYCONST double (*charge_sum)[3][3],
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const int with_openmp);
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void dym_get_dipole_dipole(double *dd, /* [natom, 3, natom, 3, (real, imag)] */
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const double *dd_q0, /* [natom, 3, 3, (real, imag)] */
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const double *G_list, /* [num_G, 3] */
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const int num_G,
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const int num_patom,
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const double *q_cart,
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const double *q_direction,
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const double *born,
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const double *dielectric,
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const double q_cart[3],
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const double q_direction[3],
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PHPYCONST double (*born)[3][3],
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PHPYCONST double dielectric[3][3],
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const double *pos, /* [natom, 3] */
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const double factor, /* 4pi/V*unit-conv */
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const double lambda,
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@ -66,15 +66,15 @@ void dym_get_dipole_dipole_q0(double *dd_q0, /* [natom, 3, 3, (real, imag)] */
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const double *G_list, /* [num_G, 3] */
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const int num_G,
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const int num_patom,
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const double *dielectric,
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PHPYCONST double dielectric[3][3],
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const double *pos, /* [natom, 3] */
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const double lambda,
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const double tolerance);
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void dym_get_charge_sum(double *charge_sum,
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void dym_get_charge_sum(double (*charge_sum)[3][3],
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const int num_patom,
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const double factor,
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const double q_cart[3],
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const double *born);
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PHPYCONST double (*born)[3][3]);
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/* fc[num_patom, num_satom, 3, 3] */
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/* dm[num_comm_points, num_patom * 3, num_patom *3] */
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/* comm_points[num_satom, num_patom, 27, 3] */
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