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/dports/biology/gemma/GEMMA-0.98.3/src/
H A Dvc.cpp85 n_vc = cPar.n_vc; in CopyFromParam()
109 cPar.n_vc = n_vc; in CopyToParam()
1317 gsl_matrix *Si_mat = gsl_matrix_alloc(n_vc, n_vc); in CalcVCss()
1517 gsl_matrix *yKrKKry = gsl_matrix_alloc(n_vc, n_vc * (n_vc + 1)); in CalcVChe()
1526 gsl_matrix *S_mat = gsl_matrix_alloc(n_vc, n_vc); in CalcVChe()
1627 gsl_matrix_submatrix(yKrKKry, 0, i * n_vc, n_vc, n_vc); in CalcVChe()
1634 gsl_matrix_submatrix(yKrKKry, 0, n_vc * n_vc, n_vc, n_vc); in CalcVChe()
1954 gsl_matrix *S1 = gsl_matrix_alloc(n_vc, n_vc); in CalcVCacl()
1955 gsl_matrix *S2 = gsl_matrix_alloc(n_vc, n_vc); in CalcVCacl()
1956 gsl_matrix *S_mat = gsl_matrix_alloc(n_vc, n_vc); in CalcVCacl()
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H A Dparam.cpp995 << n_vc << endl; in CheckData()
1328 for (size_t i = 0; i < n_vc; i++) { in compAKtoS()
1423 gsl_matrix_alloc(ni_test, (n_vc * (n_vc + 1)) / 2 * ni_test); in compKtoV()
1424 gsl_vector *trKiKj = gsl_vector_alloc(n_vc * (n_vc + 1) / 2); in compKtoV()
1434 for (size_t i = 0; i < n_vc; i++) { in compKtoV()
1450 for (size_t i = 0; i < n_vc; i++) { in compKtoV()
1469 for (size_t i = 0; i < n_vc; i++) { in compKtoV()
1474 if (l != n_vc && m != n_vc) { in compKtoV()
1526 } else if (l != n_vc && m == n_vc) { in compKtoV()
1549 } else if (l == n_vc && m != n_vc) { in compKtoV()
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H A Dgemma.cpp1953 gsl_matrix_submatrix(S, cPar.n_vc, 0, cPar.n_vc, cPar.n_vc); in BatchRun()
1999 gsl_matrix *Vq = gsl_matrix_safe_alloc(cPar.n_vc, cPar.n_vc); in BatchRun()
2115 gsl_matrix *Vq = gsl_matrix_safe_alloc(cPar.n_vc, cPar.n_vc); in BatchRun()
2136 gsl_matrix_submatrix(S, 0, 0, cPar.n_vc, cPar.n_vc); in BatchRun()
2138 gsl_matrix_submatrix(S, cPar.n_vc, 0, cPar.n_vc, cPar.n_vc); in BatchRun()
2248 cPar.n_vc = cPar.n_vc - 1; in BatchRun()
2251 gsl_matrix *Vq = gsl_matrix_safe_alloc(cPar.n_vc, cPar.n_vc); in BatchRun()
2263 gsl_matrix_submatrix(S, 0, 0, cPar.n_vc, cPar.n_vc); in BatchRun()
2265 gsl_matrix_submatrix(S, cPar.n_vc, 0, cPar.n_vc, cPar.n_vc); in BatchRun()
2397 gsl_matrix *S = gsl_matrix_safe_alloc(cPar.n_vc, cPar.n_vc); in BatchRun()
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H A Dgemma_io.cpp2640 n_vc = header.coln; in ReadFile_cat()
2642 n_vc--; in ReadFile_cat()
2645 n_vc--; in ReadFile_cat()
2648 n_vc--; in ReadFile_cat()
2651 n_vc--; in ReadFile_cat()
2654 n_vc--; in ReadFile_cat()
2657 n_vc--; in ReadFile_cat()
2723 n_vc = n_vc_tmp; in ReadFile_mcat()
2725 n_vc = max(n_vc, n_vc_tmp); in ReadFile_mcat()
3312 if (t > n_vc) { in ReadFile_wsnp()
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H A Dgemma_io.h123 size_t &n_vc);
125 size_t &n_vc);
157 bool ReadFile_wsnp(const string &file_wcat, const size_t n_vc,
H A Dvc.h63 size_t n_vc; variable
H A Dparam.h248 size_t n_vc; // Number of variance components variable
/dports/science/code_saturne/code_saturne-7.1.0/src/cdo/
H A Dcs_cdovcb_scaleq.c216 int size = n_vc + 1; in _cell_builder_create()
220 size = 2*n_vc + 3*n_ec + n_fc; in _cell_builder_create()
224 size = 2*n_ec + n_vc; in _cell_builder_create()
496 csys->mat->val[cm->n_vc*(cm->n_vc + 1)] += 0.25 * ptyc; in _svcb_conv_diff_reac()
1595 csys->rhs[cm->n_vc] += csys->source[cm->n_vc]; in cs_cdovcb_scaleq_interpolate()
1839 csys->rhs[cm->n_vc] += csys->source[cm->n_vc]; in cs_cdovcb_scaleq_solve_steady_state()
2091 csys->rhs[cm->n_vc] += csys->source[cm->n_vc]; in cs_cdovcb_scaleq_solve_implicit()
2135 csys->rhs[cm->n_vc] += dvalc * csys->val_n[cm->n_vc]; in cs_cdovcb_scaleq_solve_implicit()
2450 csys->rhs[cm->n_vc] += tcoef * csys->source[cm->n_vc]; in cs_cdovcb_scaleq_solve_theta()
2481 csys->rhs[cm->n_vc] += eqp->theta * csys->source[cm->n_vc]; in cs_cdovcb_scaleq_solve_theta()
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H A Dcs_source_term.c936 for (short int v = 0; v < cm->n_vc; v++) in cs_source_term_pvsp_by_value()
943 for (short int v = 0; v < cm->n_vc; v++) in cs_source_term_pvsp_by_value()
998 for (short int v = 0; v < cm->n_vc; v++) in cs_source_term_pvsp_by_analytic()
1039 for (int v = 0; v < cm->n_vc; v++) in cs_source_term_dcsd_by_value()
1079 for (int v = 0; v < cm->n_vc; v++) in cs_source_term_dcvd_by_value()
1122 for (int v = 0; v < cm->n_vc; v++) in cs_source_term_dcsd_by_array()
1172 for (int v = 0; v < cm->n_vc; v++) in cs_source_term_dcsd_by_dof_func()
1219 for (short int v = 0; v < cm->n_vc; v++) in cs_source_term_dcsd_bary_by_analytic()
1272 double *eval_xgv = vol_vc + cm->n_vc; in cs_source_term_dcsd_bary_by_analytic()
1708 eval[cm->n_vc] = pot_value; in cs_source_term_vcsp_by_value()
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H A Dcs_cdovb_scaleq.c146 const int n_vc = connect->n_max_vbyc; in _svb_create_cell_builder() local
148 assert(n_ec > n_vc); in _svb_create_cell_builder()
155 size = CS_MAX(4*n_ec + 3*n_vc, size); in _svb_create_cell_builder()
166 cb->loc = cs_sdm_square_create(n_vc); in _svb_create_cell_builder()
248 csys->n_dofs = cm->n_vc; in _svb_init_cell_system()
254 cs_sdm_square_init(cm->n_vc, csys->mat); in _svb_init_cell_system()
256 for (short int v = 0; v < cm->n_vc; v++) { in _svb_init_cell_system()
664 for (int v = 0; v < cm->n_vc; v++) in _svb_assemble()
677 for (int v = 0; v < cm->n_vc; v++) in _svb_assemble()
3302 pot[cm->n_vc] = 0.; in cs_cdovb_scaleq_diff_flux_in_cells()
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H A Dcs_cdovb_vecteq.c145 const int n_vc = connect->n_max_vbyc; in _vvb_create_cell_builder() local
150 BFT_MALLOC(cb->ids, n_vc, int); in _vvb_create_cell_builder()
151 memset(cb->ids, 0, n_vc*sizeof(int)); in _vvb_create_cell_builder()
154 size = CS_MAX(4*n_ec + 3*n_vc, size); in _vvb_create_cell_builder()
166 cb->loc = cs_sdm_block33_create(n_vc, n_vc); in _vvb_create_cell_builder()
244 csys->n_dofs = 3*cm->n_vc; in _vvb_init_cell_system()
251 cs_sdm_block33_init(csys->mat, cm->n_vc, cm->n_vc); in _vvb_init_cell_system()
253 for (int v = 0; v < cm->n_vc; v++) { in _vvb_init_cell_system()
292 for (int v = 0; v < cm->n_vc; v++) { in _vvb_init_cell_system()
358 for (int bi = 0; bi < cm->n_vc; bi++) { in _vvb_conv_diff_reac()
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H A Dcs_cdo_advection.c1093 ai[cm->n_vc] += coef_ic; in _vcb_stabilization_part2()
1839 cs_sdm_square_init(cm->n_vc, adv); in cs_cdo_advection_vb_upwcsv_wpty()
1925 cs_sdm_square_init(cm->n_vc, adv); in cs_cdo_advection_vb_upwcsv()
1984 cs_sdm_square_init(cm->n_vc, adv); in cs_cdo_advection_vb_cencsv()
2034 cs_sdm_square_init(cm->n_vc, adv); in cs_cdo_advection_vb_mcucsv()
2087 cs_sdm_square_init(cm->n_vc, adv); in cs_cdo_advection_vb_upwnoc_wpty()
2281 const int n_sysc = cm->n_vc + 1; in cs_cdo_advection_vcb_cw_cst()
2295 const int n_vc = cm->n_vc; in cs_cdo_advection_vcb_cw_cst() local
2362 acc[cm->n_vc] += afc[fm->n_vf]; in cs_cdo_advection_vcb_cw_cst()
2411 const int n_sysc = cm->n_vc + 1; in cs_cdo_advection_vcb()
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H A Dcs_hodge.c369 size = 2*n_vc + 3*n_ec + n_fc; in _cell_builder_create()
373 size = 2*n_ec + n_vc; in _cell_builder_create()
428 cs_sdm_square_init(cm->n_vc, sloc); in _define_vb_stiffness()
2335 cs_sdm_square_init(cm->n_vc, sloc); in cs_hodge_vb_cost_get_stiffness()
2502 cs_sdm_square_init(cm->n_vc, sloc); in cs_hodge_vb_voro_get_stiffness()
2720 const int nc_dofs = cm->n_vc + 1; in cs_hodge_vcb_get_stiffness()
2722 const int cc = nc_dofs*cm->n_vc + cm->n_vc; in cs_hodge_vcb_get_stiffness()
2929 const int msize = cm->n_vc + 1; in cs_hodge_vcb_voro_get()
2998 const int msize = cm->n_vc + 1; in cs_hodge_vcb_wbs_get()
3003 hmat->val[msize*cm->n_vc + cm->n_vc] = 0.1*cm->vol_c; in cs_hodge_vcb_wbs_get()
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H A Dcs_cdo_diffusion.c225 for (short int v = 0; v < cm->n_vc; v++) in _svb_cellwise_grd()
431 cs_sdm_square_init(cm->n_vc, bc_op); in _vb_cost_full_flux_op()
432 cs_sdm_square_init(cm->n_vc, ntrgrd_tr); in _vb_cost_full_flux_op()
475 for (int i = 0; i < cm->n_vc; i++) in _vb_cost_full_flux_op()
516 cs_sdm_square_init(cm->n_vc, ntrgrd); in _vb_wbs_normal_flux_op()
1850 cs_sdm_square_init(cm->n_vc, bc_op); in cs_cdo_diffusion_svb_cost_robin()
2000 for (int ij = 0; ij < cm->n_vc*cm->n_vc; ij++) in cs_cdo_diffusion_svb_cost_generic()
2075 cs_sdm_square_init(cm->n_vc, ntrgrd); in cs_cdo_diffusion_svb_ocs_weak_dirichlet()
2157 cs_sdm_square_init(cm->n_vc, ntrgrd); in cs_cdo_diffusion_vvb_ocs_weak_dirichlet()
2265 cs_sdm_square_init(cm->n_vc, ntrgrd); in cs_cdo_diffusion_vvb_ocs_sliding()
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H A Dcs_cdo_local.h219 short int n_vc; /*!< number of vertices in a cell */ member
419 for (short int v = 0; v < cm->n_vc; v++) in cs_cell_mesh_get_v()
492 for (short int v = 0; v < cm->n_vc; v++) v_ids[v] = -1; in cs_cell_mesh_get_f2v()
503 for (short int v = 0; v < cm->n_vc; v++) { in cs_cell_mesh_get_f2v()
H A Dcs_cdo_connect.c404 const int n_vc = c2v_idx[1] - c2v_idx[0]; in _compute_max_ent() local
407 for (short int v = 0; v < n_vc; v++) { in _compute_max_ent()
413 if (n_vc > n_max_vc) n_max_vc = n_vc; in _compute_max_ent()
445 for (short int v = 0; v < n_vc; v++) { in _compute_max_ent()
490 for (short int v = 0; v < n_vc; v++) { in _compute_max_ent()
529 int n_vc = connect->c2v->idx[c_id+1] - connect->c2v->idx[c_id]; in _get_cell_type() local
535 if (n_vc == 4 && n_ec == 6 && n_fc == 4) in _get_cell_type()
540 else if (n_vc == 5 && n_ec == 8 && n_fc == 5) in _get_cell_type()
545 else if (n_vc == 6 && n_ec == 9 && n_fc == 5) { /* Could be a prism */ in _get_cell_type()
569 else if (n_vc == 8 && n_ec == 12 && n_fc == 6) { /* Could be a hexahedron */ in _get_cell_type()
H A Dcs_cdo_local.c132 int n_vc = connect->n_max_vbyc; in cs_cdo_local_initialize() local
136 cs_cdo_local_d_buffer_size = CS_MAX(n_vc*(n_vc+1)/2, max_ent); in cs_cdo_local_initialize()
584 cm->n_vc = 0; in cs_cell_mesh_create()
675 cm->n_vc = -1; in cs_cell_mesh_reset()
768 for (short int v = 0; v < cm->n_vc; v++) in cs_cell_mesh_dump()
962 cm->n_vc = c2v_idx[1] - c2v_idx[0]; in cs_cell_mesh_build()
1146 for (short int v = 1; v < cm->n_vc; v++) in cs_cell_mesh_build()
1149 for (short int v = 0; v < cm->n_vc; v++) in cs_cell_mesh_build()
1387 for (int v = 1; v < cm->n_vc; v++) { in cs_cell_mesh_build()
1948 for (int i = 0; i < cm->n_vc; i++) { in cs_face_mesh_light_build()
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H A Dcs_reco.c1161 for (short int v = 0; v < cm->n_vc; v++) { in cs_reco_cw_scalar_pv_inside_cell()
1219 const double p_c = pot[cm->n_vc]; in cs_reco_cw_vgrd_wbs_from_pvc()
1222 for (int i = 0; i < 3*cm->n_vc; i++) vgrd[i] = 0.; in cs_reco_cw_vgrd_wbs_from_pvc()
1225 for (short int v = 0; v < cm->n_vc; v++) in cs_reco_cw_vgrd_wbs_from_pvc()
1318 const double p_c = pot[cm->n_vc]; in cs_reco_cw_cgrd_wbs_from_pvc()
1321 for (short int v = 0; v < cm->n_vc; v++) in cs_reco_cw_cgrd_wbs_from_pvc()
H A Dcs_cdo_quantities.c682 const short int n_vc = c2v_idx[1] - c2v_idx[0]; in _compute_dcell_quantities() local
687 for (short int v = 0; v < n_vc; v++) vol_vc[v] = 0.0; in _compute_dcell_quantities()
711 short int _v1 = n_vc, _v2 = n_vc; in _compute_dcell_quantities()
712 for (short int _v = 0; _v < n_vc; _v++) { in _compute_dcell_quantities()
716 CS_CDO_OMP_ASSERT(_v1 < n_vc && _v2 < n_vc); in _compute_dcell_quantities()
H A Dcs_xdef_cw_eval.c170 assert(cm->n_fc == 4 && cm->n_vc == 4); in cs_xdef_cw_eval_c_int_by_analytic()
274 assert(cm->n_fc == 4 && cm->n_vc == 4); in cs_xdef_cw_eval_fc_int_by_analytic()
708 for (short int v = 0; v < cm->n_vc; v++) { in cs_xdef_cw_eval_by_array()
769 for (short int v = 0; v < cm->n_vc; v++) in cs_xdef_cw_eval_by_field()
867 for (short int v = 0; v < cm->n_vc; v++) in cs_xdef_cw_eval_vector_at_xyz_by_array()
951 for (short int v = 0; v < cm->n_vc; v++) in cs_xdef_cw_eval_vector_at_xyz_by_field()
H A Dcs_scheme_geometry.h185 memset(wvf, 0, cm->n_vc*sizeof(cs_real_t)); in cs_compute_wvf()
H A Dcs_reco.h148 for (short int v = 0; v < cm->n_vc; v++) in cs_reco_cw_scalar_pv_at_cell_center()
H A Dcs_scheme_geometry.c508 memset(wvf, 0, cm->n_vc*sizeof(cs_real_t)); in cs_compute_wef_wvf()
/dports/science/code_saturne/code_saturne-7.1.0/tests/
H A Dcs_check_cdo.c368 cm->n_vc = 8; in _define_cm_hexa_unif()
369 for (int i = 0; i < cm->n_vc; i++) { in _define_cm_hexa_unif()
589 cm->n_vc = 4; in _define_cm_tetra_ref()
590 for (int i = 0; i < cm->n_vc; i++) { in _define_cm_tetra_ref()
804 int size = cm->n_vc*(cm->n_vc+1)/2; in _define_cm_tetra_ref()
1037 csys->n_dofs = cm->n_vc; in _test_cdovb_schemes()
1039 for (short int v = 0; v < cm->n_vc; v++) in _test_cdovb_schemes()
1132 for (int v = 0; v < cm->n_vc*cm->n_vc; v++) csys->mat->val[v] = 0.; in _test_cdovb_schemes()
1141 for (int v = 0; v < cm->n_vc*cm->n_vc; v++) csys->mat->val[v] = 0.; in _test_cdovb_schemes()
1855 csys->n_dofs = cm->n_vc; in _main_cdovb_schemes()
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H A Dcs_check_quadrature.c550 cm->n_vc = 8; in _define_cm_hexa_unif()
551 for (int i = 0; i < cm->n_vc; i++) { in _define_cm_hexa_unif()
767 cm->n_vc = 4; in _define_cm_tetra_ref()
768 for (int i = 0; i < cm->n_vc; i++) { in _define_cm_tetra_ref()
982 int size = cm->n_vc*(cm->n_vc+1)/2; in _define_cm_tetra_ref()
988 for (short int vi = 0; vi < cm->n_vc; ++vi) { in _define_cm_tetra_ref()
1377 for (int v = 0; v < cm->n_vc; v++) in _test_cdovb_source()
1403 for (int i = 0; i < cm->n_vc; i++) in _test_cdovb_source()
1427 for (int v = 0; v < cm->n_vc; v++) in _test_cdovb_source()
1462 for (int i = 0; i < cm->n_vc; i++) in _test_cdovb_source()
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