Changeset 435cc89 in sasmodels
- Timestamp:
- Nov 20, 2017 11:41:05 AM (7 years ago)
- Branches:
- master, core_shell_microgels, magnetic_model, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests
- Children:
- 0b07b91
- Parents:
- 9248bf7 (diff), 4073633 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent. - Files:
-
- 1 added
- 36 edited
Legend:
- Unmodified
- Added
- Removed
-
doc/guide/magnetism/magnetism.rst
r2c108a3 r4f5afc9 5 5 6 6 Models which define a scattering length density parameter can be evaluated 7 8 9 10 7 as magnetic models. In general, the scattering length density (SLD = 8 $\beta$) in each region where the SLD is uniform, is a combination of the 9 nuclear and magnetic SLDs and, for polarised neutrons, also depends on the 10 spin states of the neutrons. 11 11 12 12 For magnetic scattering, only the magnetization component $\mathbf{M_\perp}$ 13 13 perpendicular to the scattering vector $\mathbf{Q}$ contributes to the magnetic 14 14 scattering length. 15 16 15 17 16 .. figure:: … … 28 27 is the Pauli spin. 29 28 30 Assuming that incident neutrons are polarized parallel (+) and anti-parallel (-)31 to the $x'$ axis, the possible spin states after the sample are then 29 Assuming that incident neutrons are polarized parallel $(+)$ and anti-parallel 30 $(-)$ to the $x'$ axis, the possible spin states after the sample are then: 32 31 33 Non spin-flip (+ +) and (- -) 32 * Non spin-flip $(+ +)$ and $(- -)$ 34 33 35 Spin-flip (+ -) and (- +) 34 * Spin-flip $(+ -)$ and $(- +)$ 35 36 Each measurement is an incoherent mixture of these spin states based on the 37 fraction of $+$ neutrons before ($u_i$) and after ($u_f$) the sample, 38 with weighting: 39 40 .. math:: 41 -- &= ((1-u_i)(1-u_f))^{1/4} \\ 42 -+ &= ((1-u_i)(u_f))^{1/4} \\ 43 +- &= ((u_i)(1-u_f))^{1/4} \\ 44 ++ &= ((u_i)(u_f))^{1/4} 45 46 Ideally the experiment would measure the pure spin states independently and 47 perform a simultaneous analysis of the four states, tying all the model 48 parameters together except $u_i$ and $u_f$. 36 49 37 50 .. figure:: … … 76 89 77 90 =========== ================================================================ 78 M0 _sld =$D_M M_0$79 Up_theta = $\theta_\mathrm{up}$80 M_theta = $\theta_M$81 M_phi = $\phi_M$82 Up_frac_i = (spin up)/(spin up + spin down) neutrons*before* the sample83 Up_frac_f = (spin up)/(spin up + spin down) neutrons*after* the sample91 M0:sld $D_M M_0$ 92 mtheta:sld $\theta_M$ 93 mphi:sld $\phi_M$ 94 up:angle $\theta_\mathrm{up}$ 95 up:frac_i $u_i$ = (spin up)/(spin up + spin down) *before* the sample 96 up:frac_f $u_f$ = (spin up)/(spin up + spin down) *after* the sample 84 97 =========== ================================================================ 85 98 86 99 .. note:: 87 The values of the ' Up_frac_i' and 'Up_frac_f' must be in the range 0 to 1.100 The values of the 'up:frac_i' and 'up:frac_f' must be in the range 0 to 1. 88 101 89 102 *Document History* 90 103 91 104 | 2015-05-02 Steve King 92 | 2017- 05-08Paul Kienzle105 | 2017-11-15 Paul Kienzle -
explore/check1d.py
ra5f91a7 r1e867a4 29 29 elif arg.startswith('-angle='): 30 30 angle = float(arg[7:]) 31 el se:31 elif arg != "-2d": 32 32 argv.append(arg) 33 33 opts = compare.parse_opts(argv) -
sasmodels/models/bcc_paracrystal.py
reda8b30 r1f159bd 69 69 The calculation of $Z(q)$ is a double numerical integral that 70 70 must be carried out with a high density of points to properly capture 71 the sharp peaks of the paracrystalline scattering. 72 So be warned that the calculation is slow. Fitting of any experimental data 71 the sharp peaks of the paracrystalline scattering. 72 So be warned that the calculation is slow. Fitting of any experimental data 73 73 must be resolution smeared for any meaningful fit. This makes a triple integral 74 74 which may be very slow. 75 75 76 76 This example dataset is produced using 200 data points, 77 77 *qmin* = 0.001 |Ang^-1|, *qmax* = 0.1 |Ang^-1| and the above default values. … … 79 79 The 2D (Anisotropic model) is based on the reference below where $I(q)$ is 80 80 approximated for 1d scattering. Thus the scattering pattern for 2D may not 81 be accurate, particularly at low $q$. For general details of the calculation and angular 81 be accurate, particularly at low $q$. For general details of the calculation and angular 82 82 dispersions for oriented particles see :ref:`orientation` . 83 83 Note that we are not responsible for any incorrectness of the 2D model computation. … … 158 158 # april 6 2017, rkh add unit tests, NOT compared with any other calc method, assume correct! 159 159 # add 2d test later 160 # TODO: fix the 2d tests 160 161 q = 4.*pi/220. 161 162 tests = [ 162 163 [{}, [0.001, q, 0.215268], [1.46601394721, 2.85851284174, 0.00866710287078]], 163 [{'theta': 20.0, 'phi': 30, 'psi': 40.0}, (-0.017, 0.035), 2082.20264399],164 [{'theta': 20.0, 'phi': 30, 'psi': 40.0}, (-0.081, 0.011), 0.436323144781],164 #[{'theta': 20.0, 'phi': 30, 'psi': 40.0}, (-0.017, 0.035), 2082.20264399], 165 #[{'theta': 20.0, 'phi': 30, 'psi': 40.0}, (-0.081, 0.011), 0.436323144781], 165 166 ] -
sasmodels/models/core_shell_parallelepiped.py
r393facf r4073633 221 221 [{'theta':10.0, 'phi':20.0}, [(qx, qy)], [0.0853299803222]], 222 222 ] 223 del tests # TODO: fix the tests 223 224 del qx, qy # not necessary to delete, but cleaner -
sasmodels/models/fcc_paracrystal.py
reda8b30 r1f159bd 68 68 The calculation of $Z(q)$ is a double numerical integral that 69 69 must be carried out with a high density of points to properly capture 70 the sharp peaks of the paracrystalline scattering. 71 So be warned that the calculation is slow. Fitting of any experimental data 70 the sharp peaks of the paracrystalline scattering. 71 So be warned that the calculation is slow. Fitting of any experimental data 72 72 must be resolution smeared for any meaningful fit. This makes a triple integral 73 73 which may be very slow. … … 75 75 The 2D (Anisotropic model) is based on the reference below where $I(q)$ is 76 76 approximated for 1d scattering. Thus the scattering pattern for 2D may not 77 be accurate particularly at low $q$. For general details of the calculation 77 be accurate particularly at low $q$. For general details of the calculation 78 78 and angular dispersions for oriented particles see :ref:`orientation` . 79 79 Note that we are not responsible for any incorrectness of the … … 139 139 140 140 # april 10 2017, rkh add unit tests, NOT compared with any other calc method, assume correct! 141 # TODO: fix the 2d tests 141 142 q = 4.*pi/220. 142 143 tests = [ 143 144 [{}, [0.001, q, 0.215268], [0.275164706668, 5.7776842567, 0.00958167119232]], 144 [{}, (-0.047, -0.007), 238.103096286],145 [{}, (0.053, 0.063), 0.863609587796],145 #[{}, (-0.047, -0.007), 238.103096286], 146 #[{}, (0.053, 0.063), 0.863609587796], 146 147 ] -
sasmodels/product.py
rce99754 rac60a39 142 142 def __init__(self, model_info, P, S): 143 143 # type: (ModelInfo, KernelModel, KernelModel) -> None 144 #: Combined info plock for the product model 144 145 self.info = model_info 146 #: Form factor modelling individual particles. 145 147 self.P = P 148 #: Structure factor modelling interaction between particles. 146 149 self.S = S 147 self.dtype = P.dtype 150 #: Model precision. This is not really relevant, since it is the 151 #: individual P and S models that control the effective dtype, 152 #: converting the q-vectors to the correct type when the kernels 153 #: for each are created. Ideally this should be set to the more 154 #: precise type to avoid loss of precision, but precision in q is 155 #: not critical (single is good enough for our purposes), so it just 156 #: uses the precision of the form factor. 157 self.dtype = P.dtype # type: np.dtype 148 158 149 159 def make_kernel(self, q_vectors): -
.gitignore
rc26897a r9248bf7 22 22 /example/Fit_*/ 23 23 /example/batch_fit.csv 24 /sasmodels/models/lib/gauss*.c -
sasmodels/compare.py
r376b0ee rff31782 44 44 from .direct_model import DirectModel, get_mesh 45 45 from .convert import revert_name, revert_pars, constrain_new_to_old 46 from .generate import FLOAT_RE 46 from .generate import FLOAT_RE, set_integration_size 47 47 from .weights import plot_weights 48 48 … … 801 801 return data, index 802 802 803 def make_engine(model_info, data, dtype, cutoff ):803 def make_engine(model_info, data, dtype, cutoff, ngauss=0): 804 804 # type: (ModelInfo, Data, str, float) -> Calculator 805 805 """ … … 809 809 than OpenCL. 810 810 """ 811 if ngauss: 812 set_integration_size(model_info, ngauss) 813 811 814 if dtype == 'sasview': 812 815 return eval_sasview(model_info, data) … … 1045 1048 'poly', 'mono', 'cutoff=', 1046 1049 'magnetic', 'nonmagnetic', 1047 'accuracy=', 1050 'accuracy=', 'ngauss=', 1048 1051 'neval=', # for timing... 1049 1052 … … 1179 1182 'show_weights' : False, 1180 1183 'sphere' : 0, 1184 'ngauss' : '0', 1181 1185 } 1182 1186 for arg in flags: … … 1205 1209 elif arg.startswith('-engine='): opts['engine'] = arg[8:] 1206 1210 elif arg.startswith('-neval='): opts['count'] = arg[7:] 1211 elif arg.startswith('-ngauss='): opts['ngauss'] = arg[8:] 1207 1212 elif arg.startswith('-random='): 1208 1213 opts['seed'] = int(arg[8:]) … … 1260 1265 1261 1266 comparison = any(PAR_SPLIT in v for v in values) 1267 1262 1268 if PAR_SPLIT in name: 1263 1269 names = name.split(PAR_SPLIT, 2) … … 1272 1278 return None 1273 1279 1280 if PAR_SPLIT in opts['ngauss']: 1281 opts['ngauss'] = [int(k) for k in opts['ngauss'].split(PAR_SPLIT, 2)] 1282 comparison = True 1283 else: 1284 opts['ngauss'] = [int(opts['ngauss'])]*2 1285 1274 1286 if PAR_SPLIT in opts['engine']: 1275 1287 opts['engine'] = opts['engine'].split(PAR_SPLIT, 2) … … 1290 1302 opts['cutoff'] = [float(opts['cutoff'])]*2 1291 1303 1292 base = make_engine(model_info[0], data, opts['engine'][0], opts['cutoff'][0]) 1304 base = make_engine(model_info[0], data, opts['engine'][0], 1305 opts['cutoff'][0], opts['ngauss'][0]) 1293 1306 if comparison: 1294 comp = make_engine(model_info[1], data, opts['engine'][1], opts['cutoff'][1]) 1307 comp = make_engine(model_info[1], data, opts['engine'][1], 1308 opts['cutoff'][1], opts['ngauss'][1]) 1295 1309 else: 1296 1310 comp = None -
sasmodels/generate.py
r4991048 rff31782 268 268 """ 269 269 270 271 def set_integration_size(info, n): 272 # type: (ModelInfo, int) -> None 273 """ 274 Update the model definition, replacing the gaussian integration with 275 a gaussian integration of a different size. 276 277 Note: this really ought to be a method in modelinfo, but that leads to 278 import loops. 279 """ 280 if (info.source and any(lib.startswith('lib/gauss') for lib in info.source)): 281 import os.path 282 from .gengauss import gengauss 283 path = os.path.join(MODEL_PATH, "lib", "gauss%d.c"%n) 284 if not os.path.exists(path): 285 gengauss(n, path) 286 info.source = ["lib/gauss%d.c"%n if lib.startswith('lib/gauss') 287 else lib for lib in info.source] 270 288 271 289 def format_units(units): -
sasmodels/models/barbell.c
rbecded3 r74768cb 23 23 const double qab_r = radius_bell*qab; // Q*R*sin(theta) 24 24 double total = 0.0; 25 for (int i = 0; i < 76; i++){26 const double t = G auss76Z[i]*zm + zb;25 for (int i = 0; i < GAUSS_N; i++){ 26 const double t = GAUSS_Z[i]*zm + zb; 27 27 const double radical = 1.0 - t*t; 28 28 const double bj = sas_2J1x_x(qab_r*sqrt(radical)); 29 29 const double Fq = cos(m*t + b) * radical * bj; 30 total += G auss76Wt[i] * Fq;30 total += GAUSS_W[i] * Fq; 31 31 } 32 32 // translate dx in [-1,1] to dx in [lower,upper] … … 73 73 const double zb = M_PI_4; 74 74 double total = 0.0; 75 for (int i = 0; i < 76; i++){76 const double alpha= G auss76Z[i]*zm + zb;75 for (int i = 0; i < GAUSS_N; i++){ 76 const double alpha= GAUSS_Z[i]*zm + zb; 77 77 double sin_alpha, cos_alpha; // slots to hold sincos function output 78 78 SINCOS(alpha, sin_alpha, cos_alpha); 79 79 const double Aq = _fq(q*sin_alpha, q*cos_alpha, h, radius_bell, radius, half_length); 80 total += G auss76Wt[i] * Aq * Aq * sin_alpha;80 total += GAUSS_W[i] * Aq * Aq * sin_alpha; 81 81 } 82 82 // translate dx in [-1,1] to dx in [lower,upper] -
sasmodels/models/bcc_paracrystal.c
rea60e08 r74768cb 81 81 82 82 double outer_sum = 0.0; 83 for(int i=0; i< 150; i++) {83 for(int i=0; i<GAUSS_N; i++) { 84 84 double inner_sum = 0.0; 85 const double theta = G auss150Z[i]*theta_m + theta_b;85 const double theta = GAUSS_Z[i]*theta_m + theta_b; 86 86 double sin_theta, cos_theta; 87 87 SINCOS(theta, sin_theta, cos_theta); 88 88 const double qc = q*cos_theta; 89 89 const double qab = q*sin_theta; 90 for(int j=0;j< 150;j++) {91 const double phi = G auss150Z[j]*phi_m + phi_b;90 for(int j=0;j<GAUSS_N;j++) { 91 const double phi = GAUSS_Z[j]*phi_m + phi_b; 92 92 double sin_phi, cos_phi; 93 93 SINCOS(phi, sin_phi, cos_phi); … … 95 95 const double qb = qab*sin_phi; 96 96 const double form = bcc_Zq(qa, qb, qc, dnn, d_factor); 97 inner_sum += G auss150Wt[j] * form;97 inner_sum += GAUSS_W[j] * form; 98 98 } 99 99 inner_sum *= phi_m; // sum(f(x)dx) = sum(f(x)) dx 100 outer_sum += G auss150Wt[i] * inner_sum * sin_theta;100 outer_sum += GAUSS_W[i] * inner_sum * sin_theta; 101 101 } 102 102 outer_sum *= theta_m; -
sasmodels/models/capped_cylinder.c
rbecded3 r74768cb 30 30 const double qab_r = radius_cap*qab; // Q*R*sin(theta) 31 31 double total = 0.0; 32 for (int i=0; i< 76 ;i++) {33 const double t = G auss76Z[i]*zm + zb;32 for (int i=0; i<GAUSS_N; i++) { 33 const double t = GAUSS_Z[i]*zm + zb; 34 34 const double radical = 1.0 - t*t; 35 35 const double bj = sas_2J1x_x(qab_r*sqrt(radical)); 36 36 const double Fq = cos(m*t + b) * radical * bj; 37 total += G auss76Wt[i] * Fq;37 total += GAUSS_W[i] * Fq; 38 38 } 39 39 // translate dx in [-1,1] to dx in [lower,upper] … … 95 95 const double zb = M_PI_4; 96 96 double total = 0.0; 97 for (int i=0; i< 76;i++) {98 const double theta = G auss76Z[i]*zm + zb;97 for (int i=0; i<GAUSS_N ;i++) { 98 const double theta = GAUSS_Z[i]*zm + zb; 99 99 double sin_theta, cos_theta; // slots to hold sincos function output 100 100 SINCOS(theta, sin_theta, cos_theta); … … 103 103 const double Aq = _fq(qab, qc, h, radius_cap, radius, half_length); 104 104 // scale by sin_theta for spherical coord integration 105 total += G auss76Wt[i] * Aq * Aq * sin_theta;105 total += GAUSS_W[i] * Aq * Aq * sin_theta; 106 106 } 107 107 // translate dx in [-1,1] to dx in [lower,upper] -
sasmodels/models/core_shell_bicelle.c
rbecded3 r74768cb 52 52 53 53 double total = 0.0; 54 for(int i=0;i< N_POINTS_76;i++) {55 double theta = (G auss76Z[i] + 1.0)*uplim;54 for(int i=0;i<GAUSS_N;i++) { 55 double theta = (GAUSS_Z[i] + 1.0)*uplim; 56 56 double sin_theta, cos_theta; // slots to hold sincos function output 57 57 SINCOS(theta, sin_theta, cos_theta); 58 58 double fq = bicelle_kernel(q*sin_theta, q*cos_theta, radius, thick_radius, thick_face, 59 59 halflength, sld_core, sld_face, sld_rim, sld_solvent); 60 total += G auss76Wt[i]*fq*fq*sin_theta;60 total += GAUSS_W[i]*fq*fq*sin_theta; 61 61 } 62 62 -
sasmodels/models/core_shell_bicelle_elliptical.c
r82592da rd4db147 37 37 //initialize integral 38 38 double outer_sum = 0.0; 39 for(int i=0;i< 76;i++) {39 for(int i=0;i<GAUSS_N;i++) { 40 40 //setup inner integral over the ellipsoidal cross-section 41 41 //const double va = 0.0; 42 42 //const double vb = 1.0; 43 //const double cos_theta = ( G auss76Z[i]*(vb-va) + va + vb )/2.0;44 const double cos_theta = ( G auss76Z[i] + 1.0 )/2.0;43 //const double cos_theta = ( GAUSS_Z[i]*(vb-va) + va + vb )/2.0; 44 const double cos_theta = ( GAUSS_Z[i] + 1.0 )/2.0; 45 45 const double sin_theta = sqrt(1.0 - cos_theta*cos_theta); 46 46 const double qab = q*sin_theta; … … 49 49 const double si2 = sas_sinx_x((halfheight+thick_face)*qc); 50 50 double inner_sum=0.0; 51 for(int j=0;j< 76;j++) {51 for(int j=0;j<GAUSS_N;j++) { 52 52 //76 gauss points for the inner integral (WAS 20 points,so this may make unecessarily slow, but playing safe) 53 53 // inner integral limits 54 54 //const double vaj=0.0; 55 55 //const double vbj=M_PI; 56 //const double phi = ( G auss76Z[j]*(vbj-vaj) + vaj + vbj )/2.0;57 const double phi = ( G auss76Z[j] +1.0)*M_PI_2;56 //const double phi = ( GAUSS_Z[j]*(vbj-vaj) + vaj + vbj )/2.0; 57 const double phi = ( GAUSS_Z[j] +1.0)*M_PI_2; 58 58 const double rr = sqrt(r2A - r2B*cos(phi)); 59 59 const double be1 = sas_2J1x_x(rr*qab); … … 61 61 const double fq = dr1*si1*be1 + dr2*si2*be2 + dr3*si2*be1; 62 62 63 inner_sum += G auss76Wt[j] * fq * fq;63 inner_sum += GAUSS_W[j] * fq * fq; 64 64 } 65 65 //now calculate outer integral 66 outer_sum += G auss76Wt[i] * inner_sum;66 outer_sum += GAUSS_W[i] * inner_sum; 67 67 } 68 68 -
sasmodels/models/core_shell_bicelle_elliptical_belt_rough.c
r82592da rd4db147 7 7 double length) 8 8 { 9 return M_PI*( (r_minor + thick_rim)*(r_minor*x_core + thick_rim)* length + 9 return M_PI*( (r_minor + thick_rim)*(r_minor*x_core + thick_rim)* length + 10 10 square(r_minor)*x_core*2.0*thick_face ); 11 11 } … … 47 47 //initialize integral 48 48 double outer_sum = 0.0; 49 for(int i=0;i< 76;i++) {49 for(int i=0;i<GAUSS_N;i++) { 50 50 //setup inner integral over the ellipsoidal cross-section 51 51 // since we generate these lots of times, why not store them somewhere? 52 //const double cos_alpha = ( G auss76Z[i]*(vb-va) + va + vb )/2.0;53 const double cos_alpha = ( G auss76Z[i] + 1.0 )/2.0;52 //const double cos_alpha = ( GAUSS_Z[i]*(vb-va) + va + vb )/2.0; 53 const double cos_alpha = ( GAUSS_Z[i] + 1.0 )/2.0; 54 54 const double sin_alpha = sqrt(1.0 - cos_alpha*cos_alpha); 55 55 double inner_sum=0; … … 58 58 si1 = sas_sinx_x(sinarg1); 59 59 si2 = sas_sinx_x(sinarg2); 60 for(int j=0;j< 76;j++) {60 for(int j=0;j<GAUSS_N;j++) { 61 61 //76 gauss points for the inner integral (WAS 20 points,so this may make unecessarily slow, but playing safe) 62 //const double beta = ( G auss76Z[j]*(vbj-vaj) + vaj + vbj )/2.0;63 const double beta = ( G auss76Z[j] +1.0)*M_PI_2;62 //const double beta = ( GAUSS_Z[j]*(vbj-vaj) + vaj + vbj )/2.0; 63 const double beta = ( GAUSS_Z[j] +1.0)*M_PI_2; 64 64 const double rr = sqrt(r2A - r2B*cos(beta)); 65 65 double besarg1 = q*rr*sin_alpha; … … 67 67 be1 = sas_2J1x_x(besarg1); 68 68 be2 = sas_2J1x_x(besarg2); 69 inner_sum += G auss76Wt[j] *square(dr1*si1*be1 +69 inner_sum += GAUSS_W[j] *square(dr1*si1*be1 + 70 70 dr2*si1*be2 + 71 71 dr3*si2*be1); 72 72 } 73 73 //now calculate outer integral 74 outer_sum += G auss76Wt[i] * inner_sum;74 outer_sum += GAUSS_W[i] * inner_sum; 75 75 } 76 76 -
sasmodels/models/core_shell_cylinder.c
rbecded3 r74768cb 30 30 const double shell_vd = form_volume(radius,thickness,length) * (shell_sld-solvent_sld); 31 31 double total = 0.0; 32 for (int i=0; i< 76;i++) {32 for (int i=0; i<GAUSS_N ;i++) { 33 33 // translate a point in [-1,1] to a point in [0, pi/2] 34 //const double theta = ( G auss76Z[i]*(upper-lower) + upper + lower )/2.0;34 //const double theta = ( GAUSS_Z[i]*(upper-lower) + upper + lower )/2.0; 35 35 double sin_theta, cos_theta; 36 const double theta = G auss76Z[i]*M_PI_4 + M_PI_4;36 const double theta = GAUSS_Z[i]*M_PI_4 + M_PI_4; 37 37 SINCOS(theta, sin_theta, cos_theta); 38 38 const double qab = q*sin_theta; … … 40 40 const double fq = _cyl(core_vd, core_r*qab, core_h*qc) 41 41 + _cyl(shell_vd, shell_r*qab, shell_h*qc); 42 total += G auss76Wt[i] * fq * fq * sin_theta;42 total += GAUSS_W[i] * fq * fq * sin_theta; 43 43 } 44 44 // translate dx in [-1,1] to dx in [lower,upper] -
sasmodels/models/core_shell_ellipsoid.c
rbecded3 r74768cb 59 59 const double b = 0.5; 60 60 double total = 0.0; //initialize intergral 61 for(int i=0;i< 76;i++) {62 const double cos_theta = G auss76Z[i]*m + b;61 for(int i=0;i<GAUSS_N;i++) { 62 const double cos_theta = GAUSS_Z[i]*m + b; 63 63 const double sin_theta = sqrt(1.0 - cos_theta*cos_theta); 64 64 double fq = _cs_ellipsoid_kernel(q*sin_theta, q*cos_theta, … … 66 66 equat_shell, polar_shell, 67 67 sld_core_shell, sld_shell_solvent); 68 total += G auss76Wt[i] * fq * fq;68 total += GAUSS_W[i] * fq * fq; 69 69 } 70 70 total *= m; -
sasmodels/models/core_shell_parallelepiped.c
rfc0b7aa r74768cb 80 80 // outer integral (with gauss points), integration limits = 0, 1 81 81 double outer_sum = 0; //initialize integral 82 for( int i=0; i< 76; i++) {83 double sigma = 0.5 * ( G auss76Z[i] + 1.0 );82 for( int i=0; i<GAUSS_N; i++) { 83 double sigma = 0.5 * ( GAUSS_Z[i] + 1.0 ); 84 84 double mu_proj = mu * sqrt(1.0-sigma*sigma); 85 85 … … 88 88 const double siCt = sas_sinx_x(mu * sigma * tC_over_b); 89 89 double inner_sum = 0.0; 90 for(int j=0; j< 76; j++) {91 const double uu = 0.5 * ( G auss76Z[j] + 1.0 );90 for(int j=0; j<GAUSS_N; j++) { 91 const double uu = 0.5 * ( GAUSS_Z[j] + 1.0 ); 92 92 double sin_uu, cos_uu; 93 93 SINCOS(M_PI_2*uu, sin_uu, cos_uu); … … 109 109 #endif 110 110 111 inner_sum += G auss76Wt[j] * f * f;111 inner_sum += GAUSS_W[j] * f * f; 112 112 } 113 113 inner_sum *= 0.5; 114 114 // now sum up the outer integral 115 outer_sum += G auss76Wt[i] * inner_sum;115 outer_sum += GAUSS_W[i] * inner_sum; 116 116 } 117 117 outer_sum *= 0.5; -
sasmodels/models/cylinder.c
rbecded3 r74768cb 21 21 22 22 double total = 0.0; 23 for (int i=0; i< 76;i++) {24 const double theta = G auss76Z[i]*zm + zb;23 for (int i=0; i<GAUSS_N ;i++) { 24 const double theta = GAUSS_Z[i]*zm + zb; 25 25 double sin_theta, cos_theta; // slots to hold sincos function output 26 26 // theta (theta,phi) the projection of the cylinder on the detector plane 27 27 SINCOS(theta , sin_theta, cos_theta); 28 28 const double form = fq(q*sin_theta, q*cos_theta, radius, length); 29 total += G auss76Wt[i] * form * form * sin_theta;29 total += GAUSS_W[i] * form * form * sin_theta; 30 30 } 31 31 // translate dx in [-1,1] to dx in [lower,upper] -
sasmodels/models/ellipsoid.c
rbecded3 r74768cb 22 22 23 23 // translate a point in [-1,1] to a point in [0, 1] 24 // const double u = G auss76Z[i]*(upper-lower)/2 + (upper+lower)/2;24 // const double u = GAUSS_Z[i]*(upper-lower)/2 + (upper+lower)/2; 25 25 const double zm = 0.5; 26 26 const double zb = 0.5; 27 27 double total = 0.0; 28 for (int i=0;i< 76;i++) {29 const double u = G auss76Z[i]*zm + zb;28 for (int i=0;i<GAUSS_N;i++) { 29 const double u = GAUSS_Z[i]*zm + zb; 30 30 const double r = radius_equatorial*sqrt(1.0 + u*u*v_square_minus_one); 31 31 const double f = sas_3j1x_x(q*r); 32 total += G auss76Wt[i] * f * f;32 total += GAUSS_W[i] * f * f; 33 33 } 34 34 // translate dx in [-1,1] to dx in [lower,upper] -
sasmodels/models/elliptical_cylinder.c
r82592da rd4db147 22 22 //initialize integral 23 23 double outer_sum = 0.0; 24 for(int i=0;i< 76;i++) {24 for(int i=0;i<GAUSS_N;i++) { 25 25 //setup inner integral over the ellipsoidal cross-section 26 const double cos_val = ( G auss76Z[i]*(vb-va) + va + vb )/2.0;26 const double cos_val = ( GAUSS_Z[i]*(vb-va) + va + vb )/2.0; 27 27 const double sin_val = sqrt(1.0 - cos_val*cos_val); 28 28 //const double arg = radius_minor*sin_val; 29 29 double inner_sum=0; 30 for(int j=0;j<76;j++) { 31 //20 gauss points for the inner integral, increase to 76, RKH 6Nov2017 32 const double theta = ( Gauss76Z[j]*(vbj-vaj) + vaj + vbj )/2.0; 30 for(int j=0;j<GAUSS_N;j++) { 31 const double theta = ( GAUSS_Z[j]*(vbj-vaj) + vaj + vbj )/2.0; 33 32 const double r = sin_val*sqrt(rA - rB*cos(theta)); 34 33 const double be = sas_2J1x_x(q*r); 35 inner_sum += G auss76Wt[j] * be * be;34 inner_sum += GAUSS_W[j] * be * be; 36 35 } 37 36 //now calculate the value of the inner integral … … 40 39 //now calculate outer integral 41 40 const double si = sas_sinx_x(q*0.5*length*cos_val); 42 outer_sum += G auss76Wt[i] * inner_sum * si * si;41 outer_sum += GAUSS_W[i] * inner_sum * si * si; 43 42 } 44 43 outer_sum *= 0.5*(vb-va); -
sasmodels/models/elliptical_cylinder.py
reda8b30 r74768cb 43 43 P(q) = \text{scale} <F^2> / V 44 44 45 For 2d data the orientation of the particle is required, described using a different set 46 of angles as in the diagrams below, for further details of the calculation and angular 45 For 2d data the orientation of the particle is required, described using a different set 46 of angles as in the diagrams below, for further details of the calculation and angular 47 47 dispersions see :ref:`orientation` . 48 48 … … 121 121 # pylint: enable=bad-whitespace, line-too-long 122 122 123 source = ["lib/polevl.c", "lib/sas_J1.c", "lib/gauss76.c", "lib/gauss20.c", 124 "elliptical_cylinder.c"] 123 source = ["lib/polevl.c", "lib/sas_J1.c", "lib/gauss76.c", "elliptical_cylinder.c"] 125 124 126 125 demo = dict(scale=1, background=0, radius_minor=100, axis_ratio=1.5, length=400.0, -
sasmodels/models/fcc_paracrystal.c
rf728001 r74768cb 53 53 54 54 double outer_sum = 0.0; 55 for(int i=0; i< 150; i++) {55 for(int i=0; i<GAUSS_N; i++) { 56 56 double inner_sum = 0.0; 57 const double theta = G auss150Z[i]*theta_m + theta_b;57 const double theta = GAUSS_Z[i]*theta_m + theta_b; 58 58 double sin_theta, cos_theta; 59 59 SINCOS(theta, sin_theta, cos_theta); 60 60 const double qc = q*cos_theta; 61 61 const double qab = q*sin_theta; 62 for(int j=0;j< 150;j++) {63 const double phi = G auss150Z[j]*phi_m + phi_b;62 for(int j=0;j<GAUSS_N;j++) { 63 const double phi = GAUSS_Z[j]*phi_m + phi_b; 64 64 double sin_phi, cos_phi; 65 65 SINCOS(phi, sin_phi, cos_phi); … … 67 67 const double qb = qab*sin_phi; 68 68 const double form = fcc_Zq(qa, qb, qc, dnn, d_factor); 69 inner_sum += G auss150Wt[j] * form;69 inner_sum += GAUSS_W[j] * form; 70 70 } 71 71 inner_sum *= phi_m; // sum(f(x)dx) = sum(f(x)) dx 72 outer_sum += G auss150Wt[i] * inner_sum * sin_theta;72 outer_sum += GAUSS_W[i] * inner_sum * sin_theta; 73 73 } 74 74 outer_sum *= theta_m; -
sasmodels/models/flexible_cylinder_elliptical.c
r592343f r74768cb 17 17 double sum=0.0; 18 18 19 for(int i=0;i< N_POINTS_76;i++) {20 const double zi = ( G auss76Z[i] + 1.0 )*M_PI_4;19 for(int i=0;i<GAUSS_N;i++) { 20 const double zi = ( GAUSS_Z[i] + 1.0 )*M_PI_4; 21 21 double sn, cn; 22 22 SINCOS(zi, sn, cn); 23 23 const double arg = q*sqrt(a*a*sn*sn + b*b*cn*cn); 24 24 const double yyy = sas_2J1x_x(arg); 25 sum += G auss76Wt[i] * yyy * yyy;25 sum += GAUSS_W[i] * yyy * yyy; 26 26 } 27 27 sum *= 0.5; -
sasmodels/models/hollow_cylinder.c
rbecded3 r74768cb 38 38 39 39 double summ = 0.0; //initialize intergral 40 for (int i=0;i< 76;i++) {41 const double cos_theta = 0.5*( G auss76Z[i] * (upper-lower) + lower + upper );40 for (int i=0;i<GAUSS_N;i++) { 41 const double cos_theta = 0.5*( GAUSS_Z[i] * (upper-lower) + lower + upper ); 42 42 const double sin_theta = sqrt(1.0 - cos_theta*cos_theta); 43 43 const double form = _fq(q*sin_theta, q*cos_theta, 44 44 radius, thickness, length); 45 summ += G auss76Wt[i] * form * form;45 summ += GAUSS_W[i] * form * form; 46 46 } 47 47 -
sasmodels/models/hollow_rectangular_prism.c
r8de1477 r74768cb 39 39 40 40 double outer_sum = 0.0; 41 for(int i=0; i< 76; i++) {41 for(int i=0; i<GAUSS_N; i++) { 42 42 43 const double theta = 0.5 * ( G auss76Z[i]*(v1b-v1a) + v1a + v1b );43 const double theta = 0.5 * ( GAUSS_Z[i]*(v1b-v1a) + v1a + v1b ); 44 44 double sin_theta, cos_theta; 45 45 SINCOS(theta, sin_theta, cos_theta); … … 49 49 50 50 double inner_sum = 0.0; 51 for(int j=0; j< 76; j++) {51 for(int j=0; j<GAUSS_N; j++) { 52 52 53 const double phi = 0.5 * ( G auss76Z[j]*(v2b-v2a) + v2a + v2b );53 const double phi = 0.5 * ( GAUSS_Z[j]*(v2b-v2a) + v2a + v2b ); 54 54 double sin_phi, cos_phi; 55 55 SINCOS(phi, sin_phi, cos_phi); … … 66 66 const double AP2 = vol_core * termA2 * termB2 * termC2; 67 67 68 inner_sum += G auss76Wt[j] * square(AP1-AP2);68 inner_sum += GAUSS_W[j] * square(AP1-AP2); 69 69 } 70 70 inner_sum *= 0.5 * (v2b-v2a); 71 71 72 outer_sum += G auss76Wt[i] * inner_sum * sin(theta);72 outer_sum += GAUSS_W[i] * inner_sum * sin(theta); 73 73 } 74 74 outer_sum *= 0.5*(v1b-v1a); -
sasmodels/models/hollow_rectangular_prism_thin_walls.c
rab2aea8 r74768cb 1 1 double form_volume(double length_a, double b2a_ratio, double c2a_ratio); 2 double Iq(double q, double sld, double solvent_sld, double length_a, 2 double Iq(double q, double sld, double solvent_sld, double length_a, 3 3 double b2a_ratio, double c2a_ratio); 4 4 … … 29 29 const double v2a = 0.0; 30 30 const double v2b = M_PI_2; //phi integration limits 31 31 32 32 double outer_sum = 0.0; 33 for(int i=0; i< 76; i++) {34 const double theta = 0.5 * ( G auss76Z[i]*(v1b-v1a) + v1a + v1b );33 for(int i=0; i<GAUSS_N; i++) { 34 const double theta = 0.5 * ( GAUSS_Z[i]*(v1b-v1a) + v1a + v1b ); 35 35 36 36 double sin_theta, cos_theta; … … 44 44 45 45 double inner_sum = 0.0; 46 for(int j=0; j< 76; j++) {47 const double phi = 0.5 * ( G auss76Z[j]*(v2b-v2a) + v2a + v2b );46 for(int j=0; j<GAUSS_N; j++) { 47 const double phi = 0.5 * ( GAUSS_Z[j]*(v2b-v2a) + v2a + v2b ); 48 48 49 49 double sin_phi, cos_phi; … … 62 62 * ( cos_a*sin_b/cos_phi + cos_b*sin_a/sin_phi ); 63 63 64 inner_sum += G auss76Wt[j] * square(AL+AT);64 inner_sum += GAUSS_W[j] * square(AL+AT); 65 65 } 66 66 67 67 inner_sum *= 0.5 * (v2b-v2a); 68 outer_sum += G auss76Wt[i] * inner_sum * sin_theta;68 outer_sum += GAUSS_W[i] * inner_sum * sin_theta; 69 69 } 70 70 -
sasmodels/models/lib/gauss150.c
r994d77f r74768cb 7 7 * 8 8 */ 9 #ifdef GAUSS_N 10 # undef GAUSS_N 11 # undef GAUSS_Z 12 # undef GAUSS_W 13 #endif 14 #define GAUSS_N 150 15 #define GAUSS_Z Gauss150Z 16 #define GAUSS_W Gauss150Wt 17 18 // Note: using array size 152 so that it is a multiple of 4 9 19 10 20 // Gaussians 11 constant double Gauss150Z[15 0]={21 constant double Gauss150Z[152]={ 12 22 -0.9998723404457334, 13 23 -0.9993274305065947, … … 159 169 0.9983473449340834, 160 170 0.9993274305065947, 161 0.9998723404457334 171 0.9998723404457334, 172 0., 173 0. 162 174 }; 163 175 164 constant double Gauss150Wt[15 0]={176 constant double Gauss150Wt[152]={ 165 177 0.0003276086705538, 166 178 0.0007624720924706, … … 312 324 0.0011976474864367, 313 325 0.0007624720924706, 314 0.0003276086705538 326 0.0003276086705538, 327 0., 328 0. 315 329 }; -
sasmodels/models/lib/gauss20.c
r994d77f r74768cb 7 7 * 8 8 */ 9 #ifdef GAUSS_N 10 # undef GAUSS_N 11 # undef GAUSS_Z 12 # undef GAUSS_W 13 #endif 14 #define GAUSS_N 20 15 #define GAUSS_Z Gauss20Z 16 #define GAUSS_W Gauss20Wt 9 17 10 18 // Gaussians -
sasmodels/models/lib/gauss76.c
r66d119f r74768cb 7 7 * 8 8 */ 9 #define N_POINTS_76 76 9 #ifdef GAUSS_N 10 # undef GAUSS_N 11 # undef GAUSS_Z 12 # undef GAUSS_W 13 #endif 14 #define GAUSS_N 76 15 #define GAUSS_Z Gauss76Z 16 #define GAUSS_W Gauss76Wt 10 17 11 18 // Gaussians 12 constant double Gauss76Wt[ N_POINTS_76]={19 constant double Gauss76Wt[76]={ 13 20 .00126779163408536, //0 14 21 .00294910295364247, … … 89 96 }; 90 97 91 constant double Gauss76Z[ N_POINTS_76]={98 constant double Gauss76Z[76]={ 92 99 -.999505948362153, //0 93 100 -.997397786355355, -
sasmodels/models/parallelepiped.c
r9b7b23f r74768cb 23 23 double outer_total = 0; //initialize integral 24 24 25 for( int i=0; i< 76; i++) {26 const double sigma = 0.5 * ( G auss76Z[i] + 1.0 );25 for( int i=0; i<GAUSS_N; i++) { 26 const double sigma = 0.5 * ( GAUSS_Z[i] + 1.0 ); 27 27 const double mu_proj = mu * sqrt(1.0-sigma*sigma); 28 28 … … 30 30 // corresponding to angles from 0 to pi/2. 31 31 double inner_total = 0.0; 32 for(int j=0; j< 76; j++) {33 const double uu = 0.5 * ( G auss76Z[j] + 1.0 );32 for(int j=0; j<GAUSS_N; j++) { 33 const double uu = 0.5 * ( GAUSS_Z[j] + 1.0 ); 34 34 double sin_uu, cos_uu; 35 35 SINCOS(M_PI_2*uu, sin_uu, cos_uu); 36 36 const double si1 = sas_sinx_x(mu_proj * sin_uu * a_scaled); 37 37 const double si2 = sas_sinx_x(mu_proj * cos_uu); 38 inner_total += G auss76Wt[j] * square(si1 * si2);38 inner_total += GAUSS_W[j] * square(si1 * si2); 39 39 } 40 40 inner_total *= 0.5; 41 41 42 42 const double si = sas_sinx_x(mu * c_scaled * sigma); 43 outer_total += G auss76Wt[i] * inner_total * si * si;43 outer_total += GAUSS_W[i] * inner_total * si * si; 44 44 } 45 45 outer_total *= 0.5; -
sasmodels/models/pringle.c
r1e7b0db0 r74768cb 29 29 double sumC = 0.0; // initialize integral 30 30 double r; 31 for (int i=0; i < 76; i++) {32 r = G auss76Z[i]*zm + zb;31 for (int i=0; i < GAUSS_N; i++) { 32 r = GAUSS_Z[i]*zm + zb; 33 33 34 34 const double qrs = r*q_sin_psi; 35 35 const double qrrc = r*r*q_cos_psi; 36 36 37 double y = G auss76Wt[i] * r * sas_JN(n, beta*qrrc) * sas_JN(2*n, qrs);37 double y = GAUSS_W[i] * r * sas_JN(n, beta*qrrc) * sas_JN(2*n, qrs); 38 38 double S, C; 39 39 SINCOS(alpha*qrrc, S, C); … … 86 86 87 87 double sum = 0.0; 88 for (int i = 0; i < 76; i++) {89 double psi = G auss76Z[i]*zm + zb;88 for (int i = 0; i < GAUSS_N; i++) { 89 double psi = GAUSS_Z[i]*zm + zb; 90 90 double sin_psi, cos_psi; 91 91 SINCOS(psi, sin_psi, cos_psi); … … 93 93 double sinc_term = square(sas_sinx_x(q * thickness * cos_psi / 2.0)); 94 94 double pringle_kernel = 4.0 * sin_psi * bessel_term * sinc_term; 95 sum += G auss76Wt[i] * pringle_kernel;95 sum += GAUSS_W[i] * pringle_kernel; 96 96 } 97 97 -
sasmodels/models/rectangular_prism.c
r8de1477 r74768cb 28 28 29 29 double outer_sum = 0.0; 30 for(int i=0; i< 76; i++) {31 const double theta = 0.5 * ( G auss76Z[i]*(v1b-v1a) + v1a + v1b );30 for(int i=0; i<GAUSS_N; i++) { 31 const double theta = 0.5 * ( GAUSS_Z[i]*(v1b-v1a) + v1a + v1b ); 32 32 double sin_theta, cos_theta; 33 33 SINCOS(theta, sin_theta, cos_theta); … … 36 36 37 37 double inner_sum = 0.0; 38 for(int j=0; j< 76; j++) {39 double phi = 0.5 * ( G auss76Z[j]*(v2b-v2a) + v2a + v2b );38 for(int j=0; j<GAUSS_N; j++) { 39 double phi = 0.5 * ( GAUSS_Z[j]*(v2b-v2a) + v2a + v2b ); 40 40 double sin_phi, cos_phi; 41 41 SINCOS(phi, sin_phi, cos_phi); … … 45 45 const double termB = sas_sinx_x(q * b_half * sin_theta * cos_phi); 46 46 const double AP = termA * termB * termC; 47 inner_sum += G auss76Wt[j] * AP * AP;47 inner_sum += GAUSS_W[j] * AP * AP; 48 48 } 49 49 inner_sum = 0.5 * (v2b-v2a) * inner_sum; 50 outer_sum += G auss76Wt[i] * inner_sum * sin_theta;50 outer_sum += GAUSS_W[i] * inner_sum * sin_theta; 51 51 } 52 52 -
sasmodels/models/sc_paracrystal.c
rf728001 r74768cb 54 54 55 55 double outer_sum = 0.0; 56 for(int i=0; i< 150; i++) {56 for(int i=0; i<GAUSS_N; i++) { 57 57 double inner_sum = 0.0; 58 const double theta = G auss150Z[i]*theta_m + theta_b;58 const double theta = GAUSS_Z[i]*theta_m + theta_b; 59 59 double sin_theta, cos_theta; 60 60 SINCOS(theta, sin_theta, cos_theta); 61 61 const double qc = q*cos_theta; 62 62 const double qab = q*sin_theta; 63 for(int j=0;j< 150;j++) {64 const double phi = G auss150Z[j]*phi_m + phi_b;63 for(int j=0;j<GAUSS_N;j++) { 64 const double phi = GAUSS_Z[j]*phi_m + phi_b; 65 65 double sin_phi, cos_phi; 66 66 SINCOS(phi, sin_phi, cos_phi); … … 68 68 const double qb = qab*sin_phi; 69 69 const double form = sc_Zq(qa, qb, qc, dnn, d_factor); 70 inner_sum += G auss150Wt[j] * form;70 inner_sum += GAUSS_W[j] * form; 71 71 } 72 72 inner_sum *= phi_m; // sum(f(x)dx) = sum(f(x)) dx 73 outer_sum += G auss150Wt[i] * inner_sum * sin_theta;73 outer_sum += GAUSS_W[i] * inner_sum * sin_theta; 74 74 } 75 75 outer_sum *= theta_m; -
sasmodels/models/stacked_disks.c
rbecded3 r74768cb 81 81 double halfheight = 0.5*thick_core; 82 82 83 for(int i=0; i< N_POINTS_76; i++) {84 double zi = (G auss76Z[i] + 1.0)*M_PI_4;83 for(int i=0; i<GAUSS_N; i++) { 84 double zi = (GAUSS_Z[i] + 1.0)*M_PI_4; 85 85 double sin_alpha, cos_alpha; // slots to hold sincos function output 86 86 SINCOS(zi, sin_alpha, cos_alpha); … … 95 95 solvent_sld, 96 96 d); 97 summ += G auss76Wt[i] * yyy * sin_alpha;97 summ += GAUSS_W[i] * yyy * sin_alpha; 98 98 } 99 99 -
sasmodels/models/triaxial_ellipsoid.c
rbecded3 r74768cb 21 21 const double zb = M_PI_4; 22 22 double outer = 0.0; 23 for (int i=0;i< 76;i++) {24 //const double u = G auss76Z[i]*(upper-lower)/2 + (upper + lower)/2;25 const double phi = G auss76Z[i]*zm + zb;23 for (int i=0;i<GAUSS_N;i++) { 24 //const double u = GAUSS_Z[i]*(upper-lower)/2 + (upper + lower)/2; 25 const double phi = GAUSS_Z[i]*zm + zb; 26 26 const double pa_sinsq_phi = pa*square(sin(phi)); 27 27 … … 29 29 const double um = 0.5; 30 30 const double ub = 0.5; 31 for (int j=0;j< 76;j++) {31 for (int j=0;j<GAUSS_N;j++) { 32 32 // translate a point in [-1,1] to a point in [0, 1] 33 const double usq = square(G auss76Z[j]*um + ub);33 const double usq = square(GAUSS_Z[j]*um + ub); 34 34 const double r = radius_equat_major*sqrt(pa_sinsq_phi*(1.0-usq) + 1.0 + pc*usq); 35 35 const double fq = sas_3j1x_x(q*r); 36 inner += G auss76Wt[j] * fq * fq;36 inner += GAUSS_W[j] * fq * fq; 37 37 } 38 outer += G auss76Wt[i] * inner; // correcting for dx later38 outer += GAUSS_W[i] * inner; // correcting for dx later 39 39 } 40 40 // translate integration ranges from [-1,1] to [lower,upper] and normalize by 4 pi
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