[a7684e5] | 1 | """ |
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| 2 | SAS model constructor. |
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| 3 | |
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| 4 | Small angle scattering models are defined by a set of kernel functions: |
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| 5 | |
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| 6 | *Iq(q, p1, p2, ...)* returns the scattering at q for a form with |
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| 7 | particular dimensions averaged over all orientations. |
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| 8 | |
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| 9 | *Iqxy(qx, qy, p1, p2, ...)* returns the scattering at qx,qy for a form |
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| 10 | with particular dimensions for a single orientation. |
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| 11 | |
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| 12 | *Imagnetic(qx, qy, result[], p1, p2, ...)* returns the scattering for the |
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| 13 | polarized neutron spin states (up-up, up-down, down-up, down-down) for |
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| 14 | a form with particular dimensions for a single orientation. |
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| 15 | |
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| 16 | *form_volume(p1, p2, ...)* returns the volume of the form with particular |
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| 17 | dimension. |
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| 18 | |
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| 19 | *ER(p1, p2, ...)* returns the effective radius of the form with |
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| 20 | particular dimensions. |
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| 21 | |
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| 22 | *VR(p1, p2, ...)* returns the volume ratio for core-shell style forms. |
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| 23 | |
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| 24 | These functions are defined in a kernel module .py script and an associated |
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| 25 | set of .c files. The model constructor will use them to create models with |
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| 26 | polydispersity across volume and orientation parameters, and provide |
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| 27 | scale and background parameters for each model. |
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| 28 | |
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| 29 | *Iq*, *Iqxy*, *Imagnetic* and *form_volume* should be stylized C-99 |
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[5d4777d] | 30 | functions written for OpenCL. All functions need prototype declarations |
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| 31 | even if the are defined before they are used. OpenCL does not support |
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| 32 | *#include* preprocessor directives, so instead the list of includes needs |
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| 33 | to be given as part of the metadata in the kernel module definition. |
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| 34 | The included files should be listed using a path relative to the kernel |
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| 35 | module, or if using "lib/file.c" if it is one of the standard includes |
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| 36 | provided with the sasmodels source. The includes need to be listed in |
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| 37 | order so that functions are defined before they are used. |
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| 38 | |
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[994d77f] | 39 | Floating point values should be declared as *double*. For single precision |
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| 40 | calculations, *double* will be replaced by *float*. The single precision |
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| 41 | conversion will also tag floating point constants with "f" to make them |
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| 42 | single precision constants. When using integral values in floating point |
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| 43 | expressions, they should be expressed as floating point values by including |
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| 44 | a decimal point. This includes 0., 1. and 2. |
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[5d4777d] | 45 | |
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| 46 | OpenCL has a *sincos* function which can improve performance when both |
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| 47 | the *sin* and *cos* values are needed for a particular argument. Since |
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| 48 | this function does not exist in C99, all use of *sincos* should be |
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| 49 | replaced by the macro *SINCOS(value,sn,cn)* where *sn* and *cn* are |
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[994d77f] | 50 | previously declared *double* variables. When compiled for systems without |
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| 51 | OpenCL, *SINCOS* will be replaced by *sin* and *cos* calls. If *value* is |
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| 52 | an expression, it will appear twice in this case; whether or not it will be |
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| 53 | evaluated twice depends on the quality of the compiler. |
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[5d4777d] | 54 | |
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| 55 | If the input parameters are invalid, the scattering calculator should |
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| 56 | return a negative number. Particularly with polydispersity, there are |
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| 57 | some sets of shape parameters which lead to nonsensical forms, such |
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| 58 | as a capped cylinder where the cap radius is smaller than the |
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| 59 | cylinder radius. The polydispersity calculation will ignore these points, |
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| 60 | effectively chopping the parameter weight distributions at the boundary |
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| 61 | of the infeasible region. The resulting scattering will be set to |
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| 62 | background. This will work correctly even when polydispersity is off. |
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[a7684e5] | 63 | |
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| 64 | *ER* and *VR* are python functions which operate on parameter vectors. |
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| 65 | The constructor code will generate the necessary vectors for computing |
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| 66 | them with the desired polydispersity. |
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| 67 | |
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[ff7119b] | 68 | The available kernel parameters are defined as a list, with each parameter |
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| 69 | defined as a sublist with the following elements: |
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| 70 | |
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| 71 | *name* is the name that will be used in the call to the kernel |
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| 72 | function and the name that will be displayed to the user. Names |
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| 73 | should be lower case, with words separated by underscore. If |
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| 74 | acronyms are used, the whole acronym should be upper case. |
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| 75 | |
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| 76 | *units* should be one of *degrees* for angles, *Ang* for lengths, |
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| 77 | *1e-6/Ang^2* for SLDs. |
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| 78 | |
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| 79 | *default value* will be the initial value for the model when it |
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| 80 | is selected, or when an initial value is not otherwise specified. |
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| 81 | |
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| 82 | [*lb*, *ub*] are the hard limits on the parameter value, used to limit |
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| 83 | the polydispersity density function. In the fit, the parameter limits |
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| 84 | given to the fit are the limits on the central value of the parameter. |
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| 85 | If there is polydispersity, it will evaluate parameter values outside |
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| 86 | the fit limits, but not outside the hard limits specified in the model. |
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| 87 | If there are no limits, use +/-inf imported from numpy. |
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| 88 | |
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| 89 | *type* indicates how the parameter will be used. "volume" parameters |
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| 90 | will be used in all functions. "orientation" parameters will be used |
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| 91 | in *Iqxy* and *Imagnetic*. "magnetic* parameters will be used in |
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| 92 | *Imagnetic* only. If *type* is the empty string, the parameter will |
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| 93 | be used in all of *Iq*, *Iqxy* and *Imagnetic*. |
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| 94 | |
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| 95 | *description* is a short description of the parameter. This will |
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| 96 | be displayed in the parameter table and used as a tool tip for the |
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| 97 | parameter value in the user interface. |
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| 98 | |
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[a7684e5] | 99 | The kernel module must set variables defining the kernel meta data: |
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| 100 | |
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[cd3dba0] | 101 | *id* is an implicit variable formed from the filename. It will be |
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| 102 | a valid python identifier, and will be used as the reference into |
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| 103 | the html documentation, with '_' replaced by '-'. |
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| 104 | |
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| 105 | *name* is the model name as displayed to the user. If it is missing, |
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| 106 | it will be constructed from the id. |
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[a7684e5] | 107 | |
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| 108 | *title* is a short description of the model, suitable for a tool tip, |
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| 109 | or a one line model summary in a table of models. |
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| 110 | |
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| 111 | *description* is an extended description of the model to be displayed |
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| 112 | while the model parameters are being edited. |
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| 113 | |
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[ff7119b] | 114 | *parameters* is the list of parameters. Parameters in the kernel |
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| 115 | functions must appear in the same order as they appear in the |
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| 116 | parameters list. Two additional parameters, *scale* and *background* |
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| 117 | are added to the beginning of the parameter list. They will show up |
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| 118 | in the documentation as model parameters, but they are never sent to |
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| 119 | the kernel functions. |
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[a7684e5] | 120 | |
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[cd3dba0] | 121 | *category* is the default category for the model. Models in the |
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| 122 | *structure-factor* category do not have *scale* and *background* |
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| 123 | added. |
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| 124 | |
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[a7684e5] | 125 | *source* is the list of C-99 source files that must be joined to |
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| 126 | create the OpenCL kernel functions. The files defining the functions |
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| 127 | need to be listed before the files which use the functions. |
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| 128 | |
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| 129 | *ER* is a python function defining the effective radius. If it is |
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| 130 | not present, the effective radius is 0. |
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| 131 | |
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| 132 | *VR* is a python function defining the volume ratio. If it is not |
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| 133 | present, the volume ratio is 1. |
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| 134 | |
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[5d4777d] | 135 | *form_volume*, *Iq*, *Iqxy*, *Imagnetic* are strings containing the |
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| 136 | C source code for the body of the volume, Iq, and Iqxy functions |
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| 137 | respectively. These can also be defined in the last source file. |
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| 138 | |
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[a503bfd] | 139 | *Iq* and *Iqxy* also be instead be python functions defining the |
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| 140 | kernel. If they are marked as *Iq.vectorized = True* then the |
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| 141 | kernel is passed the entire *q* vector at once, otherwise it is |
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| 142 | passed values one *q* at a time. The performance improvement of |
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| 143 | this step is significant. |
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| 144 | |
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| 145 | *demo* is a dictionary of parameter=value defining a set of |
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[cd3dba0] | 146 | parameters to use by default when *compare* is called. Any |
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| 147 | parameter not set in *demo* gets the initial value from the |
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| 148 | parameter list. *demo* is mostly needed to set the default |
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| 149 | polydispersity values for tests. |
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[ff7119b] | 150 | |
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[a503bfd] | 151 | *oldname* is the name of the model in sasview before sasmodels |
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| 152 | was split into its own package, and *oldpars* is a dictionary |
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| 153 | of *parameter: old_parameter* pairs defining the new names for |
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| 154 | the parameters. This is used by *compare* to check the values |
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| 155 | of the new model against the values of the old model before |
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| 156 | you are ready to add the new model to sasmodels. |
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[ff7119b] | 157 | |
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[cd3dba0] | 158 | |
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| 159 | An *info* dictionary is constructed from the kernel meta data and |
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| 160 | returned to the caller. |
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| 161 | |
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[ff7119b] | 162 | The model evaluator, function call sequence consists of q inputs and the return vector, |
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| 163 | followed by the loop value/weight vector, followed by the values for |
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| 164 | the non-polydisperse parameters, followed by the lengths of the |
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| 165 | polydispersity loops. To construct the call for 1D models, the |
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| 166 | categories *fixed-1d* and *pd-1d* list the names of the parameters |
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| 167 | of the non-polydisperse and the polydisperse parameters respectively. |
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| 168 | Similarly, *fixed-2d* and *pd-2d* provide parameter names for 2D models. |
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| 169 | The *pd-rel* category is a set of those parameters which give |
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| 170 | polydispersitiy as a portion of the value (so a 10% length dispersity |
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| 171 | would use a polydispersity value of 0.1) rather than absolute |
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| 172 | dispersity such as an angle plus or minus 15 degrees. |
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| 173 | |
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| 174 | The *volume* category lists the volume parameters in order for calls |
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| 175 | to volume within the kernel (used for volume normalization) and for |
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| 176 | calls to ER and VR for effective radius and volume ratio respectively. |
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| 177 | |
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| 178 | The *orientation* and *magnetic* categories list the orientation and |
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| 179 | magnetic parameters. These are used by the sasview interface. The |
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| 180 | blank category is for parameters such as scale which don't have any |
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| 181 | other marking. |
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| 182 | |
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[a7684e5] | 183 | The doc string at the start of the kernel module will be used to |
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| 184 | construct the model documentation web pages. Embedded figures should |
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| 185 | appear in the subdirectory "img" beside the model definition, and tagged |
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| 186 | with the kernel module name to avoid collision with other models. Some |
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| 187 | file systems are case-sensitive, so only use lower case characters for |
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| 188 | file names and extensions. |
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| 189 | |
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| 190 | |
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| 191 | The function :func:`make` loads the metadata from the module and returns |
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[ff7119b] | 192 | the kernel source. The function :func:`doc` extracts the doc string |
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| 193 | and adds the parameter table to the top. The function :func:`sources` |
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| 194 | returns a list of files required by the model. |
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[a7684e5] | 195 | """ |
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| 196 | |
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| 197 | # TODO: identify model files which have changed since loading and reload them. |
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| 198 | |
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[5edfe12] | 199 | __all__ = ["make", "doc", "sources", "use_single", "use_long_double"] |
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[14de349] | 200 | |
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[5d4777d] | 201 | import sys |
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[d138d43] | 202 | from os.path import abspath, dirname, join as joinpath, exists, basename, \ |
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| 203 | splitext |
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[994d77f] | 204 | import re |
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[e88bb78] | 205 | import string |
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[14de349] | 206 | |
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| 207 | import numpy as np |
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[f734e7d] | 208 | C_KERNEL_TEMPLATE_PATH = joinpath(dirname(__file__), 'kernel_template.c') |
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[14de349] | 209 | |
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| 210 | F32 = np.dtype('float32') |
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[e1ace4d] | 211 | F64 = np.dtype('float64') |
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| 212 | try: # CRUFT: older numpy does not support float128 |
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| 213 | F128 = np.dtype('float128') |
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| 214 | except TypeError: |
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| 215 | F128 = None |
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| 216 | |
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[14de349] | 217 | |
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[ce27e21] | 218 | # Scale and background, which are parameters common to every form factor |
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| 219 | COMMON_PARAMETERS = [ |
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[33e91b1] | 220 | ["scale", "", 1, [0, np.inf], "", "Source intensity"], |
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| 221 | ["background", "1/cm", 0, [0, np.inf], "", "Source background"], |
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[ce27e21] | 222 | ] |
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| 223 | |
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| 224 | |
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[14de349] | 225 | # Conversion from units defined in the parameter table for each model |
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| 226 | # to units displayed in the sphinx documentation. |
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| 227 | RST_UNITS = { |
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| 228 | "Ang": "|Ang|", |
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[a5d0d00] | 229 | "1/Ang": "|Ang^-1|", |
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[14de349] | 230 | "1/Ang^2": "|Ang^-2|", |
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| 231 | "1e-6/Ang^2": "|1e-6Ang^-2|", |
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| 232 | "degrees": "degree", |
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| 233 | "1/cm": "|cm^-1|", |
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| 234 | "": "None", |
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| 235 | } |
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| 236 | |
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| 237 | # Headers for the parameters tables in th sphinx documentation |
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| 238 | PARTABLE_HEADERS = [ |
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[19dcb933] | 239 | "Parameter", |
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| 240 | "Description", |
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[14de349] | 241 | "Units", |
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| 242 | "Default value", |
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| 243 | ] |
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| 244 | |
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[ff7119b] | 245 | # Minimum width for a default value (this is shorter than the column header |
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| 246 | # width, so will be ignored). |
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[14de349] | 247 | PARTABLE_VALUE_WIDTH = 10 |
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| 248 | |
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[a7684e5] | 249 | # Documentation header for the module, giving the model name, its short |
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| 250 | # description and its parameter table. The remainder of the doc comes |
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| 251 | # from the module docstring. |
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[cd3dba0] | 252 | DOC_HEADER = """.. _%(id)s: |
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[a7684e5] | 253 | |
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[cd3dba0] | 254 | %(name)s |
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[a7684e5] | 255 | ======================================================= |
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| 256 | |
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| 257 | %(title)s |
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| 258 | |
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| 259 | %(parameters)s |
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| 260 | |
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[eb69cce] | 261 | %(returns)s |
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[a7684e5] | 262 | |
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| 263 | %(docs)s |
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| 264 | """ |
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[ce27e21] | 265 | |
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[4eac427] | 266 | def format_units(par): |
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| 267 | return RST_UNITS.get(par, par) |
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| 268 | |
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[19dcb933] | 269 | def make_partable(pars): |
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[ff7119b] | 270 | """ |
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| 271 | Generate the parameter table to include in the sphinx documentation. |
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| 272 | """ |
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[14de349] | 273 | column_widths = [ |
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| 274 | max(len(p[0]) for p in pars), |
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[19dcb933] | 275 | max(len(p[-1]) for p in pars), |
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[4eac427] | 276 | max(len(format_units(p[1])) for p in pars), |
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[14de349] | 277 | PARTABLE_VALUE_WIDTH, |
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| 278 | ] |
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| 279 | column_widths = [max(w, len(h)) |
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[33e91b1] | 280 | for w, h in zip(column_widths, PARTABLE_HEADERS)] |
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[14de349] | 281 | |
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| 282 | sep = " ".join("="*w for w in column_widths) |
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| 283 | lines = [ |
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| 284 | sep, |
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[33e91b1] | 285 | " ".join("%-*s" % (w, h) for w, h in zip(column_widths, PARTABLE_HEADERS)), |
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[14de349] | 286 | sep, |
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| 287 | ] |
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| 288 | for p in pars: |
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| 289 | lines.append(" ".join([ |
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[33e91b1] | 290 | "%-*s" % (column_widths[0], p[0]), |
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| 291 | "%-*s" % (column_widths[1], p[-1]), |
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[4eac427] | 292 | "%-*s" % (column_widths[2], format_units(p[1])), |
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[33e91b1] | 293 | "%*g" % (column_widths[3], p[2]), |
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[14de349] | 294 | ])) |
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| 295 | lines.append(sep) |
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| 296 | return "\n".join(lines) |
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| 297 | |
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[32c160a] | 298 | def _search(search_path, filename): |
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| 299 | """ |
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| 300 | Find *filename* in *search_path*. |
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| 301 | |
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| 302 | Raises ValueError if file does not exist. |
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| 303 | """ |
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| 304 | for path in search_path: |
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[f734e7d] | 305 | target = joinpath(path, filename) |
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| 306 | if exists(target): |
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[32c160a] | 307 | return target |
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[33e91b1] | 308 | raise ValueError("%r not found in %s" % (filename, search_path)) |
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[14de349] | 309 | |
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[ff7119b] | 310 | def sources(info): |
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| 311 | """ |
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| 312 | Return a list of the sources file paths for the module. |
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| 313 | """ |
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[33e91b1] | 314 | search_path = [dirname(info['filename']), |
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| 315 | abspath(joinpath(dirname(__file__), 'models'))] |
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[5d4777d] | 316 | return [_search(search_path, f) for f in info['source']] |
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[ff7119b] | 317 | |
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[f734e7d] | 318 | def use_single(source): |
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[ff7119b] | 319 | """ |
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[f734e7d] | 320 | Convert code from double precision to single precision. |
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[ff7119b] | 321 | """ |
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[f734e7d] | 322 | # Convert double keyword to float. Accept an 'n' parameter for vector |
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| 323 | # values, where n is 2, 4, 8 or 16. Assume complex numbers are represented |
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| 324 | # as cdouble which is typedef'd to double2. |
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| 325 | source = re.sub(r'(^|[^a-zA-Z0-9_]c?)double(([248]|16)?($|[^a-zA-Z0-9_]))', |
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| 326 | r'\1float\2', source) |
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| 327 | # Convert floating point constants to single by adding 'f' to the end. |
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| 328 | # OS/X driver complains if you don't do this. |
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| 329 | source = re.sub(r'[^a-zA-Z_](\d*[.]\d+|\d+[.]\d*)([eE][+-]?\d+)?', |
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| 330 | r'\g<0>f', source) |
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| 331 | return source |
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| 332 | |
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[5edfe12] | 333 | def use_long_double(source): |
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| 334 | """ |
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| 335 | Convert code from double precision to long double precision. |
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| 336 | """ |
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| 337 | # Convert double keyword to float. Accept an 'n' parameter for vector |
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| 338 | # values, where n is 2, 4, 8 or 16. Assume complex numbers are represented |
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| 339 | # as cdouble which is typedef'd to double2. |
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| 340 | source = re.sub(r'(^|[^a-zA-Z0-9_]c?)double(([248]|16)?($|[^a-zA-Z0-9_]))', |
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| 341 | r'\1long double\2', source) |
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| 342 | # Convert floating point constants to single by adding 'f' to the end. |
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| 343 | # OS/X driver complains if you don't do this. |
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| 344 | source = re.sub(r'[^a-zA-Z_](\d*[.]\d+|\d+[.]\d*)([eE][+-]?\d+)?', |
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| 345 | r'\g<0>L', source) |
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| 346 | return source |
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| 347 | |
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[f734e7d] | 348 | |
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| 349 | def kernel_name(info, is_2D): |
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| 350 | """ |
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| 351 | Name of the exported kernel symbol. |
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| 352 | """ |
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| 353 | return info['name'] + "_" + ("Iqxy" if is_2D else "Iq") |
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| 354 | |
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[14de349] | 355 | |
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[ce27e21] | 356 | def categorize_parameters(pars): |
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[14de349] | 357 | """ |
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[ce27e21] | 358 | Build parameter categories out of the the parameter definitions. |
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| 359 | |
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| 360 | Returns a dictionary of categories. |
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[14de349] | 361 | """ |
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[ce27e21] | 362 | partype = { |
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| 363 | 'volume': [], 'orientation': [], 'magnetic': [], '': [], |
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| 364 | 'fixed-1d': [], 'fixed-2d': [], 'pd-1d': [], 'pd-2d': [], |
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| 365 | 'pd-rel': set(), |
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[14de349] | 366 | } |
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| 367 | |
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[ce27e21] | 368 | for p in pars: |
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[33e91b1] | 369 | name, ptype = p[0], p[4] |
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[ce27e21] | 370 | if ptype == 'volume': |
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| 371 | partype['pd-1d'].append(name) |
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| 372 | partype['pd-2d'].append(name) |
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| 373 | partype['pd-rel'].add(name) |
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| 374 | elif ptype == 'magnetic': |
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| 375 | partype['fixed-2d'].append(name) |
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| 376 | elif ptype == 'orientation': |
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| 377 | partype['pd-2d'].append(name) |
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| 378 | elif ptype == '': |
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| 379 | partype['fixed-1d'].append(name) |
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| 380 | partype['fixed-2d'].append(name) |
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| 381 | else: |
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[33e91b1] | 382 | raise ValueError("unknown parameter type %r" % ptype) |
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[ce27e21] | 383 | partype[ptype].append(name) |
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[14de349] | 384 | |
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[ce27e21] | 385 | return partype |
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[14de349] | 386 | |
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[f734e7d] | 387 | def indent(s, depth): |
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| 388 | """ |
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| 389 | Indent a string of text with *depth* additional spaces on each line. |
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| 390 | """ |
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| 391 | spaces = " "*depth |
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[33e91b1] | 392 | sep = "\n" + spaces |
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[f734e7d] | 393 | return spaces + sep.join(s.split("\n")) |
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| 394 | |
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| 395 | |
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| 396 | def build_polydispersity_loops(pd_pars): |
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| 397 | """ |
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| 398 | Build polydispersity loops |
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| 399 | |
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| 400 | Returns loop opening and loop closing |
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| 401 | """ |
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[33e91b1] | 402 | LOOP_OPEN = """\ |
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[f734e7d] | 403 | for (int %(name)s_i=0; %(name)s_i < N%(name)s; %(name)s_i++) { |
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| 404 | const double %(name)s = loops[2*(%(name)s_i%(offset)s)]; |
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| 405 | const double %(name)s_w = loops[2*(%(name)s_i%(offset)s)+1];\ |
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| 406 | """ |
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| 407 | depth = 4 |
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| 408 | offset = "" |
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| 409 | loop_head = [] |
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| 410 | loop_end = [] |
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| 411 | for name in pd_pars: |
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[33e91b1] | 412 | subst = {'name': name, 'offset': offset} |
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| 413 | loop_head.append(indent(LOOP_OPEN % subst, depth)) |
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[f734e7d] | 414 | loop_end.insert(0, (" "*depth) + "}") |
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[33e91b1] | 415 | offset += '+N' + name |
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[f734e7d] | 416 | depth += 2 |
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| 417 | return "\n".join(loop_head), "\n".join(loop_end) |
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| 418 | |
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[33e91b1] | 419 | C_KERNEL_TEMPLATE = None |
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[f734e7d] | 420 | def make_model(info): |
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| 421 | """ |
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| 422 | Generate the code for the kernel defined by info, using source files |
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| 423 | found in the given search path. |
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| 424 | """ |
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| 425 | # TODO: need something other than volume to indicate dispersion parameters |
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| 426 | # No volume normalization despite having a volume parameter. |
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| 427 | # Thickness is labelled a volume in order to trigger polydispersity. |
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| 428 | # May want a separate dispersion flag, or perhaps a separate category for |
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| 429 | # disperse, but not volume. Volume parameters also use relative values |
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| 430 | # for the distribution rather than the absolute values used by angular |
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| 431 | # dispersion. Need to be careful that necessary parameters are available |
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| 432 | # for computing volume even if we allow non-disperse volume parameters. |
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| 433 | |
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| 434 | # Load template |
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| 435 | global C_KERNEL_TEMPLATE |
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| 436 | if C_KERNEL_TEMPLATE is None: |
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| 437 | with open(C_KERNEL_TEMPLATE_PATH) as fid: |
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| 438 | C_KERNEL_TEMPLATE = fid.read() |
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| 439 | |
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| 440 | # Load additional sources |
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| 441 | source = [open(f).read() for f in sources(info)] |
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| 442 | |
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| 443 | # Prepare defines |
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| 444 | defines = [] |
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| 445 | partype = info['partype'] |
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| 446 | pd_1d = partype['pd-1d'] |
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| 447 | pd_2d = partype['pd-2d'] |
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| 448 | fixed_1d = partype['fixed-1d'] |
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| 449 | fixed_2d = partype['fixed-1d'] |
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| 450 | |
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| 451 | iq_parameters = [p[0] |
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[33e91b1] | 452 | for p in info['parameters'][2:] # skip scale, background |
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| 453 | if p[0] in set(fixed_1d + pd_1d)] |
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[f734e7d] | 454 | iqxy_parameters = [p[0] |
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[33e91b1] | 455 | for p in info['parameters'][2:] # skip scale, background |
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| 456 | if p[0] in set(fixed_2d + pd_2d)] |
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[f734e7d] | 457 | volume_parameters = [p[0] |
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[33e91b1] | 458 | for p in info['parameters'] |
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| 459 | if p[4] == 'volume'] |
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[f734e7d] | 460 | |
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| 461 | # Fill in defintions for volume parameters |
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| 462 | if volume_parameters: |
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| 463 | defines.append(('VOLUME_PARAMETERS', |
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| 464 | ','.join(volume_parameters))) |
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| 465 | defines.append(('VOLUME_WEIGHT_PRODUCT', |
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[33e91b1] | 466 | '*'.join(p + '_w' for p in volume_parameters))) |
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[f734e7d] | 467 | |
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| 468 | # Generate form_volume function from body only |
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| 469 | if info['form_volume'] is not None: |
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[6137124] | 470 | if volume_parameters: |
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[33e91b1] | 471 | vol_par_decl = ', '.join('double ' + p for p in volume_parameters) |
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[6137124] | 472 | else: |
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| 473 | vol_par_decl = 'void' |
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[f734e7d] | 474 | defines.append(('VOLUME_PARAMETER_DECLARATIONS', |
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[6137124] | 475 | vol_par_decl)) |
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[f734e7d] | 476 | fn = """\ |
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| 477 | double form_volume(VOLUME_PARAMETER_DECLARATIONS); |
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| 478 | double form_volume(VOLUME_PARAMETER_DECLARATIONS) { |
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| 479 | %(body)s |
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| 480 | } |
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[33e91b1] | 481 | """ % {'body':info['form_volume']} |
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[f734e7d] | 482 | source.append(fn) |
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| 483 | |
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| 484 | # Fill in definitions for Iq parameters |
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[33e91b1] | 485 | defines.append(('IQ_KERNEL_NAME', info['name'] + '_Iq')) |
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[f734e7d] | 486 | defines.append(('IQ_PARAMETERS', ', '.join(iq_parameters))) |
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| 487 | if fixed_1d: |
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| 488 | defines.append(('IQ_FIXED_PARAMETER_DECLARATIONS', |
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[33e91b1] | 489 | ', \\\n '.join('const double %s' % p for p in fixed_1d))) |
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[f734e7d] | 490 | if pd_1d: |
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| 491 | defines.append(('IQ_WEIGHT_PRODUCT', |
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[33e91b1] | 492 | '*'.join(p + '_w' for p in pd_1d))) |
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[f734e7d] | 493 | defines.append(('IQ_DISPERSION_LENGTH_DECLARATIONS', |
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[33e91b1] | 494 | ', \\\n '.join('const int N%s' % p for p in pd_1d))) |
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[f734e7d] | 495 | defines.append(('IQ_DISPERSION_LENGTH_SUM', |
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[33e91b1] | 496 | '+'.join('N' + p for p in pd_1d))) |
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[f734e7d] | 497 | open_loops, close_loops = build_polydispersity_loops(pd_1d) |
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| 498 | defines.append(('IQ_OPEN_LOOPS', |
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[33e91b1] | 499 | open_loops.replace('\n', ' \\\n'))) |
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[f734e7d] | 500 | defines.append(('IQ_CLOSE_LOOPS', |
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[33e91b1] | 501 | close_loops.replace('\n', ' \\\n'))) |
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[f734e7d] | 502 | if info['Iq'] is not None: |
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| 503 | defines.append(('IQ_PARAMETER_DECLARATIONS', |
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[33e91b1] | 504 | ', '.join('double ' + p for p in iq_parameters))) |
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[f734e7d] | 505 | fn = """\ |
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| 506 | double Iq(double q, IQ_PARAMETER_DECLARATIONS); |
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| 507 | double Iq(double q, IQ_PARAMETER_DECLARATIONS) { |
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| 508 | %(body)s |
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| 509 | } |
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[33e91b1] | 510 | """ % {'body':info['Iq']} |
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[f734e7d] | 511 | source.append(fn) |
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| 512 | |
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| 513 | # Fill in definitions for Iqxy parameters |
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[33e91b1] | 514 | defines.append(('IQXY_KERNEL_NAME', info['name'] + '_Iqxy')) |
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[f734e7d] | 515 | defines.append(('IQXY_PARAMETERS', ', '.join(iqxy_parameters))) |
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| 516 | if fixed_2d: |
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| 517 | defines.append(('IQXY_FIXED_PARAMETER_DECLARATIONS', |
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[33e91b1] | 518 | ', \\\n '.join('const double %s' % p for p in fixed_2d))) |
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[f734e7d] | 519 | if pd_2d: |
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| 520 | defines.append(('IQXY_WEIGHT_PRODUCT', |
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[33e91b1] | 521 | '*'.join(p + '_w' for p in pd_2d))) |
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[f734e7d] | 522 | defines.append(('IQXY_DISPERSION_LENGTH_DECLARATIONS', |
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[33e91b1] | 523 | ', \\\n '.join('const int N%s' % p for p in pd_2d))) |
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[f734e7d] | 524 | defines.append(('IQXY_DISPERSION_LENGTH_SUM', |
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[33e91b1] | 525 | '+'.join('N' + p for p in pd_2d))) |
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[f734e7d] | 526 | open_loops, close_loops = build_polydispersity_loops(pd_2d) |
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| 527 | defines.append(('IQXY_OPEN_LOOPS', |
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[33e91b1] | 528 | open_loops.replace('\n', ' \\\n'))) |
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[f734e7d] | 529 | defines.append(('IQXY_CLOSE_LOOPS', |
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[33e91b1] | 530 | close_loops.replace('\n', ' \\\n'))) |
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[f734e7d] | 531 | if info['Iqxy'] is not None: |
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| 532 | defines.append(('IQXY_PARAMETER_DECLARATIONS', |
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[33e91b1] | 533 | ', '.join('double ' + p for p in iqxy_parameters))) |
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[f734e7d] | 534 | fn = """\ |
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| 535 | double Iqxy(double qx, double qy, IQXY_PARAMETER_DECLARATIONS); |
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| 536 | double Iqxy(double qx, double qy, IQXY_PARAMETER_DECLARATIONS) { |
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| 537 | %(body)s |
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| 538 | } |
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[33e91b1] | 539 | """ % {'body':info['Iqxy']} |
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[f734e7d] | 540 | source.append(fn) |
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| 541 | |
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| 542 | # Need to know if we have a theta parameter for Iqxy; it is not there |
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| 543 | # for the magnetic sphere model, for example, which has a magnetic |
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| 544 | # orientation but no shape orientation. |
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| 545 | if 'theta' in pd_2d: |
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| 546 | defines.append(('IQXY_HAS_THETA', '1')) |
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| 547 | |
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[9404dd3] | 548 | #for d in defines: print(d) |
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[33e91b1] | 549 | DEFINES = '\n'.join('#define %s %s' % (k, v) for k, v in defines) |
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| 550 | SOURCES = '\n\n'.join(source) |
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| 551 | return C_KERNEL_TEMPLATE % { |
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[f734e7d] | 552 | 'DEFINES':DEFINES, |
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| 553 | 'SOURCES':SOURCES, |
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| 554 | } |
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| 555 | |
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[cd3dba0] | 556 | def make_info(kernel_module): |
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[14de349] | 557 | """ |
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[cd3dba0] | 558 | Interpret the model definition file, categorizing the parameters. |
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[14de349] | 559 | """ |
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[9404dd3] | 560 | #print(kernelfile) |
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[cd3dba0] | 561 | category = getattr(kernel_module, 'category', None) |
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| 562 | parameters = COMMON_PARAMETERS + kernel_module.parameters |
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| 563 | # Default the demo parameters to the starting values for the individual |
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| 564 | # parameters if an explicit demo parameter set has not been specified. |
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| 565 | demo_parameters = getattr(kernel_module, 'demo', None) |
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| 566 | if demo_parameters is None: |
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| 567 | demo_parameters = dict((p[0],p[2]) for p in parameters) |
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| 568 | filename = abspath(kernel_module.__file__) |
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[d138d43] | 569 | kernel_id = splitext(basename(filename))[0] |
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[cd3dba0] | 570 | name = getattr(kernel_module, 'name', None) |
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| 571 | if name is None: |
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| 572 | name = " ".join(w.capitalize() for w in kernel_id.split('_')) |
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[32c160a] | 573 | info = dict( |
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[cd3dba0] | 574 | id = kernel_id, # string used to load the kernel |
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[33e91b1] | 575 | filename=abspath(kernel_module.__file__), |
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[cd3dba0] | 576 | name=name, |
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[33e91b1] | 577 | title=kernel_module.title, |
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| 578 | description=kernel_module.description, |
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[cd3dba0] | 579 | category=category, |
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| 580 | parameters=parameters, |
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| 581 | demo=demo_parameters, |
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[33e91b1] | 582 | source=getattr(kernel_module, 'source', []), |
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| 583 | oldname=kernel_module.oldname, |
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| 584 | oldpars=kernel_module.oldpars, |
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[32c160a] | 585 | ) |
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[5d4777d] | 586 | # Fill in attributes which default to None |
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[33e91b1] | 587 | info.update((k, getattr(kernel_module, k, None)) |
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[5d4777d] | 588 | for k in ('ER', 'VR', 'form_volume', 'Iq', 'Iqxy')) |
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| 589 | # Fill in the derived attributes |
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[33e91b1] | 590 | info['limits'] = dict((p[0], p[3]) for p in info['parameters']) |
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[32c160a] | 591 | info['partype'] = categorize_parameters(info['parameters']) |
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[33e91b1] | 592 | info['defaults'] = dict((p[0], p[2]) for p in info['parameters']) |
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[cd3dba0] | 593 | return info |
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| 594 | |
---|
| 595 | def make(kernel_module): |
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| 596 | """ |
---|
| 597 | Build an OpenCL/ctypes function from the definition in *kernel_module*. |
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[32c160a] | 598 | |
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[cd3dba0] | 599 | The module can be loaded with a normal python import statement if you |
---|
| 600 | know which module you need, or with __import__('sasmodels.model.'+name) |
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| 601 | if the name is in a string. |
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| 602 | """ |
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| 603 | info = make_info(kernel_module) |
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[f734e7d] | 604 | # Assume if one part of the kernel is python then all parts are. |
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| 605 | source = make_model(info) if not callable(info['Iq']) else None |
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[32c160a] | 606 | return source, info |
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[14de349] | 607 | |
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[e88bb78] | 608 | section_marker = re.compile(r'\A(?P<first>[%s])(?P=first)*\Z' |
---|
| 609 | %re.escape(string.punctuation)) |
---|
| 610 | def _convert_section_titles_to_boldface(lines): |
---|
| 611 | prior = None |
---|
| 612 | for line in lines: |
---|
| 613 | if prior is None: |
---|
| 614 | prior = line |
---|
| 615 | elif section_marker.match(line): |
---|
| 616 | if len(line) >= len(prior): |
---|
| 617 | yield "".join( ("**",prior,"**") ) |
---|
| 618 | prior = None |
---|
| 619 | else: |
---|
| 620 | yield prior |
---|
| 621 | prior = line |
---|
| 622 | else: |
---|
| 623 | yield prior |
---|
| 624 | prior = line |
---|
| 625 | if prior is not None: |
---|
| 626 | yield prior |
---|
| 627 | |
---|
| 628 | def convert_section_titles_to_boldface(string): |
---|
| 629 | return "\n".join(_convert_section_titles_to_boldface(string.split('\n'))) |
---|
| 630 | |
---|
[a7684e5] | 631 | def doc(kernel_module): |
---|
| 632 | """ |
---|
| 633 | Return the documentation for the model. |
---|
| 634 | """ |
---|
[eb69cce] | 635 | Iq_units = "The returned value is scaled to units of |cm^-1| |sr^-1|, absolute scale." |
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| 636 | Sq_units = "The returned value is a dimensionless structure factor, $S(q)$." |
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[cd3dba0] | 637 | info = make_info(kernel_module) |
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[eb69cce] | 638 | is_Sq = ("structure-factor" in info['category']) |
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[e88bb78] | 639 | #docs = kernel_module.__doc__ |
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| 640 | docs = convert_section_titles_to_boldface(kernel_module.__doc__) |
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[cd3dba0] | 641 | subst = dict(id=info['id'].replace('_', '-'), |
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| 642 | name=info['name'], |
---|
| 643 | title=info['title'], |
---|
| 644 | parameters=make_partable(info['parameters']), |
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[eb69cce] | 645 | returns=Sq_units if is_Sq else Iq_units, |
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[e88bb78] | 646 | docs=docs) |
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[33e91b1] | 647 | return DOC_HEADER % subst |
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[a7684e5] | 648 | |
---|
[ff7119b] | 649 | |
---|
[14de349] | 650 | |
---|
| 651 | def demo_time(): |
---|
[b3f6bc3] | 652 | from .models import cylinder |
---|
[3c56da87] | 653 | import datetime |
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[b3f6bc3] | 654 | tic = datetime.datetime.now() |
---|
[33e91b1] | 655 | make(cylinder) |
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[3c56da87] | 656 | toc = (datetime.datetime.now() - tic).total_seconds() |
---|
[9404dd3] | 657 | print("time: %g"%toc) |
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[14de349] | 658 | |
---|
[ff58110] | 659 | def main(): |
---|
| 660 | if len(sys.argv) <= 1: |
---|
[9404dd3] | 661 | print("usage: python -m sasmodels.generate modelname") |
---|
[ff58110] | 662 | else: |
---|
| 663 | name = sys.argv[1] |
---|
| 664 | import sasmodels.models |
---|
[33e91b1] | 665 | __import__('sasmodels.models.' + name) |
---|
[ff58110] | 666 | model = getattr(sasmodels.models, name) |
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[33e91b1] | 667 | source, _ = make(model) |
---|
[9404dd3] | 668 | print(source) |
---|
[14de349] | 669 | |
---|
| 670 | if __name__ == "__main__": |
---|
[ff58110] | 671 | main() |
---|