Changeset 9150036 in sasmodels for doc

Timestamp:

Mar 6, 2019 6:05:28 PM (6 years ago)

Author:

Paul Kienzle <pkienzle@…>

Branches:

master, core_shell_microgels, magnetic_model, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests

Children:

f64b154, bd91e8f, c11d09f, 02226a2

Parents:

e589e9a (diff), 37f38ff (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.

Message:

Merge branch 'master' into beta_approx

Location:

doc/guide

Files:

• plugin.rst (modified) (2 diffs)
• direct_call.png (added)
• gpu_setup.rst (modified) (4 diffs)
• scripting.rst (modified) (1 diff)

doc/guide/plugin.rst

@@ -272 +272 @@
 structure factor to account for interactions between particles.  See
 `Form_Factors`_ for more details.
+
+**model_info = ...** lets you define a model directly, for example, by
+loading and modifying existing models.  This is done implicitly by
+:func:`sasmodels.core.load_model_info`, which can create a mixture model
+from a pair of existing models.  For example::
+
+    from sasmodels.core import load_model_info
+    model_info = load_model_info('sphere+cylinder')
+
+See :class:`sasmodels.modelinfo.ModelInfo` for details about the model
+attributes that are defined.
 
 Model Parameters
@@ -894 +905 @@
              - \frac{\sin(x)}{x}\left(\frac{1}{x} - \frac{3!}{x^3} + \frac{5!}{x^5} - \frac{7!}{x^7}\right)
 
-        For small arguments ,
+        For small arguments,
 
         .. math::

doc/guide/gpu_setup.rst

@@ -94 +94 @@
 Device Selection
 ================
+**OpenCL drivers**
+
 If you have multiple GPU devices you can tell the program which device to use.
 By default, the program looks for one GPU and one CPU device from available
@@ -104 +106 @@
 was used to run the model.
 
-**If you don't want to use OpenCL, you can set** *SAS_OPENCL=None*
-**in your environment settings, and it will only use normal programs.**
-
-If you want to use one of the other devices, you can run the following
+If you want to use a specific driver and devices, you can run the following
 from the python console::
 
@@ -115 +114 @@
 This will provide a menu of different OpenCL drivers available.
 When one is selected, it will say "set PYOPENCL_CTX=..."
-Use that value as the value of *SAS_OPENCL*.
+Use that value as the value of *SAS_OPENCL=driver:device*.
+
+To use the default OpenCL device (rather than CUDA or None),
+set *SAS_OPENCL=opencl*.
+
+In batch queues, you may need to set *XDG_CACHE_HOME=~/.cache* 
+(Linux only) to a different directory, depending on how the filesystem 
+is configured.  You should also set *SAS_DLL_PATH* for CPU-only modules.
+
+    -DSAS_MODELPATH=path sets directory containing custom models
+    -DSAS_OPENCL=vendor:device|cuda:device|none sets the target GPU device
+    -DXDG_CACHE_HOME=~/.cache sets the pyopencl cache root (linux only)
+    -DSAS_COMPILER=tinycc|msvc|mingw|unix sets the DLL compiler
+    -DSAS_OPENMP=1 turns on OpenMP for the DLLs
+    -DSAS_DLL_PATH=path sets the path to the compiled modules
+
+
+**CUDA drivers**
+
+If OpenCL drivers are not available on your system, but NVidia CUDA
+drivers are available, then set *SAS_OPENCL=cuda* or
+*SAS_OPENCL=cuda:n* for a particular device number *n*.  If no device
+number is specified, then the CUDA drivers looks for look for
+*CUDA_DEVICE=n* or a file ~/.cuda-device containing n for the device number.
+
+In batch queues, the SLURM command *sbatch --gres=gpu:1 ...* will set
+*CUDA_VISIBLE_DEVICES=n*, which ought to set the correct device
+number for *SAS_OPENCL=cuda*.  If not, then set
+*CUDA_DEVICE=$CUDA_VISIBLE_DEVICES* within the batch script.  You may
+need to set the CUDA cache directory to a folder accessible across the
+cluster with *PYCUDA_CACHE_DIR* (or *PYCUDA_DISABLE_CACHE* to disable
+caching), and you may need to set environment specific compiler flags
+with *PYCUDA_DEFAULT_NVCC_FLAGS*.  You should also set *SAS_DLL_PATH* 
+for CPU-only modules.
+
+**No GPU support**
+
+If you don't want to use OpenCL or CUDA, you can set *SAS_OPENCL=None*
+in your environment settings, and it will only use normal programs.
+
+In batch queues, you may need to set *SAS_DLL_PATH* to a directory
+accessible on the compute node.
+
 
 Device Testing
@@ -154 +195 @@
 *Document History*
 
-| 2017-09-27 Paul Kienzle
+| 2018-10-15 Paul Kienzle

doc/guide/scripting.rst

@@ -188 +188 @@
 python kernel.  Once the kernel is in hand, we can then marshal a set of
 parameters into a :class:`sasmodels.details.CallDetails` object and ship it to
-the kernel using the :func:`sansmodels.direct_model.call_kernel` function.  An
-example should help, *example/cylinder_eval.py*::
-
-    from numpy import logspace
+the kernel using the :func:`sansmodels.direct_model.call_kernel` function.  To
+accesses the underlying $<F(q)>$ and $<F^2(q)>$, use
+:func:`sasmodels.direct_model.call_Fq` instead.
+
+The following example should
+help, *example/cylinder_eval.py*::
+
+    from numpy import logspace, sqrt
     from matplotlib import pyplot as plt
     from sasmodels.core import load_model
-    from sasmodels.direct_model import call_kernel
+    from sasmodels.direct_model import call_kernel, call_Fq
 
     model = load_model('cylinder')
     q = logspace(-3, -1, 200)
     kernel = model.make_kernel([q])
-    Iq = call_kernel(kernel, dict(radius=200.))
-    plt.loglog(q, Iq)
+    pars = {'radius': 200, 'radius_pd': 0.1, 'scale': 2}
+    Iq = call_kernel(kernel, pars)
+    F, Fsq, Reff, V, Vratio = call_Fq(kernel, pars)
+
+    plt.loglog(q, Iq, label='2 I(q)')
+    plt.loglog(q, F**2/V, label='<F(q)>^2/V')
+    plt.loglog(q, Fsq/V, label='<F^2(q)>/V')
+    plt.xlabel('q (1/A)')
+    plt.ylabel('I(q) (1/cm)')
+    plt.title('Cylinder with radius 200.')
+    plt.legend()
     plt.show()
 
-On windows, this can be called from the cmd prompt using sasview as::
+.. figure:: direct_call.png
+
+    Comparison between $I(q)$, $<F(q)>$ and $<F^2(q)>$ for cylinder model.
+
+This compares $I(q)$ with $<F(q)>$ and $<F^2(q)>$ for a cylinder
+with *radius=200 +/- 20* and *scale=2*. Note that *call_Fq* does not
+include scale and background, nor does it normalize by the average volume.
+The definition of $F = \rho V \hat F$ scaled by the contrast and
+volume, compared to the canonical cylinder $\hat F$, with $\hat F(0) = 1$.
+Integrating over polydispersity and orientation, the returned values are
+$\sum_{r,w\in N(r_o, r_o/10)} \sum_\theta w F(q,r_o,\theta)\sin\theta$ and
+$\sum_{r,w\in N(r_o, r_o/10)} \sum_\theta w F^2(q,r_o,\theta)\sin\theta$.
+
+On windows, this example can be called from the cmd prompt using sasview as
+as the python interpreter::
 
     SasViewCom example/cylinder_eval.py