Commit 6ae0a1c7 authored by Luka Stanisic's avatar Luka Stanisic

doc: minor fixes

parent a2585366
...@@ -310,7 +310,7 @@ ON/OFF options are presented. ...@@ -310,7 +310,7 @@ ON/OFF options are presented.
.. table:: CMake keyword options. .. table:: CMake keyword options.
+-----------------------------+---------------------------------------------------------+ +-----------------------------+---------------------------------------------------------+
| **<optionname>** | **Option** | | **<optionname>** | **Option** |
+=============================+=========================================================+ +=============================+=========================================================+
| ``USE_OPENMP`` | Enable/Disable OpenMP | | ``USE_OPENMP`` | Enable/Disable OpenMP |
+-----------------------------+---------------------------------------------------------+ +-----------------------------+---------------------------------------------------------+
...@@ -679,7 +679,7 @@ The envelope function is ...@@ -679,7 +679,7 @@ The envelope function is
.. math:: \mathrm{Env}(s)=e^{-bs^2/2}, .. math:: \mathrm{Env}(s)=e^{-bs^2/2},
where parameter :math:`b` controls the Gaussian width and modulates the where parameter :math:`b` controls the Gaussian width and modulates the
. CTF.
To calculate the BioEM posterior probability, we integrate numerically To calculate the BioEM posterior probability, we integrate numerically
the three parameters :math:`\Delta f`, :math:`b` and :math:`A`. To do the three parameters :math:`\Delta f`, :math:`b` and :math:`A`. To do
...@@ -977,19 +977,19 @@ BioEM posterior probability computation: ...@@ -977,19 +977,19 @@ BioEM posterior probability computation:
Optional keywords: Optional keywords:
^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^
- :inpar:`GRIDPOINTS_ALPHA` ``(int)``: (Integration of orientations, - :inpar:`GRIDPOINTS_ALPHA` ``(int)``: (Integration of orientations,
mandatory if quaterionions or `--ReadOrientation` are not used) mandatory if quaterionions or `--ReadOrientation` are not used)
Number of grid points used in the integration over Euler angle Number of grid points used in the integration over Euler angle
:math:`\alpha \in [-\pi,\pi]`. Here a cubic grid in Euler angle :math:`\alpha \in [-\pi,\pi]`. Here a cubic grid in Euler angle
space is performed. The integral over Euler angle :math:`\gamma` is space is performed. The integral over Euler angle :math:`\gamma` is
identical to that of :math:`\alpha`. identical to that of :math:`\alpha`.
- :inpar:`GRIDPOINTS_BETA` ``(int)``: (Integration of orientations, - :inpar:`GRIDPOINTS_BETA` ``(int)``: (Integration of orientations,
mandatory if quaterionions or `--ReadOrientation` are not used) mandatory if quaterionions or `--ReadOrientation` are not used)
Number of grid points used in the integration over Number of grid points used in the integration over
:math:`\cos(\beta) \in [-1,1]`. :math:`\cos(\beta) \in [-1,1]`.
- :inpar:`USE_QUATERNIONS`: (Integration of rientations) If using - :inpar:`USE_QUATERNIONS`: (Integration of Orientations) If using
quaternions to the describe the orientations. *Recommended* for quaternions to the describe the orientations. *Recommended* for
uniformly sampling of :math:`SO3` with the quaternions lists uniformly sampling of :math:`SO3` with the quaternions lists
available in the **Quaternions** directory. available in the **Quaternions** directory.
...@@ -999,7 +999,6 @@ Optional keywords: ...@@ -999,7 +999,6 @@ Optional keywords:
quaternion is within :math:`[-1,1]`. ``(int)`` is the number of quaternion is within :math:`[-1,1]`. ``(int)`` is the number of
grid points per dimension. grid points per dimension.
- :inpar:`ELECTRON_WAVELENGTH` ``(float)``: To change the default - :inpar:`ELECTRON_WAVELENGTH` ``(float)``: To change the default
value of the electron wavelength ``(float)`` used to calculate the value of the electron wavelength ``(float)`` used to calculate the
CTF phase with the defocus. Default 0.019688 :math:`\AA`. CTF phase with the defocus. Default 0.019688 :math:`\AA`.
...@@ -1362,7 +1361,7 @@ In this algorithm, the parallelization for GPU is now done on a lower ...@@ -1362,7 +1361,7 @@ In this algorithm, the parallelization for GPU is now done on a lower
level: the GPU (or OpenMP for the only CPU case) processes the center level: the GPU (or OpenMP for the only CPU case) processes the center
displacements, whilst the CPU with MPI processes the orientations and displacements, whilst the CPU with MPI processes the orientations and
with OpenMP the projections and convolutions. Hence, there is more with OpenMP the projections and convolutions. Hence, there is more
parallelism and better performance for the GPU for this case. parallelism and better performance for the GPU for this case.
Parallelization Parallelization
~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~
...@@ -1379,7 +1378,7 @@ We present the different parallelization options when using the ...@@ -1379,7 +1378,7 @@ We present the different parallelization options when using the
:envvar:`OMP_NUM_THREADS`. However, :envvar:`OMP_NUM_THREADS`. However,
:envvar:`BIOEM_PROJ_CONV_AT_ONCE` can also be modified as described :envvar:`BIOEM_PROJ_CONV_AT_ONCE` can also be modified as described
above. Importantly, for :envvar:`BIOEM_ALGO`\ ``=2`` the contribution of above. Importantly, for :envvar:`BIOEM_ALGO`\ ``=2`` the contribution of
:envvar:`BIOEM_PROJ_CONV_AT_ONCE` is signifcant. These :envvar:`BIOEM_PROJ_CONV_AT_ONCE` is significant. These
OMP threads are used to work in parallel on the projections, the OMP threads are used to work in parallel on the projections, the
convolutions, and if GPU is disabled on the center displacements convolutions, and if GPU is disabled on the center displacements
and comparisons. and comparisons.
...@@ -1545,11 +1544,12 @@ List of environment variables ...@@ -1545,11 +1544,12 @@ List of environment variables
.. envvar:: BIOEM_PROJ_CONV_AT_ONCE .. envvar:: BIOEM_PROJ_CONV_AT_ONCE
(Default: 1 for :envvar:`BIOEM_ALGO`\ ``=1`` and :envvar:`=OMP_NUM_THREADS` for (Default: 1 for :envvar:`BIOEM_ALGO`\ ``=1`` and ``=``\
:envvar:`BIOEM_ALGO`\ ``=2``) This defines the number of projections and :envvar:`OMP_NUM_THREADS` for :envvar:`BIOEM_ALGO`\ ``=2``) This
convolutions prepared at once. OpenMP threads (whose number is defines the number of projections and convolutions prepared at
defined by :envvar:`OMP_NUM_THREADS` environment variable) are used once. OpenMP threads (whose number is defined by
to prepare these projections and convolutions in parallel. For :envvar:`OMP_NUM_THREADS` environment variable) are used to prepare
these projections and convolutions in parallel. For
:envvar:`BIOEM_ALGO`\ ``=1`` :envvar:`BIOEM_PROJ_CONV_AT_ONCE`\ :envvar:`BIOEM_ALGO`\ ``=1`` :envvar:`BIOEM_PROJ_CONV_AT_ONCE`\
``=[x]`` is mostly relevant, if OpenMP is used, no GPU is used, ``=[x]`` is mostly relevant, if OpenMP is used, no GPU is used,
and/or the number of reference particle-image is very small. For and/or the number of reference particle-image is very small. For
......
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