Merge pull request #43 from bhourahine/bhTypos

Minor typesetting bugs
dftbplus · Jun 15, 2022 · 2be9397 · 2be9397
2 parents 354f95b + 8f7986b
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diff --git a/docs/_figures/linresp/abs-emi.png b/docs/_figures/linresp/abs-emi.png
diff --git a/docs/_figures/linresp/homo.png b/docs/_figures/linresp/homo.png
diff --git a/docs/_figures/linresp/lumo.png b/docs/_figures/linresp/lumo.png
diff --git a/docs/_figures/linresp/macromol_abs.png b/docs/_figures/linresp/macromol_abs.png
diff --git a/docs/_figures/linresp/no-tio2_abs.png b/docs/_figures/linresp/no-tio2_abs.png
diff --git a/docs/_figures/linresp/no-tio2_geo.png b/docs/_figures/linresp/no-tio2_geo.png
diff --git a/docs/_figures/moleculardynamics/md/md_spectra.png b/docs/_figures/moleculardynamics/md/md_spectra.png
diff --git a/docs/_figures/moleculardynamics/md/md_spectra.svg b/docs/_figures/moleculardynamics/md/md_spectra.svg
diff --git a/docs/interfaces/ipi/ipi.rst b/docs/interfaces/ipi/ipi.rst
@@ -114,7 +114,7 @@ Geometry optimisation
 
 [Input: `recipes/interfaces/ipi/zundel/`]
 
-An example using a Zundel ion (H:sub:`5`O:sub:`2`:sup:`+`) with
+An example using a Zundel ion (H\ :sub:`5`\ O\ :sub:`2`:sup:`+`) with
 on-site corrected DFTB2 embedded in a implicit water solvent is
 provided as an example. The implicit solvent lacks the
 hydrogen-bonding network that would be present in real water.
@@ -174,18 +174,21 @@ continued for longer) is shown below
 400 steps is insufficent to thermalise the system to the target
 temperature, but the dynamics of the individual beads, and the *path
 centroid* (i.e., the average position of the quantum particles) are
-output, along with data gathered during the run in the files ::
-
-  +----------------------+----------------+
-  |simulation.xc.xyz     | path centroid  |
-  +----------------------+----------------+
-  |RESTART               |restart data    |
-  +----------------------+----------------+
-  |simulation.out        |collected data  |
-  +----------------------+----------------+
-  |simulation.pos_\*.xyz |individual beads|
-  +----------------------+----------------+
-
+output, along with data gathered during the run in the files
+
+  +-----------------------+-----------------+
+  | File                  | Contents        |
+  +=======================+=================+
+  | simulation.xc.xyz     | path centroid   |
+  +-----------------------+-----------------+
+  | RESTART               | restart data    |
+  +-----------------------+-----------------+
+  | simulation.out        | collected data  |
+  +-----------------------+-----------------+
+  | simulation.pos_*.xyz  | individual beads|
+  +-----------------------+-----------------+
+
+
 The frequency at which these files are appended is set in `nvtPI.xml`
 
 Stopping programs

diff --git a/docs/linresp/index.rst b/docs/linresp/index.rst
@@ -1,8 +1,8 @@
 .. _linear-response:
 
-###################
-Linear response
-###################
+###########################
+Linear response excitations
+###########################
 
 In this chapter we will go through a couple of recipes for the
 computation of excited state properties using linear response

diff --git a/docs/linresp/relax.rst b/docs/linresp/relax.rst
@@ -137,7 +137,6 @@ illustrates the energetic landscape:
 
 .. _fig_aee:
 .. figure:: ../_figures/linresp/abs-emi.png
-     :height: 36ex
      :align: center
      :alt: homo real
 

diff --git a/docs/moleculardynamics/analysis.rst b/docs/moleculardynamics/analysis.rst
@@ -57,7 +57,8 @@ frequencies). The spectrum data is in frequency inits of wavenumbers
      :align: center
      :alt: Autocorrelation spectra of vibrations
 
-     Anharmonic spectra
+     Anharmonic spectra from velocity autocorrelation (excluding large
+     peak at ~0 cm\ :sup:`-1`.
 
 Try different sizes of the window and see what happens to the spectra.
 

diff --git a/docs/moleculardynamics/annealing.rst b/docs/moleculardynamics/annealing.rst
@@ -44,9 +44,10 @@ Annealing to multiple minima
 
    [Input: `recipes/moleculardynamics/annealV2/`]
    
-The annealing process can also be used to find alternative local minina. Here
-two vacancies in a graphene sheet are heated. Depending on the initial
-conditions, the system anneals to different final structures. The starting
-velocities are chosen at random, so depending on the seed value for the random
-generator (several different cases are given in the input file) a different
-final defect geometry is obtained by the same cycle of heating and cooling.
+The annealing process can also be used to find alternative local
+minina. Here two vacancies in a graphene sheet are heated. Depending
+on the initial conditions, this system anneals to different final
+structures. The starting velocities are chosen at random, so depending
+on the seed value for the random number generator (several different
+cases are given in the input file) a different final defect geometry
+is obtained by the same cycle of heating and cooling.
diff --git a/docs/moleculardynamics/plumed2.rst b/docs/moleculardynamics/plumed2.rst
@@ -67,5 +67,6 @@ by the `FILE` tag. The `PRINT` function tells PLUMED2 to print `d1` and `d2`
 every 100 steps to the file specified by the `FILE` tag. Finally, the `ENDPLUMED`
 tag indicates to PLUMED2 that input is complete.
 
-More complete information on the functionality of PLUMED2 can be found in its
-`user manual <http://plumed.github.io/doc-v2.5/user-doc/html/index.html>`_.
+More complete information on the functionality of PLUMED2 can be found
+in it's `user manual
+<http://plumed.github.io/doc-v2.5/user-doc/html/index.html>`_.
diff --git a/docs/moleculardynamics/restarting.rst b/docs/moleculardynamics/restarting.rst
@@ -90,10 +90,11 @@ Example of restarting
 
    [Input: `recipes/moleculardynamics/thermalise/`]
 
-Stop a running MD calculation by either
+Stop a running MD calculation by
 
-  * pressing `ctrl + c` or in the DFTB+ working directory create a
-    stop file ::
+  * pressing `ctrl + c` on the attached terminal
+
+  * in the DFTB+ working directory create a stop file ::
 
       touch stop_driver
 

diff --git a/docs/parallel/benchmarking.rst b/docs/parallel/benchmarking.rst
@@ -246,3 +246,9 @@ Topics to be discussed:
   calculations with spin polarisation and/or k-points.
 
 * Effects of latency on code performance.
+
+
+GPU computing
+^^^^^^^^^^^^^
+
+Description coming soon!
diff --git a/docs/parallel/introduction.rst b/docs/parallel/introduction.rst
@@ -26,8 +26,8 @@ memory per computing core).
 Types of parallel hardware
 --------------------------
 
-The two types of parallel computer that DFTB+ currently can make use of are
-either
+The types of parallel computer that DFTB+ currently can make use of
+are
 
 #. **shared memory** machines, where all processes have access to the same
    data. These are typically small to medium size systems. Most modern CPUs have
@@ -37,6 +37,11 @@ either
    typically larger scale systems with higher numbers of processors and a
    dedicated high speed network between them.
 
+#. **GPU accelerated** where either shared memory or distributed
+   systems have access to graphical processor units, which provide
+   extremely parallel calculations but currently only for ground-state
+   calculations.
+
 The different system types require distinct program models to make use of the
 hardware (however code designed for a distributed memory system can often be
 also used for shared memory architectures).
@@ -87,3 +92,9 @@ Hybrid parallelism
 DFTB+ can be compiled with both MPI and openMP parallelism combined. However
 using this can require system specific settings for thread affinity to provide
 efficiency and this is beyond the scope of this tutorial.
+
+GPU accelerated
+---------------
+
+Either the MAGMA (single node) or ELPA (distributed memory) solvers
+and libraries are required.