Stokesian Dynamics

config/Espresso.m4

@@ -74,3 +74,30 @@ AC_DEFUN([ES_ADDPATH_CHECK_HEADER],[
 ])
 
 
+
+dnl search for a library in additional paths
+AC_DEFUN([ES_ADDPATH_CHECK_LIB_2],[
+	AC_MSG_CHECKING([for lib$1])
+	es_save_LDFLAGS=$LDFLAGS
+	es_save_LIBS=$LIBS
+	es_adp_found=no
+	dnl let's see whether it's in the default paths
+	LIBS="-l$1 $es_save_LIBS"
+	AC_LINK_IFELSE([AC_LANG_CALL([],[$2])],[es_adp_found=yes],[])
+
+	if test .$es_adp_found = .no; then
+		for path in $5 /usr/lib64 /usr/local/lib64 /opt/lib64 /sw/lib /opt/local/lib /usr/lib /usr/local/lib /opt/lib; do
+			LDFLAGS="$es_save_LDFLAGS -L$path"
+			AC_LINK_IFELSE([AC_LANG_PROGRAMM([],[$2])],[es_adp_found=yes],[])
+			if test .$es_adp_found = .yes; then break; fi
+		done
+	fi
+	if test .$es_adp_found = .yes; then
+		AC_MSG_RESULT(yes)
+	else
+		AC_MSG_RESULT(no)
+		LDFLAGS=$es_save_LDFLAGS
+		LIBS=$es_save_LIBS
+	fi
+	AS_IF([test .$es_adp_found = .yes], [$3],[$4])
+])

configure.ac

@@ -268,6 +268,7 @@ AS_IF([test x$with_cuda != xno],[
     # save current libs in case CUDA is not enabled at the end
     save_LIBS=$LIBS
     save_LDFLAGS=$LDFLAGS
+    save_CPPFLAGS=$CPPFLAGS
 
     # NVCC
     AC_PROG_CUDA
@@ -301,6 +302,37 @@ AS_IF([test x$with_cuda != xno],[
         ])
     ], [$cuda_path/lib $cuda_path/lib64])
 
+    ES_ADDPATH_CHECK_LIB(cublas, cublasDgemm_v2, [], [
+        cuda_ok=no
+
+        AS_IF([test x$with_cuda = xyes],[
+            AC_MSG_FAILURE([could not find cuda BLAS library (cublas), specify location using LDFLAGS])
+        ],[
+            AC_MSG_WARN([could not find cuda BLAS library (cublas). Some features will not be available!])
+        ])
+    ], [$cuda_path/lib $cuda_path/lib64])
+
+    ES_ADDPATH_CHECK_HEADER([cublas_v2.h],, [
+    	cuda_ok=no
+
+        AS_IF([test x$with_cuda = xyes],[
+            AC_MSG_FAILURE([could not find cuda BLAS header files (cublas_v2.h), specify location using CPPFLAGS])
+        ],[
+            AC_MSG_WARN([could not find cuda BLAS header files (cublas_v2.h). Some features will not be available!])
+        ])
+    ], [$cuda_path/include])
+
+
+    ES_ADDPATH_CHECK_LIB(curand, curandCreateGenerator, [], [
+        cuda_ok=no
+
+        AS_IF([test x$with_cuda = xyes],[
+            AC_MSG_FAILURE([could not find cuda RAND library (curand), specify location using LDFLAGS])
+        ],[
+            AC_MSG_WARN([could not find cuda RAND library (curand). Some features will not be available!])
+        ])
+    ], [$cuda_path/lib $cuda_path/lib64])
+
     # NVCC compile check
     AC_MSG_CHECKING([whether CUDA compiles])
 
@@ -379,11 +411,95 @@ AS_IF([test x$with_cuda != xno],[
         # reset standard compiler options
         LIBS=$save_LIBS
         LDFLAGS=$save_LDFLAGS
+	CPPFLAGS=$save_CPPFLAGS
     ])
 ])
 
 AM_CONDITIONAL(CUDA, [test x$cuda_ok == xyes])
 
+## Checking for MAGMA
+##################################
+AS_IF([test x$with_magma = xguess || test x$with_magma = xyes || test x$with_magma = x],[
+   magma_path=/usr/local/magma
+],[test x$with_magma != xno],[
+   magma_path=$with_magma
+   with_magma=yes
+])
+
+AC_MSG_CHECKING([whether to use MAGMA])
+AC_ARG_WITH([magma],
+	AS_HELP_STRING([--with-magma],
+                       [specify whether or not to use MAGMA [guess]]),
+	, with_magma=guess)
+AC_MSG_RESULT($with_magma)
+
+AS_IF([test x$with_magma = xno], [magma_found=no],
+  [ AC_SEARCH_LIBS(magma_init, [magma], [magma_found=yes], [magma_found=no])
+    AS_IF([test x$magma_found = xyes],
+      [ AC_CHECK_HEADER([magma.h],, [magma_found=no],[[#define HAVE_CUBLAS]])
+        AS_IF([test x$magma_found = xyes],
+          [ AC_SEARCH_LIBS([lsame_], [acml acml_mp],, [magma_found=no]
+	                                              AC_MSG_WARN([MAGMA needs LAPACK. Currently only for the acml libary is searched - others have still to be added to configure.ac]) )])
+      ])
+  ])
+
+
+AS_IF([test x$magma_found = xno],[
+  AS_IF([test x$with_magma = xyes],[
+    AC_MSG_FAILURE([MAGMA requested, but MAGMA was not found!])
+    ],[ AS_IF([test x$with_magma = xguess], [
+          AC_MSG_WARN([MAGMA not found. Some features will not be available!])
+         ])
+    ])
+  ])
+AS_IF([test x$magma_found = xyes],[
+  AC_DEFINE(MAGMA,[],[Whether MAGMA is available])])
+# end of check for MAGMA
+
+
+## Checking for ARPACK
+##################################
+AS_IF([test x$with_arpack = xguess || test x$with_arpack = xyes || test x$with_arpack = x],[
+   arpack_path=/usr/local/arpack
+],[test x$with_arpack != xno],[
+   arpack_path=$with_arpack
+   with_arpack=yes
+])
+
+AC_MSG_CHECKING([whether to use ARPACK])
+AC_ARG_WITH([arpack],
+	AS_HELP_STRING([--with-arpack],
+                       [specify whether or not to use ARPACK [guess]]),
+	, with_arpack=guess)
+AC_MSG_RESULT($with_arpack)
+
+
+ES_ADDPATH_CHECK_LIB(arpack, dnaupd_, [arpack_found=yes], [
+	arpack_found=no
+
+        AS_IF([test x$with_arpack = xyes],[
+            AC_MSG_FAILURE([could not find ARPACK library, specify location using LDFLAGS])
+        ],[
+            AC_MSG_WARN([could not find ARPACK library. Some features will not be available!])
+        ])
+    ], [$arpack_path/.libs])
+
+
+
+AS_IF([test x$arpack_found = xno],[
+  AS_IF([test x$with_arpack = xyes],[
+    AC_MSG_FAILURE([ARPACK requested, but ARPACK was not found!])
+    ],[ AS_IF([test x$with_arpack = xguess], [
+          AC_MSG_WARN([ARPACK not found. Some features will not be available!])
+         ])
+    ])
+  ])
+AS_IF([test x$arpack_found = xyes],[
+  AC_DEFINE(ARPACK,[],[Whether ARPACK is available])])
+# end of check for ARPACK
+
+
+
 cat <<EOF
 ****************************************************************
 *                  Checking for Python                         *

doc/dg/dg.tex

@@ -280,7 +280,7 @@ \subsection{General issues}
 \item To see which parts of the User's guide need to be fixed or which
   documentation is missing, there is a \verb!\todo!-command where one
   can put notes about what remains to be done. In the release version,
-  the boxes are diabled so that they do not disturb the users. They
+  the boxes are disabled so that they do not disturb the users. They
   can be turned on by commenting out the appropriate line in
   \texttt{ug.tex}:
 \begin{verbatim}

doc/ug/analysis-core.tex

@@ -445,7 +445,7 @@ \subsection{Creating a correlation}
     Tensor product of $A$ and $B$, \ie $C_{i \cdot l_B + j} = A_i B_j$, with $l_B$ the length of $B$.
     \item \lit{complex_conjugate_product}
     \todo{Complex conjugate product must be defined.}
-    \item \lit{fcs_acf} \var{w_x}\var{w_y} \var{w_z} \\
+    \item \lit{fcs_acf} \var{w_x} \var{w_y} \var{w_z} \\
     Fluorescence Correlation Spectroscopy (FCS) autocorrelation function, \ie
     \begin{equation}
     G_i(\tau) = \frac{1}{N} \Bigl< \exp \Bigl( - \frac{\Delta x_i^2(\tau) }{w_x^2} - \frac{\Delta y_i^2(\tau)}{w_y^2} - \frac{\Delta z_i^2(\tau)}{w_z^2} \Bigr) \Bigr>\,,
@@ -457,7 +457,7 @@ \subsection{Creating a correlation}
     \begin{equation}
     W(x,y,z) = I_0 \exp \Bigl( - \frac{2x^2}{w_x^2} - \frac{2y^2}{w_y^2} - \frac{2z^2}{w_z^2} \Bigr)\,.
     \end{equation}
-    Equation~\ref{eq:Gtau} is a generalization of the formula presented by 
+    Equation~\eqref{eq:Gtau} is a generalization of the formula presented by 
     H\"ofling \etal~\cite{hofling11a}. For more information, see references therein.
     Per each 3 dimensions of the observable, one dimension of the correlation output
     is produced. If \lit{fcs_acf} is used with other observables than 
@@ -481,7 +481,7 @@ \subsection{Creating a correlation}
   in tau.  This is a parameter of the multiple tau correlator. If you
   want to use it, make sure that you know how it works. By default, it
   is set equal to \var{tau\_max} which results in the trivial linear
-  correlator. By setting \var{tau\_lin} < \var{tau\_max} the multiple
+  correlator. By setting \var{tau\_lin} $<$ \var{tau\_max} the multiple
   tau correlator is switched on. In many cases, \var{tau\_lin}=16 is a
   good choice but this may strongly depend on the observables you are
   correlating.  For more information, we recommend to read
@@ -549,7 +549,7 @@ \subsection{Collecting time series data for the correlation}
 updated only when the lower level buffers are filled and
 there is a need to push some values one level up. When the
 updating is stopped, a number of observable values have not
-reached the higher level, especially when \var{tau_max} 
+reached the higher level, especially when \var{tau\_max} 
 is comparable to the total simulation time
 and if there are many compression levels. In such case,
 variant \variant{3} is very useful. If \var{tau\_max} 
@@ -620,9 +620,9 @@ \subsection{The correlation algorithm: multiple tau correlator}
 \end{figure}
 
 Let us consider a set of $N$ observable values as schematically shown
-in Figures~\ref{fig:dataSet}, where a value of index $i$ was measured
+in figure~\ref{fig:dataSet}, where a value of index $i$ was measured
 in time $i\delta t$. We are interested in computing the correlation 
-function according to Equation~\ref{eq:CtauDef} for a range lag times
+function according to equation~\eqref{eq:corr.def} for a range lag times
 $\tau = (i-j)\delta t$ between the measurements $i$ and $j$.
 To simplify the notation, we further drop $\delta t$
 when referring to observables and lag times. 

doc/ug/features.tex

@@ -27,7 +27,7 @@ \chapter{Features}
 this will negatively effect \es's performance.
 
 Features can be activated in the configuration header
-\texttt{myconfig.h} (see section \vref{sec:myconfig}). Too activate
+\texttt{myconfig.hpp} (see section \vref{sec:myconfig}). Too activate
 \texttt{FEATURE}, add the following line to the header file:
 \begin{verbatim}
 #define FEATURE
@@ -145,6 +145,14 @@ \section{General features}
 \item \newfeature{LB_ELECTROHYDRODYNAMICS} Enables the implicit
   calculation of electro-hydrodynamics for charged particles and salt
   ions in an electric field.
+\item \newfeature{SD} enable Stokesian Dynamics.
+\item \newfeature{SD_NOT_PERIODIC} disable periodic boundary conditions in
+  Stokesian Dynamics.
+\item \newfeature{SD_USE_FLOAT} use float instead of double in Stokesian
+  Dynamics.
+\item \newfeature{SD_FF_ONLY} disable nearfield of Stokesian Dynamics.
+\item \newfeature{SD_DEBUG} enable debug Stokesian Dynamics.
+
 \end{itemize}
 
 \section{Interactions}
@@ -255,6 +263,8 @@ \section{Debug messages}
 \item \newfeature{FORCE\_CORE} Causes \es{} to try to provoke a core dump
   when exiting unexpectedly.
 \item \newfeature{MPI\_CORE} Causes \es{} to try this even with MPI errors.
+\item \newfeature{SD_DEBUG} Causes \es{} to check more things in the Stokesian
+  Dynamics code. If \var{warnings} is larger 1, SD prints more informations.
 \end{itemize}
 
 %%% Local Variables: 

doc/ug/installation.tex

@@ -154,6 +154,9 @@ \subsection{Options and Variables}
   i.e. everything with a Fermi chip or newer.  Note that we require at
   least compute model 1.1, that is G90. However, to use G90 (e.\,g.~Tesla
   C1060), you need to manually specificy compute model 1.1.
+\item[\texttt{--with-arpack=path} / \texttt{--without-arpack}] This switch
+  enables ARPACK support. \texttt{path} should be the path to the ARPACK
+  directory. ARPACK is currently only needed for Stokesian Dynamics support.
 \item[\texttt{LDFLAGS=\textit{linker-flags}}] This variable can be
   used to change the flags that the linker will get when linking the
   \es binaries.  This variable can be used to modify the path where

doc/ug/introduction.tex

@@ -167,6 +167,7 @@ \section{Available simulation methods}
   DPD                                 & None   & Good   \\
   Shan-Chen Multicomponent Fluid      & Group  & Group  \\
   Tunable Slip Boundary               & Single & Single \\
+  Stokesian Dynamics                  & Single & Single \\
   \multicolumn{3}{|c|}{\textbf{Analysis}} \\
   uwerr                               & None   & Good   \\
   \multicolumn{3}{|c|}{\textbf{Input/Output}} \\

doc/ug/lb.tex

@@ -130,9 +130,9 @@ \section{Setting up a LB fluid}
 the lattice constant.
 
 \begin{essyntax}
-  lbfluid save_ascii_checkpoint \var{filename}
-  lbfluid save_binary_checkpoint \var{filename}
-  lbfluid load_ascii_checkpoint \var{filename}
+  lbfluid save_ascii_checkpoint \var{filename}\\
+  lbfluid save_binary_checkpoint \var{filename}\\
+  lbfluid load_ascii_checkpoint \var{filename}\\
   lbfluid load_binary_checkpoint \var{filename}
 \end{essyntax}
 The first two save commands save all of the LB fluid nodes' populations to \var{filename} in ascii or binary format respectively.

doc/ug/otherrefs.bib

@@ -111,6 +111,19 @@ @ARTICLE{ballenegger09a
   url = {http://link.aip.org/link/?JCP/131/094107/1}
 }
 
+@article{beenakker86a,
+   author = {Beenakker, C. W. J.},
+   title = {Ewald sum of the Rotne--Prager tensor},
+   journal = {The Journal of Chemical Physics},
+   year = {1986},
+   volume = {85},
+   number = {3}, 
+   pages = {1581-1582},
+   file = {beenakker86a.pdf:beenakker86a.pdf:PDF},
+   url = {http://scitation.aip.org/content/aip/journal/jcp/85/3/10.1063/1.451199},
+   doi = {10.1063/1.451199}
+}
+
 @ARTICLE{berendsen84a,
   author = {H. J. C. Berendsen and J. P. M. Postma and W. F. van Gunsteren and
 	A. DiNola and J. R. Haak},

doc/ug/part.tex

@@ -356,6 +356,7 @@ \subsection{Getting particle properties}
 \subsection{Deleting  particles}
 \label{tcl:part:delete}
 
+\todo{What is the syntax of variant 3?}
 \begin{essyntax}
   \variant{1} part \var{pid} delete
   \variant{2} part deleteall