Move FFT routines to src/gromacs/fft/.

Adjusted the build system a bit to select the file to build at the CMake
level instead of using #ifdefs within the files. Some minor cleanup.
Also add some hacks to produce separate Doxygen docs for each of the
gmx_fft_t implementations; otherwise, they mess up each other and
produce warnings, as some of them have Doxygen comments and some do not.

Change-Id: I55d8c4ce402d68b8cd3e2e700f83d801d8b8294e

diff --git a/src/contrib/timefft.c b/src/contrib/timefft.c
index b2cc6609907d4f4b1671d4e9cec688a1a74ce3c6..fa77e433de3b332a09da01ec8050c2e04453c74d 100644 (file)
--- a/src/contrib/timefft.c
+++ b/src/contrib/timefft.c
@@ -35,19 +35,20 @@
 #include <math.h>
 #include <stdio.h>
 #include <time.h>
+
 #include "typedefs.h"
 #include "macros.h"
 #include "smalloc.h"
 #include "xvgr.h"
-#include "complex.h"
+#include "gmxcomplex.h"
 #include "copyrite.h"
-#include "gmx_fft.h"
 #include "mdrun.h"
 #include "main.h"
 #include "statutil.h"
+#include "gromacs/fft/fft.h"
 
 #ifdef GMX_MPI
-#include "gmx_parallel_3dfft.h"
+#include "gromacs/fft/parallel_3dfft.h"
 #endif
 
 #include "fftgrid.h"

diff --git a/src/gromacs/CMakeLists.txt b/src/gromacs/CMakeLists.txt
index 9703ca9b67777a3f6ff04a1a1ca4da1984f502b6..e9878f118356da72f2b2c365820f613dae82d03d 100644 (file)
--- a/src/gromacs/CMakeLists.txt
+++ b/src/gromacs/CMakeLists.txt
@@ -41,6 +41,7 @@ add_subdirectory(gmxpreprocess)
 add_subdirectory(gmxana)
 add_subdirectory(analysisdata)
 add_subdirectory(commandline)
+add_subdirectory(fft)
 add_subdirectory(linearalgebra)
 add_subdirectory(onlinehelp)
 add_subdirectory(options)

diff --git a/src/gromacs/fft/CMakeLists.txt b/src/gromacs/fft/CMakeLists.txt
new file mode 100644 (file)
index 0000000..116b807
--- /dev/null
+++ b/src/gromacs/fft/CMakeLists.txt
@@ -0,0 +1,62 @@
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2013, by the GROMACS development team, led by
+# David van der Spoel, Berk Hess, Erik Lindahl, and including many
+# others, as listed in the AUTHORS file in the top-level source
+# directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+# GLOB is used to get full paths
+file(GLOB FFT_SOURCES
+     fft.c fft5d.cpp parallel_3dfft.c)
+
+if (GMX_FFT_FFTPACK)
+    file(GLOB FFT_SPECIFIC_SOURCES fft_fftpack.c)
+    list(APPEND FFT_SPECIFIC_SOURCES
+         ${CMAKE_SOURCE_DIR}/src/external/fftpack/fftpack.c)
+endif()
+if (GMX_FFT_FFTW3)
+    file(GLOB FFT_SPECIFIC_SOURCES fft_fftw3.cpp)
+endif()
+if (GMX_FFT_MKL)
+    file(GLOB FFT_SPECIFIC_SOURCES fft_mkl.c)
+endif()
+
+set(LIBGROMACS_SOURCES
+    ${LIBGROMACS_SOURCES} ${FFT_SOURCES} ${FFT_SPECIFIC_SOURCES} PARENT_SCOPE)
+
+set(FFT_PUBLIC_HEADERS
+    fft.h)
+install(FILES ${FFT_PUBLIC_HEADERS}
+        DESTINATION ${INCL_INSTALL_DIR}/gromacs/fft
+        COMPONENT development)
+
+if (BUILD_TESTING)
+    add_subdirectory(tests)
+endif (BUILD_TESTING)

diff --git a/src/gromacs/mdlib/gmx_fft.c b/src/gromacs/fft/fft.c
similarity index 98%
rename from src/gromacs/mdlib/gmx_fft.c
rename to src/gromacs/fft/fft.c
index f131f0d06a53c6ea6283aa5b877478dd1ed90eb7..c2ae5eee45ed1306f6f15868f998c7f9f36723be 100644 (file)
--- a/src/gromacs/mdlib/gmx_fft.c
+++ b/src/gromacs/fft/fft.c
@@ -19,7 +19,6 @@
 #include <config.h>
 #endif
 
-
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
@@ -27,14 +26,13 @@
 
 #include "types/simple.h"
 #include "gmxcomplex.h"
-#include "gmx_fft.h"
-
 #include "gmx_fatal.h"
+#include "gromacs/fft/fft.h"
 
 
 /* This file contains common fft utility functions, but not
  * the actual transform implementations. Check the
- * files like gmx_fft_fftw3.c or gmx_fft_intel_mkl.c for that.
+ * files like fft_fftw3.c or fft_mkl.c for that.
  */
 
 #ifndef GMX_FFT_FFTW3

diff --git a/src/gromacs/legacyheaders/gmx_fft.h b/src/gromacs/fft/fft.h
similarity index 98%
rename from src/gromacs/legacyheaders/gmx_fft.h
rename to src/gromacs/fft/fft.h
index 8bb08eb751924c79a66b81dd145a4132b28c0883..bfe41efee1dd5d9670f974ebe95929ee60964fcb 100644 (file)
--- a/src/gromacs/legacyheaders/gmx_fft.h
+++ b/src/gromacs/fft/fft.h
@@ -15,11 +15,7 @@
  * And Hey:
  * Gnomes, ROck Monsters And Chili Sauce
  */
-
-#ifndef _GMX_FFT_H_
-#define _GMX_FFT_H_
-
-/*! \file gmx_fft.h
+/*! \file
  *  \brief Fast Fourier Transforms.
  *
  *  This file provides an abstract Gromacs interface to Fourier transforms,
@@ -32,13 +28,15 @@
  *  We also provide our own multi-dimensional transform setups even when
  *  the underlying library does not support it directly.
  *
+ * \ingroup module_fft
  */
+#ifndef GMX_FFT_FFT_H
+#define GMX_FFT_FFT_H
 
 #include <stdio.h>
 
-#include "types/simple.h"
-#include "gmxcomplex.h"
-
+#include "../legacyheaders/types/simple.h"
+#include "../legacyheaders/gmxcomplex.h"
 
 #ifdef __cplusplus
 extern "C" {
@@ -405,4 +403,4 @@ void gmx_fft_cleanup();
 }
 #endif
 
-#endif /* _GMX_FFT_H_ */
+#endif

diff --git a/src/gromacs/mdlib/fft5d.cpp b/src/gromacs/fft/fft5d.cpp
similarity index 100%
rename from src/gromacs/mdlib/fft5d.cpp
rename to src/gromacs/fft/fft5d.cpp

diff --git a/src/gromacs/mdlib/fft5d.h b/src/gromacs/fft/fft5d.h
similarity index 97%
rename from src/gromacs/mdlib/fft5d.h
rename to src/gromacs/fft/fft5d.h
index dadbb6a360a2e0425b64f24b4e5f39ad318a30aa..e84803fdfbf619f00f535d76fa1d6fc1aa7b20cf 100644 (file)
--- a/src/gromacs/mdlib/fft5d.h
+++ b/src/gromacs/fft/fft5d.h
@@ -49,9 +49,9 @@ extern "C" {
 FILE* debug;
 #endif
 
-#include <types/commrec.h>
-#include "gmxcomplex.h"
-#include "gmx_fft.h"
+#include "gromacs/legacyheaders/gmxcomplex.h"
+#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/fft/fft.h"
 
 #ifndef GMX_MPI
 double MPI_Wtime();

diff --git a/src/gromacs/mdlib/gmx_fft_fftpack.c b/src/gromacs/fft/fft_fftpack.c
similarity index 98%
rename from src/gromacs/mdlib/gmx_fft_fftpack.c
rename to src/gromacs/fft/fft_fftpack.c
index 5a6cce40b9ae5f9ed96a64ffe2cf308ddaec6f7f..b572dd9d7321a560ac2f0257398bf74de19fe742 100644 (file)
--- a/src/gromacs/mdlib/gmx_fft_fftpack.c
+++ b/src/gromacs/fft/fft_fftpack.c
@@ -19,26 +19,31 @@
 #include <config.h>
 #endif
 
-#ifdef GMX_FFT_FFTPACK
-
 #include <math.h>
 #include <stdlib.h>
 #include <string.h>
 #include <errno.h>
 
-
-#include "gmx_fft.h"
+#include "gromacs/fft/fft.h"
 #include "gmx_fatal.h"
+
 #include "external/fftpack/fftpack.h"
 
-/** Contents of the FFTPACK fft datatype.
+/*! \internal \brief
+ * Contents of the FFTPACK fft datatype.
+ *
+ * Note that this is one of several possible implementations of gmx_fft_t.
  *
  *  FFTPACK only does 1d transforms, so we use a pointers to another fft for
  *  the transform in the next dimension.
  * Thus, a 3d-structure contains a pointer to a 2d one, which in turns contains
  * a pointer to a 1d. The 1d structure has next==NULL.
  */
+#ifdef DOXYGEN
+struct gmx_fft_fftpack
+#else
 struct gmx_fft
+#endif
 {
     int             ndim;     /**< Dimensions, including our subdimensions.  */
     int             n;        /**< Number of points in this dimension.       */
@@ -471,4 +476,3 @@ gmx_fft_destroy(gmx_fft_t      fft)
 void gmx_fft_cleanup()
 {
 }
-#endif /* GMX_FFT_FFTPACK */

diff --git a/src/gromacs/mdlib/gmx_fft_fftw3.cpp b/src/gromacs/fft/fft_fftw3.cpp
similarity index 97%
rename from src/gromacs/mdlib/gmx_fft_fftw3.cpp
rename to src/gromacs/fft/fft_fftw3.cpp
index 83693c041464088a0dd48eae009c8a1d5d505d9e..461cd19d810788fe49f80efb8519f858f4d39764 100644 (file)
--- a/src/gromacs/mdlib/gmx_fft_fftw3.cpp
+++ b/src/gromacs/fft/fft_fftw3.cpp
@@ -18,14 +18,12 @@
 #include <config.h>
 #endif
 
-#ifdef GMX_FFT_FFTW3
-
 #include <errno.h>
 #include <stdlib.h>
 
 #include <fftw3.h>
 
-#include "gmx_fft.h"
+#include "gromacs/fft/fft.h"
 #include "gmx_fatal.h"
 
 #ifdef GMX_DOUBLE
@@ -49,18 +47,30 @@ static tMPI::mutex big_fftw_mutex;
      This is OK as long as the memory directly comes from malloc and is not some subarray within alloated memory.
    - This has to be fixed if any future architecute requires memory to be aligned to multiples of 32 bytes.
  */
-
+/*! \internal \brief
+ * Contents of the FFTW3 fft datatype.
+ *
+ * Note that this is one of several possible implementations of gmx_fft_t.
+ */
+#ifdef DOXYGEN
+struct gmx_fft_fftw3
+#else
 struct gmx_fft
+#endif
 {
-    /* Three alternatives (unaligned/aligned, out-of-place/in-place, forward/backward)
+    /*! \brief
+     * FFTW plans.
+     *
+     * Three alternatives (unaligned/aligned, out-of-place/in-place, forward/backward)
      * results in 8 different FFTW plans. Keep track of them with 3 array indices:
      * first index:   0=unaligned, 1=aligned
      * second index:  0=out-of-place, 1=in-place
      * third index:   0=backward, 1=forward
      */
     FFTWPREFIX(plan)         plan[2][2][2];
-    /* Catch user mistakes */
+    /** Used to catch user mistakes */
     int                      real_transform;
+    /** Number of dimensions in the FFT */
     int                      ndim;
 };
 
@@ -557,4 +567,3 @@ void gmx_fft_cleanup()
 {
     FFTWPREFIX(cleanup)();
 }
-#endif /* GMX_FFT_FFTW3 */

diff --git a/src/gromacs/mdlib/gmx_fft_mkl.c b/src/gromacs/fft/fft_mkl.c
similarity index 99%
rename from src/gromacs/mdlib/gmx_fft_mkl.c
rename to src/gromacs/fft/fft_mkl.c
index 20d3207dc367d4f1f5aa75e394812433524166fe..a0a6b0a789f6870c596de1348cb92aed0dd46659 100644 (file)
--- a/src/gromacs/mdlib/gmx_fft_mkl.c
+++ b/src/gromacs/fft/fft_mkl.c
@@ -19,16 +19,13 @@
 #include <config.h>
 #endif
 
-#ifdef GMX_FFT_MKL
-
 #include <errno.h>
 #include <stdlib.h>
 
 #include <mkl_dfti.h>
 #include <mkl_service.h>
 
-
-#include "gmx_fft.h"
+#include "gromacs/fft/fft.h"
 #include "gmx_fatal.h"
 
 
@@ -44,7 +41,8 @@
 #define GMX_DFTI_PREC  DFTI_SINGLE
 #endif
 
-/* Contents of the Intel MKL FFT fft datatype.
+/*! \internal \brief
+ * Contents of the Intel MKL FFT fft datatype.
  *
  * Note that this is one of several possible implementations of gmx_fft_t.
  *
@@ -76,9 +74,12 @@
  *  3D, ooplace real FFT: 0=FFTx, 1=FFTy, 2=r2c FFTz, 3=c2r FFTz
  *
  *  Intel people reading this: Learn from FFTW what a good interface looks like :-)
- *
  */
+#ifdef DOXYGEN
+struct gmx_fft_mkl
+#else
 struct gmx_fft
+#endif
 {
     int                ndim;          /**< Number of dimensions in FFT  */
     int                nx;            /**< Length of X transform        */
@@ -617,8 +618,3 @@ void gmx_fft_cleanup()
 {
     mkl_free_buffers();
 }
-
-#else
-int
-    gmx_fft_mkl_empty;
-#endif /* GMX_FFT_MKL */

diff --git a/src/gromacs/mdlib/gmx_parallel_3dfft.c b/src/gromacs/fft/parallel_3dfft.c
similarity index 98%
rename from src/gromacs/mdlib/gmx_parallel_3dfft.c
rename to src/gromacs/fft/parallel_3dfft.c
index cfcf557e69e83c52d43a8b762c5d24b6f7f395a9..77f7975648c8279e541c27cc8014652f9ee309cd 100644 (file)
--- a/src/gromacs/mdlib/gmx_parallel_3dfft.c
+++ b/src/gromacs/fft/parallel_3dfft.c
@@ -23,11 +23,11 @@
 #include <string.h>
 #include <errno.h>
 
+#include "gromacs/fft/parallel_3dfft.h"
+#include "gromacs/fft/fft.h"
 #include "gromacs/utility/gmxmpi.h"
 
 #include "smalloc.h"
-#include "gmx_parallel_3dfft.h"
-#include "gmx_fft.h"
 #include "gmxcomplex.h"
 #include "gmx_fatal.h"
 

diff --git a/src/gromacs/legacyheaders/gmx_parallel_3dfft.h b/src/gromacs/fft/parallel_3dfft.h
similarity index 94%
rename from src/gromacs/legacyheaders/gmx_parallel_3dfft.h
rename to src/gromacs/fft/parallel_3dfft.h
index accfec7d82ade9a976cda3da6697685ab98b5811..c5b91d61433996f393bf754a730f041ced37c519 100644 (file)
--- a/src/gromacs/legacyheaders/gmx_parallel_3dfft.h
+++ b/src/gromacs/fft/parallel_3dfft.h
@@ -16,14 +16,14 @@
  * Gnomes, ROck Monsters And Chili Sauce
  */
 
-#ifndef _gmx_parallel_3dfft_h_
-#define _gmx_parallel_3dfft_h_
+#ifndef GMX_FFT_PARALLEL_3DFFT_H
+#define GMX_FFT_PARALLEL_3DFFT_H
 
-
-#include "types/simple.h"
-#include "types/commrec.h"
-#include "gmxcomplex.h"
-#include "gmx_fft.h"
+#include "../legacyheaders/types/nrnb.h"
+#include "../legacyheaders/types/simple.h"
+#include "../legacyheaders/gmxcomplex.h"
+#include "../utility/gmxmpi.h"
+#include "fft.h"
 
 #ifdef __cplusplus
 extern "C" {
@@ -125,5 +125,4 @@ gmx_parallel_3dfft_destroy(gmx_parallel_3dfft_t    pfft_setup);
 }
 #endif
 
-
-#endif /* _gmx_parallel_3dfft_h_ */
+#endif

diff --git a/src/gromacs/fft/tests/CMakeLists.txt b/src/gromacs/fft/tests/CMakeLists.txt
new file mode 100644 (file)
index 0000000..dbb176b
--- /dev/null
+++ b/src/gromacs/fft/tests/CMakeLists.txt
@@ -0,0 +1,2 @@
+gmx_add_unit_test(FFTUnitTests fft-test
+                  fft.cpp)

diff --git a/src/gromacs/mdlib/tests/fft.cpp b/src/gromacs/fft/tests/fft.cpp
similarity index 98%
rename from src/gromacs/mdlib/tests/fft.cpp
rename to src/gromacs/fft/tests/fft.cpp
index 88d0e17bbe6ca85af41da6466f81264c88408a07..cd1fc323cd027d989fa2bb2fbb0d9b39334718c8 100644 (file)
--- a/src/gromacs/mdlib/tests/fft.cpp
+++ b/src/gromacs/fft/tests/fft.cpp
@@ -33,17 +33,16 @@
  * Tests utilities for fft calculations.
  *
  * \author Roland Schulz <roland@utk.edu>
- * \ingroup module_mdlibs
+ * \ingroup module_fft
  */
-
-#include "config.h"
 #include <vector>
-#include <complex>
+
 #include <gtest/gtest.h>
-#include "testutils/refdata.h"
+
+#include "gromacs/fft/fft.h"
+#include "gromacs/fft/parallel_3dfft.h"
 #include "gromacs/utility/stringutil.h"
-#include "gmx_fft.h"
-#include "gmx_parallel_3dfft.h"
+#include "testutils/refdata.h"
 
 namespace
 {

diff --git a/src/gromacs/mdlib/tests/refdata/7_8_25_36_60_FFTTest1D_Complex_0.xml b/src/gromacs/fft/tests/refdata/7_8_25_36_60_FFTTest1D_Complex_0.xml
similarity index 100%
rename from src/gromacs/mdlib/tests/refdata/7_8_25_36_60_FFTTest1D_Complex_0.xml
rename to src/gromacs/fft/tests/refdata/7_8_25_36_60_FFTTest1D_Complex_0.xml

diff --git a/src/gromacs/mdlib/tests/refdata/7_8_25_36_60_FFTTest1D_Complex_1.xml b/src/gromacs/fft/tests/refdata/7_8_25_36_60_FFTTest1D_Complex_1.xml
similarity index 100%
rename from src/gromacs/mdlib/tests/refdata/7_8_25_36_60_FFTTest1D_Complex_1.xml
rename to src/gromacs/fft/tests/refdata/7_8_25_36_60_FFTTest1D_Complex_1.xml

diff --git a/src/gromacs/mdlib/tests/refdata/7_8_25_36_60_FFTTest1D_Complex_2.xml b/src/gromacs/fft/tests/refdata/7_8_25_36_60_FFTTest1D_Complex_2.xml
similarity index 100%
rename from src/gromacs/mdlib/tests/refdata/7_8_25_36_60_FFTTest1D_Complex_2.xml
rename to src/gromacs/fft/tests/refdata/7_8_25_36_60_FFTTest1D_Complex_2.xml

diff --git a/src/gromacs/mdlib/tests/refdata/7_8_25_36_60_FFTTest1D_Complex_3.xml b/src/gromacs/fft/tests/refdata/7_8_25_36_60_FFTTest1D_Complex_3.xml
similarity index 100%
rename from src/gromacs/mdlib/tests/refdata/7_8_25_36_60_FFTTest1D_Complex_3.xml
rename to src/gromacs/fft/tests/refdata/7_8_25_36_60_FFTTest1D_Complex_3.xml

diff --git a/src/gromacs/mdlib/tests/refdata/7_8_25_36_60_FFTTest1D_Complex_4.xml b/src/gromacs/fft/tests/refdata/7_8_25_36_60_FFTTest1D_Complex_4.xml
similarity index 100%
rename from src/gromacs/mdlib/tests/refdata/7_8_25_36_60_FFTTest1D_Complex_4.xml
rename to src/gromacs/fft/tests/refdata/7_8_25_36_60_FFTTest1D_Complex_4.xml

diff --git a/src/gromacs/mdlib/tests/refdata/7_8_25_36_60_FFTTest1D_Real_0.xml b/src/gromacs/fft/tests/refdata/7_8_25_36_60_FFTTest1D_Real_0.xml
similarity index 100%
rename from src/gromacs/mdlib/tests/refdata/7_8_25_36_60_FFTTest1D_Real_0.xml
rename to src/gromacs/fft/tests/refdata/7_8_25_36_60_FFTTest1D_Real_0.xml

diff --git a/src/gromacs/mdlib/tests/refdata/7_8_25_36_60_FFTTest1D_Real_1.xml b/src/gromacs/fft/tests/refdata/7_8_25_36_60_FFTTest1D_Real_1.xml
similarity index 100%
rename from src/gromacs/mdlib/tests/refdata/7_8_25_36_60_FFTTest1D_Real_1.xml
rename to src/gromacs/fft/tests/refdata/7_8_25_36_60_FFTTest1D_Real_1.xml

diff --git a/src/gromacs/mdlib/tests/refdata/7_8_25_36_60_FFTTest1D_Real_2.xml b/src/gromacs/fft/tests/refdata/7_8_25_36_60_FFTTest1D_Real_2.xml
similarity index 100%
rename from src/gromacs/mdlib/tests/refdata/7_8_25_36_60_FFTTest1D_Real_2.xml
rename to src/gromacs/fft/tests/refdata/7_8_25_36_60_FFTTest1D_Real_2.xml

diff --git a/src/gromacs/mdlib/tests/refdata/7_8_25_36_60_FFTTest1D_Real_3.xml b/src/gromacs/fft/tests/refdata/7_8_25_36_60_FFTTest1D_Real_3.xml
similarity index 100%
rename from src/gromacs/mdlib/tests/refdata/7_8_25_36_60_FFTTest1D_Real_3.xml
rename to src/gromacs/fft/tests/refdata/7_8_25_36_60_FFTTest1D_Real_3.xml

diff --git a/src/gromacs/mdlib/tests/refdata/7_8_25_36_60_FFTTest1D_Real_4.xml b/src/gromacs/fft/tests/refdata/7_8_25_36_60_FFTTest1D_Real_4.xml
similarity index 100%
rename from src/gromacs/mdlib/tests/refdata/7_8_25_36_60_FFTTest1D_Real_4.xml
rename to src/gromacs/fft/tests/refdata/7_8_25_36_60_FFTTest1D_Real_4.xml

diff --git a/src/gromacs/mdlib/tests/refdata/FFFTest3D_Real5_6_9.xml b/src/gromacs/fft/tests/refdata/FFFTest3D_Real5_6_9.xml
similarity index 100%
rename from src/gromacs/mdlib/tests/refdata/FFFTest3D_Real5_6_9.xml
rename to src/gromacs/fft/tests/refdata/FFFTest3D_Real5_6_9.xml

diff --git a/src/gromacs/mdlib/tests/refdata/FFTTest_Real2DLength18_15Test.xml b/src/gromacs/fft/tests/refdata/FFTTest_Real2DLength18_15Test.xml
similarity index 100%
rename from src/gromacs/mdlib/tests/refdata/FFTTest_Real2DLength18_15Test.xml
rename to src/gromacs/fft/tests/refdata/FFTTest_Real2DLength18_15Test.xml

diff --git a/src/gromacs/mdlib/tests/refdata/ManyFFTTest_Complex1DLength48Multi5Test.xml b/src/gromacs/fft/tests/refdata/ManyFFTTest_Complex1DLength48Multi5Test.xml
similarity index 100%
rename from src/gromacs/mdlib/tests/refdata/ManyFFTTest_Complex1DLength48Multi5Test.xml
rename to src/gromacs/fft/tests/refdata/ManyFFTTest_Complex1DLength48Multi5Test.xml

diff --git a/src/gromacs/mdlib/tests/refdata/ManyFFTTest_Real1DLength48Multi5Test.xml b/src/gromacs/fft/tests/refdata/ManyFFTTest_Real1DLength48Multi5Test.xml
similarity index 100%
rename from src/gromacs/mdlib/tests/refdata/ManyFFTTest_Real1DLength48Multi5Test.xml
rename to src/gromacs/fft/tests/refdata/ManyFFTTest_Real1DLength48Multi5Test.xml

diff --git a/src/gromacs/gmxana/correl.c b/src/gromacs/gmxana/correl.c
index 142987eae58a948c0d0b87a24afc9c6a589a167c..70cc2a8bb73869d555d1660e056f3fb294bb4301 100644 (file)
--- a/src/gromacs/gmxana/correl.c
+++ b/src/gromacs/gmxana/correl.c
@@ -39,7 +39,8 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <math.h>
-#include "gmx_fft.h"
+
+#include "gromacs/fft/fft.h"
 #include "smalloc.h"
 #include "correl.h"
 

diff --git a/src/gromacs/gmxana/correl.h b/src/gromacs/gmxana/correl.h
index 63107550be67729c84bb47cf19838d7deab60394..36e16e4e1f86f093b2fb0097daf3e170638d8ae6 100644 (file)
--- a/src/gromacs/gmxana/correl.h
+++ b/src/gromacs/gmxana/correl.h
@@ -38,8 +38,7 @@
 #define _correl_h
 
 #include "typedefs.h"
-#include "gmx_fft.h"
-
+#include "gromacs/fft/fft.h"
 
 typedef struct {
     int        n;

diff --git a/src/gromacs/gmxana/gmx_dos.c b/src/gromacs/gmxana/gmx_dos.c
index 443ea04dedcdabd454499ba9f772ee750471a2fc..578d51c702402a14c6f7f95bc4cf5584aab5993b 100644 (file)
--- a/src/gromacs/gmxana/gmx_dos.c
+++ b/src/gromacs/gmxana/gmx_dos.c
@@ -58,7 +58,7 @@
 #include "xvgr.h"
 #include "correl.h"
 #include "gmx_ana.h"
-#include "gmx_fft.h"
+#include "gromacs/fft/fft.h"
 
 enum {
     VACF, MVACF, DOS, DOS_SOLID, DOS_DIFF, DOS_CP, DOS_S, DOS_A, DOS_E, DOS_NR

diff --git a/src/gromacs/gmxana/gmx_velacc.c b/src/gromacs/gmxana/gmx_velacc.c
index 06e65779d8c0881049953dbc8e0c46c0a91c2017..b49775e081309a9c647d7a707cfc66fd5493fb41 100644 (file)
--- a/src/gromacs/gmxana/gmx_velacc.c
+++ b/src/gromacs/gmxana/gmx_velacc.c
@@ -57,7 +57,7 @@
 #include "strdb.h"
 #include "xvgr.h"
 #include "gmx_ana.h"
-#include "gmx_fft.h"
+#include "gromacs/fft/fft.h"
 
 static void index_atom2mol(int *n, atom_id *index, t_block *mols)
 {

diff --git a/src/gromacs/gmxana/powerspect.c b/src/gromacs/gmxana/powerspect.c
index 1aeef2084bfd549c91b127959a85788acd221aeb..eea8ad883809b6b04799dcdaae876ced18fb8c83 100644 (file)
--- a/src/gromacs/gmxana/powerspect.c
+++ b/src/gromacs/gmxana/powerspect.c
@@ -37,10 +37,11 @@
 #ifdef HAVE_CONFIG_H
 #include <config.h>
 #endif
-#include <smalloc.h>
-#include <gmx_fft.h>
-#include <gmx_fatal.h>
-#include <futil.h>
+
+#include "smalloc.h"
+#include "gromacs/fft/fft.h"
+#include "gmx_fatal.h"
+#include "futil.h"
 #include "interf.h"
 #include "powerspect.h"
 

diff --git a/src/gromacs/mdlib/CMakeLists.txt b/src/gromacs/mdlib/CMakeLists.txt
index 96c331230b7af7e712fb69ed7442df2d746cb32f..ab083263e2ee76294fa03af4efdeccb4e590cb98 100644 (file)
--- a/src/gromacs/mdlib/CMakeLists.txt
+++ b/src/gromacs/mdlib/CMakeLists.txt
@@ -1,12 +1,6 @@
 
 file(GLOB MDLIB_SOURCES nbnxn_kernels/*.c *.c *.cpp)
-if(GMX_FFT_FFTPACK)
-list(APPEND MDLIB_SOURCES ${CMAKE_SOURCE_DIR}/src/external/fftpack/fftpack.c)
-endif()
 set(MDLIB_SOURCES ${MDLIB_SOURCES} PARENT_SCOPE)
-if (BUILD_TESTING)
-    add_subdirectory(tests)
-endif (BUILD_TESTING)
 
 if(GMX_GPU)
     add_subdirectory(nbnxn_cuda)

diff --git a/src/gromacs/mdlib/pme.c b/src/gromacs/mdlib/pme.c
index feeec50fb164d64966f1ac4cd0cae147c0e58a13..6b4ede675782d282ce548d566a949c26ecee4cb5 100644 (file)
--- a/src/gromacs/mdlib/pme.c
+++ b/src/gromacs/mdlib/pme.c
@@ -60,6 +60,7 @@
 #include <config.h>
 #endif
 
+#include "gromacs/fft/parallel_3dfft.h"
 #include "gromacs/utility/gmxmpi.h"
 
 #include <stdio.h>
@@ -80,7 +81,6 @@
 #include "nrnb.h"
 #include "copyrite.h"
 #include "gmx_wallcycle.h"
-#include "gmx_parallel_3dfft.h"
 #include "pdbio.h"
 #include "gmx_cyclecounter.h"
 #include "gmx_omp.h"

diff --git a/src/gromacs/mdlib/tests/CMakeLists.txt b/src/gromacs/mdlib/tests/CMakeLists.txt
deleted file mode 100644 (file)
index 903ed90..0000000
--- a/src/gromacs/mdlib/tests/CMakeLists.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-gmx_add_unit_test(MDLibUnitTests mdlib-test
-                  fft.cpp)