Change all C to C++ outside of TNG

Change-Id: I43464b366cfdc1b816088cf8af117b17843f9359

diff --git a/cmake/FindVMD.cmake b/cmake/FindVMD.cmake
index e390bcd7fefc633668141815630a657f1297ea6d..62b010728bfcd51dd3bcda8d9cdf0a20ca0abda8 100644 (file)
--- a/cmake/FindVMD.cmake
+++ b/cmake/FindVMD.cmake
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2013, by the GROMACS development team, led by
+# Copyright (c) 2013,2019, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -59,9 +59,9 @@ find_library(VMDXYZPLUGIN NAME "xyzplugin.so"
 
 if (VMDXYZPLUGIN)
     try_run(TESTVMD TESTVMD_COMPILED ${CMAKE_BINARY_DIR}
-        "${CMAKE_SOURCE_DIR}/cmake/TestVMD.c"
+        "${CMAKE_SOURCE_DIR}/cmake/TestVMD.cpp"
         CMAKE_FLAGS "-DLINK_LIBRARIES=${CMAKE_DL_LIBS}"
-            "-DINCLUDE_DIRECTORIES=${CMAKE_SOURCE_DIR}/src/gmxlib"
+            "-DINCLUDE_DIRECTORIES=${CMAKE_SOURCE_DIR}/src/external/vmd_molfile"
         COMPILE_DEFINITIONS "-DGMX_USE_PLUGINS"
         RUN_OUTPUT_VARIABLE TESTVMD_OUTPUT ARGS ${VMDXYZPLUGIN})
 endif()

diff --git a/cmake/TestCUDAVersion.c b/cmake/TestCUDAVersion.cpp
similarity index 100%
rename from cmake/TestCUDAVersion.c
rename to cmake/TestCUDAVersion.cpp

diff --git a/cmake/TestFileOffsetBits.c b/cmake/TestFileOffsetBits.cpp
similarity index 100%
rename from cmake/TestFileOffsetBits.c
rename to cmake/TestFileOffsetBits.cpp

diff --git a/cmake/TestFujitsuSparc64.c b/cmake/TestFujitsuSparc64.cpp
similarity index 100%
rename from cmake/TestFujitsuSparc64.c
rename to cmake/TestFujitsuSparc64.cpp

diff --git a/cmake/TestMIC.c b/cmake/TestMIC.cpp
similarity index 100%
rename from cmake/TestMIC.c
rename to cmake/TestMIC.cpp

diff --git a/cmake/TestMPI.c b/cmake/TestMPI.cpp
similarity index 100%
rename from cmake/TestMPI.c
rename to cmake/TestMPI.cpp

diff --git a/cmake/TestPipes.c b/cmake/TestPipes.cpp
similarity index 100%
rename from cmake/TestPipes.c
rename to cmake/TestPipes.cpp

diff --git a/cmake/TestSIGUSR1.c b/cmake/TestSIGUSR1.cpp
similarity index 100%
rename from cmake/TestSIGUSR1.c
rename to cmake/TestSIGUSR1.cpp

diff --git a/cmake/TestVMD.c b/cmake/TestVMD.cpp
similarity index 84%
rename from cmake/TestVMD.c
rename to cmake/TestVMD.cpp
index d0618ff9274176b3ae3050d1e6ee4dd40d4e366f..c2bd74bd63d92a622d0a21e058173f162bbe3c63 100644 (file)
--- a/cmake/TestVMD.c
+++ b/cmake/TestVMD.cpp
@@ -1,5 +1,5 @@
 #include "molfile_plugin.h"
-#include "vmddlopen.c"
+#include "vmddlopen.cpp"
 #include "stdio.h"
 
 static int register_cb(void *v, vmdplugin_t *p) {
@@ -10,7 +10,7 @@ static int register_cb(void *v, vmdplugin_t *p) {
 typedef int (*initfunc)(void);
 typedef int (*regfunc)(void *, vmdplugin_register_cb);
 
-/*run: gcc TestVMD.c -DGMX_USE_PLUGINS -Wall -ldl src/gmxlib/vmddlopen.c -I src/gmxlib && ./a.out .../xyzplugin.so ; echo $?*/
+/*run: gcc TestVMD.cpp -DGMX_USE_PLUGINS -Wall -ldl -I../src/external/vmd_molfile  -lm && ./a.out .../xyzplugin.so ; echo $?*/
 int main(int argc, char** argv)
 {
     void *handle, *ifunc, *registerfunc;

diff --git a/cmake/TestWindowsFSeek.c b/cmake/TestWindowsFSeek.cpp
similarity index 100%
rename from cmake/TestWindowsFSeek.c
rename to cmake/TestWindowsFSeek.cpp

diff --git a/cmake/TestX86.c b/cmake/TestX86.cpp
similarity index 100%
rename from cmake/TestX86.c
rename to cmake/TestX86.cpp

diff --git a/cmake/TestXDR.c b/cmake/TestXDR.cpp
similarity index 100%
rename from cmake/TestXDR.c
rename to cmake/TestXDR.cpp

diff --git a/cmake/gmxDetectClang30.cmake b/cmake/gmxDetectClang30.cmake
deleted file mode 100644 (file)
index 4deebaa..0000000
--- a/cmake/gmxDetectClang30.cmake
+++ /dev/null
@@ -1,39 +0,0 @@
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2012, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and 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.
-
-macro(gmx_detect_clang_3_0 OUT_VAR)
-    try_compile(IS_CLANG_3_0 ${CMAKE_BINARY_DIR} ${CMAKE_SOURCE_DIR}/cmake/TestClangVersion.c)
-    set(${OUT_VAR} ${IS_CLANG_3_0})
-endmacro()
-

diff --git a/cmake/gmxDetectTargetArchitecture.cmake b/cmake/gmxDetectTargetArchitecture.cmake
index eb7710b58fb9cdf3bef21d19d871d37c5f4970e4..12cc0fa97094031f2e0ff0647cbaef3ff52e5355 100644 (file)
--- a/cmake/gmxDetectTargetArchitecture.cmake
+++ b/cmake/gmxDetectTargetArchitecture.cmake
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2013,2014,2016,2018, by the GROMACS development team, led by
+# Copyright (c) 2013,2014,2016,2018,2019, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -42,11 +42,11 @@
 function(gmx_detect_target_architecture)
     if (NOT DEFINED GMX_TARGET_X86)
         try_compile(GMX_TARGET_X86 ${CMAKE_BINARY_DIR}
-            "${CMAKE_SOURCE_DIR}/cmake/TestX86.c")
+            "${CMAKE_SOURCE_DIR}/cmake/TestX86.cpp")
     endif()
     if (NOT DEFINED GMX_TARGET_MIC)
         try_compile(GMX_TARGET_MIC ${CMAKE_BINARY_DIR}
-            "${CMAKE_SOURCE_DIR}/cmake/TestMIC.c")
+            "${CMAKE_SOURCE_DIR}/cmake/TestMIC.cpp")
     endif()
     if (NOT DEFINED GMX_TARGET_ARMV7)
         try_compile(GMX_TARGET_ARMV7 ${CMAKE_BINARY_DIR}
@@ -54,6 +54,6 @@ function(gmx_detect_target_architecture)
     endif()
     if (NOT DEFINED GMX_TARGET_FUJITSU_SPARC64)
         try_compile(GMX_TARGET_FUJITSU_SPARC64 ${CMAKE_BINARY_DIR}
-            "${CMAKE_SOURCE_DIR}/cmake/TestFujitsuSparc64.c")
+            "${CMAKE_SOURCE_DIR}/cmake/TestFujitsuSparc64.cpp")
     endif()
 endfunction()

diff --git a/cmake/gmxManageGPU.cmake b/cmake/gmxManageGPU.cmake
index 6c674e5f5c7dda4989be39a5b75fa9215674e4a7..8ff10db1605dfe568d11e2e7fc9f6f25fefb6eb5 100644 (file)
--- a/cmake/gmxManageGPU.cmake
+++ b/cmake/gmxManageGPU.cmake
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -223,7 +223,7 @@ macro(gmx_gpu_setup)
             # check the generated CUDA API version against the one present in cuda_runtime_api.h
             try_compile(_get_cuda_version_compile_res
                 ${CMAKE_BINARY_DIR}
-                ${CMAKE_SOURCE_DIR}/cmake/TestCUDAVersion.c
+                ${CMAKE_SOURCE_DIR}/cmake/TestCUDAVersion.cpp
                 COMPILE_DEFINITIONS "-DGMX_CUDA_VERSION=${GMX_CUDA_VERSION}"
                 CMAKE_FLAGS "-DINCLUDE_DIRECTORIES=${CUDA_TOOLKIT_INCLUDE}"
                 OUTPUT_VARIABLE _get_cuda_version_compile_out)

diff --git a/cmake/gmxManageMPI.cmake b/cmake/gmxManageMPI.cmake
index 02db55732d049d95d626ffc6700d524eee7ba7f5..78600ba7e34d96f8f3243364c0eacfe2e5e0c72c 100644 (file)
--- a/cmake/gmxManageMPI.cmake
+++ b/cmake/gmxManageMPI.cmake
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2016,2019, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -43,7 +43,7 @@ if(GMX_MPI)
 
   # Test the CMAKE_C_COMPILER for being an MPI (wrapper) compiler
   TRY_COMPILE(MPI_FOUND ${CMAKE_BINARY_DIR}
-    "${CMAKE_SOURCE_DIR}/cmake/TestMPI.c"
+    "${CMAKE_SOURCE_DIR}/cmake/TestMPI.cpp"
     COMPILE_DEFINITIONS )
 
   # If CMAKE_C_COMPILER is not a MPI wrapper. Try to find MPI using cmake module as fall-back.

diff --git a/cmake/gmxTestLargeFiles.cmake b/cmake/gmxTestLargeFiles.cmake
index 0fe66751434e326f8cd093c983d3554080c54650..1bc9a2bb901c35e43236d1480c587190739baabb 100644 (file)
--- a/cmake/gmxTestLargeFiles.cmake
+++ b/cmake/gmxTestLargeFiles.cmake
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2009,2010,2012,2014, by the GROMACS development team, led by
+# Copyright (c) 2009,2010,2012,2014,2019, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -58,7 +58,7 @@ MACRO(GMX_TEST_LARGE_FILES VARIABLE)
 
         # First check without any special flags
         TRY_COMPILE(FILE64_OK "${CMAKE_BINARY_DIR}"
-                    "${CMAKE_SOURCE_DIR}/cmake/TestFileOffsetBits.c")
+                    "${CMAKE_SOURCE_DIR}/cmake/TestFileOffsetBits.cpp")
         if(FILE64_OK)
             MESSAGE(STATUS "Checking for 64-bit off_t - present")
         endif()
@@ -66,7 +66,7 @@ MACRO(GMX_TEST_LARGE_FILES VARIABLE)
         if(NOT FILE64_OK)
             # Test with _FILE_OFFSET_BITS=64
             TRY_COMPILE(FILE64_OK "${CMAKE_BINARY_DIR}"
-                        "${CMAKE_SOURCE_DIR}/cmake/TestFileOffsetBits.c"
+                        "${CMAKE_SOURCE_DIR}/cmake/TestFileOffsetBits.cpp"
                         COMPILE_DEFINITIONS "-D_FILE_OFFSET_BITS=64" )
             if(FILE64_OK)
                 MESSAGE(STATUS "Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64")
@@ -77,7 +77,7 @@ MACRO(GMX_TEST_LARGE_FILES VARIABLE)
         if(NOT FILE64_OK)
             # Test with _LARGE_FILES
             TRY_COMPILE(FILE64_OK "${CMAKE_BINARY_DIR}"
-                        "${CMAKE_SOURCE_DIR}/cmake/TestFileOffsetBits.c"
+                        "${CMAKE_SOURCE_DIR}/cmake/TestFileOffsetBits.cpp"
                         COMPILE_DEFINITIONS "-D_LARGE_FILES" )
             if(FILE64_OK)
                 MESSAGE(STATUS "Checking for 64-bit off_t - present with _LARGE_FILES")
@@ -88,7 +88,7 @@ MACRO(GMX_TEST_LARGE_FILES VARIABLE)
         if(NOT FILE64_OK)
             # Test with _LARGEFILE_SOURCE
             TRY_COMPILE(FILE64_OK "${CMAKE_BINARY_DIR}"
-                        "${CMAKE_SOURCE_DIR}/cmake/TestFileOffsetBits.c"
+                        "${CMAKE_SOURCE_DIR}/cmake/TestFileOffsetBits.cpp"
                         COMPILE_DEFINITIONS "-D_LARGEFILE_SOURCE" )
             if(FILE64_OK)
                 MESSAGE(STATUS "Checking for 64-bit off_t - present with _LARGEFILE_SOURCE")
@@ -103,12 +103,12 @@ MACRO(GMX_TEST_LARGE_FILES VARIABLE)
 
             # Set the flags we might have determined to be required above
             configure_file("${CMAKE_SOURCE_DIR}/cmake/TestLargeFiles.c.cmakein"
-                           "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/TestLargeFiles.c")
+                           "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/TestLargeFiles.cpp")
 
             MESSAGE(STATUS "Checking for fseeko/ftello")
             # Test if ftello/fseeko are available
             TRY_COMPILE(FSEEKO_COMPILE_OK "${CMAKE_BINARY_DIR}"
-                        "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/TestLargeFiles.c")
+                        "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/TestLargeFiles.cpp")
             if(FSEEKO_COMPILE_OK)
                 MESSAGE(STATUS "Checking for fseeko/ftello - present")
             endif()
@@ -116,7 +116,7 @@ MACRO(GMX_TEST_LARGE_FILES VARIABLE)
             if(NOT FSEEKO_COMPILE_OK)
                 # glibc 2.2 neds _LARGEFILE_SOURCE for fseeko (but not 64-bit off_t...)
                 TRY_COMPILE(FSEEKO_COMPILE_OK "${CMAKE_BINARY_DIR}"
-                            "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/TestLargeFiles.c"
+                            "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/TestLargeFiles.cpp"
                             COMPILE_DEFINITIONS "-D_LARGEFILE_SOURCE" )
                 if(FSEEKO_COMPILE_OK)
                     MESSAGE(STATUS "Checking for fseeko/ftello - present with _LARGEFILE_SOURCE")
@@ -131,7 +131,7 @@ MACRO(GMX_TEST_LARGE_FILES VARIABLE)
         if(NOT FILE64_OK)
             # now check for Windows stuff
             TRY_COMPILE(FILE64_OK "${CMAKE_BINARY_DIR}"
-                        "${CMAKE_SOURCE_DIR}/cmake/TestWindowsFSeek.c")
+                        "${CMAKE_SOURCE_DIR}/cmake/TestWindowsFSeek.cpp")
             if(FILE64_OK)
                 MESSAGE(STATUS "Checking for 64-bit off_t - present with _fseeki64")
                 set(HAVE__FSEEKI64 1 CACHE INTERNAL "64-bit off_t requires _fseeki64")

diff --git a/cmake/gmxTestPipes.cmake b/cmake/gmxTestPipes.cmake
index 5ac14cda520a212e8fc2605d9ab7e3c6b5f344f6..292d997588a5f7e49aa57667a1fb25d696e628a5 100644 (file)
--- a/cmake/gmxTestPipes.cmake
+++ b/cmake/gmxTestPipes.cmake
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2009,2014, by the GROMACS development team, led by
+# Copyright (c) 2009,2014,2019, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -46,7 +46,7 @@ MACRO(GMX_TEST_PIPES VARIABLE)
         MESSAGE(STATUS "Checking for pipe support")
 
         TRY_COMPILE(HAVE_PIPES "${CMAKE_BINARY_DIR}"
-                    "${CMAKE_SOURCE_DIR}/cmake/TestPipes.c")
+                    "${CMAKE_SOURCE_DIR}/cmake/TestPipes.cpp")
 
     ENDIF()
 ENDMACRO(GMX_TEST_PIPES VARIABLE)

diff --git a/cmake/gmxTestSignal.cmake b/cmake/gmxTestSignal.cmake
index 5756729234500f33855956394db0d096dfcf0db8..55e11b9bd4b7472b3385c3c62f0ad0936402fab2 100644 (file)
--- a/cmake/gmxTestSignal.cmake
+++ b/cmake/gmxTestSignal.cmake
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2009,2011,2014, by the GROMACS development team, led by
+# Copyright (c) 2009,2011,2014,2019, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -45,7 +45,7 @@ MACRO(GMX_TEST_SIGUSR1 VARIABLE)
         MESSAGE(STATUS "Checking for SIGUSR1")
 
         TRY_COMPILE(HAVE_${VARIABLE} "${CMAKE_BINARY_DIR}"
-                    "${CMAKE_SOURCE_DIR}/cmake/TestSIGUSR1.c")
+                    "${CMAKE_SOURCE_DIR}/cmake/TestSIGUSR1.cpp")
 
        IF(HAVE_${VARIABLE})
             MESSAGE(STATUS "Checking for SIGUSR1 - found")

diff --git a/cmake/gmxTestXDR.cmake b/cmake/gmxTestXDR.cmake
index d06385294dc4a5c5aae66e97233af241fffd3faa..6aea176c69485a947b4d415256ee7608155351a3 100644 (file)
--- a/cmake/gmxTestXDR.cmake
+++ b/cmake/gmxTestXDR.cmake
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2009,2014, by the GROMACS development team, led by
+# Copyright (c) 2009,2014,2019, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -47,7 +47,7 @@ MACRO(GMX_TEST_XDR VARIABLE)
 
        # First check without any special flags
         TRY_COMPILE(XDR_COMPILE_OK "${CMAKE_BINARY_DIR}"
-                    "${CMAKE_SOURCE_DIR}/cmake/TestXDR.c")
+                    "${CMAKE_SOURCE_DIR}/cmake/TestXDR.cpp")
 
         if(XDR_COMPILE_OK)
            MESSAGE(STATUS "Checking for system XDR support - present")

diff --git a/src/external/clFFT/src/library/CMakeLists.txt b/src/external/clFFT/src/library/CMakeLists.txt
index 2ffd46f56557a8699eda12df5d86e69b74b5e096..f16a46fc5a6295ef2107434a3d0ac90a881c7bd5 100644 (file)
--- a/src/external/clFFT/src/library/CMakeLists.txt
+++ b/src/external/clFFT/src/library/CMakeLists.txt
@@ -26,7 +26,7 @@ set( clFFT.Source     transform.cpp
                                                                generator.copy.cpp
                                                                lifetime.cpp
                                                                fft_binary_lookup.cpp
-                                                               md5sum.c
+                                                               md5sum.cpp
                                                                enqueue.cpp
                                                                stdafx.cpp )
 

diff --git a/src/external/clFFT/src/library/md5sum.c b/src/external/clFFT/src/library/md5sum.cpp
similarity index 100%
rename from src/external/clFFT/src/library/md5sum.c
rename to src/external/clFFT/src/library/md5sum.cpp

diff --git a/src/external/fftpack/fftpack.c b/src/external/fftpack/fftpack.cpp
similarity index 97%
rename from src/external/fftpack/fftpack.c
rename to src/external/fftpack/fftpack.cpp
index c913888bd190492c946ff278505c6831ae609e72..888f330d9143a577d23329a16c976c349f36de72 100644 (file)
--- a/src/external/fftpack/fftpack.c
+++ b/src/external/fftpack/fftpack.cpp
@@ -16,11 +16,6 @@ Algorithmically based on Fortran-77 FFTPACK by Paul N. Swarztrauber (Version 4,
 #define MAXFAC 13    /* maximum number of factors in factorization of n */
 #define NSPECIAL 4   /* number of factors for which we have special-case routines */
 
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-
 /* ----------------------------------------------------------------------
    passf2, passf3, passf4, passf5, passf. Complex FFT passes fwd and bwd.
 ---------------------------------------------------------------------- */
@@ -1198,26 +1193,6 @@ void fftpack_cfftf1(int n, Treal c[], Treal ch[], const Treal wa[], const int if
   } /* cfftf1 */
 
 
-void fftpack_cfftf(int n, Treal c[], Treal wsave[])
-  {
-    int iw1, iw2;
-    if (n == 1) return;
-    iw1 = 2*n;
-    iw2 = iw1 + 2*n;
-    fftpack_cfftf1(n, c, wsave, wsave+iw1, (int*)(wsave+iw2), -1);
-  } /* cfftf */
-
-
-void fftpack_cfftb(int n, Treal c[], Treal wsave[])
-  {
-    int iw1, iw2;
-    if (n == 1) return;
-    iw1 = 2*n;
-    iw2 = iw1 + 2*n;
-    fftpack_cfftf1(n, c, wsave, wsave+iw1, (int*)(wsave+iw2), +1);
-  } /* cfftb */
-
-
 static void factorize(int n, int ifac[MAXFAC+2], const int ntryh[NSPECIAL])
   /* Factorize n in factors in ntryh and rest. On exit,
 ifac[0] contains n and ifac[1] contains number of factors,
@@ -1297,16 +1272,6 @@ void fftpack_cffti1(int n, Treal wa[], int ifac[MAXFAC+2])
     }
   } /* cffti1 */
 
-
-void fftpack_cffti(int n, Treal wsave[])
- {
-    int iw1, iw2;
-    if (n == 1) return;
-    iw1 = 2*n;
-    iw2 = iw1 + 2*n;
-    fftpack_cffti1(n, wsave+iw1, (int*)(wsave+iw2));
-  } /* cffti */
-
   /* ----------------------------------------------------------------------
 rfftf1, rfftb1, rfftf, rfftb, rffti1, rffti. Treal FFTs.
 ---------------------------------------------------------------------- */
@@ -1428,20 +1393,6 @@ void fftpack_rfftb1(int n, Treal c[], Treal ch[], const Treal wa[], const int if
   } /* rfftb1 */
 
 
-void fftpack_rfftf(int n, Treal r[], Treal wsave[])
-  {
-    if (n == 1) return;
-    fftpack_rfftf1(n, r, wsave, wsave+n, (int*)(wsave+2*n));
-  } /* rfftf */
-
-
-void fftpack_rfftb(int n, Treal r[], Treal wsave[])
-  {
-    if (n == 1) return;
-    fftpack_rfftb1(n, r, wsave, wsave+n, (int*)(wsave+2*n));
-  } /* rfftb */
-
-
 void fftpack_rffti1(int n, Treal wa[], int ifac[MAXFAC+2])
   {
     static const Treal twopi = 6.28318530717959;
@@ -1484,12 +1435,4 @@ void fftpack_rffti1(int n, Treal wa[], int ifac[MAXFAC+2])
   } /* rffti1 */
 
 
-void fftpack_rffti(int n, Treal wsave[])
-  {
-    if (n == 1) return;
-    fftpack_rffti1(n, wsave+n, (int*)(wsave+2*n));
-  } /* rffti */
 
-#ifdef __cplusplus
-}
-#endif

diff --git a/src/external/fftpack/fftpack.h b/src/external/fftpack/fftpack.h
index 7a5b10d926bc79cf5ea6fef61a1a284473fa0707..92d024d9c721488618360f68091a8e7daf3f7bc8 100644 (file)
--- a/src/external/fftpack/fftpack.h
+++ b/src/external/fftpack/fftpack.h
@@ -36,12 +36,6 @@
 #ifndef _fftpack_h
 #define _fftpack_h
 
-
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
 #if GMX_DOUBLE
 #define Treal double
 #else
@@ -54,8 +48,4 @@ extern "C" {
     void fftpack_rfftf1(int n, Treal c[], Treal ch[], const Treal wa[], const int ifac[]);
     void fftpack_rfftb1(int n, Treal c[], Treal ch[], const Treal wa[], const int ifac[]);
 
-#ifdef __cplusplus
-}
-#endif
-
 #endif

diff --git a/src/external/vmd_molfile/vmddlopen.c b/src/external/vmd_molfile/vmddlopen.cpp
similarity index 100%
rename from src/external/vmd_molfile/vmddlopen.c
rename to src/external/vmd_molfile/vmddlopen.cpp

diff --git a/src/gromacs/fft/CMakeLists.txt b/src/gromacs/fft/CMakeLists.txt
index 072ca88af3aeb10114848c4504fb6a787f594729..bb9d0f9cbb217cec4e99ca4066ae71cf82600903 100644 (file)
--- a/src/gromacs/fft/CMakeLists.txt
+++ b/src/gromacs/fft/CMakeLists.txt
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2013,2014,2015,2018, by the GROMACS development team, led by
+# Copyright (c) 2013,2014,2015,2018,2019, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -42,7 +42,7 @@ gmx_add_libgromacs_sources(
 if (GMX_FFT_FFTPACK)
     gmx_add_libgromacs_sources(
         fft_fftpack.cpp
-        ${CMAKE_SOURCE_DIR}/src/external/fftpack/fftpack.c)
+        ${CMAKE_SOURCE_DIR}/src/external/fftpack/fftpack.cpp)
 endif()
 if (GMX_FFT_FFTW3 OR GMX_FFT_ARMPL_FFTW3)
     gmx_add_libgromacs_sources(fft_fftw3.cpp)

diff --git a/src/gromacs/fileio/CMakeLists.txt b/src/gromacs/fileio/CMakeLists.txt
index b7ca96feceb31d24f09c6edfbe34fc39ef3bc939..00f5a1f3dbfd1fc8407bd966ab42ee244862057a 100644 (file)
--- a/src/gromacs/fileio/CMakeLists.txt
+++ b/src/gromacs/fileio/CMakeLists.txt
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2013,2014,2015,2016,2019, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -35,7 +35,7 @@
 file(GLOB FILEIO_SOURCES *.cpp)
 
 if(GMX_USE_PLUGINS)
-  set(FILEIO_SOURCES ${FILEIO_SOURCES} ${CMAKE_SOURCE_DIR}/src/external/vmd_molfile/vmddlopen.c)
+  target_sources(libgromacs_external PRIVATE ${CMAKE_SOURCE_DIR}/src/external/vmd_molfile/vmddlopen.cpp)
 else()
   list(REMOVE_ITEM FILEIO_SOURCES ${CMAKE_CURRENT_SOURCE_DIR}/vmdio.cpp)
 endif()