Moved selection and trajana modules to src/gromacs/.

diff --git a/src/gromacs/CMakeLists.txt b/src/gromacs/CMakeLists.txt
index ce6932d5a533c83497d8701427413e58a98b874f..51d7c5fb03881549159adbaf1f4ec569a81ab814 100644 (file)
--- a/src/gromacs/CMakeLists.txt
+++ b/src/gromacs/CMakeLists.txt
@@ -6,6 +6,8 @@ add_subdirectory(mdlib)
 add_subdirectory(errorreporting)
 add_subdirectory(fatalerror)
 add_subdirectory(options)
+add_subdirectory(selection)
+list(APPEND LIBGROMACS_SOURCES trajana/trajana.cpp)
 
 file(GLOB LIBGROMACS_HEADERS *.h)
 install(FILES ${LIBGROMACS_HEADERS} DESTINATION ${INCL_INSTALL_DIR}/gromacs

diff --git a/src/gromacs/gmxlib/CMakeLists.txt b/src/gromacs/gmxlib/CMakeLists.txt
index ca25539fdf169d1117d8c01f06567f0cdf1925ff..17cea60bba687e2302f95884fbc3dbfc0cb8af74 100644 (file)
--- a/src/gromacs/gmxlib/CMakeLists.txt
+++ b/src/gromacs/gmxlib/CMakeLists.txt
@@ -3,7 +3,6 @@ include_directories(${CMAKE_CURRENT_SOURCE_DIR})
 # The nonbonded directory contains subdirectories that are only
 # conditionally built, so we cannot use a GLOB_RECURSE here.
 file(GLOB GMXLIB_SOURCES *.c 
-     selection/*.c trajana/*.c
      statistics/*.c nonbonded/*.c nonbonded/nb_kernel_c/*.c)
 
 if(GMX_DOUBLE)
@@ -69,11 +68,6 @@ endif(NOT GMX_EXTERNAL_LAPACK)
 # so they should not be included in the library
 file(GLOB_RECURSE NOT_GMXLIB_SOURCES *_test.c *\#*)
 list(REMOVE_ITEM GMXLIB_SOURCES ${NOT_GMXLIB_SOURCES})  
-# Selection has test_ instead of _test.  Removing here for special case, perhaps make general?
-if(GMX_FAHCORE)
-    file(GLOB SELECTION_TEST selection/test*)
-    list(REMOVE_ITEM GMXLIB_SOURCES ${SELECTION_TEST})
-endif(GMX_FAHCORE)
 
 # An ugly hack to get absolute paths...
 file(GLOB THREAD_MPI_SOURCES ${THREAD_MPI_SRC})

diff --git a/src/gromacs/selection/CMakeLists.txt b/src/gromacs/selection/CMakeLists.txt
new file mode 100644 (file)
index 0000000..12cdbcc
--- /dev/null
+++ b/src/gromacs/selection/CMakeLists.txt
@@ -0,0 +1,16 @@
+file(GLOB SELECTION_SOURCES *.cpp)
+set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${SELECTION_SOURCES} PARENT_SCOPE)
+
+set(SELECTION_PUBLIC_HEADERS
+    centerofmass.h
+    indexutil.h
+    nbsearch.h
+    poscalc.h
+    position.h
+    selection.h
+    selparam.h
+    selmethod.h
+    selvalue.h)
+install(FILES ${SELECTION_PUBLIC_HEADERS}
+        DESTINATION ${INCL_INSTALL_DIR}/gromacs/selection
+        COMPONENT development)

diff --git a/src/gromacs/gmxlib/trajana/centerofmass.c b/src/gromacs/selection/centerofmass.cpp
similarity index 99%
rename from src/gromacs/gmxlib/trajana/centerofmass.c
rename to src/gromacs/selection/centerofmass.cpp
index bc46cfd40889b90c2a9490bfce04d57722b05922..82a591f55e3df435fadbdadab7ba168c12230667 100644 (file)
--- a/src/gromacs/gmxlib/trajana/centerofmass.c
+++ b/src/gromacs/selection/centerofmass.cpp
@@ -39,7 +39,7 @@
 #include <pbc.h>
 #include <vec.h>
 
-#include <centerofmass.h>
+#include "gromacs/selection/centerofmass.h"
 
 /*!
  * \param[in]  top    Topology structure (unused, can be NULL).

diff --git a/src/gromacs/legacyheaders/centerofmass.h b/src/gromacs/selection/centerofmass.h
similarity index 98%
rename from src/gromacs/legacyheaders/centerofmass.h
rename to src/gromacs/selection/centerofmass.h
index b66ca76ba88aa4352339fd98bea56ad590021408..d7d3cc0d1a3386b09c781c7587c6d5ccf6c4ceb5 100644 (file)
--- a/src/gromacs/legacyheaders/centerofmass.h
+++ b/src/gromacs/selection/centerofmass.h
@@ -64,10 +64,10 @@
  * Finally, there is a function gmx_calc_comg_blocka() that takes both the
  * index group and the partitioning as a single \c t_blocka structure.
  */
-#ifndef CENTEROFMASS_H
-#define CENTEROFMASS_H
+#ifndef GMX_SELECTION_CENTEROFMASS_H
+#define GMX_SELECTION_CENTEROFMASS_H
 
-#include "typedefs.h"
+#include "../legacyheaders/typedefs.h"
 
 #ifdef __cplusplus
 extern "C"

diff --git a/src/gromacs/gmxlib/selection/compiler.c b/src/gromacs/selection/compiler.cpp
similarity index 99%
rename from src/gromacs/gmxlib/selection/compiler.c
rename to src/gromacs/selection/compiler.cpp
index 45ca192cf6e5fabedec6e18961dbf9145b20cd55..8677232ce86e00618488238662556dc35494bc33 100644 (file)
--- a/src/gromacs/gmxlib/selection/compiler.c
+++ b/src/gromacs/selection/compiler.cpp
@@ -267,10 +267,10 @@
 #include <string2.h>
 #include <vec.h>
 
-#include <indexutil.h>
-#include <poscalc.h>
-#include <selection.h>
-#include <selmethod.h>
+#include "gromacs/selection/indexutil.h"
+#include "gromacs/selection/poscalc.h"
+#include "gromacs/selection/selection.h"
+#include "gromacs/selection/selmethod.h"
 
 #include "evaluate.h"
 #include "keywords.h"

diff --git a/src/gromacs/gmxlib/selection/evaluate.c b/src/gromacs/selection/evaluate.cpp
similarity index 99%
rename from src/gromacs/gmxlib/selection/evaluate.c
rename to src/gromacs/selection/evaluate.cpp
index 9fbe3c064fd6872f689514f905c8f9e9449e9eff..fa78233827b1e6125e3fae9b38f15fc2386752a0 100644 (file)
--- a/src/gromacs/gmxlib/selection/evaluate.c
+++ b/src/gromacs/selection/evaluate.cpp
@@ -52,10 +52,10 @@
 #include <smalloc.h>
 #include <vec.h>
 
-#include <indexutil.h>
-#include <poscalc.h>
-#include <selection.h>
-#include <selmethod.h>
+#include "gromacs/selection/indexutil.h"
+#include "gromacs/selection/poscalc.h"
+#include "gromacs/selection/selection.h"
+#include "gromacs/selection/selmethod.h"
 
 #include "evaluate.h"
 #include "mempool.h"

diff --git a/src/gromacs/gmxlib/selection/evaluate.h b/src/gromacs/selection/evaluate.h
similarity index 99%
rename from src/gromacs/gmxlib/selection/evaluate.h
rename to src/gromacs/selection/evaluate.h
index 99c15c71698cc8caacfb5ba1b5ea61d3edc01179..7b5738ba76a454f961d5fb983de9c0a2b7b50f81 100644 (file)
--- a/src/gromacs/gmxlib/selection/evaluate.h
+++ b/src/gromacs/selection/evaluate.h
@@ -44,7 +44,7 @@
 
 #include <typedefs.h>
 
-#include <indexutil.h>
+#include "gromacs/selection/indexutil.h"
 
 #include "selelem.h"
 

diff --git a/src/gromacs/gmxlib/trajana/indexutil.c b/src/gromacs/selection/indexutil.cpp
similarity index 99%
rename from src/gromacs/gmxlib/trajana/indexutil.c
rename to src/gromacs/selection/indexutil.cpp
index ab5c13177887c1e905f82102afe02c2fb678b88f..79820add060fc4a8fe9f4b00769e365700672957 100644 (file)
--- a/src/gromacs/gmxlib/trajana/indexutil.c
+++ b/src/gromacs/selection/indexutil.cpp
@@ -41,7 +41,7 @@
 #include <typedefs.h>
 #include <gmx_fatal.h>
 
-#include <indexutil.h>
+#include "gromacs/selection/indexutil.h"
 
 /********************************************************************
  * gmx_ana_indexgrps_t functions

diff --git a/src/gromacs/legacyheaders/indexutil.h b/src/gromacs/selection/indexutil.h
similarity index 99%
rename from src/gromacs/legacyheaders/indexutil.h
rename to src/gromacs/selection/indexutil.h
index 6af9d9d6c0331c502ec0c9cb2b4d8647e191bcb5..62fbf9e6cd06c73a51e6d4e19893b9e47485005f 100644 (file)
--- a/src/gromacs/legacyheaders/indexutil.h
+++ b/src/gromacs/selection/indexutil.h
@@ -51,10 +51,10 @@
  * Also, the mapping functions are useful when dealing with dynamic index
  * groups.
  */
-#ifndef INDEXUTIL_H
-#define INDEXUTIL_H
+#ifndef GMX_SELECTION_INDEXUTIL_H
+#define GMX_SELECTION_INDEXUTIL_H
 
-#include "typedefs.h"
+#include "../legacyheaders/typedefs.h"
 
 #ifdef __cplusplus
 extern "C"

diff --git a/src/gromacs/gmxlib/selection/keywords.h b/src/gromacs/selection/keywords.h
similarity index 100%
rename from src/gromacs/gmxlib/selection/keywords.h
rename to src/gromacs/selection/keywords.h

diff --git a/src/gromacs/gmxlib/selection/mempool.c b/src/gromacs/selection/mempool.cpp
similarity index 99%
rename from src/gromacs/gmxlib/selection/mempool.c
rename to src/gromacs/selection/mempool.cpp
index 32d8aa0ebbb4815f02289e82ee070f609a8eae5a..8c0bf03bb1e6b96f986adb75f00e98fe7b03b504 100644 (file)
--- a/src/gromacs/gmxlib/selection/mempool.c
+++ b/src/gromacs/selection/mempool.cpp
@@ -44,7 +44,7 @@
 #include <gmx_fatal.h>
 #include <smalloc.h>
 
-#include <indexutil.h>
+#include "gromacs/selection/indexutil.h"
 
 #include "mempool.h"
 

diff --git a/src/gromacs/gmxlib/selection/mempool.h b/src/gromacs/selection/mempool.h
similarity index 100%
rename from src/gromacs/gmxlib/selection/mempool.h
rename to src/gromacs/selection/mempool.h

diff --git a/src/gromacs/gmxlib/trajana/nbsearch.c b/src/gromacs/selection/nbsearch.cpp
similarity index 99%
rename from src/gromacs/gmxlib/trajana/nbsearch.c
rename to src/gromacs/selection/nbsearch.cpp
index e991cbc2f26edb4d4acb0638025bce5195a1586e..ec0ac48aaeddff23ad32e918fa916bb4c08bfb9d 100644 (file)
--- a/src/gromacs/gmxlib/trajana/nbsearch.c
+++ b/src/gromacs/selection/nbsearch.cpp
@@ -73,8 +73,8 @@
 #include <pbc.h>
 #include <vec.h>
 
-#include <nbsearch.h>
-#include <position.h>
+#include "gromacs/selection/nbsearch.h"
+#include "gromacs/selection/position.h"
 
 /*! \internal \brief
  * Data structure for neighborhood searches.

diff --git a/src/gromacs/legacyheaders/nbsearch.h b/src/gromacs/selection/nbsearch.h
similarity index 97%
rename from src/gromacs/legacyheaders/nbsearch.h
rename to src/gromacs/selection/nbsearch.h
index 5dd73521ea0c562a40623af6b1795b2fc9956681..18bdf6a3476f3597ec12dca2744e30167ae4d03e 100644 (file)
--- a/src/gromacs/legacyheaders/nbsearch.h
+++ b/src/gromacs/selection/nbsearch.h
@@ -38,10 +38,10 @@
  * of the library.
  * The library also uses the functions internally.
  */
-#ifndef NBSEARCH_H
-#define NBSEARCH_H
+#ifndef GMX_SELECTION_NBSEARCH_H
+#define GMX_SELECTION_NBSEARCH_H
 
-#include "typedefs.h"
+#include "../legacyheaders/typedefs.h"
 
 #include "indexutil.h"
 

diff --git a/src/gromacs/gmxlib/selection/params.c b/src/gromacs/selection/params.cpp
similarity index 99%
rename from src/gromacs/gmxlib/selection/params.c
rename to src/gromacs/selection/params.cpp
index 21ae7e81915d12e567b0a402c7d16e0057b758e5..2f59faed68cbdeeb1abb32c0f772ab528c3a4ade 100644 (file)
--- a/src/gromacs/gmxlib/selection/params.c
+++ b/src/gromacs/selection/params.cpp
@@ -40,9 +40,9 @@
 #include <string2.h>
 #include <vec.h>
 
-#include <position.h>
-#include <selmethod.h>
-#include <selparam.h>
+#include "gromacs/selection/position.h"
+#include "gromacs/selection/selmethod.h"
+#include "gromacs/selection/selparam.h"
 
 #include "parsetree.h"
 #include "position.h"

diff --git a/src/gromacs/gmxlib/selection/parser.c b/src/gromacs/selection/parser.cpp
similarity index 100%
rename from src/gromacs/gmxlib/selection/parser.c
rename to src/gromacs/selection/parser.cpp

diff --git a/src/gromacs/gmxlib/selection/parser.h b/src/gromacs/selection/parser.h
similarity index 100%
rename from src/gromacs/gmxlib/selection/parser.h
rename to src/gromacs/selection/parser.h

diff --git a/src/gromacs/gmxlib/selection/parser.y b/src/gromacs/selection/parser.y
similarity index 100%
rename from src/gromacs/gmxlib/selection/parser.y
rename to src/gromacs/selection/parser.y

diff --git a/src/gromacs/gmxlib/selection/parsetree.c b/src/gromacs/selection/parsetree.cpp
similarity index 99%
rename from src/gromacs/gmxlib/selection/parsetree.c
rename to src/gromacs/selection/parsetree.cpp
index 2da5106bab0aa7ad1c12fb2204b89e47ede16da5..65b17b10c062b2cff4420f18b20284ccaafee280 100644 (file)
--- a/src/gromacs/gmxlib/selection/parsetree.c
+++ b/src/gromacs/selection/parsetree.cpp
@@ -215,9 +215,9 @@
 #include <string2.h>
 #include <gmx_fatal.h>
 
-#include <poscalc.h>
-#include <selection.h>
-#include <selmethod.h>
+#include "gromacs/selection/poscalc.h"
+#include "gromacs/selection/selection.h"
+#include "gromacs/selection/selmethod.h"
 
 #include "keywords.h"
 #include "parsetree.h"

diff --git a/src/gromacs/gmxlib/selection/parsetree.h b/src/gromacs/selection/parsetree.h
similarity index 99%
rename from src/gromacs/gmxlib/selection/parsetree.h
rename to src/gromacs/selection/parsetree.h
index 8d97d1515d5a530581e4648248f5d47efb4e67cc..0950a386934968fb907aafb704f66b424921256a 100644 (file)
--- a/src/gromacs/gmxlib/selection/parsetree.h
+++ b/src/gromacs/selection/parsetree.h
@@ -43,11 +43,9 @@
 #ifndef SELECTION_PARSETREE_H
 #define SELECTION_PARSETREE_H
 
-/*#include <typedefs.h>*/
 #include <types/simple.h>
 
-
-#include <selvalue.h>
+#include "gromacs/selection/selvalue.h"
 
 struct t_selelem;
 struct gmx_ana_indexgrps_t;

diff --git a/src/gromacs/gmxlib/trajana/poscalc.c b/src/gromacs/selection/poscalc.cpp
similarity index 99%
rename from src/gromacs/gmxlib/trajana/poscalc.c
rename to src/gromacs/selection/poscalc.cpp
index 9a319e6d6875106863f4e0696ac07d319f5951a8..76b00c68282fbb95a6966a3b9106272e381cdcf1 100644 (file)
--- a/src/gromacs/gmxlib/trajana/poscalc.c
+++ b/src/gromacs/selection/poscalc.cpp
@@ -113,10 +113,10 @@
 #include <pbc.h>
 #include <vec.h>
 
-#include <centerofmass.h>
-#include <indexutil.h>
-#include <poscalc.h>
-#include <position.h>
+#include "gromacs/selection/centerofmass.h"
+#include "gromacs/selection/indexutil.h"
+#include "gromacs/selection/poscalc.h"
+#include "gromacs/selection/position.h"
 
 /*! \internal \brief
  * Collection of \c gmx_ana_poscalc_t structures for the same topology.

diff --git a/src/gromacs/legacyheaders/poscalc.h b/src/gromacs/selection/poscalc.h
similarity index 98%
rename from src/gromacs/legacyheaders/poscalc.h
rename to src/gromacs/selection/poscalc.h
index aaac1836df6b564a05699f1608aa738bd4c58091..5503766a76fd6d162c78feaee0a7ef245649f66c 100644 (file)
--- a/src/gromacs/legacyheaders/poscalc.h
+++ b/src/gromacs/selection/poscalc.h
@@ -42,10 +42,10 @@
  * The API is documented in more detail on a separate page:
  * \ref poscalcengine.
  */
-#ifndef POSCALC_H
-#define POSCALC_H
+#ifndef GMX_SELECTION_POSCALC_H
+#define GMX_SELECTION_POSCALC_H
 
-#include "typedefs.h"
+#include "../legacyheaders/typedefs.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/gmxlib/trajana/position.c b/src/gromacs/selection/position.cpp
similarity index 99%
rename from src/gromacs/gmxlib/trajana/position.c
rename to src/gromacs/selection/position.cpp
index 4edcb46cb0afc5834ce5a117a781d55d1eb51fa3..c842b9867a152be7852abca6a2fda6323b0c48cb 100644 (file)
--- a/src/gromacs/gmxlib/trajana/position.c
+++ b/src/gromacs/selection/position.cpp
@@ -42,8 +42,8 @@
 #include <typedefs.h>
 #include <vec.h>
 
-#include <indexutil.h>
-#include <position.h>
+#include "gromacs/selection/indexutil.h"
+#include "gromacs/selection/position.h"
 
 /*!
  * \param[out] pos      Output structure.

diff --git a/src/gromacs/legacyheaders/position.h b/src/gromacs/selection/position.h
similarity index 97%
rename from src/gromacs/legacyheaders/position.h
rename to src/gromacs/selection/position.h
index 4e27d513aee22f588607f27b70c5186f88ffcabb..b0b9858057af65f9b3faef1a4a46afe5e29f3906 100644 (file)
--- a/src/gromacs/legacyheaders/position.h
+++ b/src/gromacs/selection/position.h
@@ -31,10 +31,10 @@
 /*! \file
  * \brief API for handling positions.
  */
-#ifndef POSITION_H
-#define POSITION_H
+#ifndef GMX_SELECTION_POSITION_H
+#define GMX_SELECTION_POSITION_H
 
-#include "typedefs.h"
+#include "../legacyheaders/types/simple.h"
 
 #include "indexutil.h"
 

diff --git a/src/gromacs/gmxlib/selection/regenerate_parser.sh b/src/gromacs/selection/regenerate_parser.sh
similarity index 95%
rename from src/gromacs/gmxlib/selection/regenerate_parser.sh
rename to src/gromacs/selection/regenerate_parser.sh
index 078bb48be281c1f529cc4210b735eac28a2562a0..8baa65f03189fa81420a44139819688488587c18 100755 (executable)
--- a/src/gromacs/gmxlib/selection/regenerate_parser.sh
+++ b/src/gromacs/selection/regenerate_parser.sh
@@ -13,7 +13,7 @@ fi
 
 # For convenience, change to the directory where the files are located
 # if the script is run from the root of the source tree.
-dirname=src/gromacs/gmxlib/selection
+dirname=src/gromacs/selection
 if [[ -f $dirname/parser.y && -f $dirname/scanner.l ]] ; then
     cd $dirname
 fi

diff --git a/src/gromacs/gmxlib/selection/scanner.c b/src/gromacs/selection/scanner.cpp
similarity index 100%
rename from src/gromacs/gmxlib/selection/scanner.c
rename to src/gromacs/selection/scanner.cpp

diff --git a/src/gromacs/gmxlib/selection/scanner.h b/src/gromacs/selection/scanner.h
similarity index 100%
rename from src/gromacs/gmxlib/selection/scanner.h
rename to src/gromacs/selection/scanner.h

diff --git a/src/gromacs/gmxlib/selection/scanner.l b/src/gromacs/selection/scanner.l
similarity index 100%
rename from src/gromacs/gmxlib/selection/scanner.l
rename to src/gromacs/selection/scanner.l

diff --git a/src/gromacs/gmxlib/selection/scanner_flex.h b/src/gromacs/selection/scanner_flex.h
similarity index 100%
rename from src/gromacs/gmxlib/selection/scanner_flex.h
rename to src/gromacs/selection/scanner_flex.h

diff --git a/src/gromacs/gmxlib/selection/scanner_internal.c b/src/gromacs/selection/scanner_internal.cpp
similarity index 99%
rename from src/gromacs/gmxlib/selection/scanner_internal.c
rename to src/gromacs/selection/scanner_internal.cpp
index 1e7e4f74a54590bf38f55c65c87e8f1bcebb1178..0e2311d2a51dbe827d9c728694ec42a1055e9a4c 100644 (file)
--- a/src/gromacs/gmxlib/selection/scanner_internal.c
+++ b/src/gromacs/selection/scanner_internal.cpp
@@ -52,7 +52,7 @@
 #include "string2.h"
 #include "gmx_fatal.h"
 
-#include <selmethod.h>
+#include "gromacs/selection/selmethod.h"
 
 #include "parsetree.h"
 #include "selcollection.h"

diff --git a/src/gromacs/gmxlib/selection/scanner_internal.h b/src/gromacs/selection/scanner_internal.h
similarity index 100%
rename from src/gromacs/gmxlib/selection/scanner_internal.h
rename to src/gromacs/selection/scanner_internal.h

diff --git a/src/gromacs/gmxlib/selection/selcollection.h b/src/gromacs/selection/selcollection.h
similarity index 99%
rename from src/gromacs/gmxlib/selection/selcollection.h
rename to src/gromacs/selection/selcollection.h
index 909c8781473f0d0f1cca0e2dd4a19f7fd8a97b78..91055b33b2af67fdab71bf7e6e574f8f72dc0e42 100644 (file)
--- a/src/gromacs/gmxlib/selection/selcollection.h
+++ b/src/gromacs/selection/selcollection.h
@@ -39,7 +39,7 @@
 
 #include <typedefs.h>
 
-#include <indexutil.h>
+#include "gromacs/selection/indexutil.h"
 
 /*! \internal
  * \brief

diff --git a/src/gromacs/gmxlib/selection/selection.c b/src/gromacs/selection/selection.cpp
similarity index 98%
rename from src/gromacs/gmxlib/selection/selection.c
rename to src/gromacs/selection/selection.cpp
index 17a9cf761850c8d497fa73bfdaa15d97a3a1e747..8163aed65e16a8e042e008bd71f6c74f84883bc7 100644 (file)
--- a/src/gromacs/gmxlib/selection/selection.c
+++ b/src/gromacs/selection/selection.cpp
@@ -46,9 +46,9 @@
 #include <xvgr.h>
 #include <gmx_fatal.h>
 
-#include <poscalc.h>
-#include <selection.h>
-#include <selmethod.h>
+#include "gromacs/selection/poscalc.h"
+#include "gromacs/selection/selection.h"
+#include "gromacs/selection/selmethod.h"
 
 #include "mempool.h"
 #include "selcollection.h"

diff --git a/src/gromacs/legacyheaders/selection.h b/src/gromacs/selection/selection.h
similarity index 99%
rename from src/gromacs/legacyheaders/selection.h
rename to src/gromacs/selection/selection.h
index 0b2fbe8286317e8560b4f558128ead2e7b2d5465..aa5e4da0f3ebe269d4e8b7f8583d822d1a69c517 100644 (file)
--- a/src/gromacs/legacyheaders/selection.h
+++ b/src/gromacs/selection/selection.h
@@ -35,8 +35,8 @@
  * functions in this file directly unless using the selection routines outside
  * the main trajectory analysis API.
  */
-#ifndef SELECTION_H
-#define SELECTION_H
+#ifndef GMX_SELECTION_SELECTION_H
+#define GMX_SELECTION_SELECTION_H
 
 #include "position.h"
 #include "indexutil.h"

diff --git a/src/gromacs/gmxlib/selection/selelem.c b/src/gromacs/selection/selelem.cpp
similarity index 99%
rename from src/gromacs/gmxlib/selection/selelem.c
rename to src/gromacs/selection/selelem.cpp
index 09971c053894f90799d278c1460c10ec0958ee96..294b03011bfb1544a49e96f7bd98d27a339819a0 100644 (file)
--- a/src/gromacs/gmxlib/selection/selelem.c
+++ b/src/gromacs/selection/selelem.cpp
@@ -38,10 +38,10 @@
 #include <smalloc.h>
 #include <gmx_fatal.h>
 
-#include <indexutil.h>
-#include <poscalc.h>
-#include <position.h>
-#include <selmethod.h>
+#include "gromacs/selection/indexutil.h"
+#include "gromacs/selection/poscalc.h"
+#include "gromacs/selection/position.h"
+#include "gromacs/selection/selmethod.h"
 
 #include "keywords.h"
 #include "mempool.h"

diff --git a/src/gromacs/gmxlib/selection/selelem.h b/src/gromacs/selection/selelem.h
similarity index 99%
rename from src/gromacs/gmxlib/selection/selelem.h
rename to src/gromacs/selection/selelem.h
index 571d8a127fbe50b4dd12b0aad1afcf212d53f8c0..fe36d558ecdf2f935d7549576948898e28dc2579 100644 (file)
--- a/src/gromacs/gmxlib/selection/selelem.h
+++ b/src/gromacs/selection/selelem.h
@@ -43,8 +43,8 @@
 
 #include <types/simple.h>
 
-#include <indexutil.h>
-#include <selvalue.h>
+#include "gromacs/selection/indexutil.h"
+#include "gromacs/selection/selvalue.h"
 
 struct gmx_ana_poscalc_t;
 struct gmx_ana_selparam_t;

diff --git a/src/gromacs/gmxlib/selection/selhelp.c b/src/gromacs/selection/selhelp.cpp
similarity index 99%
rename from src/gromacs/gmxlib/selection/selhelp.c
rename to src/gromacs/selection/selhelp.cpp
index 0bbe59fabac7654136541e33396261d4779a8d32..640c51512b8534fff934b7288f76fd1d62c3a26b 100644 (file)
--- a/src/gromacs/gmxlib/selection/selhelp.c
+++ b/src/gromacs/selection/selhelp.cpp
@@ -39,8 +39,9 @@
 #include <string2.h>
 #include <wman.h>
 
+#include "gromacs/selection/selmethod.h"
+
 #include "selcollection.h"
-#include "selmethod.h"
 #include "selhelp.h"
 #include "symrec.h"
 

diff --git a/src/gromacs/gmxlib/selection/selhelp.h b/src/gromacs/selection/selhelp.h
similarity index 100%
rename from src/gromacs/gmxlib/selection/selhelp.h
rename to src/gromacs/selection/selhelp.h

diff --git a/src/gromacs/gmxlib/selection/selmethod.c b/src/gromacs/selection/selmethod.cpp
similarity index 99%
rename from src/gromacs/gmxlib/selection/selmethod.c
rename to src/gromacs/selection/selmethod.cpp
index 982eaed6efe2cc8a7ba03ecab341f9b4867a83c1..56eeb6a507d3377da3250bfe0ea76cd23bb62ce8 100644 (file)
--- a/src/gromacs/gmxlib/selection/selmethod.c
+++ b/src/gromacs/selection/selmethod.cpp
@@ -41,7 +41,7 @@
 #include <macros.h>
 #include <string2.h>
 
-#include <selmethod.h>
+#include "gromacs/selection/selmethod.h"
 
 #include "selcollection.h"
 #include "symrec.h"

diff --git a/src/gromacs/legacyheaders/selmethod.h b/src/gromacs/selection/selmethod.h
similarity index 99%
rename from src/gromacs/legacyheaders/selmethod.h
rename to src/gromacs/selection/selmethod.h
index f47dc3777072df3e0419e7b8adfb5ba71c95f50c..cf8e67aa64b026a9b03b486aec98f62a7e9c3430 100644 (file)
--- a/src/gromacs/legacyheaders/selmethod.h
+++ b/src/gromacs/selection/selmethod.h
@@ -281,10 +281,10 @@
  * Instructions for implementing custom selection methods can be found
  * on a separate page: \ref selmethods
  */
-#ifndef SELMETHOD_H
-#define SELMETHOD_H
+#ifndef GMX_SELECTION_SELMETHOD_H
+#define GMX_SELECTION_SELMETHOD_H
 
-#include "typedefs.h"
+#include "../legacyheaders/typedefs.h"
 
 #include "indexutil.h"
 #include "selparam.h"

diff --git a/src/gromacs/legacyheaders/selparam.h b/src/gromacs/selection/selparam.h
similarity index 99%
rename from src/gromacs/legacyheaders/selparam.h
rename to src/gromacs/selection/selparam.h
index a10b609a9d5fba605ca7f43639c37c057820a417..2b03aa46b4750da7e4e65caad3903cb9a8125b1a 100644 (file)
--- a/src/gromacs/legacyheaders/selparam.h
+++ b/src/gromacs/selection/selparam.h
@@ -38,10 +38,8 @@
  * More details can be found on the page discussing
  * \ref selmethods "custom selection methods".
  */
-#ifndef SELPARAM_H
-#define SELPARAM_H
-
-#include "typedefs.h"
+#ifndef GMX_SELECTION_SELPARAM_H
+#define GMX_SELECTION_SELPARAM_H
 
 #include "indexutil.h"
 #include "selvalue.h"

diff --git a/src/gromacs/gmxlib/selection/selvalue.c b/src/gromacs/selection/selvalue.cpp
similarity index 97%
rename from src/gromacs/gmxlib/selection/selvalue.c
rename to src/gromacs/selection/selvalue.cpp
index 769bfa544caea4d957f9bcaea1e9fb286e9f2d6e..c3db8a77ae571f711144f3eb42753d4f1a6446bc 100644 (file)
--- a/src/gromacs/gmxlib/selection/selvalue.c
+++ b/src/gromacs/selection/selvalue.cpp
@@ -37,9 +37,9 @@
 
 #include <smalloc.h>
 
-#include <indexutil.h>
-#include <position.h>
-#include <selvalue.h>
+#include "gromacs/selection/indexutil.h"
+#include "gromacs/selection/position.h"
+#include "gromacs/selection/selvalue.h"
 
 /*!
  * \param[out] val  Output structure

diff --git a/src/gromacs/legacyheaders/selvalue.h b/src/gromacs/selection/selvalue.h
similarity index 97%
rename from src/gromacs/legacyheaders/selvalue.h
rename to src/gromacs/selection/selvalue.h
index 8460fe89a34490ea9f3e9841fef2755bc707d0b9..63a928513b2bd7da983735d6118078ba4d952e7a 100644 (file)
--- a/src/gromacs/legacyheaders/selvalue.h
+++ b/src/gromacs/selection/selvalue.h
@@ -34,10 +34,10 @@
  * There should be no need to use the data structures in this file directly
  * unless implementing a custom selection routine.
  */
-#ifndef SELVALUE_H
-#define SELVALUE_H
+#ifndef GMX_SELECTION_SELVALUE_H
+#define GMX_SELECTION_SELVALUE_H
 
-#include "types/simple.h"
+#include "../legacyheaders/types/simple.h"
 
 #ifdef __cplusplus
 extern "C"

diff --git a/src/gromacs/gmxlib/selection/sm_compare.c b/src/gromacs/selection/sm_compare.cpp
similarity index 99%
rename from src/gromacs/gmxlib/selection/sm_compare.c
rename to src/gromacs/selection/sm_compare.cpp
index 103eb9ec016b7146da16b7a4c99939a1e3667064..3aff305efc720606354e3b761250ca713f449498 100644 (file)
--- a/src/gromacs/gmxlib/selection/sm_compare.c
+++ b/src/gromacs/selection/sm_compare.cpp
@@ -41,7 +41,7 @@
 #include <smalloc.h>
 #include <gmx_fatal.h>
 
-#include <selmethod.h>
+#include "gromacs/selection/selmethod.h"
 
 /** Defines the comparison operator for comparison expressions. */
 typedef enum

diff --git a/src/gromacs/gmxlib/selection/sm_distance.c b/src/gromacs/selection/sm_distance.cpp
similarity index 98%
rename from src/gromacs/gmxlib/selection/sm_distance.c
rename to src/gromacs/selection/sm_distance.cpp
index 61ee58e7a305c3a7f233d458e2d145b45dc6fb7c..5697a93b965903648a73d2e3a7f800c753b37ca2 100644 (file)
--- a/src/gromacs/gmxlib/selection/sm_distance.c
+++ b/src/gromacs/selection/sm_distance.cpp
@@ -43,9 +43,9 @@
 #include <smalloc.h>
 #include <vec.h>
 
-#include <nbsearch.h>
-#include <position.h>
-#include <selmethod.h>
+#include "gromacs/selection/nbsearch.h"
+#include "gromacs/selection/position.h"
+#include "gromacs/selection/selmethod.h"
 
 /*! \internal \brief
  * Data structure for distance-based selection method.

diff --git a/src/gromacs/gmxlib/selection/sm_insolidangle.c b/src/gromacs/selection/sm_insolidangle.cpp
similarity index 99%
rename from src/gromacs/gmxlib/selection/sm_insolidangle.c
rename to src/gromacs/selection/sm_insolidangle.cpp
index 1f72fcf1815b40d5a71d681dd5fc80c65042d333..a2732938753802dff3d0494c801be2603f5d0db2 100644 (file)
--- a/src/gromacs/gmxlib/selection/sm_insolidangle.c
+++ b/src/gromacs/selection/sm_insolidangle.cpp
@@ -115,10 +115,10 @@
 #include <smalloc.h>
 #include <vec.h>
 
-#include <indexutil.h>
-#include <position.h>
-#include <selection.h>
-#include <selmethod.h>
+#include "gromacs/selection/indexutil.h"
+#include "gromacs/selection/position.h"
+#include "gromacs/selection/selection.h"
+#include "gromacs/selection/selmethod.h"
 
 #include "selelem.h"
 

diff --git a/src/gromacs/gmxlib/selection/sm_keywords.c b/src/gromacs/selection/sm_keywords.cpp
similarity index 99%
rename from src/gromacs/gmxlib/selection/sm_keywords.c
rename to src/gromacs/selection/sm_keywords.cpp
index afcb2e36a6f356bf4c5a55a75e4ed89301a3321f..55d212a1d311eba1c6bbf08853a5bc1e123fdfb1 100644 (file)
--- a/src/gromacs/gmxlib/selection/sm_keywords.c
+++ b/src/gromacs/selection/sm_keywords.cpp
@@ -50,7 +50,7 @@
 #include <smalloc.h>
 #include <string2.h>
 
-#include <selmethod.h>
+#include "gromacs/selection/selmethod.h"
 
 #include "keywords.h"
 #include "parsetree.h"

diff --git a/src/gromacs/gmxlib/selection/sm_merge.c b/src/gromacs/selection/sm_merge.cpp
similarity index 99%
rename from src/gromacs/gmxlib/selection/sm_merge.c
rename to src/gromacs/selection/sm_merge.cpp
index 34d2b0d740891a6199611247ac9d95addb99fe02..51bf791abc44c208d43c5c5351a6ee441bb2078f 100644 (file)
--- a/src/gromacs/gmxlib/selection/sm_merge.c
+++ b/src/gromacs/selection/sm_merge.cpp
@@ -39,8 +39,8 @@
 #include <smalloc.h>
 #include <vec.h>
 
-#include <position.h>
-#include <selmethod.h>
+#include "gromacs/selection/position.h"
+#include "gromacs/selection/selmethod.h"
 
 /*! \internal \brief
  * Data structure for the merging selection modifiers.

diff --git a/src/gromacs/gmxlib/selection/sm_permute.c b/src/gromacs/selection/sm_permute.cpp
similarity index 99%
rename from src/gromacs/gmxlib/selection/sm_permute.c
rename to src/gromacs/selection/sm_permute.cpp
index a318912eb2cf77685ae4de4d177544127eb1a328..b232228e2e78aa2a1b4a03d26c53cd0a254d14d3 100644 (file)
--- a/src/gromacs/gmxlib/selection/sm_permute.c
+++ b/src/gromacs/selection/sm_permute.cpp
@@ -39,8 +39,8 @@
 #include <smalloc.h>
 #include <vec.h>
 
-#include <position.h>
-#include <selmethod.h>
+#include "gromacs/selection/position.h"
+#include "gromacs/selection/selmethod.h"
 
 /*! \internal \brief
  * Data structure for the \p permute selection modifier.

diff --git a/src/gromacs/gmxlib/selection/sm_position.c b/src/gromacs/selection/sm_position.cpp
similarity index 98%
rename from src/gromacs/gmxlib/selection/sm_position.c
rename to src/gromacs/selection/sm_position.cpp
index 6a3ae6a3dac143e435d41dfb1601b6caaf44db34..be5827bbe33620559f266458540177bdee98534e 100644 (file)
--- a/src/gromacs/gmxlib/selection/sm_position.c
+++ b/src/gromacs/selection/sm_position.cpp
@@ -39,10 +39,10 @@
 #include <smalloc.h>
 #include <string2.h>
 
-#include <indexutil.h>
-#include <poscalc.h>
-#include <position.h>
-#include <selmethod.h>
+#include "gromacs/selection/indexutil.h"
+#include "gromacs/selection/poscalc.h"
+#include "gromacs/selection/position.h"
+#include "gromacs/selection/selmethod.h"
 
 #include "keywords.h"
 #include "selelem.h"

diff --git a/src/gromacs/gmxlib/selection/sm_same.c b/src/gromacs/selection/sm_same.cpp
similarity index 99%
rename from src/gromacs/gmxlib/selection/sm_same.c
rename to src/gromacs/selection/sm_same.cpp
index d50221e4933949ec6f309715fa311ad29aae79d8..e9bc8966973b00a586d5d998513cd672cbefe858 100644 (file)
--- a/src/gromacs/gmxlib/selection/sm_same.c
+++ b/src/gromacs/selection/sm_same.cpp
@@ -41,7 +41,7 @@
 #include <smalloc.h>
 #include <string2.h>
 
-#include <selmethod.h>
+#include "gromacs/selection/selmethod.h"
 
 #include "keywords.h"
 #include "parsetree.h"

diff --git a/src/gromacs/gmxlib/selection/sm_simple.c b/src/gromacs/selection/sm_simple.cpp
similarity index 99%
rename from src/gromacs/gmxlib/selection/sm_simple.c
rename to src/gromacs/selection/sm_simple.cpp
index 1810b12454bba5764ecaaedbbbe67452946f8e44..2a125229f50f47b208f8b5889005474edb16e52b 100644 (file)
--- a/src/gromacs/gmxlib/selection/sm_simple.c
+++ b/src/gromacs/selection/sm_simple.cpp
@@ -35,8 +35,8 @@
 #include <config.h>
 #endif
 
-#include <position.h>
-#include <selmethod.h>
+#include "gromacs/selection/position.h"
+#include "gromacs/selection/selmethod.h"
 
 /** Evaluates the \p all selection keyword. */
 static int

diff --git a/src/gromacs/gmxlib/selection/symrec.c b/src/gromacs/selection/symrec.cpp
similarity index 99%
rename from src/gromacs/gmxlib/selection/symrec.c
rename to src/gromacs/selection/symrec.cpp
index 2e40096a24d8adc59c89a461201e2c88b66e03d1..251cc4428d31daa2da1c56b988b16cb969428aa6 100644 (file)
--- a/src/gromacs/gmxlib/selection/symrec.c
+++ b/src/gromacs/selection/symrec.cpp
@@ -41,7 +41,7 @@
 #include <typedefs.h>
 #include <gmx_fatal.h>
 
-#include <poscalc.h>
+#include "gromacs/selection/poscalc.h"
 
 #include "selelem.h"
 #include "symrec.h"

diff --git a/src/gromacs/gmxlib/selection/symrec.h b/src/gromacs/selection/symrec.h
similarity index 100%
rename from src/gromacs/gmxlib/selection/symrec.h
rename to src/gromacs/selection/symrec.h

diff --git a/src/gromacs/gmxlib/trajana/trajana.c b/src/gromacs/trajana/trajana.cpp
similarity index 99%
rename from src/gromacs/gmxlib/trajana/trajana.c
rename to src/gromacs/trajana/trajana.cpp
index 4dde161ca7f584fd097c7587621dae86b933bdf7..85e4b190ab0ae8064b17823c231469209c9460a1 100644 (file)
--- a/src/gromacs/gmxlib/trajana/trajana.c
+++ b/src/gromacs/trajana/trajana.cpp
@@ -133,10 +133,10 @@
 #include <tpxio.h>
 #include <vec.h>
 
-#include <poscalc.h>
-#include <selection.h>
-#include <selmethod.h>
-#include <trajana.h>
+#include "gromacs/selection/poscalc.h"
+#include "gromacs/selection/selection.h"
+#include "gromacs/selection/selmethod.h"
+#include "gromacs/trajana/trajana.h"
 
 /*! \internal \brief
  * Data structure for trajectory analysis tools.

diff --git a/src/gromacs/legacyheaders/trajana.h b/src/gromacs/trajana/trajana.h
similarity index 98%
rename from src/gromacs/legacyheaders/trajana.h
rename to src/gromacs/trajana/trajana.h
index 8000a810334e0c4214f8b11e38b0f8fa79c93f4e..1e111d353fd93199d9e53eb85394747322440f1e 100644 (file)
--- a/src/gromacs/legacyheaders/trajana.h
+++ b/src/gromacs/trajana/trajana.h
@@ -55,12 +55,12 @@
 #ifndef TRAJANA_H
 #define TRAJANA_H
 
-#include "typedefs.h"
-#include "filenm.h"
-#include "readinp.h"
+#include "../legacyheaders/typedefs.h"
+#include "../legacyheaders/filenm.h"
+#include "../legacyheaders/readinp.h"
 
-#include "indexutil.h"
-#include "selection.h"
+#include "../selection/indexutil.h"
+#include "../selection/selection.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/tools/gmx_select.c b/src/tools/gmx_select.c
index 4361af1b73a63c154051ae8355c2194e80be9623..8b65a3a4f9462a7e151598eb43b68411c708137a 100644 (file)
--- a/src/tools/gmx_select.c
+++ b/src/tools/gmx_select.c
@@ -45,10 +45,10 @@
 #include <statutil.h>
 #include <xvgr.h>
 #include <string2.h>
-#include <trajana.h>
 #include "gmx_ana.h"
 #include "gmx_fatal.h"
 
+#include "gromacs/trajana/trajana.h"
 
 typedef struct
 {