Moved selection and trajana modules to src/gromacs/.

diff --git a/src/gmxlib/CMakeLists.txt b/src/gmxlib/CMakeLists.txt
index b78966cbfac45c27f7634ecf462d5d6c751409d5..e81ed95f72ac1d5c1c81df2c52e04242c36d593e 100644 (file)
--- a/src/gmxlib/CMakeLists.txt
+++ b/src/gmxlib/CMakeLists.txt
@@ -21,7 +21,6 @@ endif()
 # 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)
 
 # This source file is generated

diff --git a/src/gmxlib/trajana/centerofmass.c b/src/gromacs/selection/centerofmass.cpp
similarity index 99%
rename from src/gmxlib/trajana/centerofmass.c
rename to src/gromacs/selection/centerofmass.cpp
index bc46cfd40889b90c2a9490bfce04d57722b05922..8fd510c34c3bab057d7950ccc60482aa7b14eaa2 100644 (file)
--- a/src/gmxlib/trajana/centerofmass.c
+++ b/src/gromacs/selection/centerofmass.cpp
@@ -39,7 +39,7 @@
 #include <pbc.h>
 #include <vec.h>
 
-#include <centerofmass.h>
+#include "centerofmass.h"
 
 /*!
  * \param[in]  top    Topology structure (unused, can be NULL).

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

diff --git a/src/gmxlib/selection/compiler.c b/src/gromacs/selection/compiler.cpp
similarity index 99%
rename from src/gmxlib/selection/compiler.c
rename to src/gromacs/selection/compiler.cpp
index 76f40036d7ba203ff0c9f93b9cab5fe86020b6e5..13490e0b8e2e37b0c75151e10c44f161050d033e 100644 (file)
--- a/src/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 "indexutil.h"
+#include "poscalc.h"
+#include "selection.h"
+#include "selmethod.h"
 
 #include "evaluate.h"
 #include "keywords.h"

diff --git a/src/gmxlib/selection/evaluate.c b/src/gromacs/selection/evaluate.cpp
similarity index 99%
rename from src/gmxlib/selection/evaluate.c
rename to src/gromacs/selection/evaluate.cpp
index 06a4d8b7062b13aa2af56492cedaf1714a092530..dc4ac430552bf9bb3c3af4b8c3a22340c99042e7 100644 (file)
--- a/src/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 "indexutil.h"
+#include "poscalc.h"
+#include "selection.h"
+#include "selmethod.h"
 
 #include "evaluate.h"
 #include "mempool.h"

diff --git a/src/gmxlib/selection/evaluate.h b/src/gromacs/selection/evaluate.h
similarity index 99%
rename from src/gmxlib/selection/evaluate.h
rename to src/gromacs/selection/evaluate.h
index 99c15c71698cc8caacfb5ba1b5ea61d3edc01179..acb34ea653211197a0a785dc7479dfd594693a98 100644 (file)
--- a/src/gmxlib/selection/evaluate.h
+++ b/src/gromacs/selection/evaluate.h
@@ -44,7 +44,7 @@
 
 #include <typedefs.h>
 
-#include <indexutil.h>
+#include "indexutil.h"
 
 #include "selelem.h"
 

diff --git a/src/gmxlib/trajana/indexutil.c b/src/gromacs/selection/indexutil.cpp
similarity index 99%
rename from src/gmxlib/trajana/indexutil.c
rename to src/gromacs/selection/indexutil.cpp
index ab5c13177887c1e905f82102afe02c2fb678b88f..6ae45c716f62c7e79eea927f4cb38057a690e542 100644 (file)
--- a/src/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 "indexutil.h"
 
 /********************************************************************
  * gmx_ana_indexgrps_t functions

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

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

diff --git a/src/gmxlib/selection/mempool.c b/src/gromacs/selection/mempool.cpp
similarity index 99%
rename from src/gmxlib/selection/mempool.c
rename to src/gromacs/selection/mempool.cpp
index 32d8aa0ebbb4815f02289e82ee070f609a8eae5a..a13f0887d5cd79c3d2ce62717425f08f5cc17f56 100644 (file)
--- a/src/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 "indexutil.h"
 
 #include "mempool.h"
 

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

diff --git a/src/gmxlib/trajana/nbsearch.c b/src/gromacs/selection/nbsearch.cpp
similarity index 99%
rename from src/gmxlib/trajana/nbsearch.c
rename to src/gromacs/selection/nbsearch.cpp
index e991cbc2f26edb4d4acb0638025bce5195a1586e..e4e79d5a2f46514161e41ceb43b68d5f16a3ed24 100644 (file)
--- a/src/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 "nbsearch.h"
+#include "position.h"
 
 /*! \internal \brief
  * Data structure for neighborhood searches.

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

diff --git a/src/gmxlib/selection/params.c b/src/gromacs/selection/params.cpp
similarity index 99%
rename from src/gmxlib/selection/params.c
rename to src/gromacs/selection/params.cpp
index 21ae7e81915d12e567b0a402c7d16e0057b758e5..8398f491a93f36ed0b5196c2951189d1bc8e9834 100644 (file)
--- a/src/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 "position.h"
+#include "selmethod.h"
+#include "selparam.h"
 
 #include "parsetree.h"
 #include "position.h"

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

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

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

diff --git a/src/gmxlib/selection/parsetree.c b/src/gromacs/selection/parsetree.cpp
similarity index 99%
rename from src/gmxlib/selection/parsetree.c
rename to src/gromacs/selection/parsetree.cpp
index 2da5106bab0aa7ad1c12fb2204b89e47ede16da5..2971b26e67f5b6564528e986d91615d7e53611f2 100644 (file)
--- a/src/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 "poscalc.h"
+#include "selection.h"
+#include "selmethod.h"
 
 #include "keywords.h"
 #include "parsetree.h"

diff --git a/src/gmxlib/selection/parsetree.h b/src/gromacs/selection/parsetree.h
similarity index 99%
rename from src/gmxlib/selection/parsetree.h
rename to src/gromacs/selection/parsetree.h
index 8d97d1515d5a530581e4648248f5d47efb4e67cc..fce054d0dfa4e77b273b9d8bd61b16f4a4632d83 100644 (file)
--- a/src/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 "selvalue.h"
 
 struct t_selelem;
 struct gmx_ana_indexgrps_t;

diff --git a/src/gmxlib/trajana/poscalc.c b/src/gromacs/selection/poscalc.cpp
similarity index 99%
rename from src/gmxlib/trajana/poscalc.c
rename to src/gromacs/selection/poscalc.cpp
index 9a319e6d6875106863f4e0696ac07d319f5951a8..3147f951b2af8be2d7953f0b67383302f5942d37 100644 (file)
--- a/src/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 "centerofmass.h"
+#include "indexutil.h"
+#include "poscalc.h"
+#include "position.h"
 
 /*! \internal \brief
  * Collection of \c gmx_ana_poscalc_t structures for the same topology.

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

diff --git a/src/gmxlib/trajana/position.c b/src/gromacs/selection/position.cpp
similarity index 99%
rename from src/gmxlib/trajana/position.c
rename to src/gromacs/selection/position.cpp
index 4edcb46cb0afc5834ce5a117a781d55d1eb51fa3..03eaafd9ef73ac9cc8763b2b9be17d4a59858e94 100644 (file)
--- a/src/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 "indexutil.h"
+#include "position.h"
 
 /*!
  * \param[out] pos      Output structure.

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

diff --git a/src/gmxlib/selection/regenerate_parser.sh b/src/gromacs/selection/regenerate_parser.sh
similarity index 75%
rename from src/gmxlib/selection/regenerate_parser.sh
rename to src/gromacs/selection/regenerate_parser.sh
index 5b597dc34bdb5b8f4c6f21bbf715da2c15882830..df7e77cedb549daf3f9fc4844076c3f2c1ad1b2f 100755 (executable)
--- a/src/gmxlib/selection/regenerate_parser.sh
+++ b/src/gromacs/selection/regenerate_parser.sh
@@ -13,10 +13,10 @@ 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/gmxlib/selection
+dirname=src/gromacs/selection
 if [[ -f $dirname/parser.y && -f $dirname/scanner.l ]] ; then
     cd $dirname
 fi
 
-[[ $FORCE || parser.y  -nt parser.c ]]  && bison -d -t -o parser.c parser.y
-[[ $FORCE || scanner.l -nt scanner.c ]] && flex -o scanner.c scanner.l
+[[ $FORCE || parser.y  -nt parser.cpp ]]  && bison -d -t -o parser.cpp parser.y
+[[ $FORCE || scanner.l -nt scanner.cpp ]] && flex -o scanner.cpp scanner.l

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

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

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

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

diff --git a/src/gmxlib/selection/scanner_internal.c b/src/gromacs/selection/scanner_internal.cpp
similarity index 99%
rename from src/gmxlib/selection/scanner_internal.c
rename to src/gromacs/selection/scanner_internal.cpp
index 1e7e4f74a54590bf38f55c65c87e8f1bcebb1178..96f5a3dda6a7caa8a69c55459eb7846a91bb45e2 100644 (file)
--- a/src/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 "selmethod.h"
 
 #include "parsetree.h"
 #include "selcollection.h"

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

diff --git a/src/gmxlib/selection/selcollection.h b/src/gromacs/selection/selcollection.h
similarity index 99%
rename from src/gmxlib/selection/selcollection.h
rename to src/gromacs/selection/selcollection.h
index 909c8781473f0d0f1cca0e2dd4a19f7fd8a97b78..0f457e3fd50625532ba88f574e4b1d2587a57e01 100644 (file)
--- a/src/gmxlib/selection/selcollection.h
+++ b/src/gromacs/selection/selcollection.h
@@ -39,7 +39,7 @@
 
 #include <typedefs.h>
 
-#include <indexutil.h>
+#include "indexutil.h"
 
 /*! \internal
  * \brief

diff --git a/src/gmxlib/selection/selection.c b/src/gromacs/selection/selection.cpp
similarity index 99%
rename from src/gmxlib/selection/selection.c
rename to src/gromacs/selection/selection.cpp
index 17a9cf761850c8d497fa73bfdaa15d97a3a1e747..66166aabb798e360bd3c8f6286d9eb38e67c95f4 100644 (file)
--- a/src/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 "poscalc.h"
+#include "selection.h"
+#include "selmethod.h"
 
 #include "mempool.h"
 #include "selcollection.h"

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

diff --git a/src/gmxlib/selection/selelem.c b/src/gromacs/selection/selelem.cpp
similarity index 99%
rename from src/gmxlib/selection/selelem.c
rename to src/gromacs/selection/selelem.cpp
index 09971c053894f90799d278c1460c10ec0958ee96..84778d64d65de5afc3aa1399d1320efc78b767d0 100644 (file)
--- a/src/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 "indexutil.h"
+#include "poscalc.h"
+#include "position.h"
+#include "selmethod.h"
 
 #include "keywords.h"
 #include "mempool.h"

diff --git a/src/gmxlib/selection/selelem.h b/src/gromacs/selection/selelem.h
similarity index 99%
rename from src/gmxlib/selection/selelem.h
rename to src/gromacs/selection/selelem.h
index 571d8a127fbe50b4dd12b0aad1afcf212d53f8c0..bca5d6d6cb7a2ab7eff23c47a513507fe745472b 100644 (file)
--- a/src/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 "indexutil.h"
+#include "selvalue.h"
 
 struct gmx_ana_poscalc_t;
 struct gmx_ana_selparam_t;

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

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

diff --git a/src/gmxlib/selection/selmethod.c b/src/gromacs/selection/selmethod.cpp
similarity index 99%
rename from src/gmxlib/selection/selmethod.c
rename to src/gromacs/selection/selmethod.cpp
index 982eaed6efe2cc8a7ba03ecab341f9b4867a83c1..a735763ec0f0d715d0a7e56aa31e4ea2b106e169 100644 (file)
--- a/src/gmxlib/selection/selmethod.c
+++ b/src/gromacs/selection/selmethod.cpp
@@ -41,7 +41,7 @@
 #include <macros.h>
 #include <string2.h>
 
-#include <selmethod.h>
+#include "selmethod.h"
 
 #include "selcollection.h"
 #include "symrec.h"

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

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

diff --git a/src/gmxlib/selection/selvalue.c b/src/gromacs/selection/selvalue.cpp
similarity index 98%
rename from src/gmxlib/selection/selvalue.c
rename to src/gromacs/selection/selvalue.cpp
index 769bfa544caea4d957f9bcaea1e9fb286e9f2d6e..bd55f605005ffe4fd77329c77b6822767ea8be44 100644 (file)
--- a/src/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 "indexutil.h"
+#include "position.h"
+#include "selvalue.h"
 
 /*!
  * \param[out] val  Output structure

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

diff --git a/src/gmxlib/selection/sm_compare.c b/src/gromacs/selection/sm_compare.cpp
similarity index 99%
rename from src/gmxlib/selection/sm_compare.c
rename to src/gromacs/selection/sm_compare.cpp
index 103eb9ec016b7146da16b7a4c99939a1e3667064..9fc2abf23a23f568b3d428a0ec620eb1c54e2ca4 100644 (file)
--- a/src/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 "selmethod.h"
 
 /** Defines the comparison operator for comparison expressions. */
 typedef enum

diff --git a/src/gmxlib/selection/sm_distance.c b/src/gromacs/selection/sm_distance.cpp
similarity index 99%
rename from src/gmxlib/selection/sm_distance.c
rename to src/gromacs/selection/sm_distance.cpp
index 61ee58e7a305c3a7f233d458e2d145b45dc6fb7c..5f8fa2090b3871c177c1e26e714ed67a69bf912b 100644 (file)
--- a/src/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 "nbsearch.h"
+#include "position.h"
+#include "selmethod.h"
 
 /*! \internal \brief
  * Data structure for distance-based selection method.

diff --git a/src/gmxlib/selection/sm_insolidangle.c b/src/gromacs/selection/sm_insolidangle.cpp
similarity index 99%
rename from src/gmxlib/selection/sm_insolidangle.c
rename to src/gromacs/selection/sm_insolidangle.cpp
index 1f72fcf1815b40d5a71d681dd5fc80c65042d333..87a8109b5a0ce6c65f5397edc5eb0c9d05d3b7a0 100644 (file)
--- a/src/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 "indexutil.h"
+#include "position.h"
+#include "selection.h"
+#include "selmethod.h"
 
 #include "selelem.h"
 

diff --git a/src/gmxlib/selection/sm_keywords.c b/src/gromacs/selection/sm_keywords.cpp
similarity index 99%
rename from src/gmxlib/selection/sm_keywords.c
rename to src/gromacs/selection/sm_keywords.cpp
index afcb2e36a6f356bf4c5a55a75e4ed89301a3321f..dd47f7ea42248f4c07dbbcbb09be6dc66acd5261 100644 (file)
--- a/src/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 "selmethod.h"
 
 #include "keywords.h"
 #include "parsetree.h"

diff --git a/src/gmxlib/selection/sm_merge.c b/src/gromacs/selection/sm_merge.cpp
similarity index 99%
rename from src/gmxlib/selection/sm_merge.c
rename to src/gromacs/selection/sm_merge.cpp
index 34d2b0d740891a6199611247ac9d95addb99fe02..ea44d33f4eec4052a83519a5476d19e64ab21a18 100644 (file)
--- a/src/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 "position.h"
+#include "selmethod.h"
 
 /*! \internal \brief
  * Data structure for the merging selection modifiers.

diff --git a/src/gmxlib/selection/sm_permute.c b/src/gromacs/selection/sm_permute.cpp
similarity index 99%
rename from src/gmxlib/selection/sm_permute.c
rename to src/gromacs/selection/sm_permute.cpp
index a318912eb2cf77685ae4de4d177544127eb1a328..d17bf4bea20435d8cacce22d2e16b7558ef2e36a 100644 (file)
--- a/src/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 "position.h"
+#include "selmethod.h"
 
 /*! \internal \brief
  * Data structure for the \p permute selection modifier.

diff --git a/src/gmxlib/selection/sm_position.c b/src/gromacs/selection/sm_position.cpp
similarity index 99%
rename from src/gmxlib/selection/sm_position.c
rename to src/gromacs/selection/sm_position.cpp
index 6a3ae6a3dac143e435d41dfb1601b6caaf44db34..ce00ed31c594fe0a61d9a15f4cc55ea122856ec1 100644 (file)
--- a/src/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 "indexutil.h"
+#include "poscalc.h"
+#include "position.h"
+#include "selmethod.h"
 
 #include "keywords.h"
 #include "selelem.h"

diff --git a/src/gmxlib/selection/sm_same.c b/src/gromacs/selection/sm_same.cpp
similarity index 99%
rename from src/gmxlib/selection/sm_same.c
rename to src/gromacs/selection/sm_same.cpp
index d50221e4933949ec6f309715fa311ad29aae79d8..f15f3d1fe706d963e60654c87a1397a52347e7f1 100644 (file)
--- a/src/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 "selmethod.h"
 
 #include "keywords.h"
 #include "parsetree.h"

diff --git a/src/gmxlib/selection/sm_simple.c b/src/gromacs/selection/sm_simple.cpp
similarity index 99%
rename from src/gmxlib/selection/sm_simple.c
rename to src/gromacs/selection/sm_simple.cpp
index 1810b12454bba5764ecaaedbbbe67452946f8e44..1c126864f7d69c5fd606235153aa417c4c7ecb15 100644 (file)
--- a/src/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 "position.h"
+#include "selmethod.h"
 
 /** Evaluates the \p all selection keyword. */
 static int

diff --git a/src/gmxlib/selection/symrec.c b/src/gromacs/selection/symrec.cpp
similarity index 99%
rename from src/gmxlib/selection/symrec.c
rename to src/gromacs/selection/symrec.cpp
index 2e40096a24d8adc59c89a461201e2c88b66e03d1..80375c81063a2c6a5f3bf9f3ff780b5f5d08c382 100644 (file)
--- a/src/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 "poscalc.h"
 
 #include "selelem.h"
 #include "symrec.h"

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

diff --git a/src/gmxlib/trajana/trajana.c b/src/gromacs/trajana/trajana.cpp
similarity index 99%
rename from src/gmxlib/trajana/trajana.c
rename to src/gromacs/trajana/trajana.cpp
index 4dde161ca7f584fd097c7587621dae86b933bdf7..5390d91b664a384b8232a0a017f208a7fea2e4a2 100644 (file)
--- a/src/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 "../selection/poscalc.h"
+#include "../selection/selection.h"
+#include "../selection/selmethod.h"
+#include "trajana.h"
 
 /*! \internal \brief
  * Data structure for trajectory analysis tools.

diff --git a/include/trajana.h b/src/gromacs/trajana/trajana.h
similarity index 99%
rename from include/trajana.h
rename to src/gromacs/trajana/trajana.h
index 8000a810334e0c4214f8b11e38b0f8fa79c93f4e..6125e6b617b3a089964a9f6d23181f78e6779b71 100644 (file)
--- a/include/trajana.h
+++ b/src/gromacs/trajana/trajana.h
@@ -59,8 +59,8 @@
 #include "filenm.h"
 #include "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/CMakeLists.txt b/src/tools/CMakeLists.txt
index 18f8b7f6223a1bc5483e1d0f4afa843d8341f6d2..f45a39e4a05a7228a42d17936e70407da9858b93 100644 (file)
--- a/src/tools/CMakeLists.txt
+++ b/src/tools/CMakeLists.txt
@@ -1,3 +1,4 @@
+include_directories(${CMAKE_CURRENT_SOURCE_DIR}/..)
 
 add_library(gmxana 
             autocorr.c      expfit.c        polynomials.c   levenmar.c      
@@ -32,7 +33,7 @@ add_library(gmxana
             gmx_pme_error.c    )
 
 
-target_link_libraries(gmxana md gmx)
+target_link_libraries(gmxana md gmx gromacs)
 set_target_properties(gmxana PROPERTIES OUTPUT_NAME "gmxana${GMX_LIBS_SUFFIX}" SOVERSION ${SOVERSION} INSTALL_NAME_DIR "${LIB_INSTALL_DIR}")
 
 # List of programs with single corresponding .c source file,

diff --git a/src/tools/gmx_select.c b/src/tools/gmx_select.c
index 4361af1b73a63c154051ae8355c2194e80be9623..dadbd90905921edd770d1e1e10faa5b251337c19 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
 {