Move physics.* to math/units.*

- Remove some unnecessary #includes.
- Remove the dummy tests; easy to rewrite as usable tests using GTest if
  someone needs those.  They were anyways testing code that no one is
  still calling, even though it was introduced several years ago.
  Now gmxlib is free of *_test.c files.

Now, only one file using atom_id is keeping math/ dependent on
legacyheaders/.

Part of #1415.

Change-Id: I31312b92cf9f5d5129fbd90f31fcf27be2f7afaf

diff --git a/src/contrib/ehanal.c b/src/contrib/ehanal.c
index 7d488ce6e058c5ded03588b2a023b933a5d2b80a..31c6870bb89b82c82ed7166fbca0e0869300698a 100644 (file)
--- a/src/contrib/ehanal.c
+++ b/src/contrib/ehanal.c
@@ -46,7 +46,7 @@
 #include "random.h"
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/utility/futil.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/math/vec.h"
 #include "names.h"

diff --git a/src/contrib/ehdata.c b/src/contrib/ehdata.c
index 513a4a34d3ff6d4fb20f108874b92e985a4d433a..4bc06da790f45cf8f0853bf628769f221f25c417 100644 (file)
--- a/src/contrib/ehdata.c
+++ b/src/contrib/ehdata.c
@@ -45,7 +45,6 @@
 #include "random.h"
 #include "gromacs/fileio/strdb.h"
 #include "gromacs/utility/futil.h"
-#include "physics.h"
 #include "ehdata.h"
 
 typedef struct {

diff --git a/src/contrib/ehole.c b/src/contrib/ehole.c
index 36541aa6e439716568cbdddef9ea4347b4eaf589..1509e83088251423a6ef40db91117e12f6767fc6 100644 (file)
--- a/src/contrib/ehole.c
+++ b/src/contrib/ehole.c
@@ -48,7 +48,7 @@
 #include "random.h"
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/utility/futil.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "names.h"
 #include "ehdata.h"

diff --git a/src/contrib/g_anavel.c b/src/contrib/g_anavel.c
index 0573d7c69305fcdc16d0fea85722c94d274e8544..6cb062fe49d5f7a18b08cf70f5f3a38509bd0d82 100644 (file)
--- a/src/contrib/g_anavel.c
+++ b/src/contrib/g_anavel.c
@@ -42,7 +42,7 @@
 #include "random.h"
 #include "names.h"
 #include "gromacs/fileio/matio.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/utility/futil.h"
 #include "copyrite.h"

diff --git a/src/contrib/hexamer.c b/src/contrib/hexamer.c
index 21ea976763cf329bca0ee2fde1d92396a1c3eb5f..4470845988345f2866e75bc956d6d8cb78319576 100644 (file)
--- a/src/contrib/hexamer.c
+++ b/src/contrib/hexamer.c
@@ -51,7 +51,7 @@
 #include "gromacs/math/vec.h"
 #include "typedefs.h"
 #include "gbutil.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "atomprop.h"
 
 void copy_atom(t_symtab *tab,t_atoms *a1,int i1,t_atoms *a2,int i2,

diff --git a/src/contrib/mkice.c b/src/contrib/mkice.c
index b0c5bb9a30838bf51da1ea1248d90fd3ddfc71ee..7ae0d04c84aed91d7bbbb995dc4c5553393eaf1f 100644 (file)
--- a/src/contrib/mkice.c
+++ b/src/contrib/mkice.c
@@ -47,7 +47,7 @@
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/math/vec.h"
 #include "pbc.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "names.h"
 #include "txtdump.h"
 #include "gromacs/fileio/trnio.h"

diff --git a/src/contrib/test.c b/src/contrib/test.c
index f41e6c0b4b7022cbc509da27e59d86474445c972..aecb32776689f586dc88e5b66afd8c8a329495aa 100644 (file)
--- a/src/contrib/test.c
+++ b/src/contrib/test.c
@@ -49,7 +49,7 @@
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/math/vec.h"
 #include "pbc.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "names.h"
 #include "txtdump.h"
 #include "gromacs/fileio/trnio.h"

diff --git a/src/contrib/testlr.c b/src/contrib/testlr.c
index b48a0c1b93dab7a8c59a7da1aaf54553d4ee1de4..f2cc064d7344436bb1687288189f8ee857043616 100644 (file)
--- a/src/contrib/testlr.c
+++ b/src/contrib/testlr.c
@@ -36,7 +36,7 @@
 #include <string.h>
 #include "typedefs.h"
 #include "gromacs/math/vec.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "macros.h"
 #include "names.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/essentialdynamics/edsam.c b/src/gromacs/essentialdynamics/edsam.c
index 1498500cceb125555c57fa5dda6445e41787d600..317969e87ed09aa9c25547637cc134574018e55d 100644 (file)
--- a/src/gromacs/essentialdynamics/edsam.c
+++ b/src/gromacs/essentialdynamics/edsam.c
@@ -53,7 +53,6 @@
 #include "mshift.h"
 #include "mdrun.h"
 #include "update.h"
-#include "physics.h"
 #include "mtop_util.h"
 #include "gromacs/essentialdynamics/edsam.h"
 #include "gromacs/fileio/gmxfio.h"

diff --git a/src/gromacs/fileio/pdbio.c b/src/gromacs/fileio/pdbio.c
index d1974d0f69aab40dba63d029d88d993c8fac101d..7b98fb13aee049444b5387338850708ba30efce5 100644 (file)
--- a/src/gromacs/fileio/pdbio.c
+++ b/src/gromacs/fileio/pdbio.c
@@ -48,7 +48,7 @@
 #include "copyrite.h"
 #include "gromacs/utility/futil.h"
 #include "atomprop.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "pbc.h"
 #include "gmxfio.h"
 

diff --git a/src/gromacs/fileio/tngio.cpp b/src/gromacs/fileio/tngio.cpp
index 761b97501980a2ccc677810dcae2089f7dde306b..a4b72f9deeb0e4a5d1292553a32098852f8fe61d 100644 (file)
--- a/src/gromacs/fileio/tngio.cpp
+++ b/src/gromacs/fileio/tngio.cpp
@@ -47,9 +47,9 @@
 #endif
 
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/physics.h"
 
 #include "gromacs/fileio/gmxfio.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/utility/basenetwork.h"
 #include "gromacs/utility/common.h"

diff --git a/src/gromacs/fileio/tngio_for_tools.cpp b/src/gromacs/fileio/tngio_for_tools.cpp
index d6239afb1e71680ba1f7128eda3d3b4505ed562d..d81fef7fb2359d7a6d812243e79ad701e5efad09 100644 (file)
--- a/src/gromacs/fileio/tngio_for_tools.cpp
+++ b/src/gromacs/fileio/tngio_for_tools.cpp
@@ -48,8 +48,8 @@
 #endif
 
 #include "gromacs/legacyheaders/types/atoms.h"
-#include "gromacs/legacyheaders/physics.h"
 
+#include "gromacs/math/units.h"
 #include "gromacs/utility/common.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/gmxana/anadih.c b/src/gromacs/gmxana/anadih.c
index b83b1b88f19d2835955b828c1d7603fae7737b96..18746d63ea6a05daba9420782e2cdc8aa42e1ac2 100644 (file)
--- a/src/gromacs/gmxana/anadih.c
+++ b/src/gromacs/gmxana/anadih.c
@@ -41,7 +41,7 @@
 #include <math.h>
 #include <stdio.h>
 #include <string.h>
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "txtdump.h"

diff --git a/src/gromacs/gmxana/autocorr.c b/src/gromacs/gmxana/autocorr.c
index 755d330ba22b522ba037b67d35f83c0d8133ec34..d7e3e52537e303c629a4d8d4dde9992ef455bb4c 100644 (file)
--- a/src/gromacs/gmxana/autocorr.c
+++ b/src/gromacs/gmxana/autocorr.c
@@ -44,7 +44,6 @@
 
 #include "macros.h"
 #include "typedefs.h"
-#include "physics.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/utility/futil.h"

diff --git a/src/gromacs/gmxana/gmx_anaeig.c b/src/gromacs/gmxana/gmx_anaeig.c
index 014a58c147719b68717c9ffe4919883aa4a23235..370f4dc76c4f5b7aa96eabbe843946228ce549b0 100644 (file)
--- a/src/gromacs/gmxana/gmx_anaeig.c
+++ b/src/gromacs/gmxana/gmx_anaeig.c
@@ -62,7 +62,7 @@
 #include "rmpbc.h"
 #include "txtdump.h"
 #include "eigio.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "gmx_ana.h"
 
 #include "gromacs/math/do_fit.h"

diff --git a/src/gromacs/gmxana/gmx_angle.c b/src/gromacs/gmxana/gmx_angle.c
index b4778fd6de8e8444e2189e2aae4a72e6bd123aab..2795b3d2f7b792ebfe344add7a8a2caf7c951df8 100644 (file)
--- a/src/gromacs/gmxana/gmx_angle.c
+++ b/src/gromacs/gmxana/gmx_angle.c
@@ -40,7 +40,7 @@
 #include <math.h>
 #include <string.h>
 
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "typedefs.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/futil.h"

diff --git a/src/gromacs/gmxana/gmx_bar.c b/src/gromacs/gmxana/gmx_bar.c
index e71ec7e35ea5f82bd29045218b386bb71e35b2ba..b3edda4c58b42f17ed41c9782c4e22e051527c39 100644 (file)
--- a/src/gromacs/gmxana/gmx_bar.c
+++ b/src/gromacs/gmxana/gmx_bar.c
@@ -48,7 +48,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "macros.h"
 #include "gromacs/fileio/enxio.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/fileio/xvgr.h"
 #include "viewit.h"

diff --git a/src/gromacs/gmxana/gmx_bundle.c b/src/gromacs/gmxana/gmx_bundle.c
index 18326cb0cfe0e208b715e0016e27fa238f0a9473..dc9d7f1f279342a883be86f7b1e1b1938c38f5df 100644 (file)
--- a/src/gromacs/gmxana/gmx_bundle.c
+++ b/src/gromacs/gmxana/gmx_bundle.c
@@ -51,7 +51,7 @@
 #include "rmpbc.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "gmx_ana.h"
 
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/gmxana/gmx_chi.c b/src/gromacs/gmxana/gmx_chi.c
index eaddaaca926f2121f1107a0229b346dc1443216a..5cb3c68f89ebaaec63cc531a10876267ae191c36 100644 (file)
--- a/src/gromacs/gmxana/gmx_chi.c
+++ b/src/gromacs/gmxana/gmx_chi.c
@@ -49,7 +49,7 @@
 #include "gstat.h"
 #include "macros.h"
 #include "gromacs/math/utilities.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "index.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/commandline/pargs.h"

diff --git a/src/gromacs/gmxana/gmx_clustsize.c b/src/gromacs/gmxana/gmx_clustsize.c
index 2168930c64afe6ff0bf6e294510a977903c9e6c0..45b1b30e9403fceeb1195426ef95af84e336dda6 100644 (file)
--- a/src/gromacs/gmxana/gmx_clustsize.c
+++ b/src/gromacs/gmxana/gmx_clustsize.c
@@ -54,7 +54,7 @@
 #include "gromacs/utility/smalloc.h"
 #include "calcgrid.h"
 #include "nrnb.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "coulomb.h"
 #include "pme.h"
 #include "gstat.h"

diff --git a/src/gromacs/gmxana/gmx_covar.c b/src/gromacs/gmxana/gmx_covar.c
index 93128a5a44059e20754d886db0ecebba718f9068..ca5b042074f39f57e40f4a67c06854fd7e5f919a 100644 (file)
--- a/src/gromacs/gmxana/gmx_covar.c
+++ b/src/gromacs/gmxana/gmx_covar.c
@@ -62,7 +62,6 @@
 #include "txtdump.h"
 #include "gromacs/fileio/matio.h"
 #include "eigio.h"
-#include "physics.h"
 #include "gmx_ana.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/fileio/trxio.h"

diff --git a/src/gromacs/gmxana/gmx_current.c b/src/gromacs/gmxana/gmx_current.c
index 5154ae2ece25295727c0c6eed6135497379e8e3c..938f3adc0fd3cdbfa5f8c33ce79a308377b34c2a 100644 (file)
--- a/src/gromacs/gmxana/gmx_current.c
+++ b/src/gromacs/gmxana/gmx_current.c
@@ -48,7 +48,7 @@
 #include "gromacs/fileio/xvgr.h"
 #include "rmpbc.h"
 #include "pbc.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "index.h"
 #include "gromacs/statistics/statistics.h"
 #include "gmx_ana.h"

diff --git a/src/gromacs/gmxana/gmx_density.c b/src/gromacs/gmxana/gmx_density.c
index a27ccbdef25bdc1686c0f3c6c2c8903cdbd52035..ee0544ad705943fad35c310659f32915af27e8da 100644 (file)
--- a/src/gromacs/gmxana/gmx_density.c
+++ b/src/gromacs/gmxana/gmx_density.c
@@ -57,7 +57,7 @@
 #include "index.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "gmx_ana.h"
 #include "macros.h"
 

diff --git a/src/gromacs/gmxana/gmx_densorder.cpp b/src/gromacs/gmxana/gmx_densorder.cpp
index 4f79306923bc90c210c919b8054a8f1a8c800447..6cb0300791f4620aabff2dfee6000bcce715f9fe 100644 (file)
--- a/src/gromacs/gmxana/gmx_densorder.cpp
+++ b/src/gromacs/gmxana/gmx_densorder.cpp
@@ -53,7 +53,7 @@
 #include "index.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "gromacs/fileio/matio.h"
 #include "dens_filter.h"
 #include "binsearch.h"

diff --git a/src/gromacs/gmxana/gmx_dipoles.cpp b/src/gromacs/gmxana/gmx_dipoles.cpp
index ab4b6639b87678a20fbe6df1e9baa3c325f61051..adf6fc44c6aab645f7320fa1da948d8fdab7f3bc 100644 (file)
--- a/src/gromacs/gmxana/gmx_dipoles.cpp
+++ b/src/gromacs/gmxana/gmx_dipoles.cpp
@@ -57,7 +57,7 @@
 #include "index.h"
 #include "gromacs/random/random.h"
 #include "names.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "calcmu.h"
 #include "gromacs/fileio/enxio.h"
 #include "gromacs/fileio/matio.h"

diff --git a/src/gromacs/gmxana/gmx_dos.c b/src/gromacs/gmxana/gmx_dos.c
index 8024057a7944906ed7d76b0f5fdc0f9a6fbbe1f1..104e42260db6039f4affae23361687ecb1c9d111 100644 (file)
--- a/src/gromacs/gmxana/gmx_dos.c
+++ b/src/gromacs/gmxana/gmx_dos.c
@@ -48,7 +48,7 @@
 #include "gstat.h"
 #include "macros.h"
 #include "gromacs/math/utilities.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "index.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/commandline/pargs.h"

diff --git a/src/gromacs/gmxana/gmx_dyndom.c b/src/gromacs/gmxana/gmx_dyndom.c
index 0bf46e5f32c1ebe646fd3506375f9a6d7dc63812..0ebab96ddc2144a09819f24dde41bae653f87321 100644 (file)
--- a/src/gromacs/gmxana/gmx_dyndom.c
+++ b/src/gromacs/gmxana/gmx_dyndom.c
@@ -45,7 +45,7 @@
 #include "gromacs/fileio/confio.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/math/vec.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "gmx_ana.h"
 #include "macros.h"
 #include "gromacs/fileio/trxio.h"

diff --git a/src/gromacs/gmxana/gmx_editconf.c b/src/gromacs/gmxana/gmx_editconf.c
index 2b3c5ab0c532f175b6e0c88969f980a936de6af1..a85bacf9dbf5741956ed93335d6ea8ef4662d02a 100644 (file)
--- a/src/gromacs/gmxana/gmx_editconf.c
+++ b/src/gromacs/gmxana/gmx_editconf.c
@@ -52,7 +52,7 @@
 #include "gromacs/math/vec.h"
 #include "typedefs.h"
 #include "gromacs/gmxlib/conformation-utilities.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "atomprop.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"

diff --git a/src/gromacs/gmxana/gmx_enemat.c b/src/gromacs/gmxana/gmx_enemat.c
index 5d94bd078c4cc3e1a90e8ae582f5b543aea71b04..2089b90bb8b4c15d9967304a3910d00680a72441 100644 (file)
--- a/src/gromacs/gmxana/gmx_enemat.c
+++ b/src/gromacs/gmxana/gmx_enemat.c
@@ -51,7 +51,7 @@
 #include "macros.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gstat.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/strdb.h"
 #include "gmx_ana.h"

diff --git a/src/gromacs/gmxana/gmx_energy.c b/src/gromacs/gmxana/gmx_energy.c
index c73c06b561effdc50ce01322b5ed3f240aec9c36..4d3c9a3713598bf0103633f18b3846b863465511 100644 (file)
--- a/src/gromacs/gmxana/gmx_energy.c
+++ b/src/gromacs/gmxana/gmx_energy.c
@@ -54,7 +54,7 @@
 #include "macros.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gstat.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "viewit.h"

diff --git a/src/gromacs/gmxana/gmx_hbond.c b/src/gromacs/gmxana/gmx_hbond.c
index 0a0b6d88e319a09d71873b067762eb38ad5d0c95..5e8d44e777949d78e478ef86655ec3867a9cda82 100644 (file)
--- a/src/gromacs/gmxana/gmx_hbond.c
+++ b/src/gromacs/gmxana/gmx_hbond.c
@@ -44,7 +44,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "copyrite.h"
 #include "txtdump.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "macros.h"
 #include "gromacs/utility/fatalerror.h"
 #include "index.h"

diff --git a/src/gromacs/gmxana/gmx_helix.c b/src/gromacs/gmxana/gmx_helix.c
index b72d04ea57d884a468aa8f777606fafd04f1b3fa..dc009e78268110d23b5563bca0dbde4846a564b4 100644 (file)
--- a/src/gromacs/gmxana/gmx_helix.c
+++ b/src/gromacs/gmxana/gmx_helix.c
@@ -52,7 +52,6 @@
 #include "pbc.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "physics.h"
 #include "index.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/commandline/pargs.h"

diff --git a/src/gromacs/gmxana/gmx_nmeig.c b/src/gromacs/gmxana/gmx_nmeig.c
index c936ee4b0a1c63baeb2536da5560eb341191d73b..ee63c63004ad1a7ddc5c6c49987606cd7969d464 100644 (file)
--- a/src/gromacs/gmxana/gmx_nmeig.c
+++ b/src/gromacs/gmxana/gmx_nmeig.c
@@ -52,7 +52,7 @@
 #include "txtdump.h"
 #include "eigio.h"
 #include "mtop_util.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "gmx_ana.h"
 
 #include "gromacs/commandline/pargs.h"

diff --git a/src/gromacs/gmxana/gmx_nmens.c b/src/gromacs/gmxana/gmx_nmens.c
index d8859cc635420c266853b5287dc03d5eda61cab5..4ddf1300ca0ef69c802fa00ecec7dc67b1526157 100644 (file)
--- a/src/gromacs/gmxana/gmx_nmens.c
+++ b/src/gromacs/gmxana/gmx_nmens.c
@@ -53,7 +53,7 @@
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "txtdump.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "gromacs/random/random.h"
 #include "eigio.h"
 #include "gmx_ana.h"

diff --git a/src/gromacs/gmxana/gmx_nmtraj.c b/src/gromacs/gmxana/gmx_nmtraj.c
index dd972a025126a0e61ead44dad8e42f1168dbc469..b5edf8b564af9219d0dc9890761d08f30416c149 100644 (file)
--- a/src/gromacs/gmxana/gmx_nmtraj.c
+++ b/src/gromacs/gmxana/gmx_nmtraj.c
@@ -54,7 +54,7 @@
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "txtdump.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "eigio.h"
 #include "gmx_ana.h"
 

diff --git a/src/gromacs/gmxana/gmx_pme_error.cpp b/src/gromacs/gmxana/gmx_pme_error.cpp
index f67f4f9ddd3f156d42949980983dffd9dd73b7b9..b0c5e9c10478f02162842a4bee316ed1361941f8 100644 (file)
--- a/src/gromacs/gmxana/gmx_pme_error.cpp
+++ b/src/gromacs/gmxana/gmx_pme_error.cpp
@@ -46,7 +46,7 @@
 #include "checkpoint.h"
 #include "gmx_ana.h"
 #include "gromacs/random/random.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "mdatoms.h"
 #include "coulomb.h"
 #include "mtop_util.h"

diff --git a/src/gromacs/gmxana/gmx_polystat.c b/src/gromacs/gmxana/gmx_polystat.c
index afbcf2353da4a86b52285415b18cf01193a21bf3..f219ff9c43e5624c517b5bd9456fc2ae630c45ae 100644 (file)
--- a/src/gromacs/gmxana/gmx_polystat.c
+++ b/src/gromacs/gmxana/gmx_polystat.c
@@ -41,7 +41,6 @@
 #include <math.h>
 #include <string.h>
 
-#include "physics.h"
 #include "typedefs.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/futil.h"

diff --git a/src/gromacs/gmxana/gmx_rama.c b/src/gromacs/gmxana/gmx_rama.c
index eed418d1f8185cb01a93f62ccf48bce1c768c5f2..b3b2f9e8899c4dca4ddeb1f144322289ebb65799 100644 (file)
--- a/src/gromacs/gmxana/gmx_rama.c
+++ b/src/gromacs/gmxana/gmx_rama.c
@@ -47,7 +47,7 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/fileio/xvgr.h"
 #include "viewit.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "pbc.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/commandline/pargs.h"

diff --git a/src/gromacs/gmxana/gmx_rdf.c b/src/gromacs/gmxana/gmx_rdf.c
index c705891eaef03fd836d2ab972e0565b7dd1d52b8..02ec0ae7d0594fffd2eda020ae567eb35a81f1b3 100644 (file)
--- a/src/gromacs/gmxana/gmx_rdf.c
+++ b/src/gromacs/gmxana/gmx_rdf.c
@@ -51,7 +51,6 @@
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "physics.h"
 #include "index.h"
 #include "gromacs/utility/smalloc.h"
 #include "calcgrid.h"

diff --git a/src/gromacs/gmxana/gmx_rotacf.c b/src/gromacs/gmxana/gmx_rotacf.c
index 147122ddd4ec4f5847ea67f48dd8641ebab3b1bf..50b83595231347a24f7f4bf30ab585dc10aae836 100644 (file)
--- a/src/gromacs/gmxana/gmx_rotacf.c
+++ b/src/gromacs/gmxana/gmx_rotacf.c
@@ -41,7 +41,6 @@
 #include <math.h>
 #include <string.h>
 
-#include "physics.h"
 #include "typedefs.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/futil.h"

diff --git a/src/gromacs/gmxana/gmx_saxs.c b/src/gromacs/gmxana/gmx_saxs.c
index 103f299e29f235901aae35e15663f315a9f930cc..300dbf01361f2c744a912f3aee6abd05fe241b5b 100644 (file)
--- a/src/gromacs/gmxana/gmx_saxs.c
+++ b/src/gromacs/gmxana/gmx_saxs.c
@@ -49,7 +49,6 @@
 #include "gromacs/utility/futil.h"
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/tpxio.h"
-#include "physics.h"
 #include "index.h"
 #include "gromacs/utility/smalloc.h"
 #include "calcgrid.h"

diff --git a/src/gromacs/gmxana/gmx_sham.c b/src/gromacs/gmxana/gmx_sham.c
index 2cf340f10bb2d05aa156e24e637119253f6c98a3..c0193996177ecd719a22ba06fedce0b7cd0bdfc7 100644 (file)
--- a/src/gromacs/gmxana/gmx_sham.c
+++ b/src/gromacs/gmxana/gmx_sham.c
@@ -53,7 +53,7 @@
 #include "txtdump.h"
 #include "gstat.h"
 #include "gromacs/fileio/xvgr.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/matio.h"
 #include "gmx_ana.h"

diff --git a/src/gromacs/gmxana/gmx_sigeps.c b/src/gromacs/gmxana/gmx_sigeps.c
index 6241c25dc8b3c349d6cb5c634ba1c0a07e91eb30..cd97f28714283669908c4179628c607c6e03b6b0 100644 (file)
--- a/src/gromacs/gmxana/gmx_sigeps.c
+++ b/src/gromacs/gmxana/gmx_sigeps.c
@@ -50,7 +50,7 @@
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/math/vec.h"
 #include "pbc.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "names.h"
 #include "txtdump.h"
 #include "gromacs/fileio/trnio.h"

diff --git a/src/gromacs/gmxana/gmx_spol.c b/src/gromacs/gmxana/gmx_spol.c
index 280b19e715e502d5a23fe739207dd826f470e52d..edc791fa9333914cfe15f6b5864f0ade8ca3263d 100644 (file)
--- a/src/gromacs/gmxana/gmx_spol.c
+++ b/src/gromacs/gmxana/gmx_spol.c
@@ -49,7 +49,7 @@
 #include "index.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "gmx_ana.h"
 
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/gmxana/gmx_tcaf.c b/src/gromacs/gmxana/gmx_tcaf.c
index a7dfc8edba6db9b3c294829775ee89d07ce268bb..c3427883c8d90fe26364a57f8216b60f65f520c7 100644 (file)
--- a/src/gromacs/gmxana/gmx_tcaf.c
+++ b/src/gromacs/gmxana/gmx_tcaf.c
@@ -48,7 +48,7 @@
 #include "gstat.h"
 #include "macros.h"
 #include "gromacs/math/utilities.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "index.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/commandline/pargs.h"

diff --git a/src/gromacs/gmxana/gmx_traj.c b/src/gromacs/gmxana/gmx_traj.c
index 92d6e85a0275fb3e28dff77307427a94e4b023f1..66a2800d0835f87939506c55957a75a20d5b7911 100644 (file)
--- a/src/gromacs/gmxana/gmx_traj.c
+++ b/src/gromacs/gmxana/gmx_traj.c
@@ -56,7 +56,7 @@
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "rmpbc.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "gromacs/fileio/confio.h"
 #include "gmx_ana.h"
 

diff --git a/src/gromacs/gmxana/gmx_velacc.c b/src/gromacs/gmxana/gmx_velacc.c
index d951c01086bc2af4f158067a406b5e1e9906969c..1a86e56b282c91dc37a0ea815b5e324d4dc2a905 100644 (file)
--- a/src/gromacs/gmxana/gmx_velacc.c
+++ b/src/gromacs/gmxana/gmx_velacc.c
@@ -48,7 +48,7 @@
 #include "gstat.h"
 #include "macros.h"
 #include "gromacs/math/utilities.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "index.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/commandline/pargs.h"

diff --git a/src/gromacs/gmxana/gmx_wheel.c b/src/gromacs/gmxana/gmx_wheel.c
index cf7477c18b4b828f775a424ee5136a016a7bfb3f..05e63a7c236b6a2fa1517017be5a4db069691473 100644 (file)
--- a/src/gromacs/gmxana/gmx_wheel.c
+++ b/src/gromacs/gmxana/gmx_wheel.c
@@ -43,7 +43,6 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "physics.h"
 #include "typedefs.h"
 #include "gromacs/utility/smalloc.h"
 #include "macros.h"

diff --git a/src/gromacs/gmxana/hxprops.c b/src/gromacs/gmxana/hxprops.c
index 6187738528a236f5ece5a1b64f2fca6146ed8aea..5a999cec6655af0c7cac25bfd6a7590f65be86dc 100644 (file)
--- a/src/gromacs/gmxana/hxprops.c
+++ b/src/gromacs/gmxana/hxprops.c
@@ -43,7 +43,7 @@
 
 #include "typedefs.h"
 #include "macros.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "index.h"
 #include "hxprops.h"

diff --git a/src/gromacs/gmxana/pp2shift.c b/src/gromacs/gmxana/pp2shift.c
index fea240e9e351cb2eb1554b212dcbec6600cf04c6..e95d80b2b7e24f86250c2b1200c39b69ca3fde73 100644 (file)
--- a/src/gromacs/gmxana/pp2shift.c
+++ b/src/gromacs/gmxana/pp2shift.c
@@ -43,7 +43,7 @@
 #include "typedefs.h"
 #include "gromacs/utility/futil.h"
 #include "macros.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "gromacs/utility/smalloc.h"
 #include "gstat.h"
 #include "gromacs/fileio/matio.h"

diff --git a/src/gromacs/gmxlib/CMakeLists.txt b/src/gromacs/gmxlib/CMakeLists.txt
index 204fb6a66adccf61ed32968b86d25dd871b14860..c84bbcfcfc9f141da1497d3216f87183df490ed7 100644 (file)
--- a/src/gromacs/gmxlib/CMakeLists.txt
+++ b/src/gromacs/gmxlib/CMakeLists.txt
@@ -40,16 +40,11 @@ add_subdirectory(nonbonded)
 # conditionally built, so we cannot use a GLOB_RECURSE here.
 file(GLOB GMXLIB_SOURCES *.c *.cpp)
 
-# Files called xxx_test.c are test drivers with a main() function for module xxx.c,
-# 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})
-
 # gpu utils + cuda tools module
 if(GMX_GPU)
     # The log file output queries Cuda if GPU support is enabled
     add_subdirectory(cuda_tools)
-    add_subdirectory(gpu_utils)   
+    add_subdirectory(gpu_utils)
     set(GMX_GPU_LIBRARIES ${GMX_GPU_LIBRARIES} gpu_utils cuda_tools PARENT_SCOPE)
 endif()
 

diff --git a/src/gromacs/gmxlib/bondfree.c b/src/gromacs/gmxlib/bondfree.c
index 538ee5c5fed5c69c0b2c0ebabd0a4e72afbd9720..e4c0148ffbcb47f6f2ea6d413ad823e22d88c3a6 100644 (file)
--- a/src/gromacs/gmxlib/bondfree.c
+++ b/src/gromacs/gmxlib/bondfree.c
@@ -40,7 +40,7 @@
 
 #include <math.h>
 #include <assert.h>
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/math/utilities.h"
 #include "txtdump.h"

diff --git a/src/gromacs/gmxlib/calch.c b/src/gromacs/gmxlib/calch.c
index f7ac04760a54a3495522131d0b9cadc919cec26e..903fa888e3af0266d916721b3813f9b2800baab8 100644 (file)
--- a/src/gromacs/gmxlib/calch.c
+++ b/src/gromacs/gmxlib/calch.c
@@ -42,7 +42,7 @@
 #include "calch.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 
 #include "gromacs/utility/fatalerror.h"
 

diff --git a/src/gromacs/gmxlib/ewald_util.c b/src/gromacs/gmxlib/ewald_util.c
index 013c2f914739fed6aa0c509bd867d9d0e67f5c7a..b1e0223b0b1955f5105a7f666296fe663fec432f 100644 (file)
--- a/src/gromacs/gmxlib/ewald_util.c
+++ b/src/gromacs/gmxlib/ewald_util.c
@@ -46,7 +46,7 @@
 #include "gromacs/math/vec.h"
 #include "coulomb.h"
 #include "gromacs/utility/smalloc.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "txtdump.h"
 #include "gromacs/utility/futil.h"
 #include "names.h"

diff --git a/src/gromacs/gmxlib/nonbonded/nonbonded.c b/src/gromacs/gmxlib/nonbonded/nonbonded.c
index be1c17b36eae03a123f2c92853349a1cc1a2354e..2afb92f62f51084a8c95d1724bf3918065a94ce6 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nonbonded.c
+++ b/src/gromacs/gmxlib/nonbonded/nonbonded.c
@@ -54,7 +54,6 @@
 #include "force.h"
 #include "names.h"
 #include "gromacs/utility/fatalerror.h"
-#include "physics.h"
 #include "force.h"
 #include "bondf.h"
 #include "nrnb.h"

diff --git a/src/gromacs/gmxlib/physics_test.c b/src/gromacs/gmxlib/physics_test.c
deleted file mode 100644 (file)
index 7382cd2..0000000
--- a/src/gromacs/gmxlib/physics_test.c
+++ /dev/null
@@ -1,51 +0,0 @@
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2010, 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.
- */
-#include <stdio.h>
-#include "physics.h"
-
-int main(int argc, char *argv[])
-{
-    int    i;
-    double x, y, z;
-
-    x = 3.25;
-    for (i = 0; (i < eg2cNR); i++)
-    {
-        y = gmx2convert(x, i);
-        z = convert2gmx(y, i);
-        printf("Converted %g [type %d] to %g and back to %g. Diff %g\n",
-               x, i, y, z, x-z);
-    }
-}

diff --git a/src/gromacs/gmxlib/restcbt.c b/src/gromacs/gmxlib/restcbt.c
index 1309959efefc7cdce2c43a06208cf0c23ae704bb..7db21850b7bb2600e5dd070bbed0d346dbfb0bc9 100644 (file)
--- a/src/gromacs/gmxlib/restcbt.c
+++ b/src/gromacs/gmxlib/restcbt.c
@@ -37,7 +37,7 @@
 
 #include <math.h>
 #include <assert.h>
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/math/utilities.h"
 #include "txtdump.h"

diff --git a/src/gromacs/gmxpreprocess/calc_verletbuf.c b/src/gromacs/gmxpreprocess/calc_verletbuf.c
index 0a668def8ce0003950ad91580b73a39f87c7a05d..5e4349e6e1a0bed2cef11007b4d0c6743745a6a0 100644 (file)
--- a/src/gromacs/gmxpreprocess/calc_verletbuf.c
+++ b/src/gromacs/gmxpreprocess/calc_verletbuf.c
@@ -43,7 +43,7 @@
 #include <sys/types.h>
 
 #include "typedefs.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "macros.h"
 #include "gromacs/math/vec.h"
 #include "coulomb.h"

diff --git a/src/gromacs/gmxpreprocess/convparm.c b/src/gromacs/gmxpreprocess/convparm.c
index 0758399822f3e6d3a8af39f4e98f0ad22ce544d3..2e6c43636bb743db9b08c9e8f9a3b0dddf82b9cf 100644 (file)
--- a/src/gromacs/gmxpreprocess/convparm.c
+++ b/src/gromacs/gmxpreprocess/convparm.c
@@ -42,7 +42,7 @@
 #include <math.h>
 #include <string.h>
 
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/utility/smalloc.h"
 #include "typedefs.h"

diff --git a/src/gromacs/gmxpreprocess/gen_maxwell_velocities.c b/src/gromacs/gmxpreprocess/gen_maxwell_velocities.c
index 069402ca657c51534f38bcba9e6f4b075ca229ea..3e5f7ecd357b059c5dc51723cbd8f3a14ebe666a 100644 (file)
--- a/src/gromacs/gmxpreprocess/gen_maxwell_velocities.c
+++ b/src/gromacs/gmxpreprocess/gen_maxwell_velocities.c
@@ -41,7 +41,7 @@
 #include <math.h>
 #include "gromacs/random/random.h"
 #include "gromacs/utility/smalloc.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "typedefs.h"
 #include "gromacs/math/vec.h"
 #include "gen_maxwell_velocities.h"

diff --git a/src/gromacs/gmxpreprocess/gen_vsite.c b/src/gromacs/gmxpreprocess/gen_vsite.c
index 26704fa3d285b8ae250a751fd842b9a2eee9fe77..6de806c8bde1b107f9a00a2faf2b31be62f30873 100644 (file)
--- a/src/gromacs/gmxpreprocess/gen_vsite.c
+++ b/src/gromacs/gmxpreprocess/gen_vsite.c
@@ -48,7 +48,7 @@
 #include "add_par.h"
 #include "gromacs/math/vec.h"
 #include "toputil.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "index.h"
 #include "names.h"
 #include "gromacs/utility/futil.h"

diff --git a/src/gromacs/gmxpreprocess/genhydro.c b/src/gromacs/gmxpreprocess/genhydro.c
index 34ff0fc82a404e0213b94d7e66407b3e809f73ec..81f5613b5460d7dd8455d7b8d0d65069133aa976 100644 (file)
--- a/src/gromacs/gmxpreprocess/genhydro.c
+++ b/src/gromacs/gmxpreprocess/genhydro.c
@@ -48,7 +48,6 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/utility/fatalerror.h"
-#include "physics.h"
 #include "calch.h"
 #include "genhydro.h"
 #include "h_db.h"

diff --git a/src/gromacs/gmxpreprocess/hizzie.c b/src/gromacs/gmxpreprocess/hizzie.c
index eb588fefa88ec6d2a7b141a08656933eb1e46d67..f623c842a8ad444a15fb0d6ccca6989ebc4b6a02 100644 (file)
--- a/src/gromacs/gmxpreprocess/hizzie.c
+++ b/src/gromacs/gmxpreprocess/hizzie.c
@@ -45,7 +45,7 @@
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/math/vec.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "toputil.h"
 #include "pdb2top.h"
 #include "gromacs/utility/cstringutil.h"

diff --git a/src/gromacs/gmxpreprocess/nm2type.c b/src/gromacs/gmxpreprocess/nm2type.c
index a382ec7b2a5c0c0706da02b7fd9f7dbedfed84ca..7f1f21a797cb20e593674b9d254a7ae321e0eb22 100644 (file)
--- a/src/gromacs/gmxpreprocess/nm2type.c
+++ b/src/gromacs/gmxpreprocess/nm2type.c
@@ -47,7 +47,6 @@
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/confio.h"
-#include "physics.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/math/3dview.h"
 #include "txtdump.h"

diff --git a/src/gromacs/gmxpreprocess/pdb2gmx.c b/src/gromacs/gmxpreprocess/pdb2gmx.c
index d0897d07ccb59a40da5531a3607e79e9cf295ee7..caaeaea118fd63ee185b87dfe82ea38a585a3903 100644 (file)
--- a/src/gromacs/gmxpreprocess/pdb2gmx.c
+++ b/src/gromacs/gmxpreprocess/pdb2gmx.c
@@ -59,7 +59,6 @@
 #include "gromacs/fileio/pdbio.h"
 #include "toputil.h"
 #include "h_db.h"
-#include "physics.h"
 #include "pgutil.h"
 #include "calch.h"
 #include "resall.h"

diff --git a/src/gromacs/gmxpreprocess/pdb2top.cpp b/src/gromacs/gmxpreprocess/pdb2top.cpp
index 50d2a7856e34528d0eebbc7923b9c7f28a374935..fd4fee0cd11f18bbe0c5529276ff1d8f7d21f98e 100644 (file)
--- a/src/gromacs/gmxpreprocess/pdb2top.cpp
+++ b/src/gromacs/gmxpreprocess/pdb2top.cpp
@@ -57,7 +57,6 @@
 #include "resall.h"
 #include "topio.h"
 #include "gromacs/utility/cstringutil.h"
-#include "physics.h"
 #include "gromacs/fileio/pdbio.h"
 #include "gen_ad.h"
 #include "gromacs/fileio/filenm.h"

diff --git a/src/gromacs/gmxpreprocess/readir.c b/src/gromacs/gmxpreprocess/readir.c
index 8b1b8c823829f72d1a1facb7a344f7d85ee9ddcb..4b5de76c9741f9b783c0e23a709c00045f03fdae 100644 (file)
--- a/src/gromacs/gmxpreprocess/readir.c
+++ b/src/gromacs/gmxpreprocess/readir.c
@@ -43,7 +43,7 @@
 #include <limits.h>
 #include "gromacs/utility/smalloc.h"
 #include "typedefs.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "names.h"
 #include "gromacs/utility/fatalerror.h"
 #include "macros.h"

diff --git a/src/gromacs/gmxpreprocess/topio.c b/src/gromacs/gmxpreprocess/topio.c
index fd7d2e50e2e1a2c9b63c414961f4e5ac99ac238d..40dfb57220e6620423c372d778cd0677c600c1e6 100644 (file)
--- a/src/gromacs/gmxpreprocess/topio.c
+++ b/src/gromacs/gmxpreprocess/topio.c
@@ -54,7 +54,7 @@
 #include "macros.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "txtdump.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "macros.h"
 #include "names.h"
 #include "gromacs/utility/cstringutil.h"

diff --git a/src/gromacs/gmxpreprocess/topshake.c b/src/gromacs/gmxpreprocess/topshake.c
index b19f76e45fe7204c310e12dc1e7951eaa3523d84..459f011efbb7cc57ab1f77942f10a2a2d16d0d22 100644 (file)
--- a/src/gromacs/gmxpreprocess/topshake.c
+++ b/src/gromacs/gmxpreprocess/topshake.c
@@ -42,7 +42,7 @@
 #include <ctype.h>
 #include <math.h>
 
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "readir.h"
 #include "typedefs.h"
 #include "topshake.h"

diff --git a/src/gromacs/gmxpreprocess/vsite_parm.c b/src/gromacs/gmxpreprocess/vsite_parm.c
index 774bfa0ae87a0ea0ffe76b3d17792ca4f17ddabe..773266ae92c27676385bac16a503490cfe0d0acb 100644 (file)
--- a/src/gromacs/gmxpreprocess/vsite_parm.c
+++ b/src/gromacs/gmxpreprocess/vsite_parm.c
@@ -38,22 +38,22 @@
 #include <config.h>
 #endif
 
-#include <stdio.h>
-#include <math.h>
 #include <assert.h>
+#include <math.h>
+#include <stdio.h>
 #include <string.h>
+
 #include "vsite_parm.h"
 #include "gromacs/utility/smalloc.h"
 #include "resall.h"
 #include "add_par.h"
 #include "gromacs/math/vec.h"
 #include "toputil.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "index.h"
 #include "names.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/cstringutil.h"
-#include "physics.h"
 #include "macros.h"
 
 typedef struct {

diff --git a/src/gromacs/gmxpreprocess/x2top.c b/src/gromacs/gmxpreprocess/x2top.c
index 74014311d4735caa662bd95a49db18516e494057..523510e4d9e4857583b6d09a0cb0984edbf77a8a 100644 (file)
--- a/src/gromacs/gmxpreprocess/x2top.c
+++ b/src/gromacs/gmxpreprocess/x2top.c
@@ -48,7 +48,7 @@
 #include "bondf.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/confio.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "txtdump.h"
 #include "readinp.h"
 #include "names.h"

diff --git a/src/gromacs/math/3dview.c b/src/gromacs/math/3dview.c
index add531074b6a16ad09b9a31d386bf31f0e3e87fe..c2d0aaca301fd560b8f674688867bec7d57230b1 100644 (file)
--- a/src/gromacs/math/3dview.c
+++ b/src/gromacs/math/3dview.c
@@ -43,7 +43,7 @@
 #include <math.h>
 #include "gromacs/utility/smalloc.h"
 #include "macros.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "pbc.h"
 #include "gromacs/math/vec.h"
 

diff --git a/src/gromacs/math/CMakeLists.txt b/src/gromacs/math/CMakeLists.txt
index 1185590953a0cf9deac94b6147268b39fa390851..ce5ab1e7eb17bf9cae43008a88f348fc90a06cbb 100644 (file)
--- a/src/gromacs/math/CMakeLists.txt
+++ b/src/gromacs/math/CMakeLists.txt
@@ -39,6 +39,7 @@ set(MATH_PUBLIC_HEADERS
     3dview.h
     gmxcomplex.h
     do_fit.h
+    units.h
     utilities.h
     vec.h
     vectypes.h

diff --git a/src/gromacs/gmxlib/physics.c b/src/gromacs/math/units.c
similarity index 94%
rename from src/gromacs/gmxlib/physics.c
rename to src/gromacs/math/units.c
index 529eee86d96248c8dd9a97ef8dfc7673ad909f19..17ef79c28623a9fc76a8ab60f0535e17a446feca 100644 (file)
--- a/src/gromacs/gmxlib/physics.c
+++ b/src/gromacs/math/units.c
@@ -1,9 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2011,2014, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2014, 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.
@@ -34,9 +32,11 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
+#include "units.h"
+
 #include <stdio.h>
+
 #include "gromacs/utility/cstringutil.h"
-#include "physics.h"
 
 double convert2gmx(double x, int unit)
 {

diff --git a/src/gromacs/legacyheaders/physics.h b/src/gromacs/math/units.h
similarity index 98%
rename from src/gromacs/legacyheaders/physics.h
rename to src/gromacs/math/units.h
index 6134f954b5d0faa87c8338356343e59ef7cfe2f5..4859f52e377973711f1df52bd33a891762b2a3fd 100644 (file)
--- a/src/gromacs/legacyheaders/physics.h
+++ b/src/gromacs/math/units.h
@@ -34,9 +34,8 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
-
-#ifndef _physics_h
-#define _physics_h
+#ifndef GMX_MATH_UNITS_H
+#define GMX_MATH_UNITS_H
 
 /*
  * Physical constants to be used in Gromacs.
@@ -44,7 +43,7 @@
  * be anywhere else in the code.
  */
 
-#include "../math/utilities.h"
+#include "utilities.h"
 
 #ifdef __cplusplus
 extern "C" {
@@ -156,5 +155,4 @@ extern const char *unit2string(int unit);
 }
 #endif
 
-
-#endif  /* _physics_h */
+#endif

diff --git a/src/gromacs/math/vec.h b/src/gromacs/math/vec.h
index eb051e1b7783f8b1138b0df782e3c9d2fca7198a..8c748c73839b197839372ed41dde324908d90362 100644 (file)
--- a/src/gromacs/math/vec.h
+++ b/src/gromacs/math/vec.h
@@ -115,8 +115,7 @@
 
 #include <math.h>
 
-#include "../legacyheaders/physics.h"
-
+#include "units.h"
 #include "utilities.h"
 #include "vectypes.h"
 

diff --git a/src/gromacs/mdlib/calcmu.c b/src/gromacs/mdlib/calcmu.c
index c35a0e9529a33c514d1a70b5a594d0380910e505..870a96d2702b1ddbac6cd49244c600d9d250d559 100644 (file)
--- a/src/gromacs/mdlib/calcmu.c
+++ b/src/gromacs/mdlib/calcmu.c
@@ -45,7 +45,7 @@
 #include "typedefs.h"
 #include "network.h"
 #include "gromacs/math/vec.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "calcmu.h"
 #include "gmx_omp_nthreads.h"
 

diff --git a/src/gromacs/mdlib/clincs.c b/src/gromacs/mdlib/clincs.c
index 7dc2df842246d6f2b7a020794a161cbc62f28fa8..140bcb2b71e261b741d13200ad51a510688b1c6a 100644 (file)
--- a/src/gromacs/mdlib/clincs.c
+++ b/src/gromacs/mdlib/clincs.c
@@ -45,7 +45,7 @@
 #include "types/commrec.h"
 #include "constr.h"
 #include "copyrite.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "pbc.h"
 #include "mdrun.h"

diff --git a/src/gromacs/mdlib/constr.c b/src/gromacs/mdlib/constr.c
index 4cc9d4982bf4e2ee39f1552ebb2fb2a9b4d298d4..f46f3adae0835375d950e4724c2892aa4dafadb9 100644 (file)
--- a/src/gromacs/mdlib/constr.c
+++ b/src/gromacs/mdlib/constr.c
@@ -49,7 +49,6 @@
 #include "nrnb.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/math/vec.h"
-#include "physics.h"
 #include "names.h"
 #include "txtdump.h"
 #include "domdec.h"

diff --git a/src/gromacs/mdlib/coupling.c b/src/gromacs/mdlib/coupling.c
index bfc6d636b9f5a18fb1f5191546d0a4820eca178d..fd8d11f05372e1f92724e8be257a6223bca25006 100644 (file)
--- a/src/gromacs/mdlib/coupling.c
+++ b/src/gromacs/mdlib/coupling.c
@@ -45,7 +45,7 @@
 #include "update.h"
 #include "gromacs/math/vec.h"
 #include "macros.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "names.h"
 #include "gromacs/utility/fatalerror.h"
 #include "txtdump.h"

diff --git a/src/gromacs/mdlib/domdec_setup.c b/src/gromacs/mdlib/domdec_setup.c
index df6bd8770f1fee3d24c1431cb8be03a6974eabf0..d8de6ee8d58b647f8a93c24d324450a63e31320a 100644 (file)
--- a/src/gromacs/mdlib/domdec_setup.c
+++ b/src/gromacs/mdlib/domdec_setup.c
@@ -43,7 +43,6 @@
 #include "types/commrec.h"
 #include "network.h"
 #include "perf_est.h"
-#include "physics.h"
 #include "gromacs/utility/smalloc.h"
 #include "typedefs.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/mdlib/ebin.c b/src/gromacs/mdlib/ebin.c
index 7541827eeb5f56315adb90c642be5e07ad764156..ddc6102c91c6d7a867f4a2e736f5db4835cd509e 100644 (file)
--- a/src/gromacs/mdlib/ebin.c
+++ b/src/gromacs/mdlib/ebin.c
@@ -47,7 +47,7 @@
 #include "ebin.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 
 t_ebin *mk_ebin(void)
 {

diff --git a/src/gromacs/mdlib/ewald.c b/src/gromacs/mdlib/ewald.c
index 9c065b28a9f67675b9295301506c1f2d286b0d9d..2134f4cc3bc30cc352054f3dce05d3e5651712e8 100644 (file)
--- a/src/gromacs/mdlib/ewald.c
+++ b/src/gromacs/mdlib/ewald.c
@@ -47,7 +47,7 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/fatalerror.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "coulomb.h"
 #include "macros.h"
 

diff --git a/src/gromacs/mdlib/expanded.c b/src/gromacs/mdlib/expanded.c
index 5d29f85ed9bf583ffa6e34c6d197f3422c72fef4..d28a3a5066a85df76dddd67ad2af2c854abf5ab8 100644 (file)
--- a/src/gromacs/mdlib/expanded.c
+++ b/src/gromacs/mdlib/expanded.c
@@ -50,7 +50,7 @@
 #include "mshift.h"
 #include "mdrun.h"
 #include "update.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "mdatoms.h"
 #include "force.h"
 #include "bondf.h"

diff --git a/src/gromacs/mdlib/force.c b/src/gromacs/mdlib/force.c
index 73a0f565f897899b0f38ddebd0332f6c079a34a2..4ea2208bc948dfa73c5c698c7b4fe976e2448037 100644 (file)
--- a/src/gromacs/mdlib/force.c
+++ b/src/gromacs/mdlib/force.c
@@ -44,8 +44,6 @@
 
 #include "typedefs.h"
 #include "macros.h"
-#include "macros.h"
-#include "physics.h"
 #include "force.h"
 #include "nonbonded.h"
 #include "names.h"

diff --git a/src/gromacs/mdlib/forcerec.c b/src/gromacs/mdlib/forcerec.c
index 2a5b7654e6276d844c7985f33dfd330d814a648f..e0a059bb0f553a797141383ff3f1ce370c9f7f19 100644 (file)
--- a/src/gromacs/mdlib/forcerec.c
+++ b/src/gromacs/mdlib/forcerec.c
@@ -49,7 +49,7 @@
 #include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "gromacs/utility/fatalerror.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "force.h"
 #include "tables.h"
 #include "nonbonded.h"

diff --git a/src/gromacs/mdlib/genborn.c b/src/gromacs/mdlib/genborn.c
index e29eb366f7bb0e77940ddbdd95dc7eb1e8db4155..5058d568ed0e9afb080d37eba9cdc87ba8a27725 100644 (file)
--- a/src/gromacs/mdlib/genborn.c
+++ b/src/gromacs/mdlib/genborn.c
@@ -49,7 +49,7 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/fileio/pdbio.h"
 #include "names.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "domdec.h"
 #include "network.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/mdlib/genborn_allvsall.c b/src/gromacs/mdlib/genborn_allvsall.c
index 0af757ffe0e50b7c375e0b4fadc81e6c7d7b572a..7b8cce51c20efb1ddcad087eaca59052576d5dc3 100644 (file)
--- a/src/gromacs/mdlib/genborn_allvsall.c
+++ b/src/gromacs/mdlib/genborn_allvsall.c
@@ -45,7 +45,7 @@
 #include "gromacs/utility/smalloc.h"
 
 #include "network.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "genborn.h"
 #include "genborn_allvsall.h"
 

diff --git a/src/gromacs/mdlib/genborn_allvsall_sse2_double.c b/src/gromacs/mdlib/genborn_allvsall_sse2_double.c
index 841869152e4736c15c01ec2f519e622b3f80cc3d..57e304f2d054b63880fbbb9adf3d36a7e30be008 100644 (file)
--- a/src/gromacs/mdlib/genborn_allvsall_sse2_double.c
+++ b/src/gromacs/mdlib/genborn_allvsall_sse2_double.c
@@ -45,7 +45,7 @@
 #include "gromacs/utility/smalloc.h"
 
 #include "network.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "genborn.h"
 #include "genborn_allvsall.h"
 

diff --git a/src/gromacs/mdlib/genborn_allvsall_sse2_single.c b/src/gromacs/mdlib/genborn_allvsall_sse2_single.c
index 3a01a9b3caf08e01c0b579c7e33099070e8ebe9f..374a0ffcc164b6aa47ea63e0f4c13f552cf87255 100644 (file)
--- a/src/gromacs/mdlib/genborn_allvsall_sse2_single.c
+++ b/src/gromacs/mdlib/genborn_allvsall_sse2_single.c
@@ -45,7 +45,7 @@
 #include "gromacs/utility/smalloc.h"
 
 #include "network.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "genborn.h"
 #include "genborn_allvsall.h"
 

diff --git a/src/gromacs/mdlib/genborn_sse2_double.c b/src/gromacs/mdlib/genborn_sse2_double.c
index a8f367598569c6129beb9daa1df89566a8c3d7bb..3e98b33881fc4272b1b25ac3b30ee6b3203bba9c 100644 (file)
--- a/src/gromacs/mdlib/genborn_sse2_double.c
+++ b/src/gromacs/mdlib/genborn_sse2_double.c
@@ -47,7 +47,7 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/fileio/pdbio.h"
 #include "names.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "domdec.h"
 #include "network.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/mdlib/genborn_sse2_single.c b/src/gromacs/mdlib/genborn_sse2_single.c
index 17aca7ee7c219e583c7387711a2700f809771018..f0cb36106e984cd8b675a2ab4e685f6c3f07f940 100644 (file)
--- a/src/gromacs/mdlib/genborn_sse2_single.c
+++ b/src/gromacs/mdlib/genborn_sse2_single.c
@@ -47,7 +47,7 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/fileio/pdbio.h"
 #include "names.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "domdec.h"
 #include "network.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/mdlib/mdebin.c b/src/gromacs/mdlib/mdebin.c
index f7cd4a32569480ba437d50192932c365ff6ebb57..52618279a587d4491406c484b733f516b25a370e 100644 (file)
--- a/src/gromacs/mdlib/mdebin.c
+++ b/src/gromacs/mdlib/mdebin.c
@@ -45,7 +45,7 @@
 #include "typedefs.h"
 #include "mdebin.h"
 #include "gromacs/utility/smalloc.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "gromacs/fileio/enxio.h"
 #include "gromacs/math/vec.h"
 #include "disre.h"

diff --git a/src/gromacs/mdlib/perf_est.c b/src/gromacs/mdlib/perf_est.c
index febdeb5d04233bc8783c9a8b4ef430aed211d8ad..d74148f047c7472aa51bce03a86b33143932d46a 100644 (file)
--- a/src/gromacs/mdlib/perf_est.c
+++ b/src/gromacs/mdlib/perf_est.c
@@ -41,7 +41,6 @@
 #include <math.h>
 
 #include "perf_est.h"
-#include "physics.h"
 #include "gromacs/math/vec.h"
 #include "mtop_util.h"
 #include "types/commrec.h"

diff --git a/src/gromacs/mdlib/pme.c b/src/gromacs/mdlib/pme.c
index 6c7f1b981a8ed72620aac0a27b0208520fb19864..aefee8dc936c5e22fac601238566af82871134c4 100644 (file)
--- a/src/gromacs/mdlib/pme.c
+++ b/src/gromacs/mdlib/pme.c
@@ -75,7 +75,7 @@
 #include "gromacs/utility/fatalerror.h"
 #include "pme.h"
 #include "network.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "nrnb.h"
 #include "macros.h"
 

diff --git a/src/gromacs/mdlib/qm_gamess.c b/src/gromacs/mdlib/qm_gamess.c
index de7bdf7adfd212f0ee3b53bc82b8259baf575b9e..23f03fb3c381d61b7f1dafca5eb13e4811a7688e 100644 (file)
--- a/src/gromacs/mdlib/qm_gamess.c
+++ b/src/gromacs/mdlib/qm_gamess.c
@@ -44,7 +44,7 @@
 #include "typedefs.h"
 #include "macros.h"
 #include "gromacs/utility/smalloc.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "macros.h"
 #include "gromacs/math/vec.h"
 #include "force.h"

diff --git a/src/gromacs/mdlib/qm_gaussian.c b/src/gromacs/mdlib/qm_gaussian.c
index f9259bf3facee8d550e99fd2a8016677cbe6da1d..3c77505b64b61bbfcda63a1844a06bcfd84a55fb 100644 (file)
--- a/src/gromacs/mdlib/qm_gaussian.c
+++ b/src/gromacs/mdlib/qm_gaussian.c
@@ -44,7 +44,7 @@
 #include "typedefs.h"
 #include "macros.h"
 #include "gromacs/utility/smalloc.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "macros.h"
 #include "gromacs/math/vec.h"
 #include "force.h"

diff --git a/src/gromacs/mdlib/qm_mopac.c b/src/gromacs/mdlib/qm_mopac.c
index 7abd61284010f9d82bd6d4e79fbcabebb85df3ce..d14f877ad62e80773357c3390d3c18e59bc408b4 100644 (file)
--- a/src/gromacs/mdlib/qm_mopac.c
+++ b/src/gromacs/mdlib/qm_mopac.c
@@ -44,7 +44,7 @@
 #include "typedefs.h"
 #include "macros.h"
 #include "gromacs/utility/smalloc.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "macros.h"
 #include "gromacs/math/vec.h"
 #include "force.h"

diff --git a/src/gromacs/mdlib/qm_orca.c b/src/gromacs/mdlib/qm_orca.c
index dd89a19ce435f3ad70b90c8bb617a25451218294..ab20a1e0d12f4d180586d75a4c7a836570651506 100644 (file)
--- a/src/gromacs/mdlib/qm_orca.c
+++ b/src/gromacs/mdlib/qm_orca.c
@@ -42,7 +42,7 @@
 #include "typedefs.h"
 #include "macros.h"
 #include "gromacs/utility/smalloc.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "macros.h"
 #include "gromacs/math/vec.h"
 #include "force.h"

diff --git a/src/gromacs/mdlib/qmmm.c b/src/gromacs/mdlib/qmmm.c
index 4e85721b9a91e9c56616b52b91799254d599307e..ed996265de49fc1034af9cf8fd2783df7ead4e05 100644 (file)
--- a/src/gromacs/mdlib/qmmm.c
+++ b/src/gromacs/mdlib/qmmm.c
@@ -43,7 +43,7 @@
 #include "types/commrec.h"
 #include "macros.h"
 #include "gromacs/utility/smalloc.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "macros.h"
 #include "gromacs/math/vec.h"
 #include "force.h"

diff --git a/src/gromacs/mdlib/rf_util.c b/src/gromacs/mdlib/rf_util.c
index a3e3eda0fc6c7b68a6b955df181e08129ea470af..6caeb816c0443c746f296f4fbe1e29207955b5d5 100644 (file)
--- a/src/gromacs/mdlib/rf_util.c
+++ b/src/gromacs/mdlib/rf_util.c
@@ -42,7 +42,7 @@
 #include "force.h"
 #include "names.h"
 #include "gromacs/math/vec.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "copyrite.h"
 #include "pbc.h"
 

diff --git a/src/gromacs/mdlib/shellfc.c b/src/gromacs/mdlib/shellfc.c
index 28e99822074f419cdebd1857679e15ac2ac8eceb..456f00cd5ecd530174d70835114103110ccc0e3c 100644 (file)
--- a/src/gromacs/mdlib/shellfc.c
+++ b/src/gromacs/mdlib/shellfc.c
@@ -55,7 +55,7 @@
 #include "names.h"
 #include "constr.h"
 #include "domdec.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "shellfc.h"
 #include "mtop_util.h"
 #include "chargegroup.h"

diff --git a/src/gromacs/mdlib/sim_util.c b/src/gromacs/mdlib/sim_util.c
index 5897b0d3cf8b9a73fb54f9cbd61261c7b9c639a3..a817c1df005965bd4b2fe918cbb9ef6431253290 100644 (file)
--- a/src/gromacs/mdlib/sim_util.c
+++ b/src/gromacs/mdlib/sim_util.c
@@ -59,7 +59,7 @@
 #include "mdrun.h"
 #include "sim_util.h"
 #include "update.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "mdatoms.h"
 #include "force.h"
 #include "bondf.h"

diff --git a/src/gromacs/mdlib/stat.c b/src/gromacs/mdlib/stat.c
index 8ea8058a97df9fb6b697314013d0dff924ed4231..272271e31f9e72c31b45426af5c353795d553761 100644 (file)
--- a/src/gromacs/mdlib/stat.c
+++ b/src/gromacs/mdlib/stat.c
@@ -46,7 +46,6 @@
 #include "network.h"
 #include "txtdump.h"
 #include "names.h"
-#include "physics.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/math/utilities.h"
 #include "force.h"

diff --git a/src/gromacs/mdlib/tables.c b/src/gromacs/mdlib/tables.c
index 6c96f379e4e042343bb0d01e0073e23182477d08..05fddc51179680b4a4024f66c0e8cbc8fec0fe78 100644 (file)
--- a/src/gromacs/mdlib/tables.c
+++ b/src/gromacs/mdlib/tables.c
@@ -48,7 +48,7 @@
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/math/vec.h"
 #include "network.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "force.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "macros.h"

diff --git a/src/gromacs/mdlib/tpi.c b/src/gromacs/mdlib/tpi.c
index 976dc02d4857be71fc743aa53fa0d156f0391a51..d6e4bd4593c7da9d90192145d3d3c939a4206586 100644 (file)
--- a/src/gromacs/mdlib/tpi.c
+++ b/src/gromacs/mdlib/tpi.c
@@ -63,7 +63,7 @@
 #include "mdrun.h"
 #include "domdec.h"
 #include "gromacs/random/random.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "gromacs/fileio/xvgr.h"
 #include "mdatoms.h"
 #include "ns.h"

diff --git a/src/gromacs/mdlib/update.c b/src/gromacs/mdlib/update.c
index dddca371c410142f5bbadc9455a729f0ecd6a2d2..238492db7a02aac990de876f5d2523e4364aa04d 100644 (file)
--- a/src/gromacs/mdlib/update.c
+++ b/src/gromacs/mdlib/update.c
@@ -46,7 +46,7 @@
 #include "gromacs/utility/smalloc.h"
 #include "typedefs.h"
 #include "nrnb.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "macros.h"
 #include "gromacs/math/vec.h"
 #include "update.h"

diff --git a/src/gromacs/selection/sm_insolidangle.cpp b/src/gromacs/selection/sm_insolidangle.cpp
index 38766c99ebb0d76107b81d1961ed211d8125dddf..8e8f4e0221a54fb8572bad18228f04cfb69fbb21 100644 (file)
--- a/src/gromacs/selection/sm_insolidangle.cpp
+++ b/src/gromacs/selection/sm_insolidangle.cpp
@@ -118,8 +118,8 @@
 
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/pbc.h"
-#include "gromacs/legacyheaders/physics.h"
 
+#include "gromacs/math/units.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/selection/indexutil.h"

diff --git a/src/gromacs/tools/check.c b/src/gromacs/tools/check.c
index 7857d1c7ba4b1876a3a47cc87ebe913a06d9e033..4a2e01f559a8fe3075807b2a716cf155b9aa0182 100644 (file)
--- a/src/gromacs/tools/check.c
+++ b/src/gromacs/tools/check.c
@@ -49,7 +49,7 @@
 #include "atomprop.h"
 #include "gromacs/math/vec.h"
 #include "pbc.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "index.h"
 #include "gromacs/utility/smalloc.h"
 #include "names.h"

diff --git a/src/gromacs/trajectoryanalysis/modules/sasa.cpp b/src/gromacs/trajectoryanalysis/modules/sasa.cpp
index e29d7a951daaf4fcb088c68f4476391ef222fa16..bcc3dc6bd8bfc681d646fd6302bbe91d6304c274 100644 (file)
--- a/src/gromacs/trajectoryanalysis/modules/sasa.cpp
+++ b/src/gromacs/trajectoryanalysis/modules/sasa.cpp
@@ -50,7 +50,6 @@
 #include "gromacs/legacyheaders/atomprop.h"
 #include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/pbc.h"
-#include "gromacs/legacyheaders/physics.h"
 #include "gromacs/legacyheaders/symtab.h"
 
 #include "gromacs/analysisdata/analysisdata.h"
@@ -58,6 +57,7 @@
 #include "gromacs/analysisdata/modules/plot.h"
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/pdbio.h"
+#include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/filenameoption.h"

diff --git a/src/programs/mdrun/md.c b/src/programs/mdrun/md.c
index 453a6ae16794f9a83b71fcd7e15d59a6e996f205..e92a32484d5845afe9cf7c1ff3d17526cd8a3856 100644 (file)
--- a/src/programs/mdrun/md.c
+++ b/src/programs/mdrun/md.c
@@ -55,7 +55,6 @@
 #include "md_support.h"
 #include "md_logging.h"
 #include "network.h"
-#include "physics.h"
 #include "names.h"
 #include "force.h"
 #include "disre.h"

diff --git a/src/programs/mdrun/membed.c b/src/programs/mdrun/membed.c
index 0ca22c6caf0febc18e0d62849947640af2e8331e..583ca4906b0d20026e87dfe5ddc6000a848f4406 100644 (file)
--- a/src/programs/mdrun/membed.c
+++ b/src/programs/mdrun/membed.c
@@ -46,7 +46,6 @@
 #include "gromacs/utility/futil.h"
 #include "gromacs/essentialdynamics/edsam.h"
 #include "index.h"
-#include "physics.h"
 #include "names.h"
 #include "mtop_util.h"
 #include "gromacs/fileio/tpxio.h"

diff --git a/src/programs/mdrun/repl_ex.c b/src/programs/mdrun/repl_ex.c
index 5815207ea6b3dfb598b28aeccde5d66e9ce7e46a..0777244ba08d060807f3258d45b51725d2ab66c8 100644 (file)
--- a/src/programs/mdrun/repl_ex.c
+++ b/src/programs/mdrun/repl_ex.c
@@ -43,7 +43,7 @@
 #include "network.h"
 #include "gromacs/random/random.h"
 #include "gromacs/utility/smalloc.h"
-#include "physics.h"
+#include "gromacs/math/units.h"
 #include "copyrite.h"
 #include "macros.h"
 #include "gromacs/math/vec.h"