Move readinp.* and warninp.* to fileio/

These are related to reading certain file formats, so they naturally fit
there.

Change-Id: Ie39f853be580d2d0cf7f2ffd989aaaf2b7c82eb0

diff --git a/src/gromacs/gmxlib/readinp.cpp b/src/gromacs/fileio/readinp.cpp
similarity index 99%
rename from src/gromacs/gmxlib/readinp.cpp
rename to src/gromacs/fileio/readinp.cpp
index b2ea077355d24778d3a330ba0a7f49112d9e4263..6a5f63f40ab3e82496a83d155032172dd5d9510f 100644 (file)
--- a/src/gromacs/gmxlib/readinp.cpp
+++ b/src/gromacs/fileio/readinp.cpp
@@ -45,7 +45,7 @@
 #include <algorithm>
 
 #include "gromacs/fileio/gmxfio.h"
-#include "gromacs/gmxlib/warninp.h"
+#include "gromacs/fileio/warninp.h"
 #include "gromacs/mdtypes/md_enums.h"
 #include "gromacs/utility/binaryinformation.h"
 #include "gromacs/utility/cstringutil.h"

diff --git a/src/gromacs/gmxlib/readinp.h b/src/gromacs/fileio/readinp.h
similarity index 98%
rename from src/gromacs/gmxlib/readinp.h
rename to src/gromacs/fileio/readinp.h
index dba47c5d8b3303cb3543db08bf693d24dbad33c7..ead2d0d3d69cecba83fbcaa3479ba1f2285b2b77 100644 (file)
--- a/src/gromacs/gmxlib/readinp.h
+++ b/src/gromacs/fileio/readinp.h
@@ -34,12 +34,12 @@
  * 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 GMX_GMXLIB_READINP_H
-#define GMX_GMXLIB_READINP_H
+#ifndef GMX_FILEIO_READINP_H
+#define GMX_FILEIO_READINP_H
 
 #include <cstring>
 
-#include "gromacs/gmxlib/warninp.h"
+#include "gromacs/fileio/warninp.h"
 #include "gromacs/utility/basedefinitions.h"
 
 typedef struct {

diff --git a/src/gromacs/gmxlib/warninp.cpp b/src/gromacs/fileio/warninp.cpp
similarity index 100%
rename from src/gromacs/gmxlib/warninp.cpp
rename to src/gromacs/fileio/warninp.cpp

diff --git a/src/gromacs/gmxlib/warninp.h b/src/gromacs/fileio/warninp.h
similarity index 98%
rename from src/gromacs/gmxlib/warninp.h
rename to src/gromacs/fileio/warninp.h
index cedf6c542a37e45ae4bd046af879757f9c3d7f5a..1324e4996c6f16b36b68b8a83bdb3341ef43d28b 100644 (file)
--- a/src/gromacs/gmxlib/warninp.h
+++ b/src/gromacs/fileio/warninp.h
@@ -34,8 +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 GMX_GMXLIB_WARNINP_H
-#define GMX_GMXLIB_WARNINP_H
+#ifndef GMX_FILEIO_WARNINP_H
+#define GMX_FILEIO_WARNINP_H
 
 #include "gromacs/utility/basedefinitions.h"
 

diff --git a/src/gromacs/gmxana/gmx_analyze.cpp b/src/gromacs/gmxana/gmx_analyze.cpp
index 3d5f518dcbcaca82e853eed4772288c57ca5a77e..44934f3b31efcb1860811c17096c7b289705cc6f 100644 (file)
--- a/src/gromacs/gmxana/gmx_analyze.cpp
+++ b/src/gromacs/gmxana/gmx_analyze.cpp
@@ -45,10 +45,10 @@
 #include "gromacs/correlationfunctions/autocorr.h"
 #include "gromacs/correlationfunctions/expfit.h"
 #include "gromacs/correlationfunctions/integrate.h"
+#include "gromacs/fileio/readinp.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/gmxana/gstat.h"
-#include "gromacs/gmxlib/readinp.h"
 #include "gromacs/linearalgebra/matrix.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/statistics/statistics.h"

diff --git a/src/gromacs/gmxana/gmx_make_edi.cpp b/src/gromacs/gmxana/gmx_make_edi.cpp
index f92fba58955cb39b938e9baad1ba1c1b1c073994..35a78cf4fe845637e09bc4adc46b72aee08e2a69 100644 (file)
--- a/src/gromacs/gmxana/gmx_make_edi.cpp
+++ b/src/gromacs/gmxana/gmx_make_edi.cpp
@@ -46,10 +46,10 @@
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/readinp.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/eigio.h"
 #include "gromacs/gmxana/gmx_ana.h"
-#include "gromacs/gmxlib/readinp.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/topology/index.h"
 #include "gromacs/topology/topology.h"

diff --git a/src/gromacs/gmxana/gmx_pme_error.cpp b/src/gromacs/gmxana/gmx_pme_error.cpp
index 00abb4ff9843a9679ec2d77532b1acb96d0afb98..58843980f73d652853347e80d13dea6219859290 100644 (file)
--- a/src/gromacs/gmxana/gmx_pme_error.cpp
+++ b/src/gromacs/gmxana/gmx_pme_error.cpp
@@ -42,12 +42,12 @@
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/checkpoint.h"
+#include "gromacs/fileio/readinp.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/gmxlib/calcgrid.h"
 #include "gromacs/gmxlib/main.h"
 #include "gromacs/gmxlib/network.h"
-#include "gromacs/gmxlib/readinp.h"
 #include "gromacs/math/calculate-ewald-splitting-coefficient.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/gmxana/gmx_sham.cpp b/src/gromacs/gmxana/gmx_sham.cpp
index 749a211888e76e4c4b826de35c56418a3a938290..c45c306062d92d6d09fa2702ef553dc01257dbd5 100644 (file)
--- a/src/gromacs/gmxana/gmx_sham.cpp
+++ b/src/gromacs/gmxana/gmx_sham.cpp
@@ -45,10 +45,10 @@
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/readinp.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/gmxana/gstat.h"
-#include "gromacs/gmxlib/readinp.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/topology/topology.h"

diff --git a/src/gromacs/gmxana/gmx_tune_pme.cpp b/src/gromacs/gmxana/gmx_tune_pme.cpp
index 01254eebe9f5e42c8eb13c07525f5fac4a48a04c..d2191da5f2abea8dd4e7e1f47768554d5c5effa2 100644 (file)
--- a/src/gromacs/gmxana/gmx_tune_pme.cpp
+++ b/src/gromacs/gmxana/gmx_tune_pme.cpp
@@ -49,10 +49,10 @@
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/checkpoint.h"
+#include "gromacs/fileio/readinp.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/gmxlib/calcgrid.h"
-#include "gromacs/gmxlib/readinp.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/perf_est.h"

diff --git a/src/gromacs/gmxana/gmx_xpm2ps.cpp b/src/gromacs/gmxana/gmx_xpm2ps.cpp
index 88eca7f2988fef47d766d72e4283afa7c50b0cbf..a1f5afb186543d8203df76bfb98634f51a2554b9 100644 (file)
--- a/src/gromacs/gmxana/gmx_xpm2ps.cpp
+++ b/src/gromacs/gmxana/gmx_xpm2ps.cpp
@@ -46,11 +46,11 @@
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/commandline/viewit.h"
 #include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/readinp.h"
 #include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/warninp.h"
 #include "gromacs/fileio/writeps.h"
 #include "gromacs/gmxana/gmx_ana.h"
-#include "gromacs/gmxlib/readinp.h"
-#include "gromacs/gmxlib/warninp.h"
 #include "gromacs/utility/arraysize.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/gmxpreprocess/genconf.cpp b/src/gromacs/gmxpreprocess/genconf.cpp
index a9bf81d310b55e249928c1b13e61606d968ef67c..c4e3ac6ab8dd7b55db7e61f1a221c5528e8d8998 100644 (file)
--- a/src/gromacs/gmxpreprocess/genconf.cpp
+++ b/src/gromacs/gmxpreprocess/genconf.cpp
@@ -40,8 +40,8 @@
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/readinp.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/gmxlib/readinp.h"
 #include "gromacs/math/3dtransforms.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/gmxpreprocess/grompp.cpp b/src/gromacs/gmxpreprocess/grompp.cpp
index a28192aa793bc6988780d9ea2eaef7af7df31ed3..bc73d0db5a21d190c761a2379c9be658e276fb9b 100644 (file)
--- a/src/gromacs/gmxpreprocess/grompp.cpp
+++ b/src/gromacs/gmxpreprocess/grompp.cpp
@@ -53,9 +53,9 @@
 #include "gromacs/fileio/enxio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/warninp.h"
 #include "gromacs/gmxlib/calcgrid.h"
 #include "gromacs/gmxlib/splitter.h"
-#include "gromacs/gmxlib/warninp.h"
 #include "gromacs/gmxpreprocess/add_par.h"
 #include "gromacs/gmxpreprocess/convparm.h"
 #include "gromacs/gmxpreprocess/gen_maxwell_velocities.h"

diff --git a/src/gromacs/gmxpreprocess/nm2type.cpp b/src/gromacs/gmxpreprocess/nm2type.cpp
index 3f14d74c55d3a6c434404d2724c47ce98c373581..9359354cfa0c89b22887c0e1693cc2d3e9fc1a42 100644 (file)
--- a/src/gromacs/gmxpreprocess/nm2type.cpp
+++ b/src/gromacs/gmxpreprocess/nm2type.cpp
@@ -44,7 +44,7 @@
 #include <algorithm>
 
 #include "gromacs/fileio/confio.h"
-#include "gromacs/gmxlib/readinp.h"
+#include "gromacs/fileio/readinp.h"
 #include "gromacs/gmxpreprocess/fflibutil.h"
 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
 #include "gromacs/gmxpreprocess/gpp_nextnb.h"

diff --git a/src/gromacs/gmxpreprocess/pdb2gmx.cpp b/src/gromacs/gmxpreprocess/pdb2gmx.cpp
index 95430eefba71368a7a46c6242f2bc8fb6ab80b0d..d8884265f5c8516022a122d282f108c2a6caa7dc 100644 (file)
--- a/src/gromacs/gmxpreprocess/pdb2gmx.cpp
+++ b/src/gromacs/gmxpreprocess/pdb2gmx.cpp
@@ -47,8 +47,8 @@
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/readinp.h"
 #include "gromacs/gmxlib/conformation-utilities.h"
-#include "gromacs/gmxlib/readinp.h"
 #include "gromacs/gmxpreprocess/fflibutil.h"
 #include "gromacs/gmxpreprocess/genhydro.h"
 #include "gromacs/gmxpreprocess/h_db.h"

diff --git a/src/gromacs/gmxpreprocess/readir.cpp b/src/gromacs/gmxpreprocess/readir.cpp
index 081eeaf9dc9a58e6fc40f6dd784de9f61dd81d4b..c7617d82695afb772b0914ff5d3bd8e8db641a81 100644 (file)
--- a/src/gromacs/gmxpreprocess/readir.cpp
+++ b/src/gromacs/gmxpreprocess/readir.cpp
@@ -46,10 +46,10 @@
 
 #include <algorithm>
 
+#include "gromacs/fileio/readinp.h"
+#include "gromacs/fileio/warninp.h"
 #include "gromacs/gmxlib/chargegroup.h"
 #include "gromacs/gmxlib/network.h"
-#include "gromacs/gmxlib/readinp.h"
-#include "gromacs/gmxlib/warninp.h"
 #include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/gmxpreprocess/readir.h b/src/gromacs/gmxpreprocess/readir.h
index 15a0b2ef11cd56cc7cec618783e39dcfa722a436..8052c08892663a24684c673e7d0e203bd0ed1623 100644 (file)
--- a/src/gromacs/gmxpreprocess/readir.h
+++ b/src/gromacs/gmxpreprocess/readir.h
@@ -38,7 +38,7 @@
 #ifndef GMX_GMXPREPROCESS_READIR_H
 #define GMX_GMXPREPROCESS_READIR_H
 
-#include "gromacs/gmxlib/readinp.h"
+#include "gromacs/fileio/readinp.h"
 #include "gromacs/gmxpreprocess/grompp-impl.h"
 
 struct gmx_groups_t;

diff --git a/src/gromacs/gmxpreprocess/readpull.cpp b/src/gromacs/gmxpreprocess/readpull.cpp
index f894debb7a1831590e744a46a3a1ec000afda262..2234a270c87010bf4f4338e1359e1f182acc9f26 100644 (file)
--- a/src/gromacs/gmxpreprocess/readpull.cpp
+++ b/src/gromacs/gmxpreprocess/readpull.cpp
@@ -39,7 +39,7 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/gmxlib/readinp.h"
+#include "gromacs/fileio/readinp.h"
 #include "gromacs/gmxpreprocess/readir.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/mdatoms.h"

diff --git a/src/gromacs/gmxpreprocess/topio.cpp b/src/gromacs/gmxpreprocess/topio.cpp
index 6aa7e98545260f2c27832e90eeda8f79451dc51a..ba8b4807c9fdedc816441c937e2bccff9a89cb78 100644 (file)
--- a/src/gromacs/gmxpreprocess/topio.cpp
+++ b/src/gromacs/gmxpreprocess/topio.cpp
@@ -49,7 +49,7 @@
 #include <sys/types.h>
 
 #include "gromacs/fileio/gmxfio.h"
-#include "gromacs/gmxlib/warninp.h"
+#include "gromacs/fileio/warninp.h"
 #include "gromacs/gmxpreprocess/gmxcpp.h"
 #include "gromacs/gmxpreprocess/gpp_bond_atomtype.h"
 #include "gromacs/gmxpreprocess/gpp_nextnb.h"

diff --git a/src/gromacs/gmxpreprocess/toppush.cpp b/src/gromacs/gmxpreprocess/toppush.cpp
index 18942f8b30fca0ef2edfcceb9143634d2f98cb23..6da0ff1d423d0c51e2cf26ec0c257c2c95df3b24 100644 (file)
--- a/src/gromacs/gmxpreprocess/toppush.cpp
+++ b/src/gromacs/gmxpreprocess/toppush.cpp
@@ -45,7 +45,7 @@
 
 #include <algorithm>
 
-#include "gromacs/gmxlib/warninp.h"
+#include "gromacs/fileio/warninp.h"
 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
 #include "gromacs/gmxpreprocess/gpp_bond_atomtype.h"
 #include "gromacs/gmxpreprocess/notset.h"

diff --git a/src/gromacs/gmxpreprocess/toppush.h b/src/gromacs/gmxpreprocess/toppush.h
index ace6e436b0abb1092af470b874abbf27aecc3df6..da59a38a082d25f4dc2c4be7927e4d3159ad98f6 100644 (file)
--- a/src/gromacs/gmxpreprocess/toppush.h
+++ b/src/gromacs/gmxpreprocess/toppush.h
@@ -38,7 +38,7 @@
 #ifndef GMX_GMXPREPROCESS_TOPPUSH_H
 #define GMX_GMXPREPROCESS_TOPPUSH_H
 
-#include "gromacs/gmxlib/warninp.h"
+#include "gromacs/fileio/warninp.h"
 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
 #include "gromacs/gmxpreprocess/gpp_bond_atomtype.h"
 #include "gromacs/gmxpreprocess/toputil.h"

diff --git a/src/gromacs/gmxpreprocess/x2top.cpp b/src/gromacs/gmxpreprocess/x2top.cpp
index 31fdd277a371cceac26da8ca86c9b2b1880e3255..23014ecbcad401066f852d2d2a9ea08bca016a0d 100644 (file)
--- a/src/gromacs/gmxpreprocess/x2top.cpp
+++ b/src/gromacs/gmxpreprocess/x2top.cpp
@@ -43,7 +43,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/gmxfio.h"
-#include "gromacs/gmxlib/readinp.h"
+#include "gromacs/fileio/readinp.h"
 #include "gromacs/gmxpreprocess/gen_ad.h"
 #include "gromacs/gmxpreprocess/gpp_nextnb.h"
 #include "gromacs/gmxpreprocess/hackblock.h"

diff --git a/src/programs/mdrun/mdrun.cpp b/src/programs/mdrun/mdrun.cpp
index a8d6d65e45ddfef27ca56bda6422392460999fcf..d9253c26503575591d24dc8c0d3b735c1f74b57a 100644 (file)
--- a/src/programs/mdrun/mdrun.cpp
+++ b/src/programs/mdrun/mdrun.cpp
@@ -59,9 +59,9 @@
 
 #include "gromacs/commandline/filenm.h"
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/readinp.h"
 #include "gromacs/gmxlib/main.h"
 #include "gromacs/gmxlib/network.h"
-#include "gromacs/gmxlib/readinp.h"
 #include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdrunutility/handlerestart.h"
 #include "gromacs/mdtypes/commrec.h"

diff --git a/src/programs/mdrun/membed.cpp b/src/programs/mdrun/membed.cpp
index e4b4e246bfc98e422920e48fe93c80aaf274be77..1d2a93de872367a5cabab983be3986e2d651e8a7 100644 (file)
--- a/src/programs/mdrun/membed.cpp
+++ b/src/programs/mdrun/membed.cpp
@@ -41,9 +41,9 @@
 
 #include "gromacs/commandline/filenm.h"
 #include "gromacs/essentialdynamics/edsam.h"
+#include "gromacs/fileio/readinp.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/gmxlib/network.h"
-#include "gromacs/gmxlib/readinp.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/md_enums.h"