Move network.h to gmxlib/

- Suppress cyclic dependency caused by too high-level code that is
  currently present in checkpoint.cpp.
- Remove unused network.h use from forcetable.cpp to avoid another
  cyclic dependency.
- Remove all includes for network.h from other headers, and introduce
  them where required.
- Remove broken debug_gmx().
- Some cleanup.

Change-Id: Ib80787c4c2f16b12cc0f152f1017ea44dd69ecf4

diff --git a/docs/doxygen/cycle-suppressions.txt b/docs/doxygen/cycle-suppressions.txt
index 810c6ac5a9a688e3c51411cbea7860647ec72abf..5fe2068efef9f2733c6a90c858a9e20ee1b8dd45 100644 (file)
--- a/docs/doxygen/cycle-suppressions.txt
+++ b/docs/doxygen/cycle-suppressions.txt
@@ -6,6 +6,7 @@ domdec -> ewald
 domdec -> mdlib
 domdec -> pulling
 domdec -> swap
+fileio -> gmxlib
 gmxlib -> listed-forces
 mdlib -> essentialdynamics
 mdlib -> imd

diff --git a/src/gromacs/domdec/domdec.cpp b/src/gromacs/domdec/domdec.cpp
index 72de357aeafb7d0141ba0cf0351f73d3c4dbfe28..260c989ef592fbd9790a01b927f358e830d49e43 100644 (file)
--- a/src/gromacs/domdec/domdec.cpp
+++ b/src/gromacs/domdec/domdec.cpp
@@ -55,10 +55,10 @@
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/gmxlib/chargegroup.h"
 #include "gromacs/gmxlib/gmx_omp_nthreads.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/gpu_utils/gpu_utils.h"
 #include "gromacs/imd/imd.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/enums.h"

diff --git a/src/gromacs/domdec/domdec_box.cpp b/src/gromacs/domdec/domdec_box.cpp
index b8ce96f74396c6801df8fc23d7a13039786a8b04..327ad1366ed638a5ccbeec51b6bfcbb19274b0d5 100644 (file)
--- a/src/gromacs/domdec/domdec_box.cpp
+++ b/src/gromacs/domdec/domdec_box.cpp
@@ -46,7 +46,7 @@
 
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/domdec/domdec_network.h"
-#include "gromacs/legacyheaders/network.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/nsgrid.h"

diff --git a/src/gromacs/domdec/domdec_setup.cpp b/src/gromacs/domdec/domdec_setup.cpp
index 638d98be7d8e1c0a85c0bcd365e5a7abdb8abb1a..1755e18ddfb735c8d02658c8f33b62046d2ad660 100644 (file)
--- a/src/gromacs/domdec/domdec_setup.cpp
+++ b/src/gromacs/domdec/domdec_setup.cpp
@@ -50,8 +50,8 @@
 #include <cmath>
 
 #include "gromacs/domdec/domdec.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/perf_est.h"

diff --git a/src/gromacs/domdec/domdec_topology.cpp b/src/gromacs/domdec/domdec_topology.cpp
index 7f8e28deb03732270c2170e4830bb25f333d5424..9909ba4bf6d2c35f60a83c997edcebfa7cb2a6e4 100644 (file)
--- a/src/gromacs/domdec/domdec_topology.cpp
+++ b/src/gromacs/domdec/domdec_topology.cpp
@@ -56,8 +56,8 @@
 #include "gromacs/domdec/ga2la.h"
 #include "gromacs/gmxlib/chargegroup.h"
 #include "gromacs/gmxlib/gmx_omp_nthreads.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/force.h"

diff --git a/src/gromacs/essentialdynamics/edsam.cpp b/src/gromacs/essentialdynamics/edsam.cpp
index f5626dfc8de73a039b4cf1dbea8d326641c2bd53..6c06e9e3635e1fab5f05c1be0862eac8085455ca 100644 (file)
--- a/src/gromacs/essentialdynamics/edsam.cpp
+++ b/src/gromacs/essentialdynamics/edsam.cpp
@@ -44,6 +44,7 @@
 
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/types/nrnb.h"
 #include "gromacs/linearalgebra/nrjac.h"

diff --git a/src/gromacs/ewald/pme-internal.h b/src/gromacs/ewald/pme-internal.h
index eba2fa3286159773dccbfd0093f6357ee5978a90..5b95ea6a2e7bff06e42f81bac9ee97c5b1c26fc4 100644 (file)
--- a/src/gromacs/ewald/pme-internal.h
+++ b/src/gromacs/ewald/pme-internal.h
@@ -58,12 +58,12 @@
 #include <stdio.h>
 
 #include "gromacs/fft/parallel_3dfft.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/math/gmxcomplex.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/timing/walltime_accounting.h"
 #include "gromacs/utility/gmxmpi.h"
 
+struct t_commrec;
 struct t_inputrec;
 
 //@{

diff --git a/src/gromacs/ewald/pme-load-balancing.cpp b/src/gromacs/ewald/pme-load-balancing.cpp
index fec5c0864b4e4fdb6c75efad6005a621b8f9abde..8deb7eae198dab1f7c4da8d2151c3e545fdb444b 100644 (file)
--- a/src/gromacs/ewald/pme-load-balancing.cpp
+++ b/src/gromacs/ewald/pme-load-balancing.cpp
@@ -57,7 +57,7 @@
 #include "gromacs/domdec/domdec_network.h"
 #include "gromacs/gmxlib/calcgrid.h"
 #include "gromacs/gmxlib/md_logging.h"
-#include "gromacs/legacyheaders/network.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/forcerec.h"

diff --git a/src/gromacs/ewald/pme-only.cpp b/src/gromacs/ewald/pme-only.cpp
index a1404339d42b15a42ff722068a749b32778cc990..0fb5d9d3514049e76a66b06bce396422c927a9d4 100644 (file)
--- a/src/gromacs/ewald/pme-only.cpp
+++ b/src/gromacs/ewald/pme-only.cpp
@@ -69,7 +69,7 @@
 #include "gromacs/fft/parallel_3dfft.h"
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/txtdump.h"
-#include "gromacs/legacyheaders/network.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/gmxcomplex.h"

diff --git a/src/gromacs/ewald/pme-pp.cpp b/src/gromacs/ewald/pme-pp.cpp
index 65eb0e5ab33595483d551cf19556a5e26622b17f..1330a87f69b16ea440b161f7d7af08ae0d458794 100644 (file)
--- a/src/gromacs/ewald/pme-pp.cpp
+++ b/src/gromacs/ewald/pme-pp.cpp
@@ -54,8 +54,8 @@
 
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/ewald/pme.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/sighandler.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/ewald/pme.cpp b/src/gromacs/ewald/pme.cpp
index 75cce0d9ba6569d453375ef7ba8174784d962460..3608fcd921fe493baf3606a9b89b31b805b38412 100644 (file)
--- a/src/gromacs/ewald/pme.cpp
+++ b/src/gromacs/ewald/pme.cpp
@@ -83,7 +83,7 @@
 
 #include "gromacs/fft/parallel_3dfft.h"
 #include "gromacs/fileio/pdbio.h"
-#include "gromacs/legacyheaders/network.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/enums.h"

diff --git a/src/gromacs/fileio/checkpoint.cpp b/src/gromacs/fileio/checkpoint.cpp
index 6b9200150c978143bada198027f5168bec0af8fd..a00c89fff68cb1f5df427770d14cdddc35e01a76 100644 (file)
--- a/src/gromacs/fileio/checkpoint.cpp
+++ b/src/gromacs/fileio/checkpoint.cpp
@@ -59,8 +59,8 @@
 #include "gromacs/fileio/txtdump.h"
 #include "gromacs/fileio/xdr_datatype.h"
 #include "gromacs/fileio/xdrf.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/enums.h"
 #include "gromacs/legacyheaders/types/inputrec.h"

diff --git a/src/gromacs/gmxana/gmx_pme_error.cpp b/src/gromacs/gmxana/gmx_pme_error.cpp
index 1fb08234a7c75c5842895e5e4197d487cc3abe44..3e6a9cb205dfcfad9cafd83d7726d0f4e3f771fd 100644 (file)
--- a/src/gromacs/gmxana/gmx_pme_error.cpp
+++ b/src/gromacs/gmxana/gmx_pme_error.cpp
@@ -47,8 +47,8 @@
 #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/legacyheaders/network.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/calculate-ewald-splitting-coefficient.h"
 #include "gromacs/math/units.h"

diff --git a/src/gromacs/gmxlib/disre.cpp b/src/gromacs/gmxlib/disre.cpp
index 49939d1015f0e0def11079af9213a096a72b32dc..074429435b56981996005f679b4dd079ed67b1f9 100644 (file)
--- a/src/gromacs/gmxlib/disre.cpp
+++ b/src/gromacs/gmxlib/disre.cpp
@@ -49,7 +49,7 @@
 
 #include "gromacs/fileio/copyrite.h"
 #include "gromacs/gmxlib/main.h"
-#include "gromacs/legacyheaders/network.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/fcdata.h"
 #include "gromacs/legacyheaders/types/state.h"

diff --git a/src/gromacs/gmxlib/gmx_detect_hardware.cpp b/src/gromacs/gmxlib/gmx_detect_hardware.cpp
index 0ab1515926e7c76711a585ae82e5930bd1d700b8..71dd7eb6a1753833292d9a9497d1db9b7321c1b2 100644 (file)
--- a/src/gromacs/gmxlib/gmx_detect_hardware.cpp
+++ b/src/gromacs/gmxlib/gmx_detect_hardware.cpp
@@ -57,9 +57,9 @@
 #include "thread_mpi/threads.h"
 
 #include "gromacs/gmxlib/md_logging.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/gpu_utils/gpu_utils.h"
 #include "gromacs/legacyheaders/gmx_cpuid.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/enums.h"
 #include "gromacs/legacyheaders/types/hw_info.h"

diff --git a/src/gromacs/gmxlib/gmx_omp_nthreads.cpp b/src/gromacs/gmxlib/gmx_omp_nthreads.cpp
index 924d7f2e725d6c710040c84212e841b9143e4577..a4371cd7587b8e19121f29c01fe9392b4b2b303c 100644 (file)
--- a/src/gromacs/gmxlib/gmx_omp_nthreads.cpp
+++ b/src/gromacs/gmxlib/gmx_omp_nthreads.cpp
@@ -44,7 +44,7 @@
 #include <cstring>
 
 #include "gromacs/gmxlib/md_logging.h"
-#include "gromacs/legacyheaders/network.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/gmxlib/main.cpp b/src/gromacs/gmxlib/main.cpp
index 1208de8dc76c7ea1815ac97e27d24d217c0e6de5..ad4c0abdf01c9658f9062b9c771c1b2781e9f52a 100644 (file)
--- a/src/gromacs/gmxlib/main.cpp
+++ b/src/gromacs/gmxlib/main.cpp
@@ -47,7 +47,7 @@
 #include "gromacs/fileio/copyrite.h"
 #include "gromacs/fileio/filenm.h"
 #include "gromacs/fileio/gmxfio.h"
-#include "gromacs/legacyheaders/network.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/exceptions.h"
@@ -216,8 +216,6 @@ void gmx_log_open(const char *lognm, const t_commrec *cr,
     char   timebuf[STRLEN];
     FILE  *fp = *fplog;
 
-    debug_gmx();
-
     if (!bAppendFiles)
     {
         fp = gmx_fio_fopen(lognm, bAppendFiles ? "a+" : "w+" );
@@ -256,7 +254,6 @@ void gmx_log_open(const char *lognm, const t_commrec *cr,
     fprintf(fp, "\n");
 
     fflush(fp);
-    debug_gmx();
 
     *fplog = fp;
 }

diff --git a/src/gromacs/gmxlib/network.cpp b/src/gromacs/gmxlib/network.cpp
index b51556fa0afb3830a6254b5474e2acac56430813..731a39f8db3257ac119d2eb626454feb9998a8e4 100644 (file)
--- a/src/gromacs/gmxlib/network.cpp
+++ b/src/gromacs/gmxlib/network.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/network.h"
+#include "network.h"
 
 #include "config.h"
 

diff --git a/src/gromacs/legacyheaders/network.h b/src/gromacs/gmxlib/network.h
similarity index 91%
rename from src/gromacs/legacyheaders/network.h
rename to src/gromacs/gmxlib/network.h
index d452ac59300307ae5e452018027540dcaaf8292b..ddcafcbb31ec64a1bac6160e4f11dae9471153f3 100644 (file)
--- a/src/gromacs/legacyheaders/network.h
+++ b/src/gromacs/gmxlib/network.h
@@ -34,10 +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 _network_h
-#define _network_h
-
+#ifndef GMX_GMXLIB_NETWORK_H
+#define GMX_GMXLIB_NETWORK_H
 
 /*
  * This module defines the interface of the actual communication routines.
@@ -47,10 +45,6 @@
 
 #include "gromacs/utility/basedefinitions.h"
 
-#ifdef __cplusplus
-extern "C" {
-#endif
-
 struct gmx_domdec_t;
 struct gmx_multisim_t;
 struct t_commrec;
@@ -132,17 +126,4 @@ gmx_fatal_collective(int f_errno, const char *file, int line,
  * for all processes.
  */
 
-/* This doesn't currently work if enabled (needs some header cleanup). */
-#ifdef DEBUG_GMX
-#define debug_gmx() do { FILE *fp = debug ? debug : stderr; \
-                         if (bDebugMode()) { fprintf(fp, "rank=%d, %s  %d\n", gmx_mpi_initialized() ? gmx_node_rank() : -1, __FILE__, __LINE__); } fflush(fp); } while (0)
-#else
-#define debug_gmx()
 #endif
-
-#ifdef __cplusplus
-}
-#endif
-
-
-#endif  /* _network_h */

diff --git a/src/gromacs/gmxlib/orires.cpp b/src/gromacs/gmxlib/orires.cpp
index 41e73cacf0f4cd7e86fe7e342b1caa8f51e1a2ce..439f3a2822cb7375c90eac933d7f5d779120623a 100644 (file)
--- a/src/gromacs/gmxlib/orires.cpp
+++ b/src/gromacs/gmxlib/orires.cpp
@@ -42,7 +42,7 @@
 
 #include "gromacs/fileio/copyrite.h"
 #include "gromacs/gmxlib/main.h"
-#include "gromacs/legacyheaders/network.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/fcdata.h"
 #include "gromacs/legacyheaders/types/ifunc.h"

diff --git a/src/gromacs/gmxpreprocess/genhydro.cpp b/src/gromacs/gmxpreprocess/genhydro.cpp
index 66896544647750415e605251834703ca71d8c495..88fd8dd49a2f0cfac1cab3b0209275e1dbdac28b 100644 (file)
--- a/src/gromacs/gmxpreprocess/genhydro.cpp
+++ b/src/gromacs/gmxpreprocess/genhydro.cpp
@@ -42,13 +42,13 @@
 #include <time.h>
 
 #include "gromacs/fileio/confio.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxpreprocess/calch.h"
 #include "gromacs/gmxpreprocess/h_db.h"
 #include "gromacs/gmxpreprocess/notset.h"
 #include "gromacs/gmxpreprocess/pgutil.h"
 #include "gromacs/gmxpreprocess/resall.h"
 #include "gromacs/gmxpreprocess/ter_db.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/utility/cstringutil.h"
@@ -596,7 +596,6 @@ static int add_h_low(t_atoms **pdbaptr, rvec *xptr[],
                     srenew(newpdba->atom, natoms+nadd);
                     srenew(newpdba->atomname, natoms+nadd);
                 }
-                debug_gmx();
             }
             if (debug)
             {
@@ -627,7 +626,6 @@ static int add_h_low(t_atoms **pdbaptr, rvec *xptr[],
                             srenew(newpdba->atom, natoms+nadd);
                             srenew(newpdba->atomname, natoms+nadd);
                         }
-                        debug_gmx();
                     }
                     if (bUpdate_pdba)
                     {

diff --git a/src/gromacs/gmxpreprocess/readir.cpp b/src/gromacs/gmxpreprocess/readir.cpp
index fafc10ae574a2cd365855609c883c58db7050f1a..fda2171cb548c2cb922f152f51daa3024ed22813 100644 (file)
--- a/src/gromacs/gmxpreprocess/readir.cpp
+++ b/src/gromacs/gmxpreprocess/readir.cpp
@@ -47,11 +47,11 @@
 #include <algorithm>
 
 #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/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/types/ifunc.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
@@ -3247,7 +3247,6 @@ void do_index(const char* mdparin, const char *ndx,
     {
         fprintf(stderr, "processing index file...\n");
     }
-    debug_gmx();
     if (ndx == NULL)
     {
         snew(grps, 1);

diff --git a/src/gromacs/imd/imd.cpp b/src/gromacs/imd/imd.cpp
index 1250d090fec2dfa8bb1e2014dd97d2326a0b9b80..508deb0ca717f0c38b85b997ad56136aefc69074 100644 (file)
--- a/src/gromacs/imd/imd.cpp
+++ b/src/gromacs/imd/imd.cpp
@@ -64,10 +64,10 @@
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/sighandler.h"
 #include "gromacs/imd/imdsocket.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/types/inputrec.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/groupcoord.h"

diff --git a/src/gromacs/listed-forces/listed-forces.cpp b/src/gromacs/listed-forces/listed-forces.cpp
index d21c961136d33c6f741b6985216457745cb21d6d..871893a2387054a9416e60e954a068cfa8be619d 100644 (file)
--- a/src/gromacs/listed-forces/listed-forces.cpp
+++ b/src/gromacs/listed-forces/listed-forces.cpp
@@ -52,8 +52,8 @@
 #include <algorithm>
 
 #include "gromacs/gmxlib/disre.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/orires.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/types/fcdata.h"
 #include "gromacs/legacyheaders/types/force_flags.h"
@@ -699,5 +699,4 @@ do_force_listed(struct gmx_wallcycle        *wcycle,
             wallcycle_sub_stop(wcycle, ewcsLISTED_FEP);
         }
     }
-    debug_gmx();
 }

diff --git a/src/gromacs/mdlib/broadcaststructs.cpp b/src/gromacs/mdlib/broadcaststructs.cpp
index 8016064ec5751211559af018b60447e3fe0a03df..2f152e6525b69e06d7cf8cae84928de68622d87f 100644 (file)
--- a/src/gromacs/mdlib/broadcaststructs.cpp
+++ b/src/gromacs/mdlib/broadcaststructs.cpp
@@ -40,7 +40,7 @@
 #include <string.h>
 
 #include "gromacs/gmxlib/main.h"
-#include "gromacs/legacyheaders/network.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/enums.h"
 #include "gromacs/legacyheaders/types/inputrec.h"

diff --git a/src/gromacs/mdlib/calcmu.cpp b/src/gromacs/mdlib/calcmu.cpp
index 699a5e323af9ec346543595f13960c026e5bcaea..6c544c0dea2e850e0d16ce195012bf079b8fd97d 100644 (file)
--- a/src/gromacs/mdlib/calcmu.cpp
+++ b/src/gromacs/mdlib/calcmu.cpp
@@ -43,7 +43,7 @@
 #include <stdlib.h>
 
 #include "gromacs/gmxlib/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/network.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 

diff --git a/src/gromacs/mdlib/expanded.cpp b/src/gromacs/mdlib/expanded.cpp
index 44a800151c129c2390a2a99d2b763789771566b2..df9c10cfbd6695b1f991376565d8865b8ee63d21 100644 (file)
--- a/src/gromacs/mdlib/expanded.cpp
+++ b/src/gromacs/mdlib/expanded.cpp
@@ -47,9 +47,9 @@
 #include "gromacs/fileio/xtcio.h"
 #include "gromacs/gmxlib/chargegroup.h"
 #include "gromacs/gmxlib/disre.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/orires.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/mdlib/force.cpp b/src/gromacs/mdlib/force.cpp
index 3e4842675caf95aab20715b347ca4d236d2d3742..71a60a4662f3059d34458c6e62b2f2b5c0601723 100644 (file)
--- a/src/gromacs/mdlib/force.cpp
+++ b/src/gromacs/mdlib/force.cpp
@@ -50,9 +50,9 @@
 #include "gromacs/ewald/pme.h"
 #include "gromacs/fileio/txtdump.h"
 #include "gromacs/gmxlib/gmx_omp_nthreads.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/nonbonded/nonbonded.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/listed-forces/listed-forces.h"
@@ -181,8 +181,6 @@ void do_force_lowlevel(t_forcerec *fr,      t_inputrec *ir,
         box_size[i] = box[i][i];
     }
 
-    debug_gmx();
-
     /* do QMMM first if requested */
     if (fr->bQMMM)
     {
@@ -325,9 +323,6 @@ void do_force_lowlevel(t_forcerec *fr,      t_inputrec *ir,
         enerd->dvdl_lin[efptCOUL] += dvdl_nb[efptCOUL];
     }
 
-    debug_gmx();
-
-
     if (debug)
     {
         pr_rvecs(debug, 0, "fshift after SR", fr->fshift, SHIFTS);
@@ -372,7 +367,6 @@ void do_force_lowlevel(t_forcerec *fr,      t_inputrec *ir,
          */
         set_pbc_dd(&pbc, fr->ePBC, cr->dd, TRUE, box);
     }
-    debug_gmx();
 
     do_force_listed(wcycle, box, ir->fepvals, cr->ms,
                     idef, (const rvec *) x, hist, f, fr,
@@ -625,13 +619,11 @@ void do_force_lowlevel(t_forcerec *fr,      t_inputrec *ir,
         }
     }
     where();
-    debug_gmx();
 
     if (debug)
     {
         print_nrnb(debug, nrnb);
     }
-    debug_gmx();
 
 #ifdef GMX_MPI
     if (TAKETIME)

diff --git a/src/gromacs/mdlib/forcerec.cpp b/src/gromacs/mdlib/forcerec.cpp
index 6c5612a115e374e2b1ffc27cb1a576cdb5b7e61a..db84773ace33fc59f9a0f351900c224e506b3bb9 100644 (file)
--- a/src/gromacs/mdlib/forcerec.cpp
+++ b/src/gromacs/mdlib/forcerec.cpp
@@ -56,10 +56,10 @@
 #include "gromacs/gmxlib/gmx_detect_hardware.h"
 #include "gromacs/gmxlib/gmx_omp_nthreads.h"
 #include "gromacs/gmxlib/md_logging.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/gpu_utils/gpu_utils.h"
 #include "gromacs/gmxlib/nonbonded/nonbonded.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/fcdata.h"
 #include "gromacs/legacyheaders/types/group.h"

diff --git a/src/gromacs/mdlib/forcerec.h b/src/gromacs/mdlib/forcerec.h
index 727fc0fda8bd7d820c296cd659173b902c801f55..a5abedff3004ffe1c4d192f67d482d2aa5c6c119 100644 (file)
--- a/src/gromacs/mdlib/forcerec.h
+++ b/src/gromacs/mdlib/forcerec.h
@@ -37,7 +37,6 @@
 #ifndef GMX_MDLIB_FORCEREC_H
 #define GMX_MDLIB_FORCEREC_H
 
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/types/force_flags.h"
 #include "gromacs/legacyheaders/types/forcerec.h"
 #include "gromacs/mdlib/genborn.h"
@@ -45,6 +44,7 @@
 #include "gromacs/mdlib/vsite.h"
 #include "gromacs/timing/wallcycle.h"
 
+struct t_commrec;
 struct t_fcdata;
 
 /*! \brief Create a new forcerec structure */

diff --git a/src/gromacs/mdlib/genborn.cpp b/src/gromacs/mdlib/genborn.cpp
index 7dff94b2ffb0e500dd85a2b451bb741b8f06a45f..04b28fc45fb0e90a5d97b0fde6011d684e4e4cdb 100644 (file)
--- a/src/gromacs/mdlib/genborn.cpp
+++ b/src/gromacs/mdlib/genborn.cpp
@@ -47,8 +47,8 @@
 
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/fileio/pdbio.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/units.h"

diff --git a/src/gromacs/mdlib/genborn_allvsall.cpp b/src/gromacs/mdlib/genborn_allvsall.cpp
index 17d3406379e3120769827b8bf42c2ac1c481411c..e474094b250b40d4d746f4e2adae87d968a1b8fa 100644 (file)
--- a/src/gromacs/mdlib/genborn_allvsall.cpp
+++ b/src/gromacs/mdlib/genborn_allvsall.cpp
@@ -42,7 +42,7 @@
 
 #include <algorithm>
 
-#include "gromacs/legacyheaders/network.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/types/forcerec.h"
 #include "gromacs/legacyheaders/types/mdatom.h"
 #include "gromacs/math/units.h"

diff --git a/src/gromacs/mdlib/groupcoord.cpp b/src/gromacs/mdlib/groupcoord.cpp
index c8bf1a940d79513cb54bf4bdfdf207fc35e1ade2..fdf313bedd411db1e104047833ee65cc668a6381 100644 (file)
--- a/src/gromacs/mdlib/groupcoord.cpp
+++ b/src/gromacs/mdlib/groupcoord.cpp
@@ -39,7 +39,7 @@
 #include "groupcoord.h"
 
 #include "gromacs/domdec/ga2la.h"
-#include "gromacs/legacyheaders/network.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/mdlib/md_support.cpp b/src/gromacs/mdlib/md_support.cpp
index 64fb13e078942fdc315d2acb823a4224d4e7b972..c685d573e72f2e1e6d642158c1b55bb5e7dc25d1 100644 (file)
--- a/src/gromacs/mdlib/md_support.cpp
+++ b/src/gromacs/mdlib/md_support.cpp
@@ -44,6 +44,7 @@
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/fileio/trx.h"
 #include "gromacs/gmxlib/md_logging.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/types/commrec.h"
@@ -309,7 +310,6 @@ void compute_globals(FILE *fplog, gmx_global_stat_t gstat, t_commrec *cr, t_inpu
         {
             accumulate_u(cr, &(ir->opts), ekind);
         }
-        debug_gmx();
         if (bReadEkin)
         {
             restore_ekinstate_from_state(cr, ekind, &state_global->ekinstate);
@@ -318,8 +318,6 @@ void compute_globals(FILE *fplog, gmx_global_stat_t gstat, t_commrec *cr, t_inpu
         {
             calc_ke_part(state, &(ir->opts), mdatoms, ekind, nrnb, bEkinAveVel);
         }
-
-        debug_gmx();
     }
 
     /* Calculate center of mass velocity if necessary, also parallellized */

diff --git a/src/gromacs/mdlib/md_support.h b/src/gromacs/mdlib/md_support.h
index 6e4e1db810d96b4c25a6d2593a5d8fdb4b47493a..cb016589ae677df5626e18dab9bab44b9586b8a4 100644 (file)
--- a/src/gromacs/mdlib/md_support.h
+++ b/src/gromacs/mdlib/md_support.h
@@ -42,6 +42,7 @@
 #include "gromacs/timing/wallcycle.h"
 
 struct gmx_constr;
+struct gmx_multisim_t;
 struct gmx_signalling_t;
 struct t_trxframe;
 

diff --git a/src/gromacs/mdlib/mdebin.cpp b/src/gromacs/mdlib/mdebin.cpp
index 69550465dae5931824fc6f98386b773ed93c46be..ee64f4f8554cb1fceb5480c0701e57383e3660ef 100644 (file)
--- a/src/gromacs/mdlib/mdebin.cpp
+++ b/src/gromacs/mdlib/mdebin.cpp
@@ -46,9 +46,9 @@
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxlib/disre.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/orires.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/types/fcdata.h"
 #include "gromacs/legacyheaders/types/group.h"
 #include "gromacs/math/units.h"

diff --git a/src/gromacs/mdlib/mdoutf.h b/src/gromacs/mdlib/mdoutf.h
index 59603639244bb40882410f0c644deae686580903..3e12d876c80bff97f9fe5688f7bfa4e4e3b818ba 100644 (file)
--- a/src/gromacs/mdlib/mdoutf.h
+++ b/src/gromacs/mdlib/mdoutf.h
@@ -39,18 +39,14 @@
 
 #include "gromacs/fileio/enxio.h"
 #include "gromacs/fileio/filenm.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/types/inputrec.h"
 #include "gromacs/math/vectypes.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/utility/basedefinitions.h"
 
-#ifdef __cplusplus
-extern "C" {
-#endif
-
 struct gmx_mtop_t;
 struct gmx_output_env_t;
+struct t_commrec;
 
 typedef struct gmx_mdoutf *gmx_mdoutf_t;
 
@@ -65,7 +61,7 @@ gmx_mdoutf_t init_mdoutf(FILE                   *fplog,
                          int                     mdrun_flags,
                          const t_commrec        *cr,
                          const t_inputrec       *ir,
-                         struct gmx_mtop_t      *mtop,
+                         gmx_mtop_t             *mtop,
                          const gmx_output_env_t *oenv,
                          gmx_wallcycle_t         wcycle);
 
@@ -100,7 +96,7 @@ void done_mdoutf(gmx_mdoutf_t of);
 void mdoutf_write_to_trajectory_files(FILE *fplog, t_commrec *cr,
                                       gmx_mdoutf_t of,
                                       int mdof_flags,
-                                      struct gmx_mtop_t *top_global,
+                                      gmx_mtop_t *top_global,
                                       gmx_int64_t step, double t,
                                       t_state *state_local, t_state *state_global,
                                       rvec *f_local, rvec *f_global);
@@ -112,8 +108,4 @@ void mdoutf_write_to_trajectory_files(FILE *fplog, t_commrec *cr,
 #define MDOF_CPT          (1<<4)
 #define MDOF_IMD          (1<<5)
 
-#ifdef __cplusplus
-}
-#endif
-
 #endif

diff --git a/src/gromacs/mdlib/mdrun_signalling.cpp b/src/gromacs/mdlib/mdrun_signalling.cpp
index d71d0572f3a5b581e197e22fc209515aa065e638..a77041646852bf37580041b76fc2613837cbbd36 100644 (file)
--- a/src/gromacs/mdlib/mdrun_signalling.cpp
+++ b/src/gromacs/mdlib/mdrun_signalling.cpp
@@ -52,6 +52,7 @@
 
 #include <algorithm>
 
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/inputrec.h"
 #include "gromacs/mdlib/md_support.h"

diff --git a/src/gromacs/mdlib/minimize.cpp b/src/gromacs/mdlib/minimize.cpp
index bbbab8304cd8c16078d101fc51eac7725110b880..ce509c87edfe4c899235bee3251bc4b1fe4b7582 100644 (file)
--- a/src/gromacs/mdlib/minimize.cpp
+++ b/src/gromacs/mdlib/minimize.cpp
@@ -61,9 +61,9 @@
 #include "gromacs/fileio/txtdump.h"
 #include "gromacs/gmxlib/gmx_omp_nthreads.h"
 #include "gromacs/gmxlib/md_logging.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/imd/imd.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/inputrec.h"

diff --git a/src/gromacs/mdlib/ns.cpp b/src/gromacs/mdlib/ns.cpp
index 7a3beb89ea137150312e4c7269c7b65944b5725a..365487d7b82df97c99369c059d11677386a41cd8 100644 (file)
--- a/src/gromacs/mdlib/ns.cpp
+++ b/src/gromacs/mdlib/ns.cpp
@@ -48,9 +48,9 @@
 
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/fileio/txtdump.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/nonbonded/nonbonded.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/group.h"
@@ -2179,8 +2179,6 @@ static int nsgrid_core(t_commrec *cr, t_forcerec *fr,
     }
 #endif
 
-    debug_gmx();
-
     if (fr->n_tpi)
     {
         /* We only want a list for the test particle */
@@ -2512,8 +2510,6 @@ static int nsgrid_core(t_commrec *cr, t_forcerec *fr,
      * since we now save the proper long-range lists for later evaluation.
      */
 
-    debug_gmx();
-
     /* Close neighbourlists */
     close_neighbor_lists(fr, bMakeQMMMnblist);
 
@@ -2702,7 +2698,6 @@ int search_neighbours(FILE *log, t_forcerec *fr,
     {
         ns_realloc_natoms(ns, cgs->index[cgs->nr]);
     }
-    debug_gmx();
 
     /* Reset the neighbourlists */
     reset_neighbor_lists(fr, TRUE, TRUE);
@@ -2725,7 +2720,6 @@ int search_neighbours(FILE *log, t_forcerec *fr,
             grid_first(log, grid, NULL, NULL, box, grid_x0, grid_x1,
                        fr->rlistlong, grid_dens);
         }
-        debug_gmx();
 
         start = 0;
         end   = cgs->nr;
@@ -2742,7 +2736,6 @@ int search_neighbours(FILE *log, t_forcerec *fr,
             fill_grid(NULL, grid, cgs->nr, fr->cg0, fr->hcg, fr->cg_cm);
             grid->icg0 = fr->cg0;
             grid->icg1 = fr->hcg;
-            debug_gmx();
         }
 
         calc_elemnr(grid, start, end, cgs->nr);
@@ -2762,7 +2755,6 @@ int search_neighbours(FILE *log, t_forcerec *fr,
          */
         fill_grid(NULL, ns->grid, fr->hcg, fr->hcg-1, fr->hcg, fr->cg_cm);
     }
-    debug_gmx();
 
     if (fr->adress_type == eAdressOff)
     {
@@ -2812,7 +2804,6 @@ int search_neighbours(FILE *log, t_forcerec *fr,
                                  ns->bexcl, ns->simple_aaj,
                                  ngid, ns->ns_buf, put_in_list, ns->bHaveVdW);
     }
-    debug_gmx();
 
 #ifdef DEBUG
     pr_nsblock(log);

diff --git a/src/gromacs/mdlib/nsgrid.cpp b/src/gromacs/mdlib/nsgrid.cpp
index 8275abda4b2530d5d4f0e5c9c1ca7ec8e7df57cb..3314153e2b74606052c32b40aff7645bb8b5992a 100644 (file)
--- a/src/gromacs/mdlib/nsgrid.cpp
+++ b/src/gromacs/mdlib/nsgrid.cpp
@@ -48,7 +48,7 @@
 
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/fileio/pdbio.h"
-#include "gromacs/legacyheaders/network.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
@@ -683,7 +683,6 @@ void fill_grid(gmx_domdec_zones_t *dd_zones,
         fprintf(debug, "Filling grid from %d to %d\n", cg0, cg1);
     }
 
-    debug_gmx();
     if (dd_zones == NULL)
     {
         for (cg = cg0; cg < cg1; cg++)
@@ -809,7 +808,6 @@ void fill_grid(gmx_domdec_zones_t *dd_zones,
             }
         }
     }
-    debug_gmx();
 
 }
 

diff --git a/src/gromacs/mdlib/qm_gamess.cpp b/src/gromacs/mdlib/qm_gamess.cpp
index f49e90591f2ed3483bd2bc329d18374ed846d759..31b90f9f3d25ba3497109fcb227fa2bc1de07408 100644 (file)
--- a/src/gromacs/mdlib/qm_gamess.cpp
+++ b/src/gromacs/mdlib/qm_gamess.cpp
@@ -47,8 +47,8 @@
 
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/txtdump.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/units.h"

diff --git a/src/gromacs/mdlib/qm_gaussian.cpp b/src/gromacs/mdlib/qm_gaussian.cpp
index b4ff2b7046142a77ef2d89cfb1b74ea2fb60adce..4b8630989bb02b99bb03a6b695ddbb374a26aea1 100644 (file)
--- a/src/gromacs/mdlib/qm_gaussian.cpp
+++ b/src/gromacs/mdlib/qm_gaussian.cpp
@@ -47,8 +47,8 @@
 
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/txtdump.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/mdlib/qm_mopac.cpp b/src/gromacs/mdlib/qm_mopac.cpp
index 8a3754cc350462f1d9af607bc30a51503abbbe19..58cc56a04480d1cf3e865bdb0c4984a30240735e 100644 (file)
--- a/src/gromacs/mdlib/qm_mopac.cpp
+++ b/src/gromacs/mdlib/qm_mopac.cpp
@@ -47,8 +47,8 @@
 
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/txtdump.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/mdlib/qm_orca.cpp b/src/gromacs/mdlib/qm_orca.cpp
index 89bc5cfa3b29afa081dd44e1f99a5175698fde25..9d2ff860cb7e93da577fbc73e809c8c7adaa6cb2 100644 (file)
--- a/src/gromacs/mdlib/qm_orca.cpp
+++ b/src/gromacs/mdlib/qm_orca.cpp
@@ -43,8 +43,8 @@
 
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/txtdump.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/mdlib/qmmm.cpp b/src/gromacs/mdlib/qmmm.cpp
index 06754b233a9c2efa858ad19d4beb0cbd9e235a13..cdd076c72079823179b3dff0b1fee4dc70b3221e 100644 (file)
--- a/src/gromacs/mdlib/qmmm.cpp
+++ b/src/gromacs/mdlib/qmmm.cpp
@@ -51,8 +51,8 @@
 
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/txtdump.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/mdatom.h"

diff --git a/src/gromacs/mdlib/qmmm.h b/src/gromacs/mdlib/qmmm.h
index 35fa144ba5e99551d5f55ead78a25b19e05798b6..7e38f91862fba36492b627a7df7d6471608f398c 100644 (file)
--- a/src/gromacs/mdlib/qmmm.h
+++ b/src/gromacs/mdlib/qmmm.h
@@ -34,23 +34,20 @@
  * 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_MDLIB_QMMM_H
+#define GMX_MDLIB_QMMM_H
 
-#ifndef _QMMM_h
-#define _QMMM_h
-
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/math/vectypes.h"
 #include "gromacs/mdlib/tgroup.h"
 
 struct gmx_localtop_t;
+struct gmx_mtop_t;
+struct t_commrec;
 struct t_forcerec;
 struct t_inputrec;
+struct t_mdatoms;
 struct t_QMMMrec;
 
-#ifdef __cplusplus
-extern "C" {
-#endif
-
 void atomic_number(int nr, char ***atomtype, int *nucnum);
 
 t_QMMMrec *mk_QMMMrec(void);
@@ -92,8 +89,4 @@ real calculate_QMMM(t_commrec *cr,
  * called by system().
  */
 
-#ifdef __cplusplus
-}
 #endif
-
-#endif  /* _QMMM_h */

diff --git a/src/gromacs/mdlib/rbin.cpp b/src/gromacs/mdlib/rbin.cpp
index cd7fcfd285aaaabc771dfec2ef63290357f9abf2..f180b6c865c850d8718100bf738d170981ac37f0 100644 (file)
--- a/src/gromacs/mdlib/rbin.cpp
+++ b/src/gromacs/mdlib/rbin.cpp
@@ -39,7 +39,7 @@
 
 #include "rbin.h"
 
-#include "gromacs/legacyheaders/network.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/utility/smalloc.h"
 
 t_bin *mk_bin(void)

diff --git a/src/gromacs/mdlib/shellfc.cpp b/src/gromacs/mdlib/shellfc.cpp
index d6a01e497b49168fe74c732607d7aa25ad37baa9..86cc2156b9dafe217e016bc72c1d4d3959c4475b 100644 (file)
--- a/src/gromacs/mdlib/shellfc.cpp
+++ b/src/gromacs/mdlib/shellfc.cpp
@@ -46,8 +46,8 @@
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/fileio/txtdump.h"
 #include "gromacs/gmxlib/chargegroup.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/mdlib/sim_util.cpp b/src/gromacs/mdlib/sim_util.cpp
index a729eb75e5dab99daf86305497fdeb4c8a4fdd58..2de0c3296a4b03ef01f82f44c414f472566616c1 100644 (file)
--- a/src/gromacs/mdlib/sim_util.cpp
+++ b/src/gromacs/mdlib/sim_util.cpp
@@ -55,13 +55,13 @@
 #include "gromacs/gmxlib/chargegroup.h"
 #include "gromacs/gmxlib/disre.h"
 #include "gromacs/gmxlib/gmx_omp_nthreads.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/orires.h"
 #include "gromacs/gmxlib/nonbonded/nb_free_energy.h"
 #include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 #include "gromacs/gmxlib/nonbonded/nonbonded.h"
 #include "gromacs/imd/imd.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/listed-forces/bonded.h"
@@ -2842,6 +2842,4 @@ void init_md(FILE *fplog,
     clear_mat(force_vir);
     clear_mat(shake_vir);
     clear_rvec(mu_tot);
-
-    debug_gmx();
 }

diff --git a/src/gromacs/mdlib/stat.cpp b/src/gromacs/mdlib/stat.cpp
index 3237779026862ec1cddda2eafa04beb91af51eb1..8205b3bc5865ee89268158c6460b5c36ff9266b1 100644 (file)
--- a/src/gromacs/mdlib/stat.cpp
+++ b/src/gromacs/mdlib/stat.cpp
@@ -43,8 +43,8 @@
 #include "gromacs/fileio/checkpoint.h"
 #include "gromacs/fileio/txtdump.h"
 #include "gromacs/fileio/xtcio.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/group.h"
 #include "gromacs/math/utilities.h"

diff --git a/src/gromacs/mdlib/tgroup.cpp b/src/gromacs/mdlib/tgroup.cpp
index cd4e3d4468447d1287a2a3812c21783d3219bb98..d16142716893d622fda3edf3e9d93e87324c977d 100644 (file)
--- a/src/gromacs/mdlib/tgroup.cpp
+++ b/src/gromacs/mdlib/tgroup.cpp
@@ -42,7 +42,7 @@
 #include <math.h>
 
 #include "gromacs/gmxlib/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/network.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/types/group.h"
 #include "gromacs/legacyheaders/types/mdatom.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/mdlib/tpi.cpp b/src/gromacs/mdlib/tpi.cpp
index 42ba75b3f62be350e3d2cf1a3d7262feb3e514c8..74e8871bbf7679dd247a2174deb164767a1ff7f9 100644 (file)
--- a/src/gromacs/mdlib/tpi.cpp
+++ b/src/gromacs/mdlib/tpi.cpp
@@ -61,8 +61,8 @@
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxlib/chargegroup.h"
 #include "gromacs/gmxlib/conformation-utilities.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/group.h"

diff --git a/src/gromacs/mdlib/trajectory_writing.cpp b/src/gromacs/mdlib/trajectory_writing.cpp
index 0bd0cf2d8a8c2d97e57b7e077865892b7a6f5910..f179eb4b8270871803f1c0d93f04e6353edfbde5 100644 (file)
--- a/src/gromacs/mdlib/trajectory_writing.cpp
+++ b/src/gromacs/mdlib/trajectory_writing.cpp
@@ -146,7 +146,6 @@ do_md_trajectory_writing(FILE           *fplog,
         {
             (*nchkpt)++;
         }
-        debug_gmx();
         if (bLastStep && step_rel == ir->nsteps &&
             bDoConfOut && MASTER(cr) &&
             !bRerunMD)
@@ -188,7 +187,6 @@ do_md_trajectory_writing(FILE           *fplog,
             {
                 sfree(x_for_confout);
             }
-            debug_gmx();
         }
         wallcycle_stop(mdoutf_get_wcycle(outf), ewcTRAJ);
     }

diff --git a/src/gromacs/mdlib/update.cpp b/src/gromacs/mdlib/update.cpp
index e607ce389a875b00449e0808d8fda9a95e7883cb..c147cc39d036140ed6de6e96176526b758e67e23 100644 (file)
--- a/src/gromacs/mdlib/update.cpp
+++ b/src/gromacs/mdlib/update.cpp
@@ -47,6 +47,7 @@
 #include "gromacs/fileio/txtdump.h"
 #include "gromacs/gmxlib/disre.h"
 #include "gromacs/gmxlib/gmx_omp_nthreads.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/orires.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/nrnb.h"

diff --git a/src/gromacs/mdlib/vcm.cpp b/src/gromacs/mdlib/vcm.cpp
index 26e90fcd930d9a93f29479e7a8671a3ae49cf218..c371abff9bb258fa0a0d673d5718fc1dd93375a4 100644 (file)
--- a/src/gromacs/mdlib/vcm.cpp
+++ b/src/gromacs/mdlib/vcm.cpp
@@ -40,8 +40,8 @@
 #include "vcm.h"
 
 #include "gromacs/fileio/txtdump.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/mdlib/vsite.cpp b/src/gromacs/mdlib/vsite.cpp
index 479c849125902fc8691ff1525c4161356c767164..e624aec77bcefcfaeacf91d44da802dceeb15285 100644 (file)
--- a/src/gromacs/mdlib/vsite.cpp
+++ b/src/gromacs/mdlib/vsite.cpp
@@ -44,7 +44,7 @@
 
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/gmxlib/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/network.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/mdrunutility/handlerestart.cpp b/src/gromacs/mdrunutility/handlerestart.cpp
index 33a9fe7c58e974421dafea232059f543cd07c363..597e1b73397ba4386917cc1141bb80f679d8cd68 100644 (file)
--- a/src/gromacs/mdrunutility/handlerestart.cpp
+++ b/src/gromacs/mdrunutility/handlerestart.cpp
@@ -57,7 +57,7 @@
 #include "gromacs/fileio/filenm.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/gmxlib/main.h"
-#include "gromacs/legacyheaders/network.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/pulling/pull.cpp b/src/gromacs/pulling/pull.cpp
index 793a99784cc9d7e68c0d981c8d17ae625b2b7a41..3481cce59117f5bc557a6afc1109822770e08495 100644 (file)
--- a/src/gromacs/pulling/pull.cpp
+++ b/src/gromacs/pulling/pull.cpp
@@ -53,8 +53,8 @@
 #include "gromacs/fileio/filenm.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/mdatom.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/pulling/pull_rotation.cpp b/src/gromacs/pulling/pull_rotation.cpp
index 2787523992bc2655f0c2bb96f3cd18320cb9a427..5778dc00d45bf51ccb385f59d32b3a852f1f38b4 100644 (file)
--- a/src/gromacs/pulling/pull_rotation.cpp
+++ b/src/gromacs/pulling/pull_rotation.cpp
@@ -51,6 +51,7 @@
 #include "gromacs/fileio/copyrite.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/types/inputrec.h"
 #include "gromacs/linearalgebra/nrjac.h"

diff --git a/src/gromacs/pulling/pullutil.cpp b/src/gromacs/pulling/pullutil.cpp
index 2cf3732f68b42583b506cc482ab08e2edf4410c3..5a4db5f299ddd2c7cb97eb064a2af6d79559be21 100644 (file)
--- a/src/gromacs/pulling/pullutil.cpp
+++ b/src/gromacs/pulling/pullutil.cpp
@@ -43,8 +43,8 @@
 
 #include "gromacs/domdec/ga2la.h"
 #include "gromacs/fileio/confio.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/mdatom.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/swap/swapcoords.cpp b/src/gromacs/swap/swapcoords.cpp
index 5e20d19d3aeed12f93af77b70e7260311d3a3deb..e7a6f11f1642f94623dd3b2d8922dd2156ccf27f 100644 (file)
--- a/src/gromacs/swap/swapcoords.cpp
+++ b/src/gromacs/swap/swapcoords.cpp
@@ -53,8 +53,8 @@
 #include "gromacs/fileio/copyrite.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/types/inputrec.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/groupcoord.h"

diff --git a/src/gromacs/tables/forcetable.cpp b/src/gromacs/tables/forcetable.cpp
index 1f61eaa00e4f03bd8c519fb71384d6017b45f7f0..9bd2e245e3bc82a1019ac2c91b2053010a7b51d4 100644 (file)
--- a/src/gromacs/tables/forcetable.cpp
+++ b/src/gromacs/tables/forcetable.cpp
@@ -44,7 +44,6 @@
 
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/types/fcdata.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/utilities.h"

diff --git a/src/programs/mdrun/md.cpp b/src/programs/mdrun/md.cpp
index 7baa332b72eb041be019be6fde2ced916dde08aa..f1caaf3d051b7cebd081b9105b39e585b9aa6c49 100644 (file)
--- a/src/programs/mdrun/md.cpp
+++ b/src/programs/mdrun/md.cpp
@@ -54,9 +54,9 @@
 #include "gromacs/fileio/trx.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/gmxlib/md_logging.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/sighandler.h"
 #include "gromacs/imd/imd.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/enums.h"
@@ -332,7 +332,6 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
     ekind->cosacc.cos_accel = ir->cos_accel;
 
     gstat = global_stat_init(ir);
-    debug_gmx();
 
     /* Check for polarizable models and flexible constraints */
     shellfc = init_shell_flexcon(fplog,
@@ -529,8 +528,6 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
         }
     }
 
-    debug_gmx();
-
     if (IR_TWINRANGE(*ir) && repl_ex_nst % ir->nstcalclr != 0)
     {
         /* We should exchange at nstcalclr steps to get correct integration */
@@ -682,7 +679,6 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
     }
 #endif
 
-    debug_gmx();
     /***********************************************************
      *
      *             Loop over MD steps
@@ -1805,7 +1801,6 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
 
     }
     /* End of main MD loop */
-    debug_gmx();
 
     /* Closing TNG files can include compressing data. Therefore it is good to do that
      * before stopping the time measurements. */
@@ -1835,7 +1830,6 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
     }
 
     done_mdoutf(outf);
-    debug_gmx();
 
     if (bPMETune)
     {

diff --git a/src/programs/mdrun/mdrun.cpp b/src/programs/mdrun/mdrun.cpp
index e4a86f8f902d9f66226cb63263efb695d24c44a5..69136b0eb941c4a6ad55389a92c6b44084a3411b 100644 (file)
--- a/src/programs/mdrun/mdrun.cpp
+++ b/src/programs/mdrun/mdrun.cpp
@@ -60,8 +60,8 @@
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/filenm.h"
 #include "gromacs/gmxlib/main.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/readinp.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdrunutility/handlerestart.h"

diff --git a/src/programs/mdrun/membed.cpp b/src/programs/mdrun/membed.cpp
index 75d4646d075c87bf3e3b26bf7dd9db72fe288cb6..bae93fb040fbfcc87e6be8a65f7e898118ca5eef 100644 (file)
--- a/src/programs/mdrun/membed.cpp
+++ b/src/programs/mdrun/membed.cpp
@@ -41,9 +41,9 @@
 
 #include "gromacs/essentialdynamics/edsam.h"
 #include "gromacs/fileio/tpxio.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/readinp.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"

diff --git a/src/programs/mdrun/repl_ex.cpp b/src/programs/mdrun/repl_ex.cpp
index 62c8cd458ba964242d12fb197bc4a13b503a7b71..cbd74ac6541c66f5198a16976c8688914934d695 100644 (file)
--- a/src/programs/mdrun/repl_ex.cpp
+++ b/src/programs/mdrun/repl_ex.cpp
@@ -46,8 +46,8 @@
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/fileio/copyrite.h"
 #include "gromacs/gmxlib/main.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"

diff --git a/src/programs/mdrun/runner.cpp b/src/programs/mdrun/runner.cpp
index fe5e681847e92eca90a2b2a5f8b8f549958da7a4..7ff1a4e05496622d9029ae9af5ba60322631f835 100644 (file)
--- a/src/programs/mdrun/runner.cpp
+++ b/src/programs/mdrun/runner.cpp
@@ -68,12 +68,12 @@
 #include "gromacs/gmxlib/gmx_omp_nthreads.h"
 #include "gromacs/gmxlib/main.h"
 #include "gromacs/gmxlib/md_logging.h"
+#include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/orires.h"
 #include "gromacs/gmxlib/sighandler.h"
 #include "gromacs/gmxlib/thread_affinity.h"
 #include "gromacs/gmxlib/gpu_utils/gpu_utils.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
 #include "gromacs/math/calculate-ewald-splitting-coefficient.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/calc_verletbuf.h"