Move main.*, splitter.*, gmx_omp_nthreads.* to mdlib

Remove unused #includes for these headers, and remove some incorrect
uses, which showed that they are not actually used outside mdrun.
listed-forces -> mdlib dependency becomes slightly stronger with this,
but internal structure of mdrun code anyways needs a lot of work to
remove the dependency cycles.

Change-Id: If326c8da5a732ee725aa16ffad0ec72f9fefb371

diff --git a/src/gromacs/domdec/domdec.cpp b/src/gromacs/domdec/domdec.cpp
index 827c6ad5e4ee562f9ee739fc14a9d9f7f219cf3f..09d5e0dc0b104f2878b7dc057a8f1fc89155b2f8 100644 (file)
--- a/src/gromacs/domdec/domdec.cpp
+++ b/src/gromacs/domdec/domdec.cpp
@@ -54,7 +54,6 @@
 #include "gromacs/fileio/gmxfio.h"
 #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/nrnb.h"
 #include "gromacs/gpu_utils/gpu_utils.h"
@@ -67,6 +66,7 @@
 #include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/forcerec.h"
 #include "gromacs/mdlib/genborn.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
 #include "gromacs/mdlib/mdatoms.h"
 #include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/nb_verlet.h"

diff --git a/src/gromacs/domdec/domdec_constraints.cpp b/src/gromacs/domdec/domdec_constraints.cpp
index 7be14b46fd46f1716d7e976efdac08d9fbd0e6ce..2d14e388836b3041076c94fe43c1992073ea475e 100644 (file)
--- a/src/gromacs/domdec/domdec_constraints.cpp
+++ b/src/gromacs/domdec/domdec_constraints.cpp
@@ -53,9 +53,9 @@
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/domdec/domdec_struct.h"
 #include "gromacs/domdec/ga2la.h"
-#include "gromacs/gmxlib/gmx_omp_nthreads.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/topology/mtop_util.h"

diff --git a/src/gromacs/domdec/domdec_specatomcomm.cpp b/src/gromacs/domdec/domdec_specatomcomm.cpp
index ca6d2f0319262b1a9370b3285999bd9a85616b03..8d86f5f15644d42cc4b0571f95ce2b989da6881d 100644 (file)
--- a/src/gromacs/domdec/domdec_specatomcomm.cpp
+++ b/src/gromacs/domdec/domdec_specatomcomm.cpp
@@ -54,7 +54,6 @@
 #include "gromacs/domdec/domdec_network.h"
 #include "gromacs/domdec/domdec_struct.h"
 #include "gromacs/domdec/ga2la.h"
-#include "gromacs/gmxlib/gmx_omp_nthreads.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/pbcutil/ishift.h"

diff --git a/src/gromacs/domdec/domdec_topology.cpp b/src/gromacs/domdec/domdec_topology.cpp
index deb95ba3e6a76a6bf3a5ef0396e5cd4ba0b8f4a8..73df362986c43341cf6492da2ec993eef04fa2c4 100644 (file)
--- a/src/gromacs/domdec/domdec_topology.cpp
+++ b/src/gromacs/domdec/domdec_topology.cpp
@@ -56,11 +56,11 @@
 #include "gromacs/domdec/domdec_network.h"
 #include "gromacs/domdec/ga2la.h"
 #include "gromacs/gmxlib/chargegroup.h"
-#include "gromacs/gmxlib/gmx_omp_nthreads.h"
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/forcerec.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
 #include "gromacs/mdlib/vsite.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/inputrec.h"

diff --git a/src/gromacs/domdec/domdec_vsite.cpp b/src/gromacs/domdec/domdec_vsite.cpp
index be223bf8dcec0deb85cb0e2d852a2feb31412b60..d9848505351dec80dd19960b097f3ecfa0c667ca 100644 (file)
--- a/src/gromacs/domdec/domdec_vsite.cpp
+++ b/src/gromacs/domdec/domdec_vsite.cpp
@@ -53,7 +53,6 @@
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/domdec/domdec_struct.h"
 #include "gromacs/domdec/ga2la.h"
-#include "gromacs/gmxlib/gmx_omp_nthreads.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/pbcutil/ishift.h"

diff --git a/src/gromacs/gmxana/gmx_disre.cpp b/src/gromacs/gmxana/gmx_disre.cpp
index 37101cf22a9c4544a83a5442db34b8f5cd27094f..94675d62bcdc88a7659495d7abdab75440223d17 100644 (file)
--- a/src/gromacs/gmxana/gmx_disre.cpp
+++ b/src/gromacs/gmxana/gmx_disre.cpp
@@ -52,7 +52,6 @@
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/gmxana/gstat.h"
-#include "gromacs/gmxlib/main.h"
 #include "gromacs/gmxlib/nrnb.h"
 #include "gromacs/listed-forces/disre.h"
 #include "gromacs/math/do_fit.h"
@@ -955,7 +954,7 @@ int gmx_disre(int argc, char *argv[])
         }
     }
 
-    gmx_log_close(fplog);
+    gmx_ffclose(fplog);
 
     return 0;
 }

diff --git a/src/gromacs/gmxana/gmx_pme_error.cpp b/src/gromacs/gmxana/gmx_pme_error.cpp
index 58843980f73d652853347e80d13dea6219859290..fa1542d87883ae929fa3fbeb5b1b64951c1868c6 100644 (file)
--- a/src/gromacs/gmxana/gmx_pme_error.cpp
+++ b/src/gromacs/gmxana/gmx_pme_error.cpp
@@ -46,7 +46,6 @@
 #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/math/calculate-ewald-splitting-coefficient.h"
 #include "gromacs/math/units.h"

diff --git a/src/gromacs/gmxpreprocess/grompp.cpp b/src/gromacs/gmxpreprocess/grompp.cpp
index bc73d0db5a21d190c761a2379c9be658e276fb9b..e03d8eda4360b65d662d466e6a7a02128b584b77 100644 (file)
--- a/src/gromacs/gmxpreprocess/grompp.cpp
+++ b/src/gromacs/gmxpreprocess/grompp.cpp
@@ -55,7 +55,6 @@
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/warninp.h"
 #include "gromacs/gmxlib/calcgrid.h"
-#include "gromacs/gmxlib/splitter.h"
 #include "gromacs/gmxpreprocess/add_par.h"
 #include "gromacs/gmxpreprocess/convparm.h"
 #include "gromacs/gmxpreprocess/gen_maxwell_velocities.h"

diff --git a/src/gromacs/listed-forces/disre.cpp b/src/gromacs/listed-forces/disre.cpp
index 90443ff7f638231e2624cdbab1cc101024e8041e..a26023c64364f85eed4da188d986544e776d3fd0 100644 (file)
--- a/src/gromacs/listed-forces/disre.cpp
+++ b/src/gromacs/listed-forces/disre.cpp
@@ -47,9 +47,9 @@
 
 #include <algorithm>
 
-#include "gromacs/gmxlib/main.h"
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/main.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/fcdata.h"
 #include "gromacs/mdtypes/md_enums.h"

diff --git a/src/gromacs/listed-forces/manage-threading.cpp b/src/gromacs/listed-forces/manage-threading.cpp
index b4438d406a8a2ab69679e0ea04ebfede5f992340..4d0ba60c66319071e8d67b5c5b76e1c365c0e0de 100644 (file)
--- a/src/gromacs/listed-forces/manage-threading.cpp
+++ b/src/gromacs/listed-forces/manage-threading.cpp
@@ -51,8 +51,8 @@
 
 #include <algorithm>
 
-#include "gromacs/gmxlib/gmx_omp_nthreads.h"
 #include "gromacs/listed-forces/listed-forces.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/topology/ifunc.h"
 #include "gromacs/utility/exceptions.h"

diff --git a/src/gromacs/listed-forces/orires.cpp b/src/gromacs/listed-forces/orires.cpp
index 8bac1ae7890cf9b7675d89433538077457f50b7a..5dc8917e0ce23e45130f57fa6dba826de9e9cc54 100644 (file)
--- a/src/gromacs/listed-forces/orires.cpp
+++ b/src/gromacs/listed-forces/orires.cpp
@@ -40,11 +40,11 @@
 
 #include <cmath>
 
-#include "gromacs/gmxlib/main.h"
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/linearalgebra/nrjac.h"
 #include "gromacs/math/do_fit.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/main.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/fcdata.h"
 #include "gromacs/mdtypes/mdatom.h"

diff --git a/src/gromacs/mdlib/broadcaststructs.cpp b/src/gromacs/mdlib/broadcaststructs.cpp
index 789018915e2c03116179aac2c663ee64a07d4fc0..9da6b989cfd909c656db3aaf848fb44cb21443ab 100644 (file)
--- a/src/gromacs/mdlib/broadcaststructs.cpp
+++ b/src/gromacs/mdlib/broadcaststructs.cpp
@@ -39,7 +39,6 @@
 
 #include <string.h>
 
-#include "gromacs/gmxlib/main.h"
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/mdrun.h"

diff --git a/src/gromacs/mdlib/calcmu.cpp b/src/gromacs/mdlib/calcmu.cpp
index 6c544c0dea2e850e0d16ce195012bf079b8fd97d..c29e37005262a5c1ca1b0a8413865e358d9a319c 100644 (file)
--- a/src/gromacs/mdlib/calcmu.cpp
+++ b/src/gromacs/mdlib/calcmu.cpp
@@ -42,10 +42,10 @@
 #include <stdio.h>
 #include <stdlib.h>
 
-#include "gromacs/gmxlib/gmx_omp_nthreads.h"
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
 
 void calc_mu(int start, int homenr, rvec x[], real q[], real qB[],
              int nChargePerturbed,

diff --git a/src/gromacs/mdlib/clincs.cpp b/src/gromacs/mdlib/clincs.cpp
index c7520ce6f4ded8bc8481f3b47b692d8e6188bd67..6b14acc767615002f2ea044e6baca9819dcb2dab 100644 (file)
--- a/src/gromacs/mdlib/clincs.cpp
+++ b/src/gromacs/mdlib/clincs.cpp
@@ -48,11 +48,11 @@
 
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/domdec/domdec_struct.h"
-#include "gromacs/gmxlib/gmx_omp_nthreads.h"
 #include "gromacs/gmxlib/nrnb.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
 #include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/md_enums.h"

diff --git a/src/gromacs/mdlib/constr.cpp b/src/gromacs/mdlib/constr.cpp
index 289509e704da4dcf0e419a50ac7b09e28777dccd..e6c1957147b5a5029a1522a22c17660b6ba5af3b 100644 (file)
--- a/src/gromacs/mdlib/constr.cpp
+++ b/src/gromacs/mdlib/constr.cpp
@@ -51,11 +51,11 @@
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/pdbio.h"
-#include "gromacs/gmxlib/gmx_omp_nthreads.h"
 #include "gromacs/gmxlib/nrnb.h"
-#include "gromacs/gmxlib/splitter.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
 #include "gromacs/mdlib/mdrun.h"
+#include "gromacs/mdlib/splitter.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/md_enums.h"
 #include "gromacs/pbcutil/pbc.h"

diff --git a/src/gromacs/mdlib/coupling.cpp b/src/gromacs/mdlib/coupling.cpp
index 61cb4a481003302bfdd20e0b9549dd82166c582c..ff6f15ff9f3a57ae585d783043fd0b38720286a6 100644 (file)
--- a/src/gromacs/mdlib/coupling.cpp
+++ b/src/gromacs/mdlib/coupling.cpp
@@ -41,11 +41,11 @@
 #include <algorithm>
 
 #include "gromacs/domdec/domdec_struct.h"
-#include "gromacs/gmxlib/gmx_omp_nthreads.h"
 #include "gromacs/gmxlib/nrnb.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/math/vecdump.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
 #include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/sim_util.h"
 #include "gromacs/mdlib/update.h"

diff --git a/src/gromacs/mdlib/force.cpp b/src/gromacs/mdlib/force.cpp
index f076f9a3af8763193e52f785d5cdc2b60ac91d5d..cdd0daad5ca0af69a3e586fc212e8cc72acdc4a1 100644 (file)
--- a/src/gromacs/mdlib/force.cpp
+++ b/src/gromacs/mdlib/force.cpp
@@ -49,7 +49,6 @@
 #include "gromacs/ewald/ewald.h"
 #include "gromacs/ewald/long-range-correction.h"
 #include "gromacs/ewald/pme.h"
-#include "gromacs/gmxlib/gmx_omp_nthreads.h"
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/nrnb.h"
 #include "gromacs/gmxlib/nonbonded/nonbonded.h"

diff --git a/src/gromacs/mdlib/forcerec.cpp b/src/gromacs/mdlib/forcerec.cpp
index 4850834040cadff7db7b3baacbc34d47cac060bd..ba43def2816d8b579a2a9694b53b6ce549b7b681 100644 (file)
--- a/src/gromacs/mdlib/forcerec.cpp
+++ b/src/gromacs/mdlib/forcerec.cpp
@@ -52,7 +52,6 @@
 #include "gromacs/domdec/domdec_struct.h"
 #include "gromacs/ewald/ewald.h"
 #include "gromacs/fileio/filetypes.h"
-#include "gromacs/gmxlib/gmx_omp_nthreads.h"
 #include "gromacs/gmxlib/md_logging.h"
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/nonbonded/nonbonded.h"
@@ -65,6 +64,7 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/forcerec-threading.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
 #include "gromacs/mdlib/md_support.h"
 #include "gromacs/mdlib/nb_verlet.h"
 #include "gromacs/mdlib/nbnxn_atomdata.h"

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

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

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

diff --git a/src/gromacs/gmxlib/main.h b/src/gromacs/mdlib/main.h
similarity index 98%
rename from src/gromacs/gmxlib/main.h
rename to src/gromacs/mdlib/main.h
index 473c47cd19618d3db4cda9b7e213b051aad5664f..9bad47533e52bd04b7f7cd935799b85bf2f9387e 100644 (file)
--- a/src/gromacs/gmxlib/main.h
+++ b/src/gromacs/mdlib/main.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_MAIN_H
-#define GMX_GMXLIB_MAIN_H
+#ifndef GMX_MDLIB_MAIN_H
+#define GMX_MDLIB_MAIN_H
 
 #include <stdio.h>
 

diff --git a/src/gromacs/mdlib/mdatoms.cpp b/src/gromacs/mdlib/mdatoms.cpp
index 6eea20bb2f9a54e3cdc7ada08172984ffe40c704..de43bdd7bd3de21c1bb946be2b964933586ac931 100644 (file)
--- a/src/gromacs/mdlib/mdatoms.cpp
+++ b/src/gromacs/mdlib/mdatoms.cpp
@@ -40,7 +40,7 @@
 
 #include <math.h>
 
-#include "gromacs/gmxlib/gmx_omp_nthreads.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
 #include "gromacs/mdlib/qmmm.h"
 #include "gromacs/mdtypes/md_enums.h"
 #include "gromacs/topology/mtop_util.h"

diff --git a/src/gromacs/mdlib/minimize.cpp b/src/gromacs/mdlib/minimize.cpp
index 2b64a8c6f7bfa301c93f0dd93413a51322b59409..ea58576fc6811f4a2220c5f08a8d3e4ab94165e8 100644 (file)
--- a/src/gromacs/mdlib/minimize.cpp
+++ b/src/gromacs/mdlib/minimize.cpp
@@ -60,7 +60,6 @@
 #include "gromacs/ewald/pme.h"
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/mtxio.h"
-#include "gromacs/gmxlib/gmx_omp_nthreads.h"
 #include "gromacs/gmxlib/md_logging.h"
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/nrnb.h"
@@ -71,6 +70,7 @@
 #include "gromacs/mdlib/constr.h"
 #include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/forcerec.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
 #include "gromacs/mdlib/md_support.h"
 #include "gromacs/mdlib/mdatoms.h"
 #include "gromacs/mdlib/mdebin.h"

diff --git a/src/gromacs/mdlib/nbnxn_atomdata.cpp b/src/gromacs/mdlib/nbnxn_atomdata.cpp
index 9ae18bf2f0f111a4c479ed215d4b535945eac046..4827cf1b2b03cf4c2afa0d5cb99bbd9608dd4fba 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_atomdata.cpp
+++ b/src/gromacs/mdlib/nbnxn_atomdata.cpp
@@ -49,8 +49,8 @@
 
 #include "thread_mpi/atomic.h"
 
-#include "gromacs/gmxlib/gmx_omp_nthreads.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
 #include "gromacs/mdlib/nb_verlet.h"
 #include "gromacs/mdlib/nbnxn_consts.h"
 #include "gromacs/mdlib/nbnxn_internal.h"

diff --git a/src/gromacs/mdlib/nbnxn_grid.cpp b/src/gromacs/mdlib/nbnxn_grid.cpp
index b0c92a1087417444b66c774b8a292aeda68fe389..7eed056f582e68a438e7f7d2a838b1845f6148ab 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_grid.cpp
+++ b/src/gromacs/mdlib/nbnxn_grid.cpp
@@ -47,9 +47,9 @@
 #include <algorithm>
 
 #include "gromacs/domdec/domdec_struct.h"
-#include "gromacs/gmxlib/gmx_omp_nthreads.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
 #include "gromacs/mdlib/nb_verlet.h"
 #include "gromacs/mdlib/nbnxn_atomdata.h"
 #include "gromacs/mdlib/nbnxn_consts.h"

diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.cpp.pre b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.cpp.pre
index 4383a37bd651d3f03ae1f48caf4ff596bbb14296..5af77c5ce97539c9d307e68bfe699f8cd9387c4b 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.cpp.pre
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.cpp.pre
@@ -50,8 +50,8 @@
 #define GMX_SIMD_J_UNROLL_SIZE {3}
 #include "{4}"
 
-#include "gromacs/gmxlib/gmx_omp_nthreads.h"
 #include "gromacs/mdlib/force_flags.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
 #include "gromacs/simd/simd.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp
index bf7ab218241a5504bc4ea37a8cb743fd5bd4faec..cac6c13a1f029f84afc1d103029c4f50148a9d30 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp
@@ -42,9 +42,9 @@
 
 #include <cmath>
 
-#include "gromacs/gmxlib/gmx_omp_nthreads.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/force.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
 #include "gromacs/mdlib/nb_verlet.h"
 #include "gromacs/mdlib/nbnxn_consts.h"
 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"

diff --git a/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.cpp b/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.cpp
index b42443845c87173d29fc6ff27c1a059e01e73eb6..515af5b6cfa40ee8b9e0f41e930bd1ca7a07239c 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.cpp
+++ b/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.cpp
@@ -59,8 +59,8 @@
 #define GMX_SIMD_J_UNROLL_SIZE 2
 #include "nbnxn_kernel_simd_2xnn.h"
 
-#include "gromacs/gmxlib/gmx_omp_nthreads.h"
 #include "gromacs/mdlib/force_flags.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
 #include "gromacs/simd/simd.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.cpp b/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.cpp
index 0203a96a23e1ba9cea78c98786a50e7c209b364c..b57ad33376789b00fd37ea676fa1c9224a35d8ad 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.cpp
+++ b/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.cpp
@@ -58,8 +58,8 @@
 #define GMX_SIMD_J_UNROLL_SIZE 1
 #include "nbnxn_kernel_simd_4xn.h"
 
-#include "gromacs/gmxlib/gmx_omp_nthreads.h"
 #include "gromacs/mdlib/force_flags.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
 #include "gromacs/simd/simd.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/mdlib/nbnxn_search.cpp b/src/gromacs/mdlib/nbnxn_search.cpp
index 4a4e560c5575447671ee9eb64eeccfeb86cbfee0..1835f8eaab7c8678590af6e787ec23f761ee9483 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_search.cpp
+++ b/src/gromacs/mdlib/nbnxn_search.cpp
@@ -47,10 +47,10 @@
 #include <algorithm>
 
 #include "gromacs/domdec/domdec_struct.h"
-#include "gromacs/gmxlib/gmx_omp_nthreads.h"
 #include "gromacs/gmxlib/nrnb.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
 #include "gromacs/mdlib/nb_verlet.h"
 #include "gromacs/mdlib/nbnxn_atomdata.h"
 #include "gromacs/mdlib/nbnxn_consts.h"

diff --git a/src/gromacs/mdlib/sim_util.cpp b/src/gromacs/mdlib/sim_util.cpp
index 5a235a43fde72c84609b3fe3b77a648183740ab0..9c69b38f9ecdbc3243af863a6c2a319bd2187ed2 100644 (file)
--- a/src/gromacs/mdlib/sim_util.cpp
+++ b/src/gromacs/mdlib/sim_util.cpp
@@ -52,7 +52,6 @@
 #include "gromacs/essentialdynamics/edsam.h"
 #include "gromacs/ewald/pme.h"
 #include "gromacs/gmxlib/chargegroup.h"
-#include "gromacs/gmxlib/gmx_omp_nthreads.h"
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/nrnb.h"
 #include "gromacs/gmxlib/nonbonded/nb_free_energy.h"
@@ -70,6 +69,7 @@
 #include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/forcerec.h"
 #include "gromacs/mdlib/genborn.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
 #include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/nb_verlet.h"
 #include "gromacs/mdlib/nbnxn_atomdata.h"

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

diff --git a/src/gromacs/gmxlib/splitter.h b/src/gromacs/mdlib/splitter.h
similarity index 97%
rename from src/gromacs/gmxlib/splitter.h
rename to src/gromacs/mdlib/splitter.h
index 5377cbe50ed9d8cde7ec4597347dc52e7ade446d..ee784ba1f9e3ed66c1ef8bfe7c1d6ddb29e3316e 100644 (file)
--- a/src/gromacs/gmxlib/splitter.h
+++ b/src/gromacs/mdlib/splitter.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_SPLITTER_H
-#define GMX_GMXLIB_SPLITTER_H
+#ifndef GMX_MDLIB_SPLITTER_H
+#define GMX_MDLIB_SPLITTER_H
 
 #include <cstdio>
 

diff --git a/src/gromacs/mdlib/tgroup.cpp b/src/gromacs/mdlib/tgroup.cpp
index e88b99f1cc1a238735f092a735dd0865e28ce44e..e8e117b4287b59f823de629bb02c7fa0e36d8436 100644 (file)
--- a/src/gromacs/mdlib/tgroup.cpp
+++ b/src/gromacs/mdlib/tgroup.cpp
@@ -41,9 +41,9 @@
 
 #include <math.h>
 
-#include "gromacs/gmxlib/gmx_omp_nthreads.h"
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
 #include "gromacs/mdlib/rbin.h"
 #include "gromacs/mdlib/update.h"
 #include "gromacs/mdtypes/group.h"

diff --git a/src/gromacs/mdlib/update.cpp b/src/gromacs/mdlib/update.cpp
index 5b57a4d49d3f3db4f524e8878e1ec591134e6aef..185ff1af67142cf4f2bbeab51b3b6c312a5dc01d 100644 (file)
--- a/src/gromacs/mdlib/update.cpp
+++ b/src/gromacs/mdlib/update.cpp
@@ -45,7 +45,6 @@
 
 #include "gromacs/domdec/domdec_struct.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/gmxlib/gmx_omp_nthreads.h"
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/nrnb.h"
 #include "gromacs/listed-forces/disre.h"
@@ -55,6 +54,7 @@
 #include "gromacs/math/vecdump.h"
 #include "gromacs/mdlib/constr.h"
 #include "gromacs/mdlib/force.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
 #include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/sim_util.h"
 #include "gromacs/mdlib/tgroup.h"

diff --git a/src/gromacs/mdlib/vsite.cpp b/src/gromacs/mdlib/vsite.cpp
index 5e99a59387ee10456db18fadf5a8d01137ec89b5..65148c686a7d3a94c84f71a7c8dcf1c61caa12b4 100644 (file)
--- a/src/gromacs/mdlib/vsite.cpp
+++ b/src/gromacs/mdlib/vsite.cpp
@@ -44,10 +44,10 @@
 
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/domdec/domdec_struct.h"
-#include "gromacs/gmxlib/gmx_omp_nthreads.h"
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/nrnb.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"

diff --git a/src/gromacs/mdrunutility/handlerestart.cpp b/src/gromacs/mdrunutility/handlerestart.cpp
index def87e31d86ac2f55be0cd2b8e6800e64c863ff8..0b0b2acfc6ff19aa10e8f8a560f6fcdcff7836eb 100644 (file)
--- a/src/gromacs/mdrunutility/handlerestart.cpp
+++ b/src/gromacs/mdrunutility/handlerestart.cpp
@@ -56,8 +56,8 @@
 #include "gromacs/commandline/filenm.h"
 #include "gromacs/fileio/checkpoint.h"
 #include "gromacs/fileio/gmxfio.h"
-#include "gromacs/gmxlib/main.h"
 #include "gromacs/gmxlib/network.h"
+#include "gromacs/mdlib/main.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/mdrunutility/threadaffinity.cpp b/src/gromacs/mdrunutility/threadaffinity.cpp
index aabe94144d873af75a7a0676b62d47263e9cee4a..85fa39c533f590d3ccb3e1bc2bf87993b38ff84f 100644 (file)
--- a/src/gromacs/mdrunutility/threadaffinity.cpp
+++ b/src/gromacs/mdrunutility/threadaffinity.cpp
@@ -49,10 +49,10 @@
 
 #include "thread_mpi/threads.h"
 
-#include "gromacs/gmxlib/gmx_omp_nthreads.h"
 #include "gromacs/gmxlib/md_logging.h"
 #include "gromacs/hardware/hardwaretopology.h"
 #include "gromacs/hardware/hw_info.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/utility/basenetwork.h"
 #include "gromacs/utility/cstringutil.h"

diff --git a/src/programs/mdrun/mdrun.cpp b/src/programs/mdrun/mdrun.cpp
index d9253c26503575591d24dc8c0d3b735c1f74b57a..ab1e4d3be9a9f55642eae5f716279e53aff210b9 100644 (file)
--- a/src/programs/mdrun/mdrun.cpp
+++ b/src/programs/mdrun/mdrun.cpp
@@ -60,8 +60,8 @@
 #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/mdlib/main.h"
 #include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdrunutility/handlerestart.h"
 #include "gromacs/mdtypes/commrec.h"

diff --git a/src/programs/mdrun/repl_ex.cpp b/src/programs/mdrun/repl_ex.cpp
index 05867f110ea0fc3433746b8648b8b9a4f8ef81d9..3b17b7315a85fd5d9b066aa73a8b31226e0ba417 100644 (file)
--- a/src/programs/mdrun/repl_ex.cpp
+++ b/src/programs/mdrun/repl_ex.cpp
@@ -44,10 +44,10 @@
 #include <math.h>
 
 #include "gromacs/domdec/domdec.h"
-#include "gromacs/gmxlib/main.h"
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/main.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/md_enums.h"
 #include "gromacs/random/random.h"

diff --git a/src/programs/mdrun/resource-division.cpp b/src/programs/mdrun/resource-division.cpp
index 202375f246b4a5004de22b5e5b50654bfd0a9427..93acfa87f24b3a63c7bff88973fdccf6ff52393f 100644 (file)
--- a/src/programs/mdrun/resource-division.cpp
+++ b/src/programs/mdrun/resource-division.cpp
@@ -44,13 +44,13 @@
 
 #include <algorithm>
 
-#include "gromacs/gmxlib/gmx_omp_nthreads.h"
 #include "gromacs/gmxlib/md_logging.h"
 #include "gromacs/hardware/cpuinfo.h"
 #include "gromacs/hardware/detecthardware.h"
 #include "gromacs/hardware/gpu_hw_info.h"
 #include "gromacs/hardware/hardwaretopology.h"
 #include "gromacs/hardware/hw_info.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/mdtypes/md_enums.h"

diff --git a/src/programs/mdrun/runner.cpp b/src/programs/mdrun/runner.cpp
index 0038dcf5401bc06988ebf1c92f3ec7589ac748fd..c7e944d8a4be4343b7cd074218db10665603a3c3 100644 (file)
--- a/src/programs/mdrun/runner.cpp
+++ b/src/programs/mdrun/runner.cpp
@@ -62,8 +62,6 @@
 #include "gromacs/fileio/checkpoint.h"
 #include "gromacs/fileio/oenv.h"
 #include "gromacs/fileio/tpxio.h"
-#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/gpu_utils/gpu_utils.h"
@@ -76,7 +74,9 @@
 #include "gromacs/mdlib/constr.h"
 #include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/forcerec.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
 #include "gromacs/mdlib/integrator.h"
+#include "gromacs/mdlib/main.h"
 #include "gromacs/mdlib/md_support.h"
 #include "gromacs/mdlib/mdatoms.h"
 #include "gromacs/mdlib/mdrun.h"