Rename all source files from - to _ for consistency.

Refs #2839

Change-Id: I3a1af667b2b266b1fd65586445b5e7a8a1b6b618

diff --git a/docs/dev-manual/build-system.rst b/docs/dev-manual/build-system.rst
index 020a35fec069f34cf6365961750e9fb9aee2edac..fbdbedb2f462d11f9681667a63d41acf368761cc 100644 (file)
--- a/docs/dev-manual/build-system.rst
+++ b/docs/dev-manual/build-system.rst
@@ -543,6 +543,6 @@ The build system uses a few different mechanisms to influence the compilation:
   Additionally, the following file is generated by the build system:
 
   :file:`baseversion-gen.cpp`
-    Provides definitions for declarations in :file:`baseversion-gen.h` for
+    Provides definitions for declarations in :file:`baseversion_gen.h` for
     version info output.  The contents are generated either from Git version
     info, or from static version info if not building from a git repository.

diff --git a/docs/dev-manual/gmxtree.rst b/docs/dev-manual/gmxtree.rst
index 2fc13566cdab46decfece57f3c777de5757f0265..f09a9ba45ab6468e9426ab4f53927bcf4c88dc6a 100644 (file)
--- a/docs/dev-manual/gmxtree.rst
+++ b/docs/dev-manual/gmxtree.rst
@@ -90,7 +90,7 @@ module and documenting it.
     modules, using ``gmx_install_headers()``.
   * All source files must include "gmxpre.h" as the first header.
   * A source/header file should include "config.h," "gromacs/simd/simd.h",
-    or "gromacs/ewald/pme-simd.h" if and only if it uses a macro declared
+    or "gromacs/ewald/pme_simd.h" if and only if it uses a macro declared
     in such files.
   * If the file has a git attribute to identify it as a candidate for include
     sorting, the include sorter described below should not produce any

diff --git a/docs/dev-manual/naming.rst b/docs/dev-manual/naming.rst
index 8a839d26f53d301af591bce0be99ef6762bc4637..a9ba6d0ccfb3c31d5095c613c0b71016837473be 100644 (file)
--- a/docs/dev-manual/naming.rst
+++ b/docs/dev-manual/naming.rst
@@ -20,9 +20,9 @@ Files
   readability and/or usability of the API, but this should then be clearly
   documented.
 
-  There can also be a :file:`{file}-impl.h` file that declares classes or
+  There can also be a :file:`{file}_impl.h` file that declares classes or
   functions that are not accessible outside the module.  If the whole file only
-  declares symbols internal to the module, then the :file:`-impl.h` suffix is
+  declares symbols internal to the module, then the :file:`_impl.h` suffix is
   omitted.
 
   In most cases, declarations that are not used outside a single source file

diff --git a/docs/doxygen/gmxtree.py b/docs/doxygen/gmxtree.py
index b9f9be7c76181c1311866163b1510fa86762a873..8f0dc41f2241b5fd82ab9531dead6885d67ccf9e 100644 (file)
--- a/docs/doxygen/gmxtree.py
+++ b/docs/doxygen/gmxtree.py
@@ -2,7 +2,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2014,2015,2016,2017,2018, by the GROMACS development team, led by
+# Copyright (c) 2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -1079,5 +1079,5 @@ class GromacsTree(object):
         be checked."""
         return (self._files['src/config.h'],
                 self._files['src/gromacs/simd/simd.h'],
-                self._files['src/gromacs/ewald/pme-simd.h'],
+                self._files['src/gromacs/ewald/pme_simd.h'],
                 self._files['src/gromacs/mdlib/nbnxn_simd.h'])

diff --git a/docs/doxygen/lib/simd.md b/docs/doxygen/lib/simd.md
index cbdbf3bd9ad294d1ff0116fc014de9f1c45e89aa..1363f3728f5443f56adf4af1a94c87cf2effa3b6 100644 (file)
--- a/docs/doxygen/lib/simd.md
+++ b/docs/doxygen/lib/simd.md
@@ -589,7 +589,7 @@ performance problem if the code does not correctly include
 `make check-source` checks the whole code for the use of symbols defined
 in `gromacs/simd/simd.h` and requires that files using those symbols
 do the correct include. Similar checking is done for higher-level
-SIMD-management headers, e.g. `gromacs/ewald/pme-simd.h`.
+SIMD-management headers, e.g. `gromacs/ewald/pme_simd.h`.
 
 
 The SIMD math library

diff --git a/docs/doxygen/suppressions.txt b/docs/doxygen/suppressions.txt
index dcbf13ce0add7c32299c69d77660bbdd2868627b..3bfccc1c8068e536e97cbebe47a0b9dd6cc9d456 100644 (file)
--- a/docs/doxygen/suppressions.txt
+++ b/docs/doxygen/suppressions.txt
@@ -15,10 +15,10 @@ src/gromacs/utility/baseversion-gen.cpp: warning: does not include "gmxpre.h" fi
 # Exclude header files that are used for inlining code; the responsibility for
 # making the right #includes should be on the source file that uses these.
 # TODO: # Stop using the preprocessor for meta-programming!
-src/gromacs/ewald/pme-simd4.h: warning: should include "pme-simd.h"
-src/gromacs/ewald/pme-spline-work.cpp: warning: includes "simd.h" unnecessarily
-src/gromacs/ewald/pme-spline-work.h: warning: includes "simd.h" unnecessarily
-src/gromacs/ewald/pme-spread.cpp: warning: includes "simd.h" unnecessarily
+src/gromacs/ewald/pme_simd4.h: warning: should include "pme_simd.h"
+src/gromacs/ewald/pme_spline_work.cpp: warning: includes "simd.h" unnecessarily
+src/gromacs/ewald/pme_spline_work.h: warning: includes "simd.h" unnecessarily
+src/gromacs/ewald/pme_spread.cpp: warning: includes "simd.h" unnecessarily
 src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_inner.h: warning: should include "simd.h"
 src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h: warning: should include "simd.h"
 src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_inner.h: warning: should include "simd.h"

diff --git a/src/api/cpp/context.cpp b/src/api/cpp/context.cpp
index d11571e878f40708c8aec7c509a65bbecf6f2601..9c2398179c5bd43537a37a914b1fc84bc61f9a2f 100644 (file)
--- a/src/api/cpp/context.cpp
+++ b/src/api/cpp/context.cpp
@@ -70,9 +70,9 @@
 #include "gmxapi/status.h"
 #include "gmxapi/version.h"
 
-#include "context-impl.h"
+#include "context_impl.h"
 #include "createsession.h"
-#include "session-impl.h"
+#include "session_impl.h"
 #include "workflow.h"
 
 namespace gmxapi

diff --git a/src/api/cpp/context-impl.h b/src/api/cpp/context_impl.h
similarity index 98%
rename from src/api/cpp/context-impl.h
rename to src/api/cpp/context_impl.h
index 7b8ca47aae307c53af1627bb420a565c3fe7b852..0d90d1587c1ec800899f1557b57092be6aaa8d93 100644 (file)
--- a/src/api/cpp/context-impl.h
+++ b/src/api/cpp/context_impl.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/api/cpp/md.cpp b/src/api/cpp/md.cpp
index 5d235301f091f2bbfa8b6490cf932378f9edb883..6ac41b7be2a5a60bfa68147179adf6d8ac7f4d53 100644 (file)
--- a/src/api/cpp/md.cpp
+++ b/src/api/cpp/md.cpp
@@ -42,7 +42,7 @@
 #include "gmxapi/gmxapi.h"
 #include "gmxapi/md/mdmodule.h"
 
-#include "md-impl.h"
+#include "md_impl.h"
 
 namespace gmxapi
 {

diff --git a/src/api/cpp/md-impl.h b/src/api/cpp/md_impl.h
similarity index 97%
rename from src/api/cpp/md-impl.h
rename to src/api/cpp/md_impl.h
index aa2a70d9eaf952e1d067f12220e7667520700ba6..8eeda00d9efd2e496f65f6b27ce07704e458ab68 100644 (file)
--- a/src/api/cpp/md-impl.h
+++ b/src/api/cpp/md_impl.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/api/cpp/mdsignals.h b/src/api/cpp/mdsignals.h
index 2ebdd17f85474ef0465ef4b6a7e116e978546459..f5717a3f10d2e15678f5cc37ab00eb6a9487a25c 100644 (file)
--- a/src/api/cpp/mdsignals.h
+++ b/src/api/cpp/mdsignals.h
@@ -53,7 +53,7 @@
 #include "gmxapi/session.h"
 #include "gmxapi/md/mdsignals.h"
 
-#include "session-impl.h"
+#include "session_impl.h"
 
 namespace gmxapi
 {

diff --git a/src/api/cpp/session.cpp b/src/api/cpp/session.cpp
index a5bfd0d62402f00a0361eb1575a18e9ea132d60e..d1abc69eb1096d4dc3415f5b1568f05ea931a183 100644 (file)
--- a/src/api/cpp/session.cpp
+++ b/src/api/cpp/session.cpp
@@ -56,7 +56,7 @@
 
 #include "createsession.h"
 #include "mdsignals.h"
-#include "session-impl.h"
+#include "session_impl.h"
 #include "sessionresources.h"
 
 namespace gmxapi

diff --git a/src/api/cpp/session-impl.h b/src/api/cpp/session_impl.h
similarity index 98%
rename from src/api/cpp/session-impl.h
rename to src/api/cpp/session_impl.h
index 8c0d7488dfb6760753d5d3f04b807835775b8d9d..2f9373882661bb8d0df94e6c857b2429d6ea5fc4 100644 (file)
--- a/src/api/cpp/session-impl.h
+++ b/src/api/cpp/session_impl.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -59,7 +59,7 @@ namespace gmxapi
 // Forward declaration
 class MpiContextManager; // Locally defined in session.cpp
 class ContextImpl;       // locally defined in context.cpp
-class SignalManager;     // defined in mdsignals-impl.h
+class SignalManager;     // defined in mdsignals_impl.h
 
 /*!
  * \brief Implementation class for executing sessions.

diff --git a/src/api/cpp/system.cpp b/src/api/cpp/system.cpp
index 2493b0b8e3add8b5a34ac50976aee46767327e9e..666a14f4c449093aff419880f3604828ff4d60ca 100644 (file)
--- a/src/api/cpp/system.cpp
+++ b/src/api/cpp/system.cpp
@@ -47,7 +47,7 @@
 #include "gmxapi/status.h"
 #include "gmxapi/system.h"
 
-#include "system-impl.h"
+#include "system_impl.h"
 #include "workflow.h"
 
 namespace gmxapi

diff --git a/src/api/cpp/system-impl.h b/src/api/cpp/system_impl.h
similarity index 97%
rename from src/api/cpp/system-impl.h
rename to src/api/cpp/system_impl.h
index 26e400af1bc44fe31f418d150d3ac4b5720ca265..109de3f6380cc2f0d573c0f41afae91eefa15b3d 100644 (file)
--- a/src/api/cpp/system-impl.h
+++ b/src/api/cpp/system_impl.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/api/cpp/workflow.cpp b/src/api/cpp/workflow.cpp
index cf90d806fb0ba287a533390572dca524aafff7fe..5996d509ddbdab22540c882b39f54328269ed6aa 100644 (file)
--- a/src/api/cpp/workflow.cpp
+++ b/src/api/cpp/workflow.cpp
@@ -39,7 +39,7 @@
 
 #include "gromacs/utility/gmxassert.h"
 
-#include "workflow-impl.h"
+#include "workflow_impl.h"
 
 namespace gmxapi
 {

diff --git a/src/api/cpp/workflow/tests/workflow.cpp b/src/api/cpp/workflow/tests/workflow.cpp
index ec04474bb4055985b9793943b36e2376121803cc..75a92a8713f31fbe737426b57aa9d4deecba8404 100644 (file)
--- a/src/api/cpp/workflow/tests/workflow.cpp
+++ b/src/api/cpp/workflow/tests/workflow.cpp
@@ -36,7 +36,7 @@
 #include <memory>
 
 #include "api/cpp/workflow.h"
-#include "api/cpp/workflow-impl.h"
+#include "api/cpp/workflow_impl.h"
 #include "api/cpp/include/gmxapi/context.h"
 #include "api/cpp/include/gmxapi/status.h"
 #include "api/cpp/include/gmxapi/system.h"

diff --git a/src/api/cpp/workflow-impl.h b/src/api/cpp/workflow_impl.h
similarity index 97%
rename from src/api/cpp/workflow-impl.h
rename to src/api/cpp/workflow_impl.h
index 57c6161d250f8a95d827192b90c7770908d69126..20efb36b33d83c796f7685e7b46748241003621a 100644 (file)
--- a/src/api/cpp/workflow-impl.h
+++ b/src/api/cpp/workflow_impl.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/CMakeLists.txt b/src/gromacs/CMakeLists.txt
index 4e242f1cc7c6508676135fd5cb1cbce13891a0e4..b4eb9e476ff842e928386e85980be21796d11aaf 100644 (file)
--- a/src/gromacs/CMakeLists.txt
+++ b/src/gromacs/CMakeLists.txt
@@ -95,7 +95,7 @@ endfunction()
 
 add_subdirectory(gmxlib)
 add_subdirectory(mdlib)
-add_subdirectory(applied-forces)
+add_subdirectory(applied_forces)
 add_subdirectory(listed_forces)
 add_subdirectory(commandline)
 add_subdirectory(domdec)
@@ -435,12 +435,12 @@ if(GMX_USE_OPENCL)
 
     # Install the PME source and headers
     file(GLOB OPENCL_INSTALLED_FILES
-        ewald/pme-spread.clh
-        ewald/pme-solve.clh
-        ewald/pme-gather.clh
-        ewald/pme-gpu-utils.clh
-        ewald/pme-program.cl
-        ewald/pme-gpu-types.h
+        ewald/pme_spread.clh
+        ewald/pme_solve.clh
+        ewald/pme_gather.clh
+        ewald/pme_gpu_utils.clh
+        ewald/pme_program.cl
+        ewald/pme_gpu_types.h
         )
     install(FILES ${OPENCL_INSTALLED_FILES}
         DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/ewald

diff --git a/src/gromacs/applied-forces/CMakeLists.txt b/src/gromacs/applied_forces/CMakeLists.txt
similarity index 95%
rename from src/gromacs/applied-forces/CMakeLists.txt
rename to src/gromacs/applied_forces/CMakeLists.txt
index 702e776e0fd402e0e17baf7306d49ea3972b8145..1bb3b7033fe3c9857ef5dda0ea9317ec4dee1f80 100644 (file)
--- a/src/gromacs/applied-forces/CMakeLists.txt
+++ b/src/gromacs/applied_forces/CMakeLists.txt
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2015,2016,2019, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/applied-forces/electricfield.cpp b/src/gromacs/applied_forces/electricfield.cpp
similarity index 99%
rename from src/gromacs/applied-forces/electricfield.cpp
rename to src/gromacs/applied_forces/electricfield.cpp
index 730aa55c432f63d8ff4a64d77175e3ced92d529c..5b6678f8f6e89695f8b4b51953801b81eb5b3b81 100644 (file)
--- a/src/gromacs/applied-forces/electricfield.cpp
+++ b/src/gromacs/applied_forces/electricfield.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/applied-forces/electricfield.h b/src/gromacs/applied_forces/electricfield.h
similarity index 97%
rename from src/gromacs/applied-forces/electricfield.h
rename to src/gromacs/applied_forces/electricfield.h
index a5d0f8f9517bba5d4a3b1d07d43a93da9a8c9914..a68d48840baeaa5dfda3f0770f0aa2dd6d8fcdac 100644 (file)
--- a/src/gromacs/applied-forces/electricfield.h
+++ b/src/gromacs/applied_forces/electricfield.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/applied-forces/tests/CMakeLists.txt b/src/gromacs/applied_forces/tests/CMakeLists.txt
similarity index 92%
rename from src/gromacs/applied-forces/tests/CMakeLists.txt
rename to src/gromacs/applied_forces/tests/CMakeLists.txt
index 378898696114b1b7fecee6ffd004a386c95da830..d0c94c0ed3dbc054c0296e196700364fe7e8c3e3 100644 (file)
--- a/src/gromacs/applied-forces/tests/CMakeLists.txt
+++ b/src/gromacs/applied_forces/tests/CMakeLists.txt
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2015,2016,2019, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -32,6 +32,6 @@
 # To help us fund GROMACS development, we humbly ask that you cite
 # the research papers on the package. Check out http://www.gromacs.org.
 
-gmx_add_unit_test(AppliedForcesUnitTest applied-forces-test
+gmx_add_unit_test(AppliedForcesUnitTest applied_forces-test
                   electricfield.cpp
                 )

diff --git a/src/gromacs/applied-forces/tests/electricfield.cpp b/src/gromacs/applied_forces/tests/electricfield.cpp
similarity index 97%
rename from src/gromacs/applied-forces/tests/electricfield.cpp
rename to src/gromacs/applied_forces/tests/electricfield.cpp
index f9ba3950a8d5a7db2d369120a528509141e893b8..82c983e0efd94529d1b67260c033f8aa13081133 100644 (file)
--- a/src/gromacs/applied-forces/tests/electricfield.cpp
+++ b/src/gromacs/applied_forces/tests/electricfield.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/applied-forces/electricfield.h"
+#include "gromacs/applied_forces/electricfield.h"
 
 #include <gtest/gtest.h>
 

diff --git a/src/gromacs/awh/awh.cpp b/src/gromacs/awh/awh.cpp
index 1e731a6fd8ba1e7a5aaf0e7d86a5d763fa996aa8..87bc0812a2917fd7cfaf21b10ddef682be012742 100644 (file)
--- a/src/gromacs/awh/awh.cpp
+++ b/src/gromacs/awh/awh.cpp
@@ -57,12 +57,12 @@
 #include "gromacs/fileio/enxio.h"
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/math/units.h"
-#include "gromacs/mdtypes/awh-history.h"
-#include "gromacs/mdtypes/awh-params.h"
+#include "gromacs/mdtypes/awh_history.h"
+#include "gromacs/mdtypes/awh_params.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/forceoutput.h"
 #include "gromacs/mdtypes/inputrec.h"
-#include "gromacs/mdtypes/pull-params.h"
+#include "gromacs/mdtypes/pull_params.h"
 #include "gromacs/mdtypes/state.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pulling/pull.h"

diff --git a/src/gromacs/awh/bias.cpp b/src/gromacs/awh/bias.cpp
index 3c39990acbc191b760488fd51f1f5000090ba065..ecba420798f3a98d72d94f191eee63844c6ca0c7 100644 (file)
--- a/src/gromacs/awh/bias.cpp
+++ b/src/gromacs/awh/bias.cpp
@@ -60,8 +60,8 @@
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/math/utilities.h"
-#include "gromacs/mdtypes/awh-history.h"
-#include "gromacs/mdtypes/awh-params.h"
+#include "gromacs/mdtypes/awh_history.h"
+#include "gromacs/mdtypes/awh_params.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"

diff --git a/src/gromacs/awh/biasparams.cpp b/src/gromacs/awh/biasparams.cpp
index f4db497002dc7ff453a6d8e936e792b36761acdb..a02f4e4d8d93b3a4688ddc6bfecfa298c57433f0 100644 (file)
--- a/src/gromacs/awh/biasparams.cpp
+++ b/src/gromacs/awh/biasparams.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -51,7 +51,7 @@
 #include <algorithm>
 
 #include "gromacs/math/functions.h"
-#include "gromacs/mdtypes/awh-params.h"
+#include "gromacs/mdtypes/awh_params.h"
 #include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"

diff --git a/src/gromacs/awh/biassharing.cpp b/src/gromacs/awh/biassharing.cpp
index 0dfe8acec3c6c3eb94416f9e2f96c44b4665e610..ca752a9845a5fdb84a60b34e72272cfbd63e538b 100644 (file)
--- a/src/gromacs/awh/biassharing.cpp
+++ b/src/gromacs/awh/biassharing.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -48,7 +48,7 @@
 #include <vector>
 
 #include "gromacs/gmxlib/network.h"
-#include "gromacs/mdtypes/awh-params.h"
+#include "gromacs/mdtypes/awh_params.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/stringutil.h"

diff --git a/src/gromacs/awh/biasstate.cpp b/src/gromacs/awh/biasstate.cpp
index c45f8f19b5e01827195cd768beb1602bbb2c65cd..26ac4af4f3764d55ec82af5d0621a672f1263893 100644 (file)
--- a/src/gromacs/awh/biasstate.cpp
+++ b/src/gromacs/awh/biasstate.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -58,8 +58,8 @@
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/math/utilities.h"
-#include "gromacs/mdtypes/awh-history.h"
-#include "gromacs/mdtypes/awh-params.h"
+#include "gromacs/mdtypes/awh_history.h"
+#include "gromacs/mdtypes/awh_params.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/simd/simd.h"
 #include "gromacs/simd/simd_math.h"

diff --git a/src/gromacs/awh/biaswriter.cpp b/src/gromacs/awh/biaswriter.cpp
index cc45086a6e1dabf8be8f4b396c6921bd2aa7f6d4..d31ac315c16cf8976bd3c975a001e2538eacddd9 100644 (file)
--- a/src/gromacs/awh/biaswriter.cpp
+++ b/src/gromacs/awh/biaswriter.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -41,7 +41,7 @@
 #include <cmath>
 
 #include "gromacs/awh/awh.h"
-#include "gromacs/mdtypes/awh-params.h"
+#include "gromacs/mdtypes/awh_params.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/trajectory/energyframe.h"
 #include "gromacs/utility/gmxassert.h"

diff --git a/src/gromacs/awh/coordstate.cpp b/src/gromacs/awh/coordstate.cpp
index efd58c33977acce848e9d3b51a70303addba60bc..8173431b9648671b1e07ebc6ed3bd98455ff26bb 100644 (file)
--- a/src/gromacs/awh/coordstate.cpp
+++ b/src/gromacs/awh/coordstate.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -49,8 +49,8 @@
 #include <algorithm>
 
 #include "gromacs/math/utilities.h"
-#include "gromacs/mdtypes/awh-history.h"
-#include "gromacs/mdtypes/awh-params.h"
+#include "gromacs/mdtypes/awh_history.h"
+#include "gromacs/mdtypes/awh_params.h"
 #include "gromacs/random/threefry.h"
 #include "gromacs/random/uniformrealdistribution.h"
 #include "gromacs/utility/arrayref.h"

diff --git a/src/gromacs/awh/correlationhistory.cpp b/src/gromacs/awh/correlationhistory.cpp
index 47ecb44a27fea5cea9727affd7ac6dc43af9b34e..195e3d265e0832bba60c2c95de362810f6786a33 100644 (file)
--- a/src/gromacs/awh/correlationhistory.cpp
+++ b/src/gromacs/awh/correlationhistory.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -50,7 +50,7 @@
 #include <cassert>
 
 #include "gromacs/gmxlib/network.h"
-#include "gromacs/mdtypes/awh-correlation-history.h"
+#include "gromacs/mdtypes/awh_correlation_history.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/exceptions.h"

diff --git a/src/gromacs/awh/grid.cpp b/src/gromacs/awh/grid.cpp
index 6cebf587febaaf5a17996ffc184263594b2fa042..b9a188d841325a1dca74f858436d2e9d6969be5a 100644 (file)
--- a/src/gromacs/awh/grid.cpp
+++ b/src/gromacs/awh/grid.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -54,7 +54,7 @@
 
 #include "gromacs/math/functions.h"
 #include "gromacs/math/utilities.h"
-#include "gromacs/mdtypes/awh-params.h"
+#include "gromacs/mdtypes/awh_params.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"

diff --git a/src/gromacs/awh/histogramsize.cpp b/src/gromacs/awh/histogramsize.cpp
index ffcae4e4813114b0fd26be470e51f8b466962448..2810229ee1aa5b91f5ff1fba98ecb4c5725dadb6 100644 (file)
--- a/src/gromacs/awh/histogramsize.cpp
+++ b/src/gromacs/awh/histogramsize.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -52,8 +52,8 @@
 
 #include <algorithm>
 
-#include "gromacs/mdtypes/awh-history.h"
-#include "gromacs/mdtypes/awh-params.h"
+#include "gromacs/mdtypes/awh_history.h"
+#include "gromacs/mdtypes/awh_params.h"
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/stringutil.h"
 

diff --git a/src/gromacs/awh/pointstate.h b/src/gromacs/awh/pointstate.h
index 414d644ba0884c8e1328a81ce4569698939ccd8f..221534441870fe925ffcd377676d6788fc44f4ce 100644 (file)
--- a/src/gromacs/awh/pointstate.h
+++ b/src/gromacs/awh/pointstate.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -52,8 +52,8 @@
 
 #include <cmath>
 
-#include "gromacs/mdtypes/awh-history.h"
-#include "gromacs/mdtypes/awh-params.h"
+#include "gromacs/mdtypes/awh_history.h"
+#include "gromacs/mdtypes/awh_params.h"
 #include "gromacs/utility/gmxassert.h"
 
 #include "biasparams.h"

diff --git a/src/gromacs/awh/read-params.cpp b/src/gromacs/awh/read_params.cpp
similarity index 99%
rename from src/gromacs/awh/read-params.cpp
rename to src/gromacs/awh/read_params.cpp
index db83a07584c0700c7e19a63785aa95b4990582c5..a02b54fc4ac00165174f2c3d5dca001ac7771847 100644 (file)
--- a/src/gromacs/awh/read-params.cpp
+++ b/src/gromacs/awh/read_params.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "read-params.h"
+#include "read_params.h"
 
 #include "gromacs/awh/awh.h"
 #include "gromacs/fileio/readinp.h"
@@ -44,10 +44,10 @@
 #include "gromacs/math/units.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/mdtypes/awh-params.h"
+#include "gromacs/mdtypes/awh_params.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/mdtypes/md_enums.h"
-#include "gromacs/mdtypes/pull-params.h"
+#include "gromacs/mdtypes/pull_params.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pulling/pull.h"
 #include "gromacs/random/seed.h"

diff --git a/src/gromacs/awh/read-params.h b/src/gromacs/awh/read_params.h
similarity index 97%
rename from src/gromacs/awh/read-params.h
rename to src/gromacs/awh/read_params.h
index 5c5be7a4f9010dfb6e7bbe9e42e604f0141548d0..fa953974ea39ff96843b45a8c5556134d6190857 100644 (file)
--- a/src/gromacs/awh/read-params.h
+++ b/src/gromacs/awh/read_params.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/awh/tests/bias.cpp b/src/gromacs/awh/tests/bias.cpp
index 8e4475ed5cfc0d72bbc1e1e11640474e49977db5..4477b7239d515b68466eacdb11b958b784cd83a4 100644 (file)
--- a/src/gromacs/awh/tests/bias.cpp
+++ b/src/gromacs/awh/tests/bias.cpp
@@ -47,7 +47,7 @@
 
 #include "gromacs/awh/correlationgrid.h"
 #include "gromacs/awh/pointstate.h"
-#include "gromacs/mdtypes/awh-params.h"
+#include "gromacs/mdtypes/awh_params.h"
 #include "gromacs/utility/stringutil.h"
 
 #include "testutils/refdata.h"

diff --git a/src/gromacs/awh/tests/biasstate.cpp b/src/gromacs/awh/tests/biasstate.cpp
index 06c871608d41ec9c5283f8db5252250f88722364..2d65d5be682fc0041b2786ffc16b816bfd35f65c 100644 (file)
--- a/src/gromacs/awh/tests/biasstate.cpp
+++ b/src/gromacs/awh/tests/biasstate.cpp
@@ -47,7 +47,7 @@
 #include "gromacs/awh/grid.h"
 #include "gromacs/awh/pointstate.h"
 #include "gromacs/math/functions.h"
-#include "gromacs/mdtypes/awh-params.h"
+#include "gromacs/mdtypes/awh_params.h"
 #include "gromacs/utility/smalloc.h"
 
 #include "testutils/testasserts.h"

diff --git a/src/gromacs/awh/tests/grid.cpp b/src/gromacs/awh/tests/grid.cpp
index 772490e0a1480c485a4104828d5a57b07ae24e36..04adccf90a5be15436a36828c1e7dfc5cd24a425 100644 (file)
--- a/src/gromacs/awh/tests/grid.cpp
+++ b/src/gromacs/awh/tests/grid.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -44,7 +44,7 @@
 #include <gmock/gmock.h>
 #include <gtest/gtest.h>
 
-#include "gromacs/mdtypes/awh-params.h"
+#include "gromacs/mdtypes/awh_params.h"
 #include "gromacs/utility/gmxassert.h"
 
 #include "testutils/testasserts.h"

diff --git a/src/gromacs/commandline/cmdlinehelpmodule.h b/src/gromacs/commandline/cmdlinehelpmodule.h
index 497d87d700ff66916e8a371eb0f9f209a4e2b894..8ff0bdeb825ea215ddeeedb8a1a96e7ce36527ee 100644 (file)
--- a/src/gromacs/commandline/cmdlinehelpmodule.h
+++ b/src/gromacs/commandline/cmdlinehelpmodule.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013,2014,2015,2018, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -46,7 +46,7 @@
 #include "gromacs/onlinehelp/ihelptopic.h"
 #include "gromacs/utility/classhelpers.h"
 
-#include "cmdlinemodulemanager-impl.h"
+#include "cmdlinemodulemanager_impl.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/commandline/cmdlinemodulemanager.cpp b/src/gromacs/commandline/cmdlinemodulemanager.cpp
index d9ff26e43c60a91aee84e1ecb3bb59c22d1ac6c8..85e88e344b4f1890c3328383fcd92e4e3c59a2a2 100644 (file)
--- a/src/gromacs/commandline/cmdlinemodulemanager.cpp
+++ b/src/gromacs/commandline/cmdlinemodulemanager.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -66,7 +66,7 @@
 #include "gromacs/utility/sysinfo.h"
 
 #include "cmdlinehelpmodule.h"
-#include "cmdlinemodulemanager-impl.h"
+#include "cmdlinemodulemanager_impl.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/commandline/cmdlinemodulemanager-impl.h b/src/gromacs/commandline/cmdlinemodulemanager_impl.h
similarity index 98%
rename from src/gromacs/commandline/cmdlinemodulemanager-impl.h
rename to src/gromacs/commandline/cmdlinemodulemanager_impl.h
index 53b54c8664ffdeec330796ec92391c7ad7ee2641..0141f24138a53267b7e14847f74399d431e788e2 100644 (file)
--- a/src/gromacs/commandline/cmdlinemodulemanager-impl.h
+++ b/src/gromacs/commandline/cmdlinemodulemanager_impl.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/domdec/domdec.cpp b/src/gromacs/domdec/domdec.cpp
index d4a5169b6c4a43ac0bcbee8fee28b03d4e9127c7..3a7a230a66a97179c5cf7271e92a06b1aa9d1b76 100644 (file)
--- a/src/gromacs/domdec/domdec.cpp
+++ b/src/gromacs/domdec/domdec.cpp
@@ -60,7 +60,7 @@
 #include "gromacs/gmxlib/nrnb.h"
 #include "gromacs/gpu_utils/gpu_utils.h"
 #include "gromacs/hardware/hw_info.h"
-#include "gromacs/listed_forces/manage-threading.h"
+#include "gromacs/listed_forces/manage_threading.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/math/vectypes.h"
 #include "gromacs/mdlib/calc_verletbuf.h"

diff --git a/src/gromacs/ewald/CMakeLists.txt b/src/gromacs/ewald/CMakeLists.txt
index 05654eda2d630cec135b3df512462dcfbcb55935..318a36c6c3c89452b4b11ce43e8381179384b16c 100644 (file)
--- a/src/gromacs/ewald/CMakeLists.txt
+++ b/src/gromacs/ewald/CMakeLists.txt
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2014,2015,2016,2017,2018, by the GROMACS development team, led by
+# Copyright (c) 2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -33,55 +33,55 @@
 # the research papers on the package. Check out http://www.gromacs.org.
 
 gmx_add_libgromacs_sources(
-    calculate-spline-moduli.cpp
+    calculate_spline_moduli.cpp
     ewald.cpp
-    ewald-utils.cpp
-    long-range-correction.cpp
+    ewald_utils.cpp
+    long_range_correction.cpp
     pme.cpp
-    pme-gather.cpp
-    pme-grid.cpp
-    pme-load-balancing.cpp
-    pme-only.cpp
-    pme-pp.cpp
-    pme-redistribute.cpp
-    pme-solve.cpp
-    pme-spline-work.cpp
-    pme-spread.cpp
+    pme_gather.cpp
+    pme_grid.cpp
+    pme_load_balancing.cpp
+    pme_only.cpp
+    pme_pp.cpp
+    pme_redistribute.cpp
+    pme_solve.cpp
+    pme_spline_work.cpp
+    pme_spread.cpp
     # Files that implement stubs
-    pme-gpu-program.cpp
+    pme_gpu_program.cpp
     )
 if (GMX_USE_CUDA)
     gmx_add_libgromacs_sources(
         # CUDA-specific sources
-        pme-gather.cu
-        pme-gpu-3dfft.cu
-        pme-solve.cu
-        pme-spread.cu
-        pme-gpu-program-impl.cu
+        pme_gather.cu
+        pme_gpu_3dfft.cu
+        pme_solve.cu
+        pme_spread.cu
+        pme_gpu_program_impl.cu
         # GPU-specific sources
-        pme-gpu.cpp
-        pme-gpu-internal.cpp
-        pme-gpu-timings.cpp
+        pme_gpu.cpp
+        pme_gpu_internal.cpp
+        pme_gpu_timings.cpp
         )
     gmx_compile_cpp_as_cuda(
-        pme-gpu-internal.cpp
-        pme-gpu-program.cpp
-        pme-gpu-timings.cpp
+        pme_gpu_internal.cpp
+        pme_gpu_program.cpp
+        pme_gpu_timings.cpp
         )
 elseif (GMX_USE_OPENCL)
     gmx_add_libgromacs_sources(
         # OpenCL-specific sources
-        pme-gpu-3dfft-ocl.cpp
-        pme-gpu-program-impl-ocl.cpp
+        pme_gpu_3dfft_ocl.cpp
+        pme_gpu_program_impl_ocl.cpp
         # GPU-specific sources
-        pme-gpu.cpp
-        pme-gpu-internal.cpp
-        pme-gpu-timings.cpp
+        pme_gpu.cpp
+        pme_gpu_internal.cpp
+        pme_gpu_timings.cpp
         )
 else()
     gmx_add_libgromacs_sources(
         # Files that implement stubs
-        pme-gpu-program-impl.cpp
+        pme_gpu_program_impl.cpp
         )
 endif()
 

diff --git a/src/gromacs/ewald/calculate-spline-moduli.cpp b/src/gromacs/ewald/calculate_spline_moduli.cpp
similarity index 97%
rename from src/gromacs/ewald/calculate-spline-moduli.cpp
rename to src/gromacs/ewald/calculate_spline_moduli.cpp
index d25620e9cb8654ae4b3b74ef6dea47193c83daf2..ac2136e5c0fa173be1ee007609958d41de25e698 100644 (file)
--- a/src/gromacs/ewald/calculate-spline-moduli.cpp
+++ b/src/gromacs/ewald/calculate_spline_moduli.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "calculate-spline-moduli.h"
+#include "calculate_spline_moduli.h"
 
 #include <cmath>
 
@@ -48,7 +48,7 @@
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "pme-internal.h"
+#include "pme_internal.h"
 
 static void make_dft_mod(real *mod,
                          const double *data, int splineOrder, int ndata)

diff --git a/src/gromacs/ewald/calculate-spline-moduli.h b/src/gromacs/ewald/calculate_spline_moduli.h
similarity index 95%
rename from src/gromacs/ewald/calculate-spline-moduli.h
rename to src/gromacs/ewald/calculate_spline_moduli.h
index 3e33e6a0532959f370e3e92f1575aa444771b108..35746f60e5fb3423be74451b706c2630f13f47c2 100644 (file)
--- a/src/gromacs/ewald/calculate-spline-moduli.h
+++ b/src/gromacs/ewald/calculate_spline_moduli.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -37,7 +37,7 @@
 #ifndef GMX_EWALD_CALCULATE_SPLINE_MODULI_H
 #define GMX_EWALD_CALCULATE_SPLINE_MODULI_H
 
-#include "pme-internal.h"
+#include "pme_internal.h"
 
 /* Calulate plain SPME B-spline interpolation */
 void make_bspline_moduli(splinevec bsp_mod,

diff --git a/src/gromacs/ewald/ewald.cpp b/src/gromacs/ewald/ewald.cpp
index 696a47c9d38e7b77b1ddd8f6b6c22fcf342e6465..a16f0599ab6f824ce43bf4d68becbe7a97412ed2 100644 (file)
--- a/src/gromacs/ewald/ewald.cpp
+++ b/src/gromacs/ewald/ewald.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -55,7 +55,7 @@
 
 #include <algorithm>
 
-#include "gromacs/ewald/ewald-utils.h"
+#include "gromacs/ewald/ewald_utils.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/math/gmxcomplex.h"
 #include "gromacs/math/units.h"

diff --git a/src/gromacs/ewald/ewald-utils.cpp b/src/gromacs/ewald/ewald_utils.cpp
similarity index 96%
rename from src/gromacs/ewald/ewald-utils.cpp
rename to src/gromacs/ewald/ewald_utils.cpp
index 5bab76eadc297d6b1357ae34e263cde237ff039a..be6727af06235b99620e5cb5524f1ed684d5b8ea 100644 (file)
--- a/src/gromacs/ewald/ewald-utils.cpp
+++ b/src/gromacs/ewald/ewald_utils.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "ewald-utils.h"
+#include "ewald_utils.h"
 
 #include <cmath>
 

diff --git a/src/gromacs/ewald/ewald-utils.h b/src/gromacs/ewald/ewald_utils.h
similarity index 98%
rename from src/gromacs/ewald/ewald-utils.h
rename to src/gromacs/ewald/ewald_utils.h
index 39ca3e81b3e3fbbbc5162cf1a604e2f3f2a4b582..ab760f8efb14f94feb5dabfeed96f5aecac82e48 100644 (file)
--- a/src/gromacs/ewald/ewald-utils.h
+++ b/src/gromacs/ewald/ewald_utils.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2017,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/ewald/long-range-correction.cpp b/src/gromacs/ewald/long_range_correction.cpp
similarity index 99%
rename from src/gromacs/ewald/long-range-correction.cpp
rename to src/gromacs/ewald/long_range_correction.cpp
index 0a83727190a1587b4647a4ef12f27fbd991fa540..6a93d0a57dafd363774dae0b55c63ac0ffa2d631 100644 (file)
--- a/src/gromacs/ewald/long-range-correction.cpp
+++ b/src/gromacs/ewald/long_range_correction.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -36,11 +36,11 @@
  */
 #include "gmxpre.h"
 
-#include "long-range-correction.h"
+#include "long_range_correction.h"
 
 #include <cmath>
 
-#include "gromacs/ewald/ewald-utils.h"
+#include "gromacs/ewald/ewald_utils.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/utilities.h"
@@ -52,7 +52,7 @@
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxassert.h"
 
-#include "pme-internal.h"
+#include "pme_internal.h"
 
 /* There's nothing special to do here if just masses are perturbed,
  * but if either charge or type is perturbed then the implementation

diff --git a/src/gromacs/ewald/long-range-correction.h b/src/gromacs/ewald/long_range_correction.h
similarity index 97%
rename from src/gromacs/ewald/long-range-correction.h
rename to src/gromacs/ewald/long_range_correction.h
index 37108de07f06d48aaf6c78194c168738696725f4..c060deb764572d47c90b7a3cdb0145275b322eac 100644 (file)
--- a/src/gromacs/ewald/long-range-correction.h
+++ b/src/gromacs/ewald/long_range_correction.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/ewald/pme.cpp b/src/gromacs/ewald/pme.cpp
index fab79704649cff8be4fedd79c54a1970b67a37d6..f906a04e45a9d120cd6d8cf9bea7ba9474d644ad 100644 (file)
--- a/src/gromacs/ewald/pme.cpp
+++ b/src/gromacs/ewald/pme.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -83,7 +83,7 @@
 #include <list>
 
 #include "gromacs/domdec/domdec.h"
-#include "gromacs/ewald/ewald-utils.h"
+#include "gromacs/ewald/ewald_utils.h"
 #include "gromacs/fft/parallel_3dfft.h"
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/gmxlib/network.h"
@@ -115,15 +115,15 @@
 #include "gromacs/utility/stringutil.h"
 #include "gromacs/utility/unique_cptr.h"
 
-#include "calculate-spline-moduli.h"
-#include "pme-gather.h"
-#include "pme-gpu-internal.h"
-#include "pme-grid.h"
-#include "pme-internal.h"
-#include "pme-redistribute.h"
-#include "pme-solve.h"
-#include "pme-spline-work.h"
-#include "pme-spread.h"
+#include "calculate_spline_moduli.h"
+#include "pme_gather.h"
+#include "pme_gpu_internal.h"
+#include "pme_grid.h"
+#include "pme_internal.h"
+#include "pme_redistribute.h"
+#include "pme_solve.h"
+#include "pme_spline_work.h"
+#include "pme_spread.h"
 
 /*! \brief Help build a descriptive message in \c error if there are
  * \c errorReasons why PME on GPU is not supported.

diff --git a/src/gromacs/ewald/pme.cuh b/src/gromacs/ewald/pme.cuh
index fd18de2c0df4ede3502826f86d4a319b866a06f2..3994a84d8382ca554ebf53019aa407ca3d1f7287 100644 (file)
--- a/src/gromacs/ewald/pme.cuh
+++ b/src/gromacs/ewald/pme.cuh
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -45,9 +45,9 @@
 
 #include "gromacs/math/vectypes.h" // for DIM
 
-#include "pme-gpu-constants.h"
-#include "pme-gpu-internal.h"      // for GridOrdering
-#include "pme-gpu-types.h"
+#include "pme_gpu_constants.h"
+#include "pme_gpu_internal.h"      // for GridOrdering
+#include "pme_gpu_types.h"
 
 /*! \brief \internal
  * A single structure encompassing all the PME data used in CUDA kernels.

diff --git a/src/gromacs/ewald/pme-gather.clh b/src/gromacs/ewald/pme_gather.clh
similarity index 98%
rename from src/gromacs/ewald/pme-gather.clh
rename to src/gromacs/ewald/pme_gather.clh
index e795d4dd7086f7862b46327cd04a61481a17cb1f..8b19f474a5f9f9d5dbf82dfee8edde8d1647c472 100644 (file)
--- a/src/gromacs/ewald/pme-gather.clh
+++ b/src/gromacs/ewald/pme_gather.clh
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -37,7 +37,7 @@
  *  \brief Implements PME OpenCL force gathering kernel.
  * When including this and other PME OpenCL kernel files, plenty of common
  * constants/macros are expected to be defined (such as "order" which is PME interpolation order).
- * For details, please see how pme-program.cl is compiled in pme-gpu-program-impl-ocl.cpp.
+ * For details, please see how pme_program.cl is compiled in pme_gpu_program_impl_ocl.cpp.
  *
  * This file's kernels specifically expect the following definitions:
  *
@@ -51,8 +51,8 @@
  *  \author Aleksei Iupinov <a.yupinov@gmail.com>
  */
 
-#include "pme-gpu-types.h"
-#include "pme-gpu-utils.clh"
+#include "pme_gpu_types.h"
+#include "pme_gpu_utils.clh"
 
 #ifndef COMPILE_GATHER_HELPERS_ONCE
 #define COMPILE_GATHER_HELPERS_ONCE

diff --git a/src/gromacs/ewald/pme-gather.cpp b/src/gromacs/ewald/pme_gather.cpp
similarity index 98%
rename from src/gromacs/ewald/pme-gather.cpp
rename to src/gromacs/ewald/pme_gather.cpp
index b939468ab6abad20435cc0863a5a7ff6e7e36bd8..0802005eabb0ff4e8fb0e4257ac0ae9e17e09026 100644 (file)
--- a/src/gromacs/ewald/pme-gather.cpp
+++ b/src/gromacs/ewald/pme_gather.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -37,7 +37,7 @@
 
 #include "gmxpre.h"
 
-#include "pme-gather.h"
+#include "pme_gather.h"
 
 #include "gromacs/math/vec.h"
 #include "gromacs/simd/simd.h"
@@ -46,9 +46,9 @@
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/typetraits.h"
 
-#include "pme-internal.h"
-#include "pme-simd.h"
-#include "pme-spline-work.h"
+#include "pme_internal.h"
+#include "pme_simd.h"
+#include "pme_spline_work.h"
 
 using namespace gmx; // TODO: Remove when this file is moved into gmx namespace
 

diff --git a/src/gromacs/ewald/pme-gather.cu b/src/gromacs/ewald/pme_gather.cu
similarity index 99%
rename from src/gromacs/ewald/pme-gather.cu
rename to src/gromacs/ewald/pme_gather.cu
index b8297c4d68012f5cab472c1e07a0fc48bf7743a4..e9775a5dd0b379f502ade3dadfda43e034b53c60 100644 (file)
--- a/src/gromacs/ewald/pme-gather.cu
+++ b/src/gromacs/ewald/pme_gather.cu
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -44,7 +44,7 @@
 #include <cassert>
 
 #include "pme.cuh"
-#include "pme-gpu-utils.h"
+#include "pme_gpu_utils.h"
 
 /*! \brief
  * An inline CUDA function: unroll the dynamic index accesses to the constant grid sizes to avoid local memory operations.

diff --git a/src/gromacs/ewald/pme-gather.h b/src/gromacs/ewald/pme_gather.h
similarity index 94%
rename from src/gromacs/ewald/pme-gather.h
rename to src/gromacs/ewald/pme_gather.h
index 864eda3be218f6aba195afcce8b02298cfe576ee..384c72598d5f00eedab1e31a60bbef699216181f 100644 (file)
--- a/src/gromacs/ewald/pme-gather.h
+++ b/src/gromacs/ewald/pme_gather.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014,2015,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -37,7 +37,7 @@
 
 #include "gromacs/utility/real.h"
 
-#include "pme-internal.h"
+#include "pme_internal.h"
 
 void
 gather_f_bsplines(const struct gmx_pme_t *pme, const real *grid,

diff --git a/src/gromacs/ewald/pme-gpu.cpp b/src/gromacs/ewald/pme_gpu.cpp
similarity index 98%
rename from src/gromacs/ewald/pme-gpu.cpp
rename to src/gromacs/ewald/pme_gpu.cpp
index 40c653bb83ec4646870d0e5e68f07d4e79b74e52..efe4a60235e557cac1b0c84ffaddf09bbd74f509 100644 (file)
--- a/src/gromacs/ewald/pme-gpu.cpp
+++ b/src/gromacs/ewald/pme_gpu.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -46,7 +46,7 @@
 
 #include <list>
 
-#include "gromacs/ewald/ewald-utils.h"
+#include "gromacs/ewald/ewald_utils.h"
 #include "gromacs/ewald/pme.h"
 #include "gromacs/fft/parallel_3dfft.h"
 #include "gromacs/math/invertmatrix.h"
@@ -59,10 +59,10 @@
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/stringutil.h"
 
-#include "pme-gpu-internal.h"
-#include "pme-grid.h"
-#include "pme-internal.h"
-#include "pme-solve.h"
+#include "pme_gpu_internal.h"
+#include "pme_grid.h"
+#include "pme_internal.h"
+#include "pme_solve.h"
 
 void pme_gpu_reset_timings(const gmx_pme_t *pme)
 {

diff --git a/src/gromacs/ewald/pme-gpu-3dfft.cu b/src/gromacs/ewald/pme_gpu_3dfft.cu
similarity index 96%
rename from src/gromacs/ewald/pme-gpu-3dfft.cu
rename to src/gromacs/ewald/pme_gpu_3dfft.cu
index 4445e2475d6100aafecac39b3afe945cfb91522d..c36d440b14339089656ab7fabcfa6d224f27429d 100644 (file)
--- a/src/gromacs/ewald/pme-gpu-3dfft.cu
+++ b/src/gromacs/ewald/pme_gpu_3dfft.cu
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -42,15 +42,15 @@
 
 #include "gmxpre.h"
 
-#include "pme-gpu-3dfft.h"
+#include "pme_gpu_3dfft.h"
 
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxassert.h"
 
 #include "pme.cuh"
-#include "pme-gpu-types.h"
-#include "pme-gpu-types-host.h"
-#include "pme-gpu-types-host-impl.h"
+#include "pme_gpu_types.h"
+#include "pme_gpu_types_host.h"
+#include "pme_gpu_types_host_impl.h"
 
 static void handleCufftError(cufftResult_t status, const char *msg)
 {

diff --git a/src/gromacs/ewald/pme-gpu-3dfft.h b/src/gromacs/ewald/pme_gpu_3dfft.h
similarity index 97%
rename from src/gromacs/ewald/pme-gpu-3dfft.h
rename to src/gromacs/ewald/pme_gpu_3dfft.h
index 6da6b86d85b4fc98e8475448673a98a7e48f65fc..cee64552e8bda2679508b76ea09230effc0b0682 100644 (file)
--- a/src/gromacs/ewald/pme-gpu-3dfft.h
+++ b/src/gromacs/ewald/pme_gpu_3dfft.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/ewald/pme-gpu-3dfft-ocl.cpp b/src/gromacs/ewald/pme_gpu_3dfft_ocl.cpp
similarity index 97%
rename from src/gromacs/ewald/pme-gpu-3dfft-ocl.cpp
rename to src/gromacs/ewald/pme_gpu_3dfft_ocl.cpp
index 729a32a07d807d84d04745cc877c33056bbc41d0..e2019ba5581bc06dca340a7929532d64c1fb0c60 100644 (file)
--- a/src/gromacs/ewald/pme-gpu-3dfft-ocl.cpp
+++ b/src/gromacs/ewald/pme_gpu_3dfft_ocl.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -48,10 +48,10 @@
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/stringutil.h"
 
-#include "pme-gpu-3dfft.h"
-#include "pme-gpu-internal.h"
-#include "pme-gpu-types.h"
-#include "pme-gpu-types-host-impl.h"
+#include "pme_gpu_3dfft.h"
+#include "pme_gpu_internal.h"
+#include "pme_gpu_types.h"
+#include "pme_gpu_types_host_impl.h"
 
 //! Throws the exception on clFFT error
 static void handleClfftError(clfftStatus status, const char *msg)

diff --git a/src/gromacs/ewald/pme-gpu-constants.h b/src/gromacs/ewald/pme_gpu_constants.h
similarity index 99%
rename from src/gromacs/ewald/pme-gpu-constants.h
rename to src/gromacs/ewald/pme_gpu_constants.h
index ca108915e28f8a717341c773b92f3a4fc878ad8d..695a9e220caa252630287dba0349d9ebdb28a61a 100644 (file)
--- a/src/gromacs/ewald/pme-gpu-constants.h
+++ b/src/gromacs/ewald/pme_gpu_constants.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/ewald/pme-gpu-internal.cpp b/src/gromacs/ewald/pme_gpu_internal.cpp
similarity index 99%
rename from src/gromacs/ewald/pme-gpu-internal.cpp
rename to src/gromacs/ewald/pme_gpu_internal.cpp
index a8d98e96cf11f71a92630bc24d76d2a2b4bf22fc..27da475ac8c3e0eec0e428d4afbaee39252d87ab 100644 (file)
--- a/src/gromacs/ewald/pme-gpu-internal.cpp
+++ b/src/gromacs/ewald/pme_gpu_internal.cpp
@@ -47,7 +47,7 @@
 
 #include "gmxpre.h"
 
-#include "pme-gpu-internal.h"
+#include "pme_gpu_internal.h"
 
 #include "config.h"
 
@@ -55,7 +55,7 @@
 #include <memory>
 #include <string>
 
-#include "gromacs/ewald/ewald-utils.h"
+#include "gromacs/ewald/ewald_utils.h"
 #include "gromacs/gpu_utils/gpu_utils.h"
 #include "gromacs/math/invertmatrix.h"
 #include "gromacs/math/units.h"
@@ -76,17 +76,17 @@
 
 #include "gromacs/ewald/pme.h"
 
-#include "pme-gpu-3dfft.h"
-#include "pme-gpu-constants.h"
-#include "pme-gpu-program-impl.h"
-#include "pme-gpu-timings.h"
-#include "pme-gpu-types.h"
-#include "pme-gpu-types-host.h"
-#include "pme-gpu-types-host-impl.h"
-#include "pme-gpu-utils.h"
-#include "pme-grid.h"
-#include "pme-internal.h"
-#include "pme-solve.h"
+#include "pme_gpu_3dfft.h"
+#include "pme_gpu_constants.h"
+#include "pme_gpu_program_impl.h"
+#include "pme_gpu_timings.h"
+#include "pme_gpu_types.h"
+#include "pme_gpu_types_host.h"
+#include "pme_gpu_types_host_impl.h"
+#include "pme_gpu_utils.h"
+#include "pme_grid.h"
+#include "pme_internal.h"
+#include "pme_solve.h"
 
 /*! \internal \brief
  * Wrapper for getting a pointer to the plain C++ part of the GPU kernel parameters structure.

diff --git a/src/gromacs/ewald/pme-gpu-internal.h b/src/gromacs/ewald/pme_gpu_internal.h
similarity index 98%
rename from src/gromacs/ewald/pme-gpu-internal.h
rename to src/gromacs/ewald/pme_gpu_internal.h
index 652c7f7aa5c3a07127ef600d774613252824dcf1..afe3bf65abcfce0c6e979b663796a106d9fa0631 100644 (file)
--- a/src/gromacs/ewald/pme-gpu-internal.h
+++ b/src/gromacs/ewald/pme_gpu_internal.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -37,7 +37,7 @@
  *
  * \brief This file contains internal function definitions for performing the PME calculations on GPU.
  * These are not meant to be exposed outside of the PME GPU code.
- * As of now, their bodies are still in the common pme-gpu.cpp files.
+ * As of now, their bodies are still in the common pme_gpu.cpp files.
  *
  * \author Aleksei Iupinov <a.yupinov@gmail.com>
  * \ingroup module_ewald
@@ -50,7 +50,7 @@
 #include "gromacs/gpu_utils/gpu_macros.h"      // for the GPU_FUNC_ macros
 #include "gromacs/utility/arrayref.h"
 
-#include "pme-gpu-types-host.h"                     // for the inline functions accessing PmeGpu members
+#include "pme_gpu_types_host.h"                     // for the inline functions accessing PmeGpu members
 
 struct gmx_hw_info_t;
 struct gmx_gpu_opt_t;
@@ -356,7 +356,7 @@ void pme_gpu_reinit_3dfft(const PmeGpu *pmeGpu);
  */
 void pme_gpu_destroy_3dfft(const PmeGpu *pmeGpu);
 
-/* Several GPU event-based timing functions that live in pme-gpu-timings.cpp */
+/* Several GPU event-based timing functions that live in pme_gpu_timings.cpp */
 
 /*! \libinternal \brief
  * Finalizes all the active PME GPU stage timings for the current computation. Should be called at the end of every computation.
@@ -529,7 +529,7 @@ inline bool pme_gpu_is_testing(const PmeGpu *pmeGpu)
     return pmeGpu->settings.copyAllOutputs;
 }
 
-/* A block of C++ functions that live in pme-gpu-internal.cpp */
+/* A block of C++ functions that live in pme_gpu_internal.cpp */
 
 /*! \libinternal \brief
  * Returns the energy and virial GPU outputs, useful for testing.

diff --git a/src/gromacs/ewald/pme-gpu-program.cpp b/src/gromacs/ewald/pme_gpu_program.cpp
similarity index 97%
rename from src/gromacs/ewald/pme-gpu-program.cpp
rename to src/gromacs/ewald/pme_gpu_program.cpp
index fbb1a8eeb7973050e87a3bd1958dc2cb9888da84..67e6a4e1c901e584b6a4b1886b01358df8057497 100644 (file)
--- a/src/gromacs/ewald/pme-gpu-program.cpp
+++ b/src/gromacs/ewald/pme_gpu_program.cpp
@@ -45,11 +45,11 @@
 
 #include "gmxpre.h"
 
-#include "pme-gpu-program.h"
+#include "pme_gpu_program.h"
 
 #include <memory>
 
-#include "pme-gpu-program-impl.h"
+#include "pme_gpu_program_impl.h"
 
 PmeGpuProgram::PmeGpuProgram(const gmx_device_info_t *deviceInfo) :
     impl_(std::make_unique<PmeGpuProgramImpl>(deviceInfo))

diff --git a/src/gromacs/ewald/pme-gpu-program.h b/src/gromacs/ewald/pme_gpu_program.h
similarity index 97%
rename from src/gromacs/ewald/pme-gpu-program.h
rename to src/gromacs/ewald/pme_gpu_program.h
index 76045e32bff207eaf5b99e90d36853d61f138034..de4eb562a6788350f41506669f97bc5c39d1d02e 100644 (file)
--- a/src/gromacs/ewald/pme-gpu-program.h
+++ b/src/gromacs/ewald/pme_gpu_program.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/ewald/pme-gpu-program-impl.cpp b/src/gromacs/ewald/pme_gpu_program_impl.cpp
similarity index 95%
rename from src/gromacs/ewald/pme-gpu-program-impl.cpp
rename to src/gromacs/ewald/pme_gpu_program_impl.cpp
index 47297e3ece21f8270cbcdb47dd7fac809b8352da..cb993bea8be2a26b2068643ee3ecbf1d44b5e46d 100644 (file)
--- a/src/gromacs/ewald/pme-gpu-program-impl.cpp
+++ b/src/gromacs/ewald/pme_gpu_program_impl.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -43,7 +43,7 @@
 
 #include "gmxpre.h"
 
-#include "pme-gpu-program-impl.h"
+#include "pme_gpu_program_impl.h"
 
 PmeGpuProgramImpl::PmeGpuProgramImpl(const gmx_device_info_t * /*unused*/) :
     warpSize(0),

diff --git a/src/gromacs/ewald/pme-gpu-program-impl.cu b/src/gromacs/ewald/pme_gpu_program_impl.cu
similarity index 95%
rename from src/gromacs/ewald/pme-gpu-program-impl.cu
rename to src/gromacs/ewald/pme_gpu_program_impl.cu
index db2f1b178db2eb78b7eda59b23aa3893d4f4d48e..087d85f50e51c523b9f280f36775423f879a6ace 100644 (file)
--- a/src/gromacs/ewald/pme-gpu-program-impl.cu
+++ b/src/gromacs/ewald/pme_gpu_program_impl.cu
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -43,11 +43,11 @@
  */
 #include "gmxpre.h"
 
-#include "pme-gpu-program-impl.h"
+#include "pme_gpu_program_impl.h"
 
-#include "pme-gpu-constants.h"
-#include "pme-gpu-internal.h"                    // for GridOrdering enum
-#include "pme-gpu-types-host.h"
+#include "pme_gpu_constants.h"
+#include "pme_gpu_internal.h"                    // for GridOrdering enum
+#include "pme_gpu_types_host.h"
 
 // PME interpolation order
 constexpr int  c_pmeOrder = 4;

diff --git a/src/gromacs/ewald/pme-gpu-program-impl.h b/src/gromacs/ewald/pme_gpu_program_impl.h
similarity index 98%
rename from src/gromacs/ewald/pme-gpu-program-impl.h
rename to src/gromacs/ewald/pme_gpu_program_impl.h
index 2f2bf685648d975e0bc1114483001038f6b468c2..f1c114115fea72a0dcc20bd03913e3f254369142 100644 (file)
--- a/src/gromacs/ewald/pme-gpu-program-impl.h
+++ b/src/gromacs/ewald/pme_gpu_program_impl.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/ewald/pme-gpu-program-impl-ocl.cpp b/src/gromacs/ewald/pme_gpu_program_impl_ocl.cpp
similarity index 96%
rename from src/gromacs/ewald/pme-gpu-program-impl-ocl.cpp
rename to src/gromacs/ewald/pme_gpu_program_impl_ocl.cpp
index 16bfac9aadf8fad87810782969f209c7f1cfde69..a3558005608581aa08af5fc05eaa6b57aa517ea2 100644 (file)
--- a/src/gromacs/ewald/pme-gpu-program-impl-ocl.cpp
+++ b/src/gromacs/ewald/pme_gpu_program_impl_ocl.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -47,11 +47,11 @@
 #include "gromacs/gpu_utils/ocl_compiler.h"
 #include "gromacs/utility/stringutil.h"
 
-#include "pme-gpu-constants.h"
-#include "pme-gpu-internal.h" // for GridOrdering enum
-#include "pme-gpu-program-impl.h"
-#include "pme-gpu-types-host.h"
-#include "pme-grid.h"
+#include "pme_gpu_constants.h"
+#include "pme_gpu_internal.h" // for GridOrdering enum
+#include "pme_gpu_program_impl.h"
+#include "pme_gpu_types_host.h"
+#include "pme_grid.h"
 
 PmeGpuProgramImpl::PmeGpuProgramImpl(const gmx_device_info_t *deviceInfo)
 {
@@ -145,9 +145,9 @@ void PmeGpuProgramImpl::compileKernels(const gmx_device_info_t *deviceInfo)
                     "-Dorder=%d "
                     "-DatomsPerWarp=%zd "
                     "-DthreadsPerAtom=%d "
-                    // forwarding from pme-grid.h, used for spline computation table sizes only
+                    // forwarding from pme_grid.h, used for spline computation table sizes only
                     "-Dc_pmeMaxUnitcellShift=%f "
-                    // forwarding PME behavior constants from pme-gpu-constants.h
+                    // forwarding PME behavior constants from pme_gpu_constants.h
                     "-Dc_usePadding=%d "
                     "-Dc_skipNeutralAtoms=%d "
                     "-Dc_virialAndEnergyCount=%d "
@@ -177,7 +177,7 @@ void PmeGpuProgramImpl::compileKernels(const gmx_device_info_t *deviceInfo)
                the log output here should be written there */
             program = gmx::ocl::compileProgram(stderr,
                                                "gromacs/ewald",
-                                               "pme-program.cl",
+                                               "pme_program.cl",
                                                commonDefines,
                                                context,
                                                deviceInfo->ocl_gpu_id.ocl_device_id,
@@ -218,7 +218,7 @@ void PmeGpuProgramImpl::compileKernels(const gmx_device_info_t *deviceInfo)
             GMX_THROW(gmx::InternalError(errorString));
         }
 
-        // The names below must correspond to those defined in pme-program.cl
+        // The names below must correspond to those defined in pme_program.cl
         // TODO use a map with string key instead?
         if (!strcmp(kernelNamesBuffer.data(), "pmeSplineKernel"))
         {

diff --git a/src/gromacs/ewald/pme-gpu-timings.cpp b/src/gromacs/ewald/pme_gpu_timings.cpp
similarity index 96%
rename from src/gromacs/ewald/pme-gpu-timings.cpp
rename to src/gromacs/ewald/pme_gpu_timings.cpp
index 5c218c14104d13657f49d1e51e22c385365ffc85..58361a59f0b55dba063d44695630a897ea6c5f9a 100644 (file)
--- a/src/gromacs/ewald/pme-gpu-timings.cpp
+++ b/src/gromacs/ewald/pme_gpu_timings.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -42,13 +42,13 @@
 
 #include "gmxpre.h"
 
-#include "pme-gpu-timings.h"
+#include "pme_gpu_timings.h"
 
 #include "gromacs/utility/gmxassert.h"
 
-#include "pme-gpu-internal.h"
-#include "pme-gpu-types-host.h"
-#include "pme-gpu-types-host-impl.h"
+#include "pme_gpu_internal.h"
+#include "pme_gpu_types_host.h"
+#include "pme_gpu_types_host_impl.h"
 
 /*! \brief
  * Tells if CUDA-based performance tracking is enabled for PME.

diff --git a/src/gromacs/ewald/pme-gpu-timings.h b/src/gromacs/ewald/pme_gpu_timings.h
similarity index 97%
rename from src/gromacs/ewald/pme-gpu-timings.h
rename to src/gromacs/ewald/pme_gpu_timings.h
index 08ee83d42d1dfe254d5fc1770af0b2fb282bc9d3..df8c80398b3658aa1a188c21f874a89fb2a2d87f 100644 (file)
--- a/src/gromacs/ewald/pme-gpu-timings.h
+++ b/src/gromacs/ewald/pme_gpu_timings.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/ewald/pme-gpu-types.h b/src/gromacs/ewald/pme_gpu_types.h
similarity index 99%
rename from src/gromacs/ewald/pme-gpu-types.h
rename to src/gromacs/ewald/pme_gpu_types.h
index 6fb6cae82726120279bb3a0a6329949fac3be110..0598aacbbff6e5e9e49bfae50823295d915d8448 100644 (file)
--- a/src/gromacs/ewald/pme-gpu-types.h
+++ b/src/gromacs/ewald/pme_gpu_types.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/ewald/pme-gpu-types-host.h b/src/gromacs/ewald/pme_gpu_types_host.h
similarity index 99%
rename from src/gromacs/ewald/pme-gpu-types-host.h
rename to src/gromacs/ewald/pme_gpu_types_host.h
index 5a780ecba217b3d74dc38a40e8be5ed067e0c8b9..eacc911dfb5d504b9facc142cf78f301c62caae7 100644 (file)
--- a/src/gromacs/ewald/pme-gpu-types-host.h
+++ b/src/gromacs/ewald/pme_gpu_types_host.h
@@ -54,7 +54,7 @@
 #include <vector>
 
 #include "gromacs/ewald/pme.h"
-#include "gromacs/ewald/pme-gpu-program.h"
+#include "gromacs/ewald/pme_gpu_program.h"
 #include "gromacs/gpu_utils/gpu_utils.h"      // for GpuApiCallBehavior
 #include "gromacs/gpu_utils/hostallocator.h"
 #include "gromacs/math/vectypes.h"

diff --git a/src/gromacs/ewald/pme-gpu-types-host-impl.h b/src/gromacs/ewald/pme_gpu_types_host_impl.h
similarity index 98%
rename from src/gromacs/ewald/pme-gpu-types-host-impl.h
rename to src/gromacs/ewald/pme_gpu_types_host_impl.h
index e005552400fb806a16ec77dd570ce32b3f5d78f4..6949bde60f66deaeff8e889ab6b9299adb103fdc 100644 (file)
--- a/src/gromacs/ewald/pme-gpu-types-host-impl.h
+++ b/src/gromacs/ewald/pme_gpu_types_host_impl.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -35,7 +35,7 @@
 
 /*! \internal \file
  * \brief Defines the host-side PME GPU data structure, which is dependent on the GPU types.
- * It's included by pointer in the general PmeGpu host structure in pme-gpu-types-host.h.
+ * It's included by pointer in the general PmeGpu host structure in pme_gpu_types_host.h.
  *
  * \author Aleksei Iupinov <a.yupinov@gmail.com>
  * \ingroup module_ewald

diff --git a/src/gromacs/ewald/pme-gpu-utils.clh b/src/gromacs/ewald/pme_gpu_utils.clh
similarity index 96%
rename from src/gromacs/ewald/pme-gpu-utils.clh
rename to src/gromacs/ewald/pme_gpu_utils.clh
index fe0531dc490aed086bf8a5ad782cf66a2989edfb..5f611e9510b8546dbff90e79f9c3e6d29863001a 100644 (file)
--- a/src/gromacs/ewald/pme-gpu-utils.clh
+++ b/src/gromacs/ewald/pme_gpu_utils.clh
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -37,11 +37,11 @@
 
 /*! \internal \file
  * \brief This file defines the small PME OpenCL inline device functions.
- * This closely mirrors pme-gpu-utils.h (which is used in CUDA and unit tests), except with no templates.
+ * This closely mirrors pme_gpu_utils.h (which is used in CUDA and unit tests), except with no templates.
  * Instead of templated parameters this file expects following defines during compilation:
  * - order - PME interpolation order;
  * - atomsPerWarp - number of atoms processed by a warp (fixed for spread and gather kernels to be the same);
- * - c_usePadding and c_skipNeutralAtoms - same as in pme-gpu-constants.h.
+ * - c_usePadding and c_skipNeutralAtoms - same as in pme_gpu_constants.h.
  *
  * \author Aleksei Iupinov <a.yupinov@gmail.com>
  * \ingroup module_ewald

diff --git a/src/gromacs/ewald/pme-gpu-utils.h b/src/gromacs/ewald/pme_gpu_utils.h
similarity index 97%
rename from src/gromacs/ewald/pme-gpu-utils.h
rename to src/gromacs/ewald/pme_gpu_utils.h
index e576a5604503a969973f8448429284844e0e3436..c706f071ecdc95670112cfd0cf29aa18ddedda04 100644 (file)
--- a/src/gromacs/ewald/pme-gpu-utils.h
+++ b/src/gromacs/ewald/pme_gpu_utils.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -38,7 +38,7 @@
 /*! \internal \file
  * \brief This file defines small PME GPU inline host/device functions.
  * Note that OpenCL device-side functions can't use C++ features, so they are
- * located in a similar file pme-gpu-utils.clh.
+ * located in a similar file pme_gpu_utils.clh.
  * Be sure to keep the logic in sync in both files when changing it!
  *
  * \author Aleksei Iupinov <a.yupinov@gmail.com>
@@ -49,7 +49,7 @@
 
 #include <cassert>
 
-#include "pme-gpu-constants.h"
+#include "pme_gpu_constants.h"
 
 //! A macro for inline GPU functions.
 #if GMX_GPU == GMX_GPU_CUDA

diff --git a/src/gromacs/ewald/pme-grid.cpp b/src/gromacs/ewald/pme_grid.cpp
similarity index 99%
rename from src/gromacs/ewald/pme-grid.cpp
rename to src/gromacs/ewald/pme_grid.cpp
index a2a0dfaff072a00207ccde2a44343cd28bda086a..2f1b16d720e6a66a57d2bc297fb5f177b7d5bfd6 100644 (file)
--- a/src/gromacs/ewald/pme-grid.cpp
+++ b/src/gromacs/ewald/pme_grid.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -37,7 +37,7 @@
 /* TODO find out what this file should be called */
 #include "gmxpre.h"
 
-#include "pme-grid.h"
+#include "pme_grid.h"
 
 #include "config.h"
 
@@ -50,7 +50,7 @@
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "pme-internal.h"
+#include "pme_internal.h"
 
 #ifdef DEBUG_PME
 #include "gromacs/fileio/pdbio.h"
@@ -58,7 +58,7 @@
 #include "gromacs/utility/futil.h"
 #endif
 
-#include "pme-simd.h"
+#include "pme_simd.h"
 
 /* GMX_CACHE_SEP should be a multiple of the SIMD and SIMD4 register size
  * to preserve alignment.

diff --git a/src/gromacs/ewald/pme-grid.h b/src/gromacs/ewald/pme_grid.h
similarity index 97%
rename from src/gromacs/ewald/pme-grid.h
rename to src/gromacs/ewald/pme_grid.h
index f86199759580fea40d420ec5f64961ccb6e486d8..52fd095ca4032df1e8c78bd7ac4a220dda525071 100644 (file)
--- a/src/gromacs/ewald/pme-grid.h
+++ b/src/gromacs/ewald/pme_grid.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/ewald/pme-internal.h b/src/gromacs/ewald/pme_internal.h
similarity index 99%
rename from src/gromacs/ewald/pme-internal.h
rename to src/gromacs/ewald/pme_internal.h
index 9dcfdf38c84f081266fc8807a753969d7bf4ceeb..76aa3c090f1c54a7c5bb9c31807c300aef96c716 100644 (file)
--- a/src/gromacs/ewald/pme-internal.h
+++ b/src/gromacs/ewald/pme_internal.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -59,7 +59,7 @@
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/gmxmpi.h"
 
-#include "pme-gpu-types-host.h"
+#include "pme_gpu_types_host.h"
 
 //! A repeat of typedef from parallel_3dfft.h
 typedef struct gmx_parallel_3dfft *gmx_parallel_3dfft_t;

diff --git a/src/gromacs/ewald/pme-load-balancing.cpp b/src/gromacs/ewald/pme_load_balancing.cpp
similarity index 99%
rename from src/gromacs/ewald/pme-load-balancing.cpp
rename to src/gromacs/ewald/pme_load_balancing.cpp
index a975b49788c517b1c8bba48e498109ee63f39396..8ff5939072338d9b96b05c6ca7f491a289e3932d 100644 (file)
--- a/src/gromacs/ewald/pme-load-balancing.cpp
+++ b/src/gromacs/ewald/pme_load_balancing.cpp
@@ -43,7 +43,7 @@
  */
 #include "gmxpre.h"
 
-#include "pme-load-balancing.h"
+#include "pme_load_balancing.h"
 
 #include <cassert>
 #include <cmath>
@@ -55,7 +55,7 @@
 #include "gromacs/domdec/domdec_network.h"
 #include "gromacs/domdec/domdec_struct.h"
 #include "gromacs/domdec/partition.h"
-#include "gromacs/ewald/ewald-utils.h"
+#include "gromacs/ewald/ewald_utils.h"
 #include "gromacs/ewald/pme.h"
 #include "gromacs/fft/calcgrid.h"
 #include "gromacs/gmxlib/network.h"
@@ -79,7 +79,7 @@
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/strconvert.h"
 
-#include "pme-internal.h"
+#include "pme_internal.h"
 
 /*! \brief Parameters and settings for one PP-PME setup */
 struct pme_setup_t {

diff --git a/src/gromacs/ewald/pme-load-balancing.h b/src/gromacs/ewald/pme_load_balancing.h
similarity index 97%
rename from src/gromacs/ewald/pme-load-balancing.h
rename to src/gromacs/ewald/pme_load_balancing.h
index b660ef397074472b420e333d58e330ccc72cc538..11ea28cb869f3dc781e2af49dfbb4d16f497e41e 100644 (file)
--- a/src/gromacs/ewald/pme-load-balancing.h
+++ b/src/gromacs/ewald/pme_load_balancing.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/ewald/pme-only.cpp b/src/gromacs/ewald/pme_only.cpp
similarity index 99%
rename from src/gromacs/ewald/pme-only.cpp
rename to src/gromacs/ewald/pme_only.cpp
index e448d45426fdcfe95f0c63ae2a1db68a87911208..9fd7a138e9e359cb8c04ca2a24fe37a36634ce55 100644 (file)
--- a/src/gromacs/ewald/pme-only.cpp
+++ b/src/gromacs/ewald/pme_only.cpp
@@ -92,9 +92,9 @@
 #include "gromacs/utility/gmxomp.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "pme-gpu-internal.h"
-#include "pme-internal.h"
-#include "pme-pp-communication.h"
+#include "pme_gpu_internal.h"
+#include "pme_internal.h"
+#include "pme_pp_communication.h"
 
 //! Contains information about the PP ranks that partner this PME rank.
 struct PpRanks

diff --git a/src/gromacs/ewald/pme-pp.cpp b/src/gromacs/ewald/pme_pp.cpp
similarity index 98%
rename from src/gromacs/ewald/pme-pp.cpp
rename to src/gromacs/ewald/pme_pp.cpp
index fcad69f0af1beb8cddbae0d7e9b817a6b90cbc38..a15e1b57cd6e1b95c19ed1f0a2fb17ce5f3b2f5e 100644 (file)
--- a/src/gromacs/ewald/pme-pp.cpp
+++ b/src/gromacs/ewald/pme_pp.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -66,8 +66,8 @@
 #include "gromacs/utility/gmxmpi.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "pme-internal.h"
-#include "pme-pp-communication.h"
+#include "pme_internal.h"
+#include "pme_pp_communication.h"
 
 /*! \brief Block to wait for communication to PME ranks to complete
  *

diff --git a/src/gromacs/ewald/pme-pp-communication.h b/src/gromacs/ewald/pme_pp_communication.h
similarity index 98%
rename from src/gromacs/ewald/pme-pp-communication.h
rename to src/gromacs/ewald/pme_pp_communication.h
index 5d66cf3d5d36beefdbb876219d8acabc1efab790..31c0bb717da099e4c6403ca19080cfba5e00b7c8 100644 (file)
--- a/src/gromacs/ewald/pme-pp-communication.h
+++ b/src/gromacs/ewald/pme_pp_communication.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/ewald/pme-program.cl b/src/gromacs/ewald/pme_program.cl
similarity index 92%
rename from src/gromacs/ewald/pme-program.cl
rename to src/gromacs/ewald/pme_program.cl
index afbf17273d895f1d89bc27c117c0796dcbc5f457..58fa2c6c31c76c6e9760e7fcd1cbddd8ad9fb5b2 100644 (file)
--- a/src/gromacs/ewald/pme-program.cl
+++ b/src/gromacs/ewald/pme_program.cl
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -38,7 +38,7 @@
  * This file includes all the PME OpenCL kernel files multiple times, with additional defines.
  * Plenty of common constants/macros are also expected to be already defined by the compiler
  * (such as "order" which is PME interpolation order).
- * For details, please see how pme-program.cl is compiled in pme-gpu-program-impl-ocl.cpp.
+ * For details, please see how pme_program.cl is compiled in pme_gpu_program_impl_ocl.cpp.
  *
  * This file specifically expects the following work size definitions:
  *
@@ -63,7 +63,7 @@
 #define computeSplines 1
 #define spreadCharges 1
 #define CUSTOMIZED_KERNEL_NAME(x) pmeSplineAndSpreadKernel
-#include "pme-spread.clh"
+#include "pme_spread.clh"
 #undef computeSplines
 #undef spreadCharges
 #undef CUSTOMIZED_KERNEL_NAME
@@ -72,7 +72,7 @@
 #define computeSplines 1
 #define spreadCharges 0
 #define CUSTOMIZED_KERNEL_NAME(x) pmeSplineKernel
-#include "pme-spread.clh"
+#include "pme_spread.clh"
 #undef computeSplines
 #undef spreadCharges
 #undef CUSTOMIZED_KERNEL_NAME
@@ -81,7 +81,7 @@
 #define computeSplines 0
 #define spreadCharges 1
 #define CUSTOMIZED_KERNEL_NAME(x) pmeSpreadKernel
-#include "pme-spread.clh"
+#include "pme_spread.clh"
 #undef computeSplines
 #undef spreadCharges
 #undef CUSTOMIZED_KERNEL_NAME
@@ -97,14 +97,14 @@
 // gather
 #define overwriteForces 1
 #define CUSTOMIZED_KERNEL_NAME(x) pmeGatherKernel
-#include "pme-gather.clh"
+#include "pme_gather.clh"
 #undef overwriteForces
 #undef CUSTOMIZED_KERNEL_NAME
 
 // gather with reduction
 #define overwriteForces 0
 #define CUSTOMIZED_KERNEL_NAME(x) pmeGatherReduceWithInputKernel
-#include "pme-gather.clh"
+#include "pme_gather.clh"
 #undef overwriteForces
 #undef CUSTOMIZED_KERNEL_NAME
 
@@ -121,7 +121,7 @@
 #define gridOrdering YZX
 #define computeEnergyAndVirial 0
 #define CUSTOMIZED_KERNEL_NAME(x) pmeSolveYZXKernel
-#include "pme-solve.clh"
+#include "pme_solve.clh"
 #undef gridOrdering
 #undef computeEnergyAndVirial
 #undef CUSTOMIZED_KERNEL_NAME
@@ -130,7 +130,7 @@
 #define gridOrdering YZX
 #define computeEnergyAndVirial 1
 #define CUSTOMIZED_KERNEL_NAME(x) pmeSolveYZXEnergyKernel
-#include "pme-solve.clh"
+#include "pme_solve.clh"
 #undef gridOrdering
 #undef computeEnergyAndVirial
 #undef CUSTOMIZED_KERNEL_NAME
@@ -139,7 +139,7 @@
 #define gridOrdering XYZ
 #define computeEnergyAndVirial 0
 #define CUSTOMIZED_KERNEL_NAME(x) pmeSolveXYZKernel
-#include "pme-solve.clh"
+#include "pme_solve.clh"
 #undef gridOrdering
 #undef computeEnergyAndVirial
 #undef CUSTOMIZED_KERNEL_NAME
@@ -148,7 +148,7 @@
 #define gridOrdering XYZ
 #define computeEnergyAndVirial 1
 #define CUSTOMIZED_KERNEL_NAME(x) pmeSolveXYZEnergyKernel
-#include "pme-solve.clh"
+#include "pme_solve.clh"
 #undef gridOrdering
 #undef computeEnergyAndVirial
 #undef CUSTOMIZED_KERNEL_NAME

diff --git a/src/gromacs/ewald/pme-redistribute.cpp b/src/gromacs/ewald/pme_redistribute.cpp
similarity index 98%
rename from src/gromacs/ewald/pme-redistribute.cpp
rename to src/gromacs/ewald/pme_redistribute.cpp
index bbef6bf975ae20594779900ba36e1e1be0afd84c..3db06d32d8e73f78c222a9ab15177091444223cc 100644 (file)
--- a/src/gromacs/ewald/pme-redistribute.cpp
+++ b/src/gromacs/ewald/pme_redistribute.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "pme-redistribute.h"
+#include "pme_redistribute.h"
 
 #include "config.h"
 
@@ -49,8 +49,8 @@
 #include "gromacs/utility/gmxmpi.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "pme-internal.h"
-#include "pme-simd.h"
+#include "pme_internal.h"
+#include "pme_simd.h"
 
 static void pme_calc_pidx(int start, int end,
                           matrix recipbox, rvec x[],

diff --git a/src/gromacs/ewald/pme-redistribute.h b/src/gromacs/ewald/pme_redistribute.h
similarity index 95%
rename from src/gromacs/ewald/pme-redistribute.h
rename to src/gromacs/ewald/pme_redistribute.h
index 2508611039225168fad5e31e4de8548e86ef3ee3..dc30592b844f63491d4808d7f8cb21cc5c415cd0 100644 (file)
--- a/src/gromacs/ewald/pme-redistribute.h
+++ b/src/gromacs/ewald/pme_redistribute.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014,2015,2018, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -35,7 +35,7 @@
 #ifndef GMX_EWALD_PME_REDISTRIBUTE_H
 #define GMX_EWALD_PME_REDISTRIBUTE_H
 
-#include "pme-internal.h"
+#include "pme_internal.h"
 
 void
 pme_realloc_atomcomm_things(pme_atomcomm_t *atc);

diff --git a/src/gromacs/ewald/pme-simd.h b/src/gromacs/ewald/pme_simd.h
similarity index 97%
rename from src/gromacs/ewald/pme-simd.h
rename to src/gromacs/ewald/pme_simd.h
index 7bbbc25b83ad0bf9359a375d0ca24e0194bc679b..2e4475e346af87bc435239ea2b9c726950ec6603 100644 (file)
--- a/src/gromacs/ewald/pme-simd.h
+++ b/src/gromacs/ewald/pme_simd.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/ewald/pme-simd4.h b/src/gromacs/ewald/pme_simd4.h
similarity index 98%
rename from src/gromacs/ewald/pme-simd4.h
rename to src/gromacs/ewald/pme_simd4.h
index d1d40bd825abe9e5fab341d6ad74f6d892be552b..0fdc3170b1ed147e36c8ceaf536f7ab899ae3143 100644 (file)
--- a/src/gromacs/ewald/pme-simd4.h
+++ b/src/gromacs/ewald/pme_simd4.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/ewald/pme-solve.clh b/src/gromacs/ewald/pme_solve.clh
similarity index 98%
rename from src/gromacs/ewald/pme-solve.clh
rename to src/gromacs/ewald/pme_solve.clh
index b85b1ecc24ea8e7782a6de20564f57479bd6657b..a4b877e0dd82f9ee4b70b53bb01428fe37218304 100644 (file)
--- a/src/gromacs/ewald/pme-solve.clh
+++ b/src/gromacs/ewald/pme_solve.clh
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -37,7 +37,7 @@
  *  \brief Implements PME OpenCL solving kernel.
  * When including this and other PME OpenCL kernel files, plenty of common
  * constants/macros are expected to be defined.
- * For details, please see how pme-program.cl is compiled in pme-gpu-program-impl-ocl.cpp.
+ * For details, please see how pme_program.cl is compiled in pme_gpu_program_impl_ocl.cpp.
  *
  * This file's solving kernel specifically expects the following definitions for its flavors:
  *
@@ -49,7 +49,7 @@
  *  \author Aleksei Iupinov <a.yupinov@gmail.com>
  */
 
-#include "pme-gpu-types.h"
+#include "pme_gpu_types.h"
 #include "gromacs/gpu_utils/vectype_ops.clh"
 
 /*! \brief

diff --git a/src/gromacs/ewald/pme-solve.cpp b/src/gromacs/ewald/pme_solve.cpp
similarity index 99%
rename from src/gromacs/ewald/pme-solve.cpp
rename to src/gromacs/ewald/pme_solve.cpp
index 863b81ccee336d78cd2a8fa65cae09e002c86661..1e944bce10867d32826fd630e05bf73c3dc40df5 100644 (file)
--- a/src/gromacs/ewald/pme-solve.cpp
+++ b/src/gromacs/ewald/pme_solve.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -37,7 +37,7 @@
 
 #include "gmxpre.h"
 
-#include "pme-solve.h"
+#include "pme_solve.h"
 
 #include <cmath>
 
@@ -51,7 +51,7 @@
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "pme-internal.h"
+#include "pme_internal.h"
 
 #if GMX_SIMD_HAVE_REAL
 /* Turn on arbitrary width SIMD intrinsics for PME solve */

diff --git a/src/gromacs/ewald/pme-solve.cu b/src/gromacs/ewald/pme_solve.cu
similarity index 99%
rename from src/gromacs/ewald/pme-solve.cu
rename to src/gromacs/ewald/pme_solve.cu
index c00ec9df0edff0641bb89161ae5688a58fa5d250..3aec442c7b57c31b499958143c4d868bec15a0fc 100644 (file)
--- a/src/gromacs/ewald/pme-solve.cu
+++ b/src/gromacs/ewald/pme_solve.cu
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/ewald/pme-solve.h b/src/gromacs/ewald/pme_solve.h
similarity index 97%
rename from src/gromacs/ewald/pme-solve.h
rename to src/gromacs/ewald/pme_solve.h
index 0252fd5adf2114f488b2debd00a569e0611e92cd..ed6457dcdd8691c09474706537f871a5a66a0933 100644 (file)
--- a/src/gromacs/ewald/pme-solve.h
+++ b/src/gromacs/ewald/pme_solve.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/ewald/pme-spline-work.cpp b/src/gromacs/ewald/pme_spline_work.cpp
similarity index 95%
rename from src/gromacs/ewald/pme-spline-work.cpp
rename to src/gromacs/ewald/pme_spline_work.cpp
index ef2da9253e315bf539914afc3ebd1d9627ebf366..09f9ebdc0762870e00ca9e7524fafab4c7541e31 100644 (file)
--- a/src/gromacs/ewald/pme-spline-work.cpp
+++ b/src/gromacs/ewald/pme_spline_work.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -37,7 +37,7 @@
 
 #include "gmxpre.h"
 
-#include "pme-spline-work.h"
+#include "pme_spline_work.h"
 
 #include "gromacs/simd/simd.h"
 #include "gromacs/utility/alignedallocator.h"
@@ -45,7 +45,7 @@
 #include "gromacs/utility/real.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "pme-simd.h"
+#include "pme_simd.h"
 
 using namespace gmx; // TODO: Remove when this file is moved into gmx namespace
 

diff --git a/src/gromacs/ewald/pme-spline-work.h b/src/gromacs/ewald/pme_spline_work.h
similarity index 95%
rename from src/gromacs/ewald/pme-spline-work.h
rename to src/gromacs/ewald/pme_spline_work.h
index 6e77f6cdf01464c68c1583ea8a7c8a5a8c0e6941..1d0ad410a7694cc5c8e549ab16df06c0dbb56f11 100644 (file)
--- a/src/gromacs/ewald/pme-spline-work.h
+++ b/src/gromacs/ewald/pme_spline_work.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014,2015,2018, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -37,7 +37,7 @@
 
 #include "gromacs/simd/simd.h"
 
-#include "pme-simd.h"
+#include "pme_simd.h"
 
 struct pme_spline_work
 {

diff --git a/src/gromacs/ewald/pme-spread.clh b/src/gromacs/ewald/pme_spread.clh
similarity index 99%
rename from src/gromacs/ewald/pme-spread.clh
rename to src/gromacs/ewald/pme_spread.clh
index 5916e162c3985b64d11a552792a4a22087a5b2ce..2b140133c11adb06eec94e9e2542927b496160b2 100644 (file)
--- a/src/gromacs/ewald/pme-spread.clh
+++ b/src/gromacs/ewald/pme_spread.clh
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -37,7 +37,7 @@
  *  \brief Implements PME OpenCL spline parameter computation and charge spread kernels.
  * When including this and other PME OpenCL kernel files, plenty of common
  * constants/macros are expected to be defined (such as "order" which is PME interpolation order).
- * For details, please see how pme-program.cl is compiled in pme-gpu-program-impl-ocl.cpp.
+ * For details, please see how pme_program.cl is compiled in pme_gpu_program_impl_ocl.cpp.
  *
  * This file's kernels specifically expect the following definitions:
  *
@@ -51,8 +51,8 @@
  *  \author Aleksei Iupinov <a.yupinov@gmail.com>
  */
 
-#include "pme-gpu-types.h"
-#include "pme-gpu-utils.clh"
+#include "pme_gpu_types.h"
+#include "pme_gpu_utils.clh"
 #include "gromacs/gpu_utils/vectype_ops.clh"
 
 /*

diff --git a/src/gromacs/ewald/pme-spread.cpp b/src/gromacs/ewald/pme_spread.cpp
similarity index 99%
rename from src/gromacs/ewald/pme-spread.cpp
rename to src/gromacs/ewald/pme_spread.cpp
index 6ee5381967a77e66ac65be003cbe84a08e1b9123..deed63f025ac7a7f88167b58d17b3cae4d8fdd89 100644 (file)
--- a/src/gromacs/ewald/pme-spread.cpp
+++ b/src/gromacs/ewald/pme_spread.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "pme-spread.h"
+#include "pme_spread.h"
 
 #include "config.h"
 
@@ -52,10 +52,10 @@
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "pme-grid.h"
-#include "pme-internal.h"
-#include "pme-simd.h"
-#include "pme-spline-work.h"
+#include "pme_grid.h"
+#include "pme_internal.h"
+#include "pme_simd.h"
+#include "pme_spline_work.h"
 
 /* TODO consider split of pme-spline from this file */
 
@@ -377,7 +377,7 @@ static void spread_coefficients_bsplines_thread(const pmegrid_t
 #define PME_SPREAD_SIMD4_ALIGNED
 #define PME_ORDER 4
 #endif
-#include "pme-simd4.h"
+#include "pme_simd4.h"
 #else
                     DO_BSPLINE(4);
 #endif
@@ -386,7 +386,7 @@ static void spread_coefficients_bsplines_thread(const pmegrid_t
 #ifdef PME_SIMD4_SPREAD_GATHER
 #define PME_SPREAD_SIMD4_ALIGNED
 #define PME_ORDER 5
-#include "pme-simd4.h"
+#include "pme_simd4.h"
 #else
                     DO_BSPLINE(5);
 #endif

diff --git a/src/gromacs/ewald/pme-spread.cu b/src/gromacs/ewald/pme_spread.cu
similarity index 99%
rename from src/gromacs/ewald/pme-spread.cu
rename to src/gromacs/ewald/pme_spread.cu
index 030367fd3088e21a1cb9b69f2b48cb2769fe1723..728300c815d945b190b8695bfb2c6b93ff074856 100644 (file)
--- a/src/gromacs/ewald/pme-spread.cu
+++ b/src/gromacs/ewald/pme_spread.cu
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013-2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013-2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -49,8 +49,8 @@
 #include "gromacs/gpu_utils/cuda_kernel_utils.cuh"
 
 #include "pme.cuh"
-#include "pme-gpu-utils.h"
-#include "pme-grid.h"
+#include "pme_gpu_utils.h"
+#include "pme_grid.h"
 
 /*
  * This define affects the spline calculation behaviour in the kernel.

diff --git a/src/gromacs/ewald/pme-spread.h b/src/gromacs/ewald/pme_spread.h
similarity index 95%
rename from src/gromacs/ewald/pme-spread.h
rename to src/gromacs/ewald/pme_spread.h
index 78d8fbef69531376eecd41ea2da231d09dc259d2..23e07318533cdcfbe1a9df4070fbbf7159db5e39 100644 (file)
--- a/src/gromacs/ewald/pme-spread.h
+++ b/src/gromacs/ewald/pme_spread.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -39,7 +39,7 @@
 
 #include "gromacs/utility/real.h"
 
-#include "pme-internal.h"
+#include "pme_internal.h"
 
 void
 spread_on_grid(const gmx_pme_t *pme,

diff --git a/src/gromacs/ewald/tests/pmebsplinetest.cpp b/src/gromacs/ewald/tests/pmebsplinetest.cpp
index b57d2dd91bcd931ed3b7b9a1b33b35d6c01fec3f..c7a952a7143d4d43a031d96deec3304603c419a5 100644 (file)
--- a/src/gromacs/ewald/tests/pmebsplinetest.cpp
+++ b/src/gromacs/ewald/tests/pmebsplinetest.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -46,7 +46,7 @@
 
 #include <gmock/gmock.h>
 
-#include "gromacs/ewald/pme-internal.h"
+#include "gromacs/ewald/pme_internal.h"
 #include "gromacs/math/vectypes.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/utility/stringutil.h"

diff --git a/src/gromacs/ewald/tests/pmetestcommon.cpp b/src/gromacs/ewald/tests/pmetestcommon.cpp
index 6fa0627777e4bdff414a3daf1f51aee713d37564..625a077afa7dee5a53405a7ddcaaef5f450cbe64 100644 (file)
--- a/src/gromacs/ewald/tests/pmetestcommon.cpp
+++ b/src/gromacs/ewald/tests/pmetestcommon.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -48,12 +48,12 @@
 #include <algorithm>
 
 #include "gromacs/domdec/domdec.h"
-#include "gromacs/ewald/pme-gather.h"
-#include "gromacs/ewald/pme-gpu-internal.h"
-#include "gromacs/ewald/pme-grid.h"
-#include "gromacs/ewald/pme-internal.h"
-#include "gromacs/ewald/pme-solve.h"
-#include "gromacs/ewald/pme-spread.h"
+#include "gromacs/ewald/pme_gather.h"
+#include "gromacs/ewald/pme_gpu_internal.h"
+#include "gromacs/ewald/pme_grid.h"
+#include "gromacs/ewald/pme_internal.h"
+#include "gromacs/ewald/pme_solve.h"
+#include "gromacs/ewald/pme_spread.h"
 #include "gromacs/fft/parallel_3dfft.h"
 #include "gromacs/gpu_utils/gpu_utils.h"
 #include "gromacs/math/invertmatrix.h"

diff --git a/src/gromacs/ewald/tests/pmetestcommon.h b/src/gromacs/ewald/tests/pmetestcommon.h
index d4f4027e2f83dd0d86d1e1f4c238a7fdaa65b13b..3b353b026ad1e3d05c5bc889d7fb3382cb91b3de 100644 (file)
--- a/src/gromacs/ewald/tests/pmetestcommon.h
+++ b/src/gromacs/ewald/tests/pmetestcommon.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -49,7 +49,7 @@
 #include <gtest/gtest.h>
 
 #include "gromacs/ewald/pme.h"
-#include "gromacs/ewald/pme-gpu-internal.h"
+#include "gromacs/ewald/pme_gpu_internal.h"
 #include "gromacs/math/gmxcomplex.h"
 #include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/unique_cptr.h"

diff --git a/src/gromacs/ewald/tests/testhardwarecontexts.h b/src/gromacs/ewald/tests/testhardwarecontexts.h
index f364c466d4fb3f93e6ad921e6483f984e05b99e5..f733e230951025da3f25b8dd4878e3b9fc190dfb 100644 (file)
--- a/src/gromacs/ewald/tests/testhardwarecontexts.h
+++ b/src/gromacs/ewald/tests/testhardwarecontexts.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -48,7 +48,7 @@
 
 #include <gtest/gtest.h>
 
-#include "gromacs/ewald/pme-gpu-program.h"
+#include "gromacs/ewald/pme_gpu_program.h"
 #include "gromacs/hardware/gpu_hw_info.h"
 
 struct gmx_hw_info_t;

diff --git a/src/gromacs/fileio/checkpoint.cpp b/src/gromacs/fileio/checkpoint.cpp
index a3a7a094932894617943ee32053865ae83392bf2..555c6e790b7aaef9c99d2a0c3a38cfb48a664cd8 100644 (file)
--- a/src/gromacs/fileio/checkpoint.cpp
+++ b/src/gromacs/fileio/checkpoint.cpp
@@ -57,15 +57,15 @@
 #include "buildinfo.h"
 #include "gromacs/fileio/filetypes.h"
 #include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/gmxfio-xdr.h"
+#include "gromacs/fileio/gmxfio_xdr.h"
 #include "gromacs/fileio/xdr_datatype.h"
 #include "gromacs/fileio/xdrf.h"
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/math/vecdump.h"
 #include "gromacs/math/vectypes.h"
-#include "gromacs/mdtypes/awh-correlation-history.h"
-#include "gromacs/mdtypes/awh-history.h"
+#include "gromacs/mdtypes/awh_correlation_history.h"
+#include "gromacs/mdtypes/awh_history.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/df_history.h"
 #include "gromacs/mdtypes/edsamhistory.h"

diff --git a/src/gromacs/fileio/enxio.cpp b/src/gromacs/fileio/enxio.cpp
index dc0a177c9ff4609568915a5d4946297e06b0a8c6..cc2ac96df42e1ee83055f6919b95962391323f0d 100644 (file)
--- a/src/gromacs/fileio/enxio.cpp
+++ b/src/gromacs/fileio/enxio.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -44,7 +44,7 @@
 #include <algorithm>
 
 #include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/gmxfio-xdr.h"
+#include "gromacs/fileio/gmxfio_xdr.h"
 #include "gromacs/fileio/xdrf.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/fileio/gmxfio.cpp b/src/gromacs/fileio/gmxfio.cpp
index bf7749b9f7a4bc53dc4073896dc271005d8556e3..a9fc9c0b057fab7765f2ded23bec6592a1ef88ae 100644 (file)
--- a/src/gromacs/fileio/gmxfio.cpp
+++ b/src/gromacs/fileio/gmxfio.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -62,7 +62,7 @@
 #include "gromacs/utility/mutex.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "gmxfio-impl.h"
+#include "gmxfio_impl.h"
 
 /* This is the new improved and thread safe version of gmxfio. */
 

diff --git a/src/gromacs/fileio/gmxfio-impl.h b/src/gromacs/fileio/gmxfio_impl.h
similarity index 97%
rename from src/gromacs/fileio/gmxfio-impl.h
rename to src/gromacs/fileio/gmxfio_impl.h
index 0b455979dd6fb23c18c77202b81a6fe2e97349c6..1cc7d40b31d9ea00a8970b482c99877930cf76fb 100644 (file)
--- a/src/gromacs/fileio/gmxfio-impl.h
+++ b/src/gromacs/fileio/gmxfio_impl.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/fileio/gmxfio-xdr.cpp b/src/gromacs/fileio/gmxfio_xdr.cpp
similarity index 99%
rename from src/gromacs/fileio/gmxfio-xdr.cpp
rename to src/gromacs/fileio/gmxfio_xdr.cpp
index 87a672112e572c928dd50fe7bc12418cc72a12f9..9a40af48dd457493d5f9e5d8f760097682f59d37 100644 (file)
--- a/src/gromacs/fileio/gmxfio-xdr.cpp
+++ b/src/gromacs/fileio/gmxfio_xdr.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gmxfio-xdr.h"
+#include "gmxfio_xdr.h"
 
 #include <cstdio>
 #include <cstring>
@@ -47,7 +47,7 @@
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "gmxfio-impl.h"
+#include "gmxfio_impl.h"
 
 /* Enumerated for data types in files */
 enum {

diff --git a/src/gromacs/fileio/gmxfio-xdr.h b/src/gromacs/fileio/gmxfio_xdr.h
similarity index 98%
rename from src/gromacs/fileio/gmxfio-xdr.h
rename to src/gromacs/fileio/gmxfio_xdr.h
index 848e936c801cc274091c09016f11bf4bb44e239c..27811f3030f10f8b1c8e859639ccc7bba01432bd 100644 (file)
--- a/src/gromacs/fileio/gmxfio-xdr.h
+++ b/src/gromacs/fileio/gmxfio_xdr.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/fileio/mtxio.cpp b/src/gromacs/fileio/mtxio.cpp
index 7a48bc64ffca1617a322e1c5bd5c03b885ebfa9b..542a6ae08267b6a84de8501ac4da3e1cca439657 100644 (file)
--- a/src/gromacs/fileio/mtxio.cpp
+++ b/src/gromacs/fileio/mtxio.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -44,7 +44,7 @@
  */
 
 #include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/gmxfio-xdr.h"
+#include "gromacs/fileio/gmxfio_xdr.h"
 #include "gromacs/linearalgebra/sparsematrix.h"
 #include "gromacs/utility/baseversion.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/fileio/tpxio.cpp b/src/gromacs/fileio/tpxio.cpp
index 8891f103cd96cb6f517c0d2e0b14388f06595908..fb04ec0ee2801f356e6f106f971f6d754053c813 100644 (file)
--- a/src/gromacs/fileio/tpxio.cpp
+++ b/src/gromacs/fileio/tpxio.cpp
@@ -50,14 +50,14 @@
 
 #include "gromacs/fileio/filetypes.h"
 #include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/gmxfio-xdr.h"
+#include "gromacs/fileio/gmxfio_xdr.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/mdtypes/awh-history.h"
-#include "gromacs/mdtypes/awh-params.h"
+#include "gromacs/mdtypes/awh_history.h"
+#include "gromacs/mdtypes/awh_params.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/mdtypes/md_enums.h"
-#include "gromacs/mdtypes/pull-params.h"
+#include "gromacs/mdtypes/pull_params.h"
 #include "gromacs/mdtypes/state.h"
 #include "gromacs/pbcutil/boxutilities.h"
 #include "gromacs/pbcutil/pbc.h"

diff --git a/src/gromacs/fileio/trrio.cpp b/src/gromacs/fileio/trrio.cpp
index 2fe6ff8afb0b306c6159c2a53e5128f760602807..b69811cb8631e504830ae8455eb4fd67cc97a2c1 100644 (file)
--- a/src/gromacs/fileio/trrio.cpp
+++ b/src/gromacs/fileio/trrio.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -41,7 +41,7 @@
 #include <cstring>
 
 #include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/gmxfio-xdr.h"
+#include "gromacs/fileio/gmxfio_xdr.h"
 #include "gromacs/mdtypes/md_enums.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"

diff --git a/src/gromacs/fileio/trxio.cpp b/src/gromacs/fileio/trxio.cpp
index f655a3cb26e8efd2286ea18a587c82bd63796dc2..f9a33fefac166d668280adb6786602c12c3328d8 100644 (file)
--- a/src/gromacs/fileio/trxio.cpp
+++ b/src/gromacs/fileio/trxio.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -49,7 +49,7 @@
 #include "gromacs/fileio/filetypes.h"
 #include "gromacs/fileio/g96io.h"
 #include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/gmxfio-xdr.h"
+#include "gromacs/fileio/gmxfio_xdr.h"
 #include "gromacs/fileio/groio.h"
 #include "gromacs/fileio/oenv.h"
 #include "gromacs/fileio/pdbio.h"

diff --git a/src/gromacs/fileio/xtcio.cpp b/src/gromacs/fileio/xtcio.cpp
index bd705f2b765609fca9cea9d979ee021d785931ab..09f0d8cab7fd0af87295885f5d299e8d3465dfd5 100644 (file)
--- a/src/gromacs/fileio/xtcio.cpp
+++ b/src/gromacs/fileio/xtcio.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -41,7 +41,7 @@
 #include <cstring>
 
 #include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/gmxfio-xdr.h"
+#include "gromacs/fileio/gmxfio_xdr.h"
 #include "gromacs/fileio/xdrf.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/gmxana/gmx_awh.cpp b/src/gromacs/gmxana/gmx_awh.cpp
index e17343a925c27345dbf6b057b9ec4e12f161c4ba..1d7463bdaa6d8535d2c2f9f22e7fc66f1abddcf3 100644 (file)
--- a/src/gromacs/gmxana/gmx_awh.cpp
+++ b/src/gromacs/gmxana/gmx_awh.cpp
@@ -60,7 +60,7 @@
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/math/units.h"
-#include "gromacs/mdtypes/awh-params.h"
+#include "gromacs/mdtypes/awh_params.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/topology/mtop_util.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 48ed788268d30ecf4221efe43e3017767fbdf5c3..bc87405672b5aa3ecc18c77868c98a56411a0fcf 100644 (file)
--- a/src/gromacs/gmxana/gmx_pme_error.cpp
+++ b/src/gromacs/gmxana/gmx_pme_error.cpp
@@ -41,7 +41,7 @@
 #include <algorithm>
 
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/ewald/ewald-utils.h"
+#include "gromacs/ewald/ewald_utils.h"
 #include "gromacs/ewald/pme.h"
 #include "gromacs/fft/calcgrid.h"
 #include "gromacs/fileio/checkpoint.h"

diff --git a/src/gromacs/gmxana/gmx_wham.cpp b/src/gromacs/gmxana/gmx_wham.cpp
index 307a04485c79ac0b54dc09132505739f7da48084..12d9d1d2276e4e6bb68c64725d744c161e52ed07 100644 (file)
--- a/src/gromacs/gmxana/gmx_wham.cpp
+++ b/src/gromacs/gmxana/gmx_wham.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -63,7 +63,7 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/mdtypes/md_enums.h"
-#include "gromacs/mdtypes/pull-params.h"
+#include "gromacs/mdtypes/pull_params.h"
 #include "gromacs/mdtypes/state.h"
 #include "gromacs/pulling/pull.h"
 #include "gromacs/random/tabulatednormaldistribution.h"

diff --git a/src/gromacs/gmxlib/conformation-utilities.cpp b/src/gromacs/gmxlib/conformation_utilities.cpp
similarity index 97%
rename from src/gromacs/gmxlib/conformation-utilities.cpp
rename to src/gromacs/gmxlib/conformation_utilities.cpp
index 5f93fd7573172eda4259af3bc819fc2cd5c9ec8d..c3d6dbd11813339886f00faacd0afcf6f503c7dd 100644 (file)
--- a/src/gromacs/gmxlib/conformation-utilities.cpp
+++ b/src/gromacs/gmxlib/conformation_utilities.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014,2015,2018, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -37,7 +37,7 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
-#include "conformation-utilities.h"
+#include "conformation_utilities.h"
 
 #include <cmath>
 

diff --git a/src/gromacs/gmxlib/conformation-utilities.h b/src/gromacs/gmxlib/conformation_utilities.h
similarity index 96%
rename from src/gromacs/gmxlib/conformation-utilities.h
rename to src/gromacs/gmxlib/conformation_utilities.h
index 9c20592da6d8c686da18c8bdec0930cf56b24866..b3dbc96f39570af4fbcf9c23f8c4cda62be57f22 100644 (file)
--- a/src/gromacs/gmxlib/conformation-utilities.h
+++ b/src/gromacs/gmxlib/conformation_utilities.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014,2018, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/gmxpreprocess/add_par.cpp b/src/gromacs/gmxpreprocess/add_par.cpp
index aca94d8a2d576b0defa360a0329a983723200eb7..741452d69a9a7b9d49bdc32c533ad141e088ffac 100644 (file)
--- a/src/gromacs/gmxpreprocess/add_par.cpp
+++ b/src/gromacs/gmxpreprocess/add_par.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2014,2015,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2011,2014,2015,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -43,7 +43,7 @@
 
 #include <algorithm>
 
-#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp_impl.h"
 #include "gromacs/gmxpreprocess/hackblock.h"
 #include "gromacs/gmxpreprocess/notset.h"
 #include "gromacs/gmxpreprocess/toputil.h"

diff --git a/src/gromacs/gmxpreprocess/convparm.cpp b/src/gromacs/gmxpreprocess/convparm.cpp
index a28d9918da62659bdc38ce1bdbf76bab0000612f..df6889d52a3b6c61e48df38b907a1066551cecc3 100644 (file)
--- a/src/gromacs/gmxpreprocess/convparm.cpp
+++ b/src/gromacs/gmxpreprocess/convparm.cpp
@@ -46,7 +46,7 @@
 #include <memory>
 
 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
-#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp_impl.h"
 #include "gromacs/gmxpreprocess/topio.h"
 #include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/math/functions.h"

diff --git a/src/gromacs/gmxpreprocess/editconf.cpp b/src/gromacs/gmxpreprocess/editconf.cpp
index 58347b87a82f80534a51f6bc0380419df97bc4f7..dcbd52a49d123a93bcbb57cb7f5633a7129c5623 100644 (file)
--- a/src/gromacs/gmxpreprocess/editconf.cpp
+++ b/src/gromacs/gmxpreprocess/editconf.cpp
@@ -51,7 +51,7 @@
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/gmxana/princ.h"
-#include "gromacs/gmxlib/conformation-utilities.h"
+#include "gromacs/gmxlib/conformation_utilities.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/gmxpreprocess/gen_ad.cpp b/src/gromacs/gmxpreprocess/gen_ad.cpp
index c77553fb31b2d1c426bc8963ec4c8f57e726c86d..671147624388fa9f5a1490028dcfd8678f366d6d 100644 (file)
--- a/src/gromacs/gmxpreprocess/gen_ad.cpp
+++ b/src/gromacs/gmxpreprocess/gen_ad.cpp
@@ -48,7 +48,7 @@
 
 #include "gromacs/fileio/confio.h"
 #include "gromacs/gmxpreprocess/gpp_nextnb.h"
-#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp_impl.h"
 #include "gromacs/gmxpreprocess/hackblock.h"
 #include "gromacs/gmxpreprocess/notset.h"
 #include "gromacs/gmxpreprocess/pgutil.h"

diff --git a/src/gromacs/gmxpreprocess/gen_vsite.cpp b/src/gromacs/gmxpreprocess/gen_vsite.cpp
index b55d8a37f478836cabcc01020c33f4504de1406b..1bc33529d795ed86d363d7ff0edf4f35fc791e3d 100644 (file)
--- a/src/gromacs/gmxpreprocess/gen_vsite.cpp
+++ b/src/gromacs/gmxpreprocess/gen_vsite.cpp
@@ -50,7 +50,7 @@
 #include "gromacs/gmxpreprocess/add_par.h"
 #include "gromacs/gmxpreprocess/fflibutil.h"
 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
-#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp_impl.h"
 #include "gromacs/gmxpreprocess/hackblock.h"
 #include "gromacs/gmxpreprocess/notset.h"
 #include "gromacs/gmxpreprocess/resall.h"

diff --git a/src/gromacs/gmxpreprocess/gpp_atomtype.cpp b/src/gromacs/gmxpreprocess/gpp_atomtype.cpp
index a5b905f6ef7051dbc2badc5686a91e4adebbc77e..3fe7003ccd3575b4749e33ca0235d7ec6d706c18 100644 (file)
--- a/src/gromacs/gmxpreprocess/gpp_atomtype.cpp
+++ b/src/gromacs/gmxpreprocess/gpp_atomtype.cpp
@@ -42,7 +42,7 @@
 #include <cmath>
 #include <cstring>
 
-#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp_impl.h"
 #include "gromacs/gmxpreprocess/notset.h"
 #include "gromacs/gmxpreprocess/topdirs.h"
 #include "gromacs/gmxpreprocess/toputil.h"

diff --git a/src/gromacs/gmxpreprocess/gpp_nextnb.cpp b/src/gromacs/gmxpreprocess/gpp_nextnb.cpp
index 66ef693a6bd379b3b3f1486f28ba593d65c8ec8f..74c2fa32261712dfdd061869a382a4fa22375a0f 100644 (file)
--- a/src/gromacs/gmxpreprocess/gpp_nextnb.cpp
+++ b/src/gromacs/gmxpreprocess/gpp_nextnb.cpp
@@ -41,7 +41,7 @@
 
 #include <cstdlib>
 
-#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp_impl.h"
 #include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/topology/ifunc.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/gmxpreprocess/grompp.cpp b/src/gromacs/gmxpreprocess/grompp.cpp
index 4e0922fd84cc496c32fb067617fc0a4554526950..08ce54c750b9b5404ba3388005bc0dbcf3901370 100644 (file)
--- a/src/gromacs/gmxpreprocess/grompp.cpp
+++ b/src/gromacs/gmxpreprocess/grompp.cpp
@@ -49,9 +49,9 @@
 
 #include <sys/types.h>
 
-#include "gromacs/awh/read-params.h"
+#include "gromacs/awh/read_params.h"
 #include "gromacs/commandline/pargs.h"
-#include "gromacs/ewald/ewald-utils.h"
+#include "gromacs/ewald/ewald_utils.h"
 #include "gromacs/ewald/pme.h"
 #include "gromacs/fft/calcgrid.h"
 #include "gromacs/fileio/confio.h"
@@ -63,7 +63,7 @@
 #include "gromacs/gmxpreprocess/convparm.h"
 #include "gromacs/gmxpreprocess/gen_maxwell_velocities.h"
 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
-#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp_impl.h"
 #include "gromacs/gmxpreprocess/notset.h"
 #include "gromacs/gmxpreprocess/readir.h"
 #include "gromacs/gmxpreprocess/tomorse.h"

diff --git a/src/gromacs/gmxpreprocess/grompp-impl.h b/src/gromacs/gmxpreprocess/grompp_impl.h
similarity index 100%
rename from src/gromacs/gmxpreprocess/grompp-impl.h
rename to src/gromacs/gmxpreprocess/grompp_impl.h

diff --git a/src/gromacs/gmxpreprocess/insert-molecules.cpp b/src/gromacs/gmxpreprocess/insert_molecules.cpp
similarity index 99%
rename from src/gromacs/gmxpreprocess/insert-molecules.cpp
rename to src/gromacs/gmxpreprocess/insert_molecules.cpp
index 268b56e125bfea63d613b9513a5c24e3640f862e..572c385516faf0094710afd2bfaeb227ca9dfcde 100644 (file)
--- a/src/gromacs/gmxpreprocess/insert-molecules.cpp
+++ b/src/gromacs/gmxpreprocess/insert_molecules.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "insert-molecules.h"
+#include "insert_molecules.h"
 
 #include <algorithm>
 #include <memory>
@@ -48,7 +48,7 @@
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/filetypes.h"
 #include "gromacs/fileio/xvgr.h"
-#include "gromacs/gmxlib/conformation-utilities.h"
+#include "gromacs/gmxlib/conformation_utilities.h"
 #include "gromacs/gmxpreprocess/makeexclusiondistances.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/math/utilities.h"

diff --git a/src/gromacs/gmxpreprocess/insert-molecules.h b/src/gromacs/gmxpreprocess/insert_molecules.h
similarity index 96%
rename from src/gromacs/gmxpreprocess/insert-molecules.h
rename to src/gromacs/gmxpreprocess/insert_molecules.h
index 8392f92277a8665d73bb137f94d086985693cefe..37601f2748a07fafd752b2e9d562198054617514 100644 (file)
--- a/src/gromacs/gmxpreprocess/insert-molecules.h
+++ b/src/gromacs/gmxpreprocess/insert_molecules.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014,2015,2018, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/gmxpreprocess/nm2type.cpp b/src/gromacs/gmxpreprocess/nm2type.cpp
index 836cec2227df606370d0c2698ef531d9e410ad50..3926d6137abc65f9f74031c22a563dfcc517be2b 100644 (file)
--- a/src/gromacs/gmxpreprocess/nm2type.cpp
+++ b/src/gromacs/gmxpreprocess/nm2type.cpp
@@ -49,7 +49,7 @@
 #include "gromacs/gmxpreprocess/fflibutil.h"
 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
 #include "gromacs/gmxpreprocess/gpp_nextnb.h"
-#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp_impl.h"
 #include "gromacs/gmxpreprocess/notset.h"
 #include "gromacs/gmxpreprocess/pdb2top.h"
 #include "gromacs/gmxpreprocess/toppush.h"

diff --git a/src/gromacs/gmxpreprocess/pdb2gmx.cpp b/src/gromacs/gmxpreprocess/pdb2gmx.cpp
index cab4521a434e0e22298c8bff8b7cfb7c247a343d..6f613f901cda6f70f112ab012af4bd7fecbece43 100644 (file)
--- a/src/gromacs/gmxpreprocess/pdb2gmx.cpp
+++ b/src/gromacs/gmxpreprocess/pdb2gmx.cpp
@@ -53,10 +53,10 @@
 #include "gromacs/fileio/filetypes.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/pdbio.h"
-#include "gromacs/gmxlib/conformation-utilities.h"
+#include "gromacs/gmxlib/conformation_utilities.h"
 #include "gromacs/gmxpreprocess/fflibutil.h"
 #include "gromacs/gmxpreprocess/genhydro.h"
-#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp_impl.h"
 #include "gromacs/gmxpreprocess/h_db.h"
 #include "gromacs/gmxpreprocess/hackblock.h"
 #include "gromacs/gmxpreprocess/hizzie.h"

diff --git a/src/gromacs/gmxpreprocess/pdb2top.cpp b/src/gromacs/gmxpreprocess/pdb2top.cpp
index ecb7f264a8ce89982bc45c7960fc88a00b2ed360..292397645c1063253d4adb5e8d8b51baeb1ee43a 100644 (file)
--- a/src/gromacs/gmxpreprocess/pdb2top.cpp
+++ b/src/gromacs/gmxpreprocess/pdb2top.cpp
@@ -53,7 +53,7 @@
 #include "gromacs/gmxpreprocess/gen_ad.h"
 #include "gromacs/gmxpreprocess/gen_vsite.h"
 #include "gromacs/gmxpreprocess/gpp_nextnb.h"
-#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp_impl.h"
 #include "gromacs/gmxpreprocess/h_db.h"
 #include "gromacs/gmxpreprocess/hackblock.h"
 #include "gromacs/gmxpreprocess/notset.h"

diff --git a/src/gromacs/gmxpreprocess/readir.cpp b/src/gromacs/gmxpreprocess/readir.cpp
index 9e6a9d1ee27ed9344189168d7a7eb57b24deff8a..1960170bb067e973c9c7a32167f5b1b48191eb55 100644 (file)
--- a/src/gromacs/gmxpreprocess/readir.cpp
+++ b/src/gromacs/gmxpreprocess/readir.cpp
@@ -46,7 +46,7 @@
 #include <algorithm>
 #include <string>
 
-#include "gromacs/awh/read-params.h"
+#include "gromacs/awh/read_params.h"
 #include "gromacs/fileio/readinp.h"
 #include "gromacs/fileio/warninp.h"
 #include "gromacs/gmxlib/chargegroup.h"
@@ -60,7 +60,7 @@
 #include "gromacs/mdrunutility/mdmodules.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/mdtypes/md_enums.h"
-#include "gromacs/mdtypes/pull-params.h"
+#include "gromacs/mdtypes/pull_params.h"
 #include "gromacs/options/options.h"
 #include "gromacs/options/treesupport.h"
 #include "gromacs/pbcutil/pbc.h"

diff --git a/src/gromacs/gmxpreprocess/readpull.cpp b/src/gromacs/gmxpreprocess/readpull.cpp
index f910615911fb9912b9a8fad5a165d1d32530131b..16f00271e791882196cf1426218ab7de66758227 100644 (file)
--- a/src/gromacs/gmxpreprocess/readpull.cpp
+++ b/src/gromacs/gmxpreprocess/readpull.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -49,7 +49,7 @@
 #include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/mdtypes/md_enums.h"
-#include "gromacs/mdtypes/pull-params.h"
+#include "gromacs/mdtypes/pull_params.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pulling/pull.h"
 #include "gromacs/topology/topology.h"

diff --git a/src/gromacs/gmxpreprocess/resall.cpp b/src/gromacs/gmxpreprocess/resall.cpp
index 0c67d5abd66db8d37ab889c7291c104cfb1bf0a7..ea89de540a78496649e49dab719cb670fc8e6849 100644 (file)
--- a/src/gromacs/gmxpreprocess/resall.cpp
+++ b/src/gromacs/gmxpreprocess/resall.cpp
@@ -48,7 +48,7 @@
 
 #include "gromacs/gmxpreprocess/fflibutil.h"
 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
-#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp_impl.h"
 #include "gromacs/gmxpreprocess/hackblock.h"
 #include "gromacs/gmxpreprocess/notset.h"
 #include "gromacs/gmxpreprocess/pgutil.h"

diff --git a/src/gromacs/gmxpreprocess/solvate.cpp b/src/gromacs/gmxpreprocess/solvate.cpp
index 40405d567016736b2042e80d7ea692dba70527e5..60fa35e97cd941905fa394c0208f3cd9db5ec6b3 100644 (file)
--- a/src/gromacs/gmxpreprocess/solvate.cpp
+++ b/src/gromacs/gmxpreprocess/solvate.cpp
@@ -46,7 +46,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/pdbio.h"
-#include "gromacs/gmxlib/conformation-utilities.h"
+#include "gromacs/gmxlib/conformation_utilities.h"
 #include "gromacs/gmxpreprocess/makeexclusiondistances.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/math/units.h"

diff --git a/src/gromacs/gmxpreprocess/ter_db.cpp b/src/gromacs/gmxpreprocess/ter_db.cpp
index 866f8103688d61c79bd70b4db9def8cc8793cfd5..6f78669d25530358020e3b09a1822248846b456f 100644 (file)
--- a/src/gromacs/gmxpreprocess/ter_db.cpp
+++ b/src/gromacs/gmxpreprocess/ter_db.cpp
@@ -47,7 +47,7 @@
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/gmxpreprocess/fflibutil.h"
 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
-#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp_impl.h"
 #include "gromacs/gmxpreprocess/h_db.h"
 #include "gromacs/gmxpreprocess/hackblock.h"
 #include "gromacs/gmxpreprocess/notset.h"

diff --git a/src/gromacs/gmxpreprocess/tests/CMakeLists.txt b/src/gromacs/gmxpreprocess/tests/CMakeLists.txt
index f3d52e323747768cd8f34e837f1d691c1c01eba4..ecb8c960dd359b0d7bfc1bde57c02274cd514cb3 100644 (file)
--- a/src/gromacs/gmxpreprocess/tests/CMakeLists.txt
+++ b/src/gromacs/gmxpreprocess/tests/CMakeLists.txt
@@ -34,7 +34,7 @@
 
 gmx_add_unit_test(GmxPreprocessTests gmxpreprocess-test
     genconf.cpp
-    insert-molecules.cpp
+    insert_molecules.cpp
     readir.cpp
     solvate.cpp
     topdirs.cpp

diff --git a/src/gromacs/gmxpreprocess/tests/insert-molecules.cpp b/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp
similarity index 96%
rename from src/gromacs/gmxpreprocess/tests/insert-molecules.cpp
rename to src/gromacs/gmxpreprocess/tests/insert_molecules.cpp
index ff603a6e1d1746786a1b0be4b012382765f90b06..39699fdb150945ad3e753dee670428525f33632c 100644 (file)
--- a/src/gromacs/gmxpreprocess/tests/insert-molecules.cpp
+++ b/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/gmxpreprocess/insert-molecules.h"
+#include "gromacs/gmxpreprocess/insert_molecules.h"
 
 #include "testutils/cmdlinetest.h"
 #include "testutils/refdata.h"

diff --git a/src/gromacs/gmxpreprocess/tomorse.cpp b/src/gromacs/gmxpreprocess/tomorse.cpp
index 7cef8dfee78e671fbe6676ec1246204129d793ec..90b296274648f90130d60b32b0691b95c3f5ef0d 100644 (file)
--- a/src/gromacs/gmxpreprocess/tomorse.cpp
+++ b/src/gromacs/gmxpreprocess/tomorse.cpp
@@ -45,7 +45,7 @@
 #include <cstring>
 
 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
-#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp_impl.h"
 #include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/topology/ifunc.h"
 #include "gromacs/utility/cstringutil.h"

diff --git a/src/gromacs/gmxpreprocess/topdirs.cpp b/src/gromacs/gmxpreprocess/topdirs.cpp
index 87da79bf201f910a7aa0e405295e65602ca9bcdf..89f4374b1f07778d13931c4e5cba0c4251ada26e 100644 (file)
--- a/src/gromacs/gmxpreprocess/topdirs.cpp
+++ b/src/gromacs/gmxpreprocess/topdirs.cpp
@@ -49,7 +49,7 @@
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
-/* Must correspond to the Directive enum in grompp-impl.h */
+/* Must correspond to the Directive enum in grompp_impl.h */
 static gmx::EnumerationArray<Directive, const char *> directive_names
     = { {
             "defaults",

diff --git a/src/gromacs/gmxpreprocess/topio.cpp b/src/gromacs/gmxpreprocess/topio.cpp
index 10f6d39b9c53fc17870738da29536701460a0857..97a5ff7f9939ccf0128d093e31171e2a255963b3 100644 (file)
--- a/src/gromacs/gmxpreprocess/topio.cpp
+++ b/src/gromacs/gmxpreprocess/topio.cpp
@@ -57,7 +57,7 @@
 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
 #include "gromacs/gmxpreprocess/gpp_bond_atomtype.h"
 #include "gromacs/gmxpreprocess/gpp_nextnb.h"
-#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp_impl.h"
 #include "gromacs/gmxpreprocess/readir.h"
 #include "gromacs/gmxpreprocess/topdirs.h"
 #include "gromacs/gmxpreprocess/toppush.h"

diff --git a/src/gromacs/gmxpreprocess/toppush.cpp b/src/gromacs/gmxpreprocess/toppush.cpp
index 6828bb0703b429ccdb205ebe07229a4458a8752c..abf5722ddfc16cdebb888604a5e9d1a3f7073f79 100644 (file)
--- a/src/gromacs/gmxpreprocess/toppush.cpp
+++ b/src/gromacs/gmxpreprocess/toppush.cpp
@@ -49,7 +49,7 @@
 #include "gromacs/fileio/warninp.h"
 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
 #include "gromacs/gmxpreprocess/gpp_bond_atomtype.h"
-#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp_impl.h"
 #include "gromacs/gmxpreprocess/notset.h"
 #include "gromacs/gmxpreprocess/readir.h"
 #include "gromacs/gmxpreprocess/topdirs.h"

diff --git a/src/gromacs/gmxpreprocess/topshake.cpp b/src/gromacs/gmxpreprocess/topshake.cpp
index 93ae99953cd9df4b5d3a0bbc7773a30f04b85f0d..5c54f19db79fd6335059ab12e65474659c39b3e0 100644 (file)
--- a/src/gromacs/gmxpreprocess/topshake.cpp
+++ b/src/gromacs/gmxpreprocess/topshake.cpp
@@ -42,7 +42,7 @@
 #include <cctype>
 #include <cmath>
 
-#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp_impl.h"
 #include "gromacs/gmxpreprocess/notset.h"
 #include "gromacs/gmxpreprocess/readir.h"
 #include "gromacs/gmxpreprocess/topdirs.h"

diff --git a/src/gromacs/gmxpreprocess/toputil.cpp b/src/gromacs/gmxpreprocess/toputil.cpp
index facc152e5a684eeedcf898f3669581f1f3dc03ba..c5a69f6014fd05e18cc241ab0a010617c4878c6a 100644 (file)
--- a/src/gromacs/gmxpreprocess/toputil.cpp
+++ b/src/gromacs/gmxpreprocess/toputil.cpp
@@ -45,7 +45,7 @@
 #include <algorithm>
 
 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
-#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp_impl.h"
 #include "gromacs/gmxpreprocess/notset.h"
 #include "gromacs/gmxpreprocess/topdirs.h"
 #include "gromacs/topology/block.h"

diff --git a/src/gromacs/gmxpreprocess/vsite_parm.cpp b/src/gromacs/gmxpreprocess/vsite_parm.cpp
index 9917af8b912eea1bf6b44bae60e687643e911a43..548456d453372ea0f46ae535391910d3629e3209 100644 (file)
--- a/src/gromacs/gmxpreprocess/vsite_parm.cpp
+++ b/src/gromacs/gmxpreprocess/vsite_parm.cpp
@@ -46,7 +46,7 @@
 
 #include "gromacs/gmxpreprocess/add_par.h"
 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
-#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp_impl.h"
 #include "gromacs/gmxpreprocess/notset.h"
 #include "gromacs/gmxpreprocess/resall.h"
 #include "gromacs/gmxpreprocess/toputil.h"

diff --git a/src/gromacs/gmxpreprocess/x2top.cpp b/src/gromacs/gmxpreprocess/x2top.cpp
index fdbe302c147adc926eea32f5d68b7473e98ecf46..22a84e45bffce94494e2ca28d18f310c0fb0afc0 100644 (file)
--- a/src/gromacs/gmxpreprocess/x2top.cpp
+++ b/src/gromacs/gmxpreprocess/x2top.cpp
@@ -47,7 +47,7 @@
 #include "gromacs/gmxpreprocess/gen_ad.h"
 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
 #include "gromacs/gmxpreprocess/gpp_nextnb.h"
-#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp_impl.h"
 #include "gromacs/gmxpreprocess/hackblock.h"
 #include "gromacs/gmxpreprocess/nm2type.h"
 #include "gromacs/gmxpreprocess/notset.h"

diff --git a/src/gromacs/gmxpreprocess/xlate.cpp b/src/gromacs/gmxpreprocess/xlate.cpp
index be603334b5c77f4650da1d0acbb981d8b7d30f41..da4df8ca2c083b50b23a55b806f34d90318f88aa 100644 (file)
--- a/src/gromacs/gmxpreprocess/xlate.cpp
+++ b/src/gromacs/gmxpreprocess/xlate.cpp
@@ -45,7 +45,7 @@
 #include <vector>
 
 #include "gromacs/gmxpreprocess/fflibutil.h"
-#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/grompp_impl.h"
 #include "gromacs/gmxpreprocess/hackblock.h"
 #include "gromacs/topology/residuetypes.h"
 #include "gromacs/topology/symtab.h"

diff --git a/src/gromacs/gpu_utils/tests/hostallocator.cpp b/src/gromacs/gpu_utils/tests/hostallocator.cpp
index 203fac342238d1ca6b6cf919fccde782b1413166..c7613dd1843b18af27af427a7ce59052793a8677 100644 (file)
--- a/src/gromacs/gpu_utils/tests/hostallocator.cpp
+++ b/src/gromacs/gpu_utils/tests/hostallocator.cpp
@@ -381,4 +381,4 @@ TYPED_TEST_CASE(AllocatorTest, AllocatorTypesToTest);
 } // namespace gmx
 
 // Includes tests common to all allocation policies.
-#include "gromacs/utility/tests/alignedallocator-impl.h"
+#include "gromacs/utility/tests/alignedallocator_impl.h"

diff --git a/src/gromacs/listed_forces/CMakeLists.txt b/src/gromacs/listed_forces/CMakeLists.txt
index bd97c81fe1b3b53a84605087192297b6d9a0596e..22936e1e5b4be51197832c9e2777fffb27c71396 100644 (file)
--- a/src/gromacs/listed_forces/CMakeLists.txt
+++ b/src/gromacs/listed_forces/CMakeLists.txt
@@ -35,19 +35,19 @@
 gmx_add_libgromacs_sources(
     bonded.cpp
     disre.cpp
-    gpubonded-impl.cpp
+    gpubonded_impl.cpp
     listed_forces.cpp
-    listed-internal.cpp
-    manage-threading.cpp
+    listed_internal.cpp
+    manage_threading.cpp
     orires.cpp
     pairs.cpp
-    position-restraints.cpp
+    position_restraints.cpp
     restcbt.cpp
     )
 
 if(GMX_USE_CUDA)
     gmx_add_libgromacs_sources(
-       gpubonded-impl.cu
+       gpubonded_impl.cu
        gpubondedkernels.cu
        )
 endif()

diff --git a/src/gromacs/listed_forces/bonded.cpp b/src/gromacs/listed_forces/bonded.cpp
index 0ae06d19af587562abcf334359eb52d343a9908d..8c03e0a29ab7572931e766648a0024c5fac88820 100644 (file)
--- a/src/gromacs/listed_forces/bonded.cpp
+++ b/src/gromacs/listed_forces/bonded.cpp
@@ -63,7 +63,7 @@
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "gromacs/pbcutil/pbc-simd.h"
+#include "gromacs/pbcutil/pbc_simd.h"
 #include "gromacs/simd/simd.h"
 #include "gromacs/simd/simd_math.h"
 #include "gromacs/simd/vector_operations.h"
@@ -72,7 +72,7 @@
 #include "gromacs/utility/real.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "listed-internal.h"
+#include "listed_internal.h"
 #include "restcbt.h"
 
 using namespace gmx; // TODO: Remove when this file is moved into gmx namespace

diff --git a/src/gromacs/listed_forces/gpubonded-impl.cpp b/src/gromacs/listed_forces/gpubonded_impl.cpp
similarity index 100%
rename from src/gromacs/listed_forces/gpubonded-impl.cpp
rename to src/gromacs/listed_forces/gpubonded_impl.cpp

diff --git a/src/gromacs/listed_forces/gpubonded-impl.cu b/src/gromacs/listed_forces/gpubonded_impl.cu
similarity index 99%
rename from src/gromacs/listed_forces/gpubonded-impl.cu
rename to src/gromacs/listed_forces/gpubonded_impl.cu
index 8da1a9ffd052fbe3068f7e1603f025672515c9c4..40f2c6dd186b906c271ce339d2e89ce261bb375e 100644 (file)
--- a/src/gromacs/listed_forces/gpubonded-impl.cu
+++ b/src/gromacs/listed_forces/gpubonded_impl.cu
@@ -45,7 +45,7 @@
 
 #include "gmxpre.h"
 
-#include "gpubonded-impl.h"
+#include "gpubonded_impl.h"
 
 #include "gromacs/gpu_utils/cudautils.cuh"
 #include "gromacs/gpu_utils/devicebuffer.h"

diff --git a/src/gromacs/listed_forces/gpubonded-impl.h b/src/gromacs/listed_forces/gpubonded_impl.h
similarity index 100%
rename from src/gromacs/listed_forces/gpubonded-impl.h
rename to src/gromacs/listed_forces/gpubonded_impl.h

diff --git a/src/gromacs/listed_forces/gpubondedkernels.cu b/src/gromacs/listed_forces/gpubondedkernels.cu
index 2f7848634057b8bed9112b5802d8e319ff2403bb..a804553d1f742e7a22aa3ea4e4889d6ce3b73715 100644 (file)
--- a/src/gromacs/listed_forces/gpubondedkernels.cu
+++ b/src/gromacs/listed_forces/gpubondedkernels.cu
@@ -69,7 +69,7 @@
 #include "gromacs/topology/ifunc.h"
 #include "gromacs/utility/gmxassert.h"
 
-#include "gpubonded-impl.h"
+#include "gpubonded_impl.h"
 
 #if defined(_MSVC)
 #include <limits>

diff --git a/src/gromacs/listed_forces/listed_forces.cpp b/src/gromacs/listed_forces/listed_forces.cpp
index 97255fe9a954599a780bceb4d27fc63573d204e6..d99dcfe8c8fa5e0f4e3c0bc78b4dd95d29d55333 100644 (file)
--- a/src/gromacs/listed_forces/listed_forces.cpp
+++ b/src/gromacs/listed_forces/listed_forces.cpp
@@ -56,7 +56,7 @@
 #include "gromacs/listed_forces/disre.h"
 #include "gromacs/listed_forces/orires.h"
 #include "gromacs/listed_forces/pairs.h"
-#include "gromacs/listed_forces/position-restraints.h"
+#include "gromacs/listed_forces/position_restraints.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/force.h"
 #include "gromacs/mdlib/force_flags.h"
@@ -74,7 +74,7 @@
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "listed-internal.h"
+#include "listed_internal.h"
 #include "utilities.h"
 
 struct BondedInteractions

diff --git a/src/gromacs/listed_forces/listed-internal.cpp b/src/gromacs/listed_forces/listed_internal.cpp
similarity index 98%
rename from src/gromacs/listed_forces/listed-internal.cpp
rename to src/gromacs/listed_forces/listed_internal.cpp
index 2161bff3c5567090fb6703c8aef9e7a12561dd70..fe883968e8bcc55ed426e1d41489941205ca6279 100644 (file)
--- a/src/gromacs/listed_forces/listed-internal.cpp
+++ b/src/gromacs/listed_forces/listed_internal.cpp
@@ -41,7 +41,7 @@
  */
 #include "gmxpre.h"
 
-#include "listed-internal.h"
+#include "listed_internal.h"
 
 #include <cstdlib>
 

diff --git a/src/gromacs/listed_forces/listed-internal.h b/src/gromacs/listed_forces/listed_internal.h
similarity index 100%
rename from src/gromacs/listed_forces/listed-internal.h
rename to src/gromacs/listed_forces/listed_internal.h

diff --git a/src/gromacs/listed_forces/manage-threading.cpp b/src/gromacs/listed_forces/manage_threading.cpp
similarity index 99%
rename from src/gromacs/listed_forces/manage-threading.cpp
rename to src/gromacs/listed_forces/manage_threading.cpp
index 5aa96feb880b5762321d0af5de86abf11c079f38..9b1ff77f69eff58075aefe5842a4a622205f4cc1 100644 (file)
--- a/src/gromacs/listed_forces/manage-threading.cpp
+++ b/src/gromacs/listed_forces/manage_threading.cpp
@@ -43,7 +43,7 @@
  */
 #include "gmxpre.h"
 
-#include "manage-threading.h"
+#include "manage_threading.h"
 
 #include "config.h"
 
@@ -64,7 +64,7 @@
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "listed-internal.h"
+#include "listed_internal.h"
 #include "utilities.h"
 
 /*! \brief struct for passing all data required for a function type */

diff --git a/src/gromacs/listed_forces/manage-threading.h b/src/gromacs/listed_forces/manage_threading.h
similarity index 100%
rename from src/gromacs/listed_forces/manage-threading.h
rename to src/gromacs/listed_forces/manage_threading.h

diff --git a/src/gromacs/listed_forces/pairs.cpp b/src/gromacs/listed_forces/pairs.cpp
index e910e592275cb495faadd988ba2de3c7b8e45a48..283c7cbb706186f898f180342649788d3ceb3116 100644 (file)
--- a/src/gromacs/listed_forces/pairs.cpp
+++ b/src/gromacs/listed_forces/pairs.cpp
@@ -55,7 +55,7 @@
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "gromacs/pbcutil/pbc-simd.h"
+#include "gromacs/pbcutil/pbc_simd.h"
 #include "gromacs/simd/simd.h"
 #include "gromacs/simd/simd_math.h"
 #include "gromacs/simd/vector_operations.h"
@@ -64,7 +64,7 @@
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxassert.h"
 
-#include "listed-internal.h"
+#include "listed_internal.h"
 
 using namespace gmx; // TODO: Remove when this file is moved into gmx namespace
 

diff --git a/src/gromacs/listed_forces/position-restraints.cpp b/src/gromacs/listed_forces/position_restraints.cpp
similarity index 99%
rename from src/gromacs/listed_forces/position-restraints.cpp
rename to src/gromacs/listed_forces/position_restraints.cpp
index f6c865b30ba91a6d12acfe01096891198b0218bd..9e1a41c994fd86703aeb951cbd99f9d0f8762447 100644 (file)
--- a/src/gromacs/listed_forces/position-restraints.cpp
+++ b/src/gromacs/listed_forces/position_restraints.cpp
@@ -44,7 +44,7 @@
 
 #include "gmxpre.h"
 
-#include "position-restraints.h"
+#include "position_restraints.h"
 
 #include <cassert>
 #include <cmath>

diff --git a/src/gromacs/listed_forces/position-restraints.h b/src/gromacs/listed_forces/position_restraints.h
similarity index 100%
rename from src/gromacs/listed_forces/position-restraints.h
rename to src/gromacs/listed_forces/position_restraints.h

diff --git a/src/gromacs/mdlib/broadcaststructs.cpp b/src/gromacs/mdlib/broadcaststructs.cpp
index 61768551a74c13e8d2f639da562d2747c176044d..51fd02767e9d8253d18aacde08fa2da2a4bb3cbf 100644 (file)
--- a/src/gromacs/mdlib/broadcaststructs.cpp
+++ b/src/gromacs/mdlib/broadcaststructs.cpp
@@ -47,11 +47,11 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/tgroup.h"
-#include "gromacs/mdtypes/awh-params.h"
+#include "gromacs/mdtypes/awh_params.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/mdtypes/md_enums.h"
-#include "gromacs/mdtypes/pull-params.h"
+#include "gromacs/mdtypes/pull_params.h"
 #include "gromacs/mdtypes/state.h"
 #include "gromacs/topology/mtop_util.h"
 #include "gromacs/topology/symtab.h"

diff --git a/src/gromacs/mdlib/calc_verletbuf.cpp b/src/gromacs/mdlib/calc_verletbuf.cpp
index 0807282c85e871438dfa52c770bcf21a0003283c..fd07917451e74dfbdd4d6e24c9f3505b1e736139 100644 (file)
--- a/src/gromacs/mdlib/calc_verletbuf.cpp
+++ b/src/gromacs/mdlib/calc_verletbuf.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -41,7 +41,7 @@
 
 #include <algorithm>
 
-#include "gromacs/ewald/ewald-utils.h"
+#include "gromacs/ewald/ewald_utils.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/mdlib/compute_io.cpp b/src/gromacs/mdlib/compute_io.cpp
index ec5b613b24430035723c88bffce153e5a1c7e4af..4849bcfe288dcbc685ee379198f2d7d72cc73576 100644 (file)
--- a/src/gromacs/mdlib/compute_io.cpp
+++ b/src/gromacs/mdlib/compute_io.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014,2015,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -43,7 +43,7 @@
 
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/mdtypes/md_enums.h"
-#include "gromacs/mdtypes/pull-params.h"
+#include "gromacs/mdtypes/pull_params.h"
 #include "gromacs/topology/topology.h"
 
 static int div_nsteps(int nsteps, int nst)

diff --git a/src/gromacs/mdlib/force.cpp b/src/gromacs/mdlib/force.cpp
index 7847aaa8cc8595e067505c3dc16a1a308cbec6e4..09f54fc4f8aa13ab59b3a3ce93537162067cd045 100644 (file)
--- a/src/gromacs/mdlib/force.cpp
+++ b/src/gromacs/mdlib/force.cpp
@@ -47,7 +47,7 @@
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/domdec/domdec_struct.h"
 #include "gromacs/ewald/ewald.h"
-#include "gromacs/ewald/long-range-correction.h"
+#include "gromacs/ewald/long_range_correction.h"
 #include "gromacs/ewald/pme.h"
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/nrnb.h"
@@ -56,7 +56,7 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/math/vecdump.h"
 #include "gromacs/mdlib/force_flags.h"
-#include "gromacs/mdlib/forcerec-threading.h"
+#include "gromacs/mdlib/forcerec_threading.h"
 #include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/ns.h"
 #include "gromacs/mdlib/qmmm.h"

diff --git a/src/gromacs/mdlib/forcerec.cpp b/src/gromacs/mdlib/forcerec.cpp
index dec8a2a0222866127825d9e9c5e5ab1c4cebf003..5d7872a3ff44a6120be90504e72d28fe8a0f1fa1 100644 (file)
--- a/src/gromacs/mdlib/forcerec.cpp
+++ b/src/gromacs/mdlib/forcerec.cpp
@@ -52,21 +52,21 @@
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/domdec/domdec_struct.h"
 #include "gromacs/ewald/ewald.h"
-#include "gromacs/ewald/ewald-utils.h"
+#include "gromacs/ewald/ewald_utils.h"
 #include "gromacs/fileio/filetypes.h"
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/nonbonded/nonbonded.h"
 #include "gromacs/gpu_utils/gpu_utils.h"
 #include "gromacs/hardware/hw_info.h"
 #include "gromacs/listed_forces/gpubonded.h"
-#include "gromacs/listed_forces/manage-threading.h"
+#include "gromacs/listed_forces/manage_threading.h"
 #include "gromacs/listed_forces/pairs.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/force.h"
-#include "gromacs/mdlib/forcerec-threading.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"

diff --git a/src/gromacs/mdlib/forcerec-threading.h b/src/gromacs/mdlib/forcerec_threading.h
similarity index 96%
rename from src/gromacs/mdlib/forcerec-threading.h
rename to src/gromacs/mdlib/forcerec_threading.h
index 9bf01ceadec09fd353a3590b3618985a6b1577ae..26d40570a07bd1185db5217e5017d9ef763a7a14 100644 (file)
--- a/src/gromacs/mdlib/forcerec-threading.h
+++ b/src/gromacs/mdlib/forcerec_threading.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014,2015,2018, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/mdlib/lincs.cpp b/src/gromacs/mdlib/lincs.cpp
index 44f1415c0778ea0c2315bedaddc1784723d8ff85..ac37a7b54ecd837eb2295caf351e3712fb7914e9 100644 (file)
--- a/src/gromacs/mdlib/lincs.cpp
+++ b/src/gromacs/mdlib/lincs.cpp
@@ -69,7 +69,7 @@
 #include "gromacs/mdtypes/md_enums.h"
 #include "gromacs/mdtypes/mdatom.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "gromacs/pbcutil/pbc-simd.h"
+#include "gromacs/pbcutil/pbc_simd.h"
 #include "gromacs/simd/simd.h"
 #include "gromacs/simd/simd_math.h"
 #include "gromacs/simd/vector_operations.h"

diff --git a/src/gromacs/mdlib/mdsetup.cpp b/src/gromacs/mdlib/mdsetup.cpp
index 5a5bb53164779213b7163f194dde1401c69e4ac3..c3dffae4f52497616160f201db2b45d8cfdb73fb 100644 (file)
--- a/src/gromacs/mdlib/mdsetup.cpp
+++ b/src/gromacs/mdlib/mdsetup.cpp
@@ -39,7 +39,7 @@
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/domdec/domdec_struct.h"
 #include "gromacs/ewald/pme.h"
-#include "gromacs/listed_forces/manage-threading.h"
+#include "gromacs/listed_forces/manage_threading.h"
 #include "gromacs/mdlib/constr.h"
 #include "gromacs/mdlib/mdatoms.h"
 #include "gromacs/mdlib/shellfc.h"

diff --git a/src/gromacs/mdlib/resethandler.cpp b/src/gromacs/mdlib/resethandler.cpp
index 17bd7df8e357e29b58c49ff6521802a11b5fa93c..0e1e06993fcae38e1d52404ed45df174f539f9ef 100644 (file)
--- a/src/gromacs/mdlib/resethandler.cpp
+++ b/src/gromacs/mdlib/resethandler.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -46,7 +46,7 @@
 
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/ewald/pme.h"
-#include "gromacs/ewald/pme-load-balancing.h"
+#include "gromacs/ewald/pme_load_balancing.h"
 #include "gromacs/gmxlib/nrnb.h"
 #include "gromacs/gpu_utils/gpu_utils.h"
 #include "gromacs/mdlib/nbnxn_gpu_data_mgmt.h"

diff --git a/src/gromacs/mdlib/settle.cpp b/src/gromacs/mdlib/settle.cpp
index 8bcbfd1008cf9e7399892eb26c259f0a1d9b2783..3263c0ddd2ce1a2e9b6009c809fa6ff73cadaf20 100644 (file)
--- a/src/gromacs/mdlib/settle.cpp
+++ b/src/gromacs/mdlib/settle.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -58,7 +58,7 @@
 #include "gromacs/mdtypes/mdatom.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "gromacs/pbcutil/pbc-simd.h"
+#include "gromacs/pbcutil/pbc_simd.h"
 #include "gromacs/simd/simd.h"
 #include "gromacs/simd/simd_math.h"
 #include "gromacs/topology/idef.h"

diff --git a/src/gromacs/mdlib/sim_util.cpp b/src/gromacs/mdlib/sim_util.cpp
index c6c02e77a0179fb27a5f1fa47ab2d462b80e2b1b..5e3656bd0caf8109a865b48f1f3e0044e15c94e3 100644 (file)
--- a/src/gromacs/mdlib/sim_util.cpp
+++ b/src/gromacs/mdlib/sim_util.cpp
@@ -64,7 +64,7 @@
 #include "gromacs/listed_forces/bonded.h"
 #include "gromacs/listed_forces/disre.h"
 #include "gromacs/listed_forces/gpubonded.h"
-#include "gromacs/listed_forces/manage-threading.h"
+#include "gromacs/listed_forces/manage_threading.h"
 #include "gromacs/listed_forces/orires.h"
 #include "gromacs/math/arrayrefwithpadding.h"
 #include "gromacs/math/functions.h"

diff --git a/src/gromacs/mdrun/md.cpp b/src/gromacs/mdrun/md.cpp
index 1825b36b1b0e25cd2b5d0d5aea14ff9b16f3097f..8d38a7c068db9838e715cdccea0e0f0f79a923eb 100644 (file)
--- a/src/gromacs/mdrun/md.cpp
+++ b/src/gromacs/mdrun/md.cpp
@@ -60,13 +60,13 @@
 #include "gromacs/domdec/partition.h"
 #include "gromacs/essentialdynamics/edsam.h"
 #include "gromacs/ewald/pme.h"
-#include "gromacs/ewald/pme-load-balancing.h"
+#include "gromacs/ewald/pme_load_balancing.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/nrnb.h"
 #include "gromacs/gpu_utils/gpu_utils.h"
 #include "gromacs/imd/imd.h"
-#include "gromacs/listed_forces/manage-threading.h"
+#include "gromacs/listed_forces/manage_threading.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
@@ -100,8 +100,8 @@
 #include "gromacs/mdlib/update.h"
 #include "gromacs/mdlib/vcm.h"
 #include "gromacs/mdlib/vsite.h"
-#include "gromacs/mdtypes/awh-history.h"
-#include "gromacs/mdtypes/awh-params.h"
+#include "gromacs/mdtypes/awh_history.h"
+#include "gromacs/mdtypes/awh_params.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/df_history.h"
 #include "gromacs/mdtypes/energyhistory.h"

diff --git a/src/gromacs/mdrun/mimic.cpp b/src/gromacs/mdrun/mimic.cpp
index ffa3117749d7409329b75f6349d1dc859658b69f..c77e5637a5899d30b04f6a306277a82ae5328c94 100644 (file)
--- a/src/gromacs/mdrun/mimic.cpp
+++ b/src/gromacs/mdrun/mimic.cpp
@@ -59,13 +59,13 @@
 #include "gromacs/domdec/partition.h"
 #include "gromacs/essentialdynamics/edsam.h"
 #include "gromacs/ewald/pme.h"
-#include "gromacs/ewald/pme-load-balancing.h"
+#include "gromacs/ewald/pme_load_balancing.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/nrnb.h"
 #include "gromacs/gpu_utils/gpu_utils.h"
 #include "gromacs/imd/imd.h"
-#include "gromacs/listed_forces/manage-threading.h"
+#include "gromacs/listed_forces/manage_threading.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
@@ -99,8 +99,8 @@
 #include "gromacs/mdlib/update.h"
 #include "gromacs/mdlib/vcm.h"
 #include "gromacs/mdlib/vsite.h"
-#include "gromacs/mdtypes/awh-history.h"
-#include "gromacs/mdtypes/awh-params.h"
+#include "gromacs/mdtypes/awh_history.h"
+#include "gromacs/mdtypes/awh_params.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/df_history.h"
 #include "gromacs/mdtypes/energyhistory.h"

diff --git a/src/gromacs/mdrun/minimize.cpp b/src/gromacs/mdrun/minimize.cpp
index d7f720018e2dc98a837c79cdfda38446b66d9ae5..ee8c8ac0dee81e71e0ddfad8094d549f56478628 100644 (file)
--- a/src/gromacs/mdrun/minimize.cpp
+++ b/src/gromacs/mdrun/minimize.cpp
@@ -65,7 +65,7 @@
 #include "gromacs/gmxlib/nrnb.h"
 #include "gromacs/imd/imd.h"
 #include "gromacs/linearalgebra/sparsematrix.h"
-#include "gromacs/listed_forces/manage-threading.h"
+#include "gromacs/listed_forces/manage_threading.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/constr.h"

diff --git a/src/gromacs/mdrun/rerun.cpp b/src/gromacs/mdrun/rerun.cpp
index aba3f6fc9514e14b449cacd670b12949e15d3704..53bcd23b84d7935e36ee3e34482b9286ceed2c36 100644 (file)
--- a/src/gromacs/mdrun/rerun.cpp
+++ b/src/gromacs/mdrun/rerun.cpp
@@ -60,13 +60,13 @@
 #include "gromacs/domdec/partition.h"
 #include "gromacs/essentialdynamics/edsam.h"
 #include "gromacs/ewald/pme.h"
-#include "gromacs/ewald/pme-load-balancing.h"
+#include "gromacs/ewald/pme_load_balancing.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/nrnb.h"
 #include "gromacs/gpu_utils/gpu_utils.h"
 #include "gromacs/imd/imd.h"
-#include "gromacs/listed_forces/manage-threading.h"
+#include "gromacs/listed_forces/manage_threading.h"
 #include "gromacs/math/functions.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
@@ -100,8 +100,8 @@
 #include "gromacs/mdlib/update.h"
 #include "gromacs/mdlib/vcm.h"
 #include "gromacs/mdlib/vsite.h"
-#include "gromacs/mdtypes/awh-history.h"
-#include "gromacs/mdtypes/awh-params.h"
+#include "gromacs/mdtypes/awh_history.h"
+#include "gromacs/mdtypes/awh_params.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/df_history.h"
 #include "gromacs/mdtypes/energyhistory.h"

diff --git a/src/gromacs/mdrun/runner.cpp b/src/gromacs/mdrun/runner.cpp
index 5f38a12d47810bd41b24cae0f2b849a9510dac2d..92ac8c69b3182577abc88e475d3f73b0b6726292 100644 (file)
--- a/src/gromacs/mdrun/runner.cpp
+++ b/src/gromacs/mdrun/runner.cpp
@@ -60,9 +60,9 @@
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/domdec/domdec_struct.h"
 #include "gromacs/domdec/localatomsetmanager.h"
-#include "gromacs/ewald/ewald-utils.h"
+#include "gromacs/ewald/ewald_utils.h"
 #include "gromacs/ewald/pme.h"
-#include "gromacs/ewald/pme-gpu-program.h"
+#include "gromacs/ewald/pme_gpu_program.h"
 #include "gromacs/fileio/checkpoint.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/oenv.h"

diff --git a/src/gromacs/mdrun/tpi.cpp b/src/gromacs/mdrun/tpi.cpp
index 5aaf23de06a4b5987bb051f17b287fcc0909fa34..cebc50de14f0703d2325e847c0f5426adf539092 100644 (file)
--- a/src/gromacs/mdrun/tpi.cpp
+++ b/src/gromacs/mdrun/tpi.cpp
@@ -59,7 +59,7 @@
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxlib/chargegroup.h"
-#include "gromacs/gmxlib/conformation-utilities.h"
+#include "gromacs/gmxlib/conformation_utilities.h"
 #include "gromacs/gmxlib/network.h"
 #include "gromacs/gmxlib/nrnb.h"
 #include "gromacs/math/units.h"

diff --git a/src/gromacs/mdrunutility/mdmodules.cpp b/src/gromacs/mdrunutility/mdmodules.cpp
index 039a11e774d868651ab9f79264572fd075c94af5..f0eab395c7372a0900c7acfb203589588dd9f920 100644 (file)
--- a/src/gromacs/mdrunutility/mdmodules.cpp
+++ b/src/gromacs/mdrunutility/mdmodules.cpp
@@ -38,7 +38,7 @@
 
 #include <memory>
 
-#include "gromacs/applied-forces/electricfield.h"
+#include "gromacs/applied_forces/electricfield.h"
 #include "gromacs/mdtypes/iforceprovider.h"
 #include "gromacs/mdtypes/imdmodule.h"
 #include "gromacs/mdtypes/imdoutputprovider.h"

diff --git a/src/gromacs/mdrunutility/tests/CMakeLists.txt b/src/gromacs/mdrunutility/tests/CMakeLists.txt
index b765917e95944891f071c7c470d896f76c457443..97b3f485134c600bc722c12496de4e24c38edf39 100644 (file)
--- a/src/gromacs/mdrunutility/tests/CMakeLists.txt
+++ b/src/gromacs/mdrunutility/tests/CMakeLists.txt
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2016,2017, by the GROMACS development team, led by
+# Copyright (c) 2016,2017,2019, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -40,5 +40,5 @@ gmx_add_unit_test(MdrunUtilityUnitTests mdrunutility-test
                   $<TARGET_OBJECTS:mdrunutility-test-shared>)
 
 gmx_add_mpi_unit_test(MdrunUtilityMpiUnitTests mdrunutility-mpi-test 4
-                      threadaffinity-mpi.cpp
+                      threadaffinity_mpi.cpp
                       $<TARGET_OBJECTS:mdrunutility-test-shared>)

diff --git a/src/gromacs/mdrunutility/tests/threadaffinity-mpi.cpp b/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp
similarity index 99%
rename from src/gromacs/mdrunutility/tests/threadaffinity-mpi.cpp
rename to src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp
index 7ed0397a8ccef49677e2823872a094a8d0713423..c0bb431f8fc14197b3fb7a8de68c27bbb0522e28 100644 (file)
--- a/src/gromacs/mdrunutility/tests/threadaffinity-mpi.cpp
+++ b/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/mdtypes/awh-correlation-history.h b/src/gromacs/mdtypes/awh_correlation_history.h
similarity index 98%
rename from src/gromacs/mdtypes/awh-correlation-history.h
rename to src/gromacs/mdtypes/awh_correlation_history.h
index b0d8b58231bf6be862b96b13744cccfc1950dd9c..56fd4426481aef895448578631e6c907761add50 100644 (file)
--- a/src/gromacs/mdtypes/awh-correlation-history.h
+++ b/src/gromacs/mdtypes/awh_correlation_history.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/mdtypes/awh-history.h b/src/gromacs/mdtypes/awh_history.h
similarity index 97%
rename from src/gromacs/mdtypes/awh-history.h
rename to src/gromacs/mdtypes/awh_history.h
index ad00f270d0855394603788a816aa53c3a804d2db..b33f7e5a33ae156cd0b74096522bfa70313cc4d5 100644 (file)
--- a/src/gromacs/mdtypes/awh-history.h
+++ b/src/gromacs/mdtypes/awh_history.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -49,7 +49,7 @@
 
 #include <vector>
 
-#include "gromacs/mdtypes/awh-correlation-history.h"
+#include "gromacs/mdtypes/awh_correlation_history.h"
 #include "gromacs/utility/basedefinitions.h"
 
 namespace gmx

diff --git a/src/gromacs/mdtypes/awh-params.h b/src/gromacs/mdtypes/awh_params.h
similarity index 98%
rename from src/gromacs/mdtypes/awh-params.h
rename to src/gromacs/mdtypes/awh_params.h
index 6eef443fdad35c0c4c7beb6e5d2cb1b707a2c9ce..f01286deb15018817934595de9d4f79b47905af4 100644 (file)
--- a/src/gromacs/mdtypes/awh-params.h
+++ b/src/gromacs/mdtypes/awh_params.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/mdtypes/inputrec.cpp b/src/gromacs/mdtypes/inputrec.cpp
index 6edc255c4f4dc6796515ffb5bca9d3ac07a3297e..46d58cf5021d698259f747247bd26d079a4dc9e6 100644 (file)
--- a/src/gromacs/mdtypes/inputrec.cpp
+++ b/src/gromacs/mdtypes/inputrec.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2010, The GROMACS development team.
- * Copyright (c) 2012,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -46,9 +46,9 @@
 
 #include "gromacs/math/veccompare.h"
 #include "gromacs/math/vecdump.h"
-#include "gromacs/mdtypes/awh-params.h"
+#include "gromacs/mdtypes/awh_params.h"
 #include "gromacs/mdtypes/md_enums.h"
-#include "gromacs/mdtypes/pull-params.h"
+#include "gromacs/mdtypes/pull_params.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/compare.h"
 #include "gromacs/utility/cstringutil.h"

diff --git a/src/gromacs/mdtypes/pull-params.h b/src/gromacs/mdtypes/pull_params.h
similarity index 98%
rename from src/gromacs/mdtypes/pull-params.h
rename to src/gromacs/mdtypes/pull_params.h
index ab58be708f46095de5b8123fa3141885b3d4d392..3ec189d076531a53d60a63092f984521f3fb6d10 100644 (file)
--- a/src/gromacs/mdtypes/pull-params.h
+++ b/src/gromacs/mdtypes/pull_params.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016,2018, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/mdtypes/state.cpp b/src/gromacs/mdtypes/state.cpp
index 10ae4e9d294f657135b0bcd3dcaac5f31c795e0d..ef9956a9c8bbf761b9361852f18dd67fb5d53d2e 100644 (file)
--- a/src/gromacs/mdtypes/state.cpp
+++ b/src/gromacs/mdtypes/state.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -46,11 +46,11 @@
 #include "gromacs/math/paddedvector.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/math/veccompare.h"
-#include "gromacs/mdtypes/awh-history.h"
+#include "gromacs/mdtypes/awh_history.h"
 #include "gromacs/mdtypes/df_history.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/mdtypes/md_enums.h"
-#include "gromacs/mdtypes/pull-params.h"
+#include "gromacs/mdtypes/pull_params.h"
 #include "gromacs/mdtypes/swaphistory.h"
 #include "gromacs/pbcutil/boxutilities.h"
 #include "gromacs/pbcutil/pbc.h"

diff --git a/src/gromacs/onlinehelp-doc.h b/src/gromacs/onlinehelp_doc.h
similarity index 97%
rename from src/gromacs/onlinehelp-doc.h
rename to src/gromacs/onlinehelp_doc.h
index 13acaaa2f9eb376a52dfb1caaca8b27c75c1de29..a83e61f3feb81ebd268ca1c9b439852590b8eb63 100644 (file)
--- a/src/gromacs/onlinehelp-doc.h
+++ b/src/gromacs/onlinehelp_doc.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2015,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/options/abstractsection.cpp b/src/gromacs/options/abstractsection.cpp
index bb056cf8d7c1a61c7a447f5c1b621939e2cce92c..8f3fe770a70d994403cb3e8d9e6b93eac30748dc 100644 (file)
--- a/src/gromacs/options/abstractsection.cpp
+++ b/src/gromacs/options/abstractsection.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2016, by the GROMACS development team, led by
+ * Copyright (c) 2016,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -43,7 +43,7 @@
 
 #include "abstractsection.h"
 
-#include "options-impl.h"
+#include "options_impl.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/options/options.cpp b/src/gromacs/options/options.cpp
index c8de6e435a8a2ea3b99d02a902e71e21622289bc..79fbb16c30991872d8ee677a8bdf06a36918b0a5 100644 (file)
--- a/src/gromacs/options/options.cpp
+++ b/src/gromacs/options/options.cpp
@@ -54,7 +54,7 @@
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/stringutil.h"
 
-#include "options-impl.h"
+#include "options_impl.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/options/options-impl.h b/src/gromacs/options/options_impl.h
similarity index 98%
rename from src/gromacs/options/options-impl.h
rename to src/gromacs/options/options_impl.h
index acaccc8c261ce2850a127b1c97bbfa178661c902..d95dc90c678147d7895b65badf0af7291017c39b 100644 (file)
--- a/src/gromacs/options/options-impl.h
+++ b/src/gromacs/options/options_impl.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2018, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/options/optionsassigner.cpp b/src/gromacs/options/optionsassigner.cpp
index f9cb896873d49ec42703fbd5f95f9630211f86d8..d2b9856e969d3a573db4744650face05a7806a0c 100644 (file)
--- a/src/gromacs/options/optionsassigner.cpp
+++ b/src/gromacs/options/optionsassigner.cpp
@@ -51,7 +51,7 @@
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
 
-#include "options-impl.h"
+#include "options_impl.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/options/optionsvisitor.cpp b/src/gromacs/options/optionsvisitor.cpp
index c628d3a5a1c951b5896fa8e52e5b890dbb090274..cb950a37fb86e3a8d007df9118a2751085035653 100644 (file)
--- a/src/gromacs/options/optionsvisitor.cpp
+++ b/src/gromacs/options/optionsvisitor.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2012,2014,2015,2016,2018, by the GROMACS development team, led by
+ * Copyright (c) 2010,2012,2014,2015,2016,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -47,7 +47,7 @@
 #include "gromacs/options/options.h"
 #include "gromacs/options/optionsection.h"
 
-#include "options-impl.h"
+#include "options_impl.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/pbcutil/pbc-simd.cpp b/src/gromacs/pbcutil/pbc_simd.cpp
similarity index 97%
rename from src/gromacs/pbcutil/pbc-simd.cpp
rename to src/gromacs/pbcutil/pbc_simd.cpp
index fb9addd5655fadf2d2a79946bda98833a3ebfc34..92700e830ff72681439ab80f475fd3ce3213c596 100644 (file)
--- a/src/gromacs/pbcutil/pbc-simd.cpp
+++ b/src/gromacs/pbcutil/pbc_simd.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -42,7 +42,7 @@
  */
 #include "gmxpre.h"
 
-#include "pbc-simd.h"
+#include "pbc_simd.h"
 
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"

diff --git a/src/gromacs/pbcutil/pbc-simd.h b/src/gromacs/pbcutil/pbc_simd.h
similarity index 98%
rename from src/gromacs/pbcutil/pbc-simd.h
rename to src/gromacs/pbcutil/pbc_simd.h
index 2040b8efa0d135da90de8b6a4a67f0638df8efff..e5e64d9d2387dc483bfcefaa6715219dc4ea34c0 100644 (file)
--- a/src/gromacs/pbcutil/pbc-simd.h
+++ b/src/gromacs/pbcutil/pbc_simd.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/pulling/pull.h b/src/gromacs/pulling/pull.h
index 9fd108e3fb1aeb6ff4d63b29ff5b1ff2d9f1c744..9ae87394d065c828f7f4e28f3fd651926b1828e7 100644 (file)
--- a/src/gromacs/pulling/pull.h
+++ b/src/gromacs/pulling/pull.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -54,7 +54,7 @@
 
 #include "gromacs/math/vectypes.h"
 #include "gromacs/mdlib/mdrun.h"
-#include "gromacs/mdtypes/pull-params.h"
+#include "gromacs/mdtypes/pull_params.h"
 #include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/real.h"

diff --git a/src/gromacs/pulling/pull_internal.h b/src/gromacs/pulling/pull_internal.h
index 9084b077149ad8546d64226b8b0f4226659e7eb7..b6351a9d52779f48ad7cfdd4177e3cb35c7cbd67 100644 (file)
--- a/src/gromacs/pulling/pull_internal.h
+++ b/src/gromacs/pulling/pull_internal.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -54,7 +54,7 @@
 #include <vector>
 
 #include "gromacs/domdec/localatomset.h"
-#include "gromacs/mdtypes/pull-params.h"
+#include "gromacs/mdtypes/pull_params.h"
 #include "gromacs/utility/gmxmpi.h"
 
 /*! \brief Determines up to what local atom count a pull group gets processed single-threaded.

diff --git a/src/gromacs/restraint/restraintmdmodule.cpp b/src/gromacs/restraint/restraintmdmodule.cpp
index 590516dfc011190bc5010ad6fb5ef602489f3d17..32c0d01861d4521f7e116603bcb455d647bd9ad6 100644 (file)
--- a/src/gromacs/restraint/restraintmdmodule.cpp
+++ b/src/gromacs/restraint/restraintmdmodule.cpp
@@ -42,7 +42,7 @@
 #include "gromacs/mdtypes/forceoutput.h"
 #include "gromacs/mdtypes/iforceprovider.h"
 
-#include "restraintmdmodule-impl.h"
+#include "restraintmdmodule_impl.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/restraint/restraintmdmodule-impl.h b/src/gromacs/restraint/restraintmdmodule_impl.h
similarity index 99%
rename from src/gromacs/restraint/restraintmdmodule-impl.h
rename to src/gromacs/restraint/restraintmdmodule_impl.h
index 67cce4a59a3ce042b6576ab378afaeb34ef11661..3895c3c19b87deb65091feb5cf84afb648305804 100644 (file)
--- a/src/gromacs/restraint/restraintmdmodule-impl.h
+++ b/src/gromacs/restraint/restraintmdmodule_impl.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/selection/compiler.cpp b/src/gromacs/selection/compiler.cpp
index 8438dbe00cfc2fbd3b37eecdd85ae4c25ab2f400..5e35fc407e32bbd008f6251776e02edfd58ee7d8 100644 (file)
--- a/src/gromacs/selection/compiler.cpp
+++ b/src/gromacs/selection/compiler.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -289,7 +289,7 @@
 #include "keywords.h"
 #include "mempool.h"
 #include "poscalc.h"
-#include "selectioncollection-impl.h"
+#include "selectioncollection_impl.h"
 #include "selelem.h"
 #include "selmethod.h"
 

diff --git a/src/gromacs/selection/evaluate.cpp b/src/gromacs/selection/evaluate.cpp
index c5659dbb2bc36aa3ba873953a7e59c74074a2134..59a4aa27f3008a1b6fbd239ef2d0d489dcdef11d 100644 (file)
--- a/src/gromacs/selection/evaluate.cpp
+++ b/src/gromacs/selection/evaluate.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -68,7 +68,7 @@
 
 #include "mempool.h"
 #include "poscalc.h"
-#include "selectioncollection-impl.h"
+#include "selectioncollection_impl.h"
 #include "selelem.h"
 #include "selmethod.h"
 

diff --git a/src/gromacs/selection/parsetree.cpp b/src/gromacs/selection/parsetree.cpp
index 6f2596c11312a398023503b88137195598a68700..1b504071cc08d14999842e8b423e614d7d0fa5ab 100644 (file)
--- a/src/gromacs/selection/parsetree.cpp
+++ b/src/gromacs/selection/parsetree.cpp
@@ -240,7 +240,7 @@
 #include "keywords.h"
 #include "poscalc.h"
 #include "scanner.h"
-#include "selectioncollection-impl.h"
+#include "selectioncollection_impl.h"
 #include "selelem.h"
 #include "selmethod.h"
 #include "symrec.h"

diff --git a/src/gromacs/selection/scanner_internal.cpp b/src/gromacs/selection/scanner_internal.cpp
index b04366c8805b36fb9d5c069fc55fbe3e59d71d1b..abb96a5d6c6d6840b32eefd18d967fc8a7be011c 100644 (file)
--- a/src/gromacs/selection/scanner_internal.cpp
+++ b/src/gromacs/selection/scanner_internal.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2009,2010,2011,2012,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -69,7 +69,7 @@
 #include "parser.h"
 #include "parsetree.h"
 #include "scanner.h"
-#include "selectioncollection-impl.h"
+#include "selectioncollection_impl.h"
 #include "selelem.h"
 #include "selmethod.h"
 #include "symrec.h"

diff --git a/src/gromacs/selection/selectioncollection.cpp b/src/gromacs/selection/selectioncollection.cpp
index c2a6218fb86c65b22ccac31f40e8922840634087..bd45bcb90dd4c7325515f374d256c927218c6f9c 100644 (file)
--- a/src/gromacs/selection/selectioncollection.cpp
+++ b/src/gromacs/selection/selectioncollection.cpp
@@ -71,7 +71,7 @@
 #include "parser.h"
 #include "poscalc.h"
 #include "scanner.h"
-#include "selectioncollection-impl.h"
+#include "selectioncollection_impl.h"
 #include "selelem.h"
 #include "selmethod.h"
 #include "symrec.h"

diff --git a/src/gromacs/selection/selectioncollection-impl.h b/src/gromacs/selection/selectioncollection_impl.h
similarity index 98%
rename from src/gromacs/selection/selectioncollection-impl.h
rename to src/gromacs/selection/selectioncollection_impl.h
index 56d62fc327ca7e8be7112e6b14194bac8582df9a..c8028af48fb2f6da40b8187e575643855221a960 100644 (file)
--- a/src/gromacs/selection/selectioncollection-impl.h
+++ b/src/gromacs/selection/selectioncollection_impl.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/selection/selmethod.cpp b/src/gromacs/selection/selmethod.cpp
index bf9b2ee572d843db3311003ab78e08d57dadfffa..8aecaaa4aea17244e6a1876d95802e658a8a0c94 100644 (file)
--- a/src/gromacs/selection/selmethod.cpp
+++ b/src/gromacs/selection/selmethod.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2009,2010,2011,2012,2014,2015,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2014,2015,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -51,7 +51,7 @@
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/stringutil.h"
 
-#include "selmethod-impl.h"
+#include "selmethod_impl.h"
 #include "symrec.h"
 
 /*! \internal \brief

diff --git a/src/gromacs/selection/selmethod-impl.h b/src/gromacs/selection/selmethod_impl.h
similarity index 98%
rename from src/gromacs/selection/selmethod-impl.h
rename to src/gromacs/selection/selmethod_impl.h
index 184d8ae2fc76b187be8266de0d4c514a09677a4e..12af47cfda4f717e8c3630f0de8db95af0aa8916 100644 (file)
--- a/src/gromacs/selection/selmethod-impl.h
+++ b/src/gromacs/selection/selmethod_impl.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/selection/sm_distance.cpp b/src/gromacs/selection/sm_distance.cpp
index ca0d1ad38b99987ea28ea7f5e1c2a9d6d9a9cb0b..0bb083101830aaed07b61eb6a238e0e26bd9ec2b 100644 (file)
--- a/src/gromacs/selection/sm_distance.cpp
+++ b/src/gromacs/selection/sm_distance.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -51,7 +51,7 @@
 #include "gromacs/utility/exceptions.h"
 
 #include "selmethod.h"
-#include "selmethod-impl.h"
+#include "selmethod_impl.h"
 
 /*! \internal
  * \brief

diff --git a/src/gromacs/selection/sm_insolidangle.cpp b/src/gromacs/selection/sm_insolidangle.cpp
index cd5cc97d5cb752a7f3dd552a2e2db8aa67d382e2..fd90c036f30f647843762120af0319ea94e9b7e4 100644 (file)
--- a/src/gromacs/selection/sm_insolidangle.cpp
+++ b/src/gromacs/selection/sm_insolidangle.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -132,7 +132,7 @@
 
 #include "selelem.h"
 #include "selmethod.h"
-#include "selmethod-impl.h"
+#include "selmethod_impl.h"
 
 using std::min;
 using std::max;

diff --git a/src/gromacs/selection/sm_merge.cpp b/src/gromacs/selection/sm_merge.cpp
index 26298901c1eca62048d78bb5d000afd1ef3a899f..e681239e245c15a8822f66dd47a9c1174053b8e6 100644 (file)
--- a/src/gromacs/selection/sm_merge.cpp
+++ b/src/gromacs/selection/sm_merge.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -49,7 +49,7 @@
 #include "gromacs/utility/smalloc.h"
 
 #include "selmethod.h"
-#include "selmethod-impl.h"
+#include "selmethod_impl.h"
 
 /*! \internal \brief
  * Data structure for the merging selection modifiers.

diff --git a/src/gromacs/selection/sm_permute.cpp b/src/gromacs/selection/sm_permute.cpp
index 0b942e54451e6da51f57129047bab2b3711185e3..a90e00cf0d85a773044789152fb32dd78f1bf6c8 100644 (file)
--- a/src/gromacs/selection/sm_permute.cpp
+++ b/src/gromacs/selection/sm_permute.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -49,7 +49,7 @@
 #include "gromacs/utility/stringutil.h"
 
 #include "selmethod.h"
-#include "selmethod-impl.h"
+#include "selmethod_impl.h"
 
 /*! \internal \brief
  * Data structure for the \p permute selection modifier.

diff --git a/src/gromacs/selection/sm_position.cpp b/src/gromacs/selection/sm_position.cpp
index 569957c7005012089ed7f087de10cf5af38a2505..dad8060cd84e3d6a15ab7f39161a19131333bce6 100644 (file)
--- a/src/gromacs/selection/sm_position.cpp
+++ b/src/gromacs/selection/sm_position.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -51,7 +51,7 @@
 #include "poscalc.h"
 #include "selelem.h"
 #include "selmethod.h"
-#include "selmethod-impl.h"
+#include "selmethod_impl.h"
 
 /*! \internal \brief
  * Data structure for position keyword evaluation.

diff --git a/src/gromacs/selection/sm_same.cpp b/src/gromacs/selection/sm_same.cpp
index ec4beace5e3a0058ce45cc388ed3c1a9a66c790b..26d7c5d16c63d95eb73a70a58731c8d213c6253e 100644 (file)
--- a/src/gromacs/selection/sm_same.cpp
+++ b/src/gromacs/selection/sm_same.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -52,7 +52,7 @@
 #include "parsetree.h"
 #include "selelem.h"
 #include "selmethod.h"
-#include "selmethod-impl.h"
+#include "selmethod_impl.h"
 
 /*! \internal
  * \brief

diff --git a/src/gromacs/selection/sm_simple.cpp b/src/gromacs/selection/sm_simple.cpp
index a61cd5e73f01be645bf8872fb2a9cba75a6ff3bf..6e3440d9c3bcc62033b8795e71dc13b673f852dc 100644 (file)
--- a/src/gromacs/selection/sm_simple.cpp
+++ b/src/gromacs/selection/sm_simple.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -51,7 +51,7 @@
 #include "gromacs/utility/gmxassert.h"
 
 #include "selmethod.h"
-#include "selmethod-impl.h"
+#include "selmethod_impl.h"
 
 /** Evaluates the \p all selection keyword. */
 static void

diff --git a/src/gromacs/tools/report-methods.cpp b/src/gromacs/tools/report_methods.cpp
similarity index 99%
rename from src/gromacs/tools/report-methods.cpp
rename to src/gromacs/tools/report_methods.cpp
index 253895ea737db00657c1c2b4ff0a02cb00822436..882e18d08a54f705c88098f3f7d1bc598f6032bb 100644 (file)
--- a/src/gromacs/tools/report-methods.cpp
+++ b/src/gromacs/tools/report_methods.cpp
@@ -34,7 +34,7 @@
  */
 #include "gmxpre.h"
 
-#include "report-methods.h"
+#include "report_methods.h"
 
 #include "gromacs/commandline/cmdlineoptionsmodule.h"
 #include "gromacs/fileio/confio.h"

diff --git a/src/gromacs/tools/report-methods.h b/src/gromacs/tools/report_methods.h
similarity index 98%
rename from src/gromacs/tools/report-methods.h
rename to src/gromacs/tools/report_methods.h
index 221cdf2e4f465ec0f742175b4273822221fa21be..dc918badc7d8502424aef25a3f2e22b3910dc1ba 100644 (file)
--- a/src/gromacs/tools/report-methods.h
+++ b/src/gromacs/tools/report_methods.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/tools/tests/CMakeLists.txt b/src/gromacs/tools/tests/CMakeLists.txt
index d543a8ce81749d026f83cc57c6259e445ed843cd..9eee06a2f60c05b988e72fa223058f5c2d098d54 100644 (file)
--- a/src/gromacs/tools/tests/CMakeLists.txt
+++ b/src/gromacs/tools/tests/CMakeLists.txt
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2018, by the GROMACS development team, led by
+# Copyright (c) 2018,2019, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -33,5 +33,5 @@
 # the research papers on the package. Check out http://www.gromacs.org.
 
 gmx_add_unit_test(ToolUnitTests tool-test
-                  report-methods.cpp)
+                  report_methods.cpp)
 

diff --git a/src/gromacs/tools/tests/report-methods.cpp b/src/gromacs/tools/tests/report_methods.cpp
similarity index 98%
rename from src/gromacs/tools/tests/report-methods.cpp
rename to src/gromacs/tools/tests/report_methods.cpp
index d84fb3328be1e646dec5ecfd1c08cf80ddae940b..74bb402a40c4d0fd0c75c27608fa27b7cb81543c 100644 (file)
--- a/src/gromacs/tools/tests/report-methods.cpp
+++ b/src/gromacs/tools/tests/report_methods.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -40,7 +40,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/tools/report-methods.h"
+#include "gromacs/tools/report_methods.h"
 
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/gmxpreprocess/grompp.h"

diff --git a/src/gromacs/trajectoryanalysis/analysissettings.cpp b/src/gromacs/trajectoryanalysis/analysissettings.cpp
index 165c01097618115d3491b30bf0e3cb65b2994107..c54d3801f7c9a68dec41f39cee36338235a54f50 100644 (file)
--- a/src/gromacs/trajectoryanalysis/analysissettings.cpp
+++ b/src/gromacs/trajectoryanalysis/analysissettings.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -48,7 +48,7 @@
 #include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/gmxassert.h"
 
-#include "analysissettings-impl.h"
+#include "analysissettings_impl.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/trajectoryanalysis/analysissettings-impl.h b/src/gromacs/trajectoryanalysis/analysissettings_impl.h
similarity index 97%
rename from src/gromacs/trajectoryanalysis/analysissettings-impl.h
rename to src/gromacs/trajectoryanalysis/analysissettings_impl.h
index 4bd75f2cd0736b71fcc586d8f55a7b2db9414610..edc2b3c5b3fa59fa8ed62c64be78535b9d20bc58 100644 (file)
--- a/src/gromacs/trajectoryanalysis/analysissettings-impl.h
+++ b/src/gromacs/trajectoryanalysis/analysissettings_impl.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2014,2015,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/trajectoryanalysis/runnercommon.cpp b/src/gromacs/trajectoryanalysis/runnercommon.cpp
index 3341d040964ed1186ff76d17edaeaec46280ddd6..93e47cec84907ae0c8eb9361595f7332f8daeb1e 100644 (file)
--- a/src/gromacs/trajectoryanalysis/runnercommon.cpp
+++ b/src/gromacs/trajectoryanalysis/runnercommon.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -71,7 +71,7 @@
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/stringutil.h"
 
-#include "analysissettings-impl.h"
+#include "analysissettings_impl.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/utility/baseversion-gen.cpp.cmakein b/src/gromacs/utility/baseversion-gen.cpp.cmakein
index 441cefebd35f1d642c95773446a2ee9255eefc12..17daa56644906bc0256bd4157acb262ae9b21adb 100644 (file)
--- a/src/gromacs/utility/baseversion-gen.cpp.cmakein
+++ b/src/gromacs/utility/baseversion-gen.cpp.cmakein
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2012,2014,2015,2018, by the GROMACS development team, led by
+ * Copyright (c) 2010,2012,2014,2015,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -32,7 +32,7 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
-#include "gromacs/utility/baseversion-gen.h"
+#include "gromacs/utility/baseversion_gen.h"
 
 const char _gmx_ver_string[] = "@GMX_VERSION_STRING_FULL@";
 const char _gmx_full_git_hash[] = "@GMX_VERSION_FULL_HASH@";

diff --git a/src/gromacs/utility/baseversion.cpp b/src/gromacs/utility/baseversion.cpp
index 1cf7cc0652fe6b7d4b5daa472ef3d6e65e5b8e14..ee195b2b3f7a833bf01d5fe51c71785e79a1496d 100644 (file)
--- a/src/gromacs/utility/baseversion.cpp
+++ b/src/gromacs/utility/baseversion.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014,2015,2018, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -38,7 +38,7 @@
 
 #include "config.h"
 
-#include "baseversion-gen.h"
+#include "baseversion_gen.h"
 
 const char *gmx_version()
 {

diff --git a/src/gromacs/utility/baseversion-gen.h b/src/gromacs/utility/baseversion_gen.h
similarity index 96%
rename from src/gromacs/utility/baseversion-gen.h
rename to src/gromacs/utility/baseversion_gen.h
index 1efca7a64e7c1eb7bb22b83219378f9f14c8b585..ee793533a5b516372b91d22c2ef68093bed57eb6 100644 (file)
--- a/src/gromacs/utility/baseversion-gen.h
+++ b/src/gromacs/utility/baseversion_gen.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2012,2013,2014,2015,2018, by the GROMACS development team, led by
+ * Copyright (c) 2010,2012,2013,2014,2015,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/utility/tests/CMakeLists.txt b/src/gromacs/utility/tests/CMakeLists.txt
index c88bf29fcea871c7b5d34440c6db9f47efd55411..39fdf059ab76f2111d87b0aadc4a7017a878de97 100644 (file)
--- a/src/gromacs/utility/tests/CMakeLists.txt
+++ b/src/gromacs/utility/tests/CMakeLists.txt
@@ -52,5 +52,5 @@ gmx_add_unit_test(UtilityUnitTests utility-test
                   )
 
 gmx_add_mpi_unit_test(UtilityMpiUnitTests utility-mpi-test 4
-                  physicalnodecommunicator-mpi.cpp
+                  physicalnodecommunicator_mpi.cpp
                   )

diff --git a/src/gromacs/utility/tests/alignedallocator.cpp b/src/gromacs/utility/tests/alignedallocator.cpp
index d046a24c6b565642336d5a411a886a65301dab02..7e21cc933ab078fb4e2decbfb57e5801cfa95aa8 100644 (file)
--- a/src/gromacs/utility/tests/alignedallocator.cpp
+++ b/src/gromacs/utility/tests/alignedallocator.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2015,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -70,7 +70,7 @@ TYPED_TEST_CASE(AllocatorTest, AllocatorTypesToTest);
 }  // namespace gmx
 
 // Includes tests common to all allocation policies.
-#include "gromacs/utility/tests/alignedallocator-impl.h"
+#include "gromacs/utility/tests/alignedallocator_impl.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/utility/tests/alignedallocator-impl.h b/src/gromacs/utility/tests/alignedallocator_impl.h
similarity index 98%
rename from src/gromacs/utility/tests/alignedallocator-impl.h
rename to src/gromacs/utility/tests/alignedallocator_impl.h
index 045da902c4b767674fc8412aeed0b31702fe3ddc..8d240fec74b30e4cb3e4a102e2b004817a3f016a 100644 (file)
--- a/src/gromacs/utility/tests/alignedallocator-impl.h
+++ b/src/gromacs/utility/tests/alignedallocator_impl.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2015,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/gromacs/utility/tests/physicalnodecommunicator-mpi.cpp b/src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp
similarity index 96%
rename from src/gromacs/utility/tests/physicalnodecommunicator-mpi.cpp
rename to src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp
index b88421aca73de44cfe9489f3c11d976db9de98f6..a97e344a88e618f22fc1de730ecc99844c69bfc5 100644 (file)
--- a/src/gromacs/utility/tests/physicalnodecommunicator-mpi.cpp
+++ b/src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/programs/legacymodules.cpp b/src/programs/legacymodules.cpp
index 4e3381216633846c9ab428bee8b6dbd17b85f823..e3a6f1cb192902f757abe436ceb5325d40857538 100644 (file)
--- a/src/programs/legacymodules.cpp
+++ b/src/programs/legacymodules.cpp
@@ -52,14 +52,14 @@
 #include "gromacs/gmxpreprocess/genion.h"
 #include "gromacs/gmxpreprocess/genrestr.h"
 #include "gromacs/gmxpreprocess/grompp.h"
-#include "gromacs/gmxpreprocess/insert-molecules.h"
+#include "gromacs/gmxpreprocess/insert_molecules.h"
 #include "gromacs/gmxpreprocess/pdb2gmx.h"
 #include "gromacs/gmxpreprocess/solvate.h"
 #include "gromacs/gmxpreprocess/x2top.h"
 #include "gromacs/tools/check.h"
 #include "gromacs/tools/convert_tpr.h"
 #include "gromacs/tools/dump.h"
-#include "gromacs/tools/report-methods.h"
+#include "gromacs/tools/report_methods.h"
 
 #include "mdrun/mdrun_main.h"
 #include "view/view.h"

diff --git a/src/testutils/CMakeLists.txt b/src/testutils/CMakeLists.txt
index 5bcc6993b69900749a5457cc0040bee70854b34f..0747669960b52e325c4b98640e15b1a902e38029 100644 (file)
--- a/src/testutils/CMakeLists.txt
+++ b/src/testutils/CMakeLists.txt
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+# Copyright (c) 2011,2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -44,10 +44,10 @@ set(TESTUTILS_SOURCES
     filematchers.cpp
     interactivetest.cpp
     loggertest.cpp
-    mpi-printer.cpp
+    mpi_printer.cpp
     mpitest.cpp
     refdata.cpp
-    refdata-xml.cpp
+    refdata_xml.cpp
     simulationdatabase.cpp
     stdiohelper.cpp
     stringtest.cpp

diff --git a/src/testutils/mpi-printer.cpp b/src/testutils/mpi_printer.cpp
similarity index 98%
rename from src/testutils/mpi-printer.cpp
rename to src/testutils/mpi_printer.cpp
index 1d09b365b2073ecbbfe854d1989a04290ed72886..a193d1276321d30a5c0465940d970fe8077d8f88 100644 (file)
--- a/src/testutils/mpi-printer.cpp
+++ b/src/testutils/mpi_printer.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -34,7 +34,7 @@
  */
 #include "gmxpre.h"
 
-#include "mpi-printer.h"
+#include "mpi_printer.h"
 
 #include "config.h"
 

diff --git a/src/testutils/mpi-printer.h b/src/testutils/mpi_printer.h
similarity index 97%
rename from src/testutils/mpi-printer.h
rename to src/testutils/mpi_printer.h
index f771049020e602bc844a0b8a0b3fb36049f7fa3e..434fabd5da70b18efd4fa86939c7e3f5272e0aab 100644 (file)
--- a/src/testutils/mpi-printer.h
+++ b/src/testutils/mpi_printer.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.

diff --git a/src/testutils/refdata.cpp b/src/testutils/refdata.cpp
index 98043304be8de5e236f1b4e6e534c5401e6f8db4..1e22a71f7bbaba35372ce6bd96e301848e1616b4 100644 (file)
--- a/src/testutils/refdata.cpp
+++ b/src/testutils/refdata.cpp
@@ -62,9 +62,9 @@
 #include "gromacs/utility/real.h"
 #include "gromacs/utility/stringutil.h"
 
-#include "testutils/refdata-checkers.h"
-#include "testutils/refdata-impl.h"
-#include "testutils/refdata-xml.h"
+#include "testutils/refdata_checkers.h"
+#include "testutils/refdata_impl.h"
+#include "testutils/refdata_xml.h"
 #include "testutils/testasserts.h"
 #include "testutils/testexceptions.h"
 #include "testutils/testfilemanager.h"

diff --git a/src/testutils/refdata-checkers.h b/src/testutils/refdata_checkers.h
similarity index 98%
rename from src/testutils/refdata-checkers.h
rename to src/testutils/refdata_checkers.h
index 32656d27fda588d635c9e577948732ef322e3f04..0d3fda7aabb6d0a11b4b8cce6e74048d0043aa46 100644 (file)
--- a/src/testutils/refdata-checkers.h
+++ b/src/testutils/refdata_checkers.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -55,7 +55,7 @@
 #include "gromacs/utility/strconvert.h"
 #include "gromacs/utility/stringutil.h"
 
-#include "testutils/refdata-impl.h"
+#include "testutils/refdata_impl.h"
 #include "testutils/testasserts.h"
 #include "testutils/testexceptions.h"
 

diff --git a/src/testutils/refdata-impl.h b/src/testutils/refdata_impl.h
similarity index 100%
rename from src/testutils/refdata-impl.h
rename to src/testutils/refdata_impl.h

diff --git a/src/testutils/refdata-xml.cpp b/src/testutils/refdata_xml.cpp
similarity index 98%
rename from src/testutils/refdata-xml.cpp
rename to src/testutils/refdata_xml.cpp
index 0b7a8269444dcf20a678865e51196d1cff54fd33..50e2e6f4e8e30388ed7eefb6e33081367faf690d 100644 (file)
--- a/src/testutils/refdata-xml.cpp
+++ b/src/testutils/refdata_xml.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -42,13 +42,13 @@
  */
 #include "gmxpre.h"
 
-#include "refdata-xml.h"
+#include "refdata_xml.h"
 
 #include <tinyxml2.h>
 
 #include "gromacs/utility/exceptions.h"
 
-#include "testutils/refdata-impl.h"
+#include "testutils/refdata_impl.h"
 #include "testutils/testexceptions.h"
 
 namespace gmx

diff --git a/src/testutils/refdata-xml.h b/src/testutils/refdata_xml.h
similarity index 96%
rename from src/testutils/refdata-xml.h
rename to src/testutils/refdata_xml.h
index ef8c703e9983be5a5d85eb3c4076a66c24609d89..fd56e346525470e2757926d7b6b6fe99e2b7cc08 100644 (file)
--- a/src/testutils/refdata-xml.h
+++ b/src/testutils/refdata_xml.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -44,7 +44,7 @@
 
 #include <string>
 
-#include "testutils/refdata-impl.h"
+#include "testutils/refdata_impl.h"
 
 namespace gmx
 {

diff --git a/src/testutils/testinit.cpp b/src/testutils/testinit.cpp
index e87b9ea88f0859f27ff5d7b4c2353b1448ba3998..5acb4558690cab641d1d37e659cea4b38ad9582a 100644 (file)
--- a/src/testutils/testinit.cpp
+++ b/src/testutils/testinit.cpp
@@ -67,7 +67,7 @@
 #include "gromacs/utility/programcontext.h"
 #include "gromacs/utility/textwriter.h"
 
-#include "testutils/mpi-printer.h"
+#include "testutils/mpi_printer.h"
 #include "testutils/refdata.h"
 #include "testutils/testfilemanager.h"
 #include "testutils/testoptions.h"

diff --git a/src/testutils/testutils-doc.h b/src/testutils/testutils_doc.h
similarity index 96%
rename from src/testutils/testutils-doc.h
rename to src/testutils/testutils_doc.h
index eb111256d0d3adc34e59f78658b75f38d410da94..f59a1aaebc9742946dd82dfe9054dbb05ef98e65 100644 (file)
--- a/src/testutils/testutils-doc.h
+++ b/src/testutils/testutils_doc.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2015,2017,2019, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -82,12 +82,12 @@
  *  - gmx::test::StdioTestHelper provides a helper class for tests that need to
  *    execute legacy code where `stdin` reading cannot be easily mocked.
  *
- * Additionally, testinit.h and mpi-printer.h, and their corresponding source
+ * Additionally, testinit.h and mpi_printer.h, and their corresponding source
  * files, provide functionality that is not visible on the API level: they
  * provide initialization routines for the above functionality, which are
  * automatically called by the %main() function provided in unittest_main.cpp.
  *
- * mpi-printer.h provides a Google Test listener that is installed when the
+ * mpi_printer.h provides a Google Test listener that is installed when the
  * tests are compiled with MPI.  This listener allows the test binary to be run
  * on multiple MPI ranks, and synchronizes the execution and output from the
  * test cases, as well as makes the test fail on even if an assertion fails