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`
   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.
     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",
     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
     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.
 
   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
   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
   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.
 #
 #
 # 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.
 # 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'],
         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'])
                 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
 `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
 
 
 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!
 # 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"
 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 "gmxapi/status.h"
 #include "gmxapi/version.h"
 

-#include "context-impl.h"
+#include "context_impl.h"

 #include "createsession.h"
 #include "createsession.h"

-#include "session-impl.h"
+#include "session_impl.h"

 #include "workflow.h"
 
 namespace gmxapi
 #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.
  *
 /*
  * 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.
  * 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 "gmxapi/gmxapi.h"
 #include "gmxapi/md/mdmodule.h"
 

-#include "md-impl.h"
+#include "md_impl.h"

 
 namespace gmxapi
 {
 
 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.
  *
 /*
  * 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.
  * 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 "gmxapi/session.h"
 #include "gmxapi/md/mdsignals.h"
 

-#include "session-impl.h"
+#include "session_impl.h"

 
 namespace gmxapi
 {
 
 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 "createsession.h"
 #include "mdsignals.h"

-#include "session-impl.h"
+#include "session_impl.h"

 #include "sessionresources.h"
 
 namespace gmxapi
 #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.
  *
 /*
  * 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.
  * 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
 // 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.
 
 /*!
  * \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 "gmxapi/status.h"
 #include "gmxapi/system.h"
 

-#include "system-impl.h"
+#include "system_impl.h"

 #include "workflow.h"
 
 namespace gmxapi
 #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.
  *
 /*
  * 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.
  * 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 "gromacs/utility/gmxassert.h"
 

-#include "workflow-impl.h"
+#include "workflow_impl.h"

 
 namespace gmxapi
 {
 
 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 <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"
 #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.
  *
 /*
  * 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.
  * 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(gmxlib)
 add_subdirectory(mdlib)

-add_subdirectory(applied-forces)
+add_subdirectory(applied_forces)

 add_subdirectory(listed_forces)
 add_subdirectory(commandline)
 add_subdirectory(domdec)
 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
 
     # 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
         )
     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.
 #
 #
 # 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.
 # 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.
  *
 /*
  * 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.
  * 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.
  *
 /*
  * 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.
  * 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.
 #
 #
 # 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.
 # 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.
 
 # 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
                 )
                   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.
  *
 /*
  * 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.
  * 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 "gmxpre.h"
 

-#include "gromacs/applied-forces/electricfield.h"
+#include "gromacs/applied_forces/electricfield.h"

 
 #include <gtest/gtest.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/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/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"
 #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/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"
 #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.
  *
 /*
  * 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.
  * 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 <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"
 #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.
  *
 /*
  * 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.
  * 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 <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"
 #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.
  *
 /*
  * 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.
  * 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/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"
 #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.
  *
 /*
  * 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.
  * 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 <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"
 #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.
  *
 /*
  * 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.
  * 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 <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"
 #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.
  *
 /*
  * 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.
  * 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 <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"
 #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.
  *
 /*
  * 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.
  * 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/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"
 #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.
  *
 /*
  * 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.
  * 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 <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"
 
 #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.
  *
 /*
  * 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.
  * 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 <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"
 #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) 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.
  * 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 "gmxpre.h"
 

-#include "read-params.h"
+#include "read_params.h"

 
 #include "gromacs/awh/awh.h"
 #include "gromacs/fileio/readinp.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/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/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"
 #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.
  *
 /*
  * 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.
  * 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/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"
 #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/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"
 #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.
  *
 /*
  * 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.
  * 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 <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"
 #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.
  *
 /*
  * 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.
  * 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 "gromacs/onlinehelp/ihelptopic.h"
 #include "gromacs/utility/classhelpers.h"
 

-#include "cmdlinemodulemanager-impl.h"
+#include "cmdlinemodulemanager_impl.h"

 
 namespace gmx
 {
 
 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.
  *
 /*
  * 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.
  * 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 "gromacs/utility/sysinfo.h"
 
 #include "cmdlinehelpmodule.h"

-#include "cmdlinemodulemanager-impl.h"
+#include "cmdlinemodulemanager_impl.h"

 
 namespace gmx
 {
 
 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.
  *
 /*
  * 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.
  * 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/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"
 #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.
 #
 #
 # 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.
 # 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(
 # 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.cpp

-    ewald-utils.cpp
-    long-range-correction.cpp
+    ewald_utils.cpp
+    long_range_correction.cpp

     pme.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
     # Files that implement stubs

-    pme-gpu-program.cpp
+    pme_gpu_program.cpp

     )
 if (GMX_USE_CUDA)
     gmx_add_libgromacs_sources(
         # CUDA-specific sources
     )
 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
         # 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(
         )
     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
         )
 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
         # 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
         )
 else()
     gmx_add_libgromacs_sources(
         # Files that implement stubs

-        pme-gpu-program-impl.cpp
+        pme_gpu_program_impl.cpp

         )
 endif()
 
         )
 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) 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.
  * 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 "gmxpre.h"
 

-#include "calculate-spline-moduli.h"
+#include "calculate_spline_moduli.h"

 
 #include <cmath>
 
 
 #include <cmath>
 


@@ -48,7 +48,7 @@
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/smalloc.h"
 
 #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)
 
 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) 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.
  * 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
 
 #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,
 
 /* 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) 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.
  * 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 <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"
 #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) 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.
  * 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 "gmxpre.h"
 

-#include "ewald-utils.h"
+#include "ewald_utils.h"

 
 #include <cmath>
 
 
 #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) 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.
  * 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) 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.
  * 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 "gmxpre.h"
 

-#include "long-range-correction.h"
+#include "long_range_correction.h"

 
 #include <cmath>
 
 
 #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"
 #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 "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
 
 /* 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) 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.
  * 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) 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.
  * 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 <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"
 #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 "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.
 
 /*! \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.
  *
 /*
  * 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.
  * 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 "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.
 
 /*! \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.
  *
 /*
  * 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.
  * 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).
  *  \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:
  *
  *
  * This file's kernels specifically expect the following definitions:
  *


@@ -51,8 +51,8 @@
  *  \author Aleksei Iupinov <a.yupinov@gmail.com>
  */
 
  *  \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
 
 #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) 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.
  * 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 "gmxpre.h"
 

-#include "pme-gather.h"
+#include "pme_gather.h"

 
 #include "gromacs/math/vec.h"
 #include "gromacs/simd/simd.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 "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
 
 
 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.
  *
 /*
  * 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.
  * 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 <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.
 
 /*! \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.
  *
 /*
  * 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.
  * 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 "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,
 
 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.
  *
 /*
  * 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.
  * 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 <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"
 #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 "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)
 {
 
 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.
  *
 /*
  * 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.
  * 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 "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 "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)
 {
 
 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.
  *
 /*
  * 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.
  * 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.
  *
 /*
  * 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.
  * 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 "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)
 
 //! 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.
  *
 /*
  * 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.
  * 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 "gmxpre.h"
 

-#include "pme-gpu-internal.h"
+#include "pme_gpu_internal.h"

 
 #include "config.h"
 
 
 #include "config.h"
 


@@ -55,7 +55,7 @@
 #include <memory>
 #include <string>
 
 #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"
 #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 "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.
 
 /*! \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.
  *
 /*
  * 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.
  * 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.
  *
  * \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
  *
  * \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 "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;
 
 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);
 
  */
 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.
 
 /*! \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;
 }
 
     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.
 
 /*! \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 "gmxpre.h"
 

-#include "pme-gpu-program.h"
+#include "pme_gpu_program.h"

 
 #include <memory>
 
 
 #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))
 
 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.
  *
 /*
  * 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.
  * 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.
  *
 /*
  * 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.
  * 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 "gmxpre.h"
 

-#include "pme-gpu-program-impl.h"
+#include "pme_gpu_program_impl.h"

 
 PmeGpuProgramImpl::PmeGpuProgramImpl(const gmx_device_info_t * /*unused*/) :
     warpSize(0),
 
 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.
  *
 /*
  * 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.
  * 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 "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;
 
 // 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.
  *
 /*
  * 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.
  * 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.
  *
 /*
  * 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.
  * 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 "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)
 {
 
 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 "
                     "-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 "
                     "-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 "
                     "-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",
                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,
                                                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));
         }
 
             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"))
         {
         // 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.
  *
 /*
  * 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.
  * 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 "gmxpre.h"
 

-#include "pme-gpu-timings.h"
+#include "pme_gpu_timings.h"

 
 #include "gromacs/utility/gmxassert.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.
 
 /*! \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.
  *
 /*
  * 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.
  * 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.
  *
 /*
  * 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.
  * 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 <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"
 #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.
  *
 /*
  * 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.
  * 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.
 
 /*! \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
  *
  * \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.
  *
 /*
  * 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.
  * 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.
 
 /*! \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);
  * 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
  *
  * \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.
  *
 /*
  * 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.
  * 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
 /*! \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>
  * 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 <cassert>
 

-#include "pme-gpu-constants.h"
+#include "pme_gpu_constants.h"

 
 //! A macro for inline GPU functions.
 #if GMX_GPU == GMX_GPU_CUDA
 
 //! 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) 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.
  * 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"
 
 /* TODO find out what this file should be called */
 #include "gmxpre.h"
 

-#include "pme-grid.h"
+#include "pme_grid.h"

 
 #include "config.h"
 
 
 #include "config.h"
 


@@ -50,7 +50,7 @@
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
 #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"
 
 #ifdef DEBUG_PME
 #include "gromacs/fileio/pdbio.h"


@@ -58,7 +58,7 @@
 #include "gromacs/utility/futil.h"
 #endif
 
 #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.
 
 /* 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.
  *
 /*
  * 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.
  * 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) 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.
  * 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 "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;
 
 //! 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 "gmxpre.h"
 

-#include "pme-load-balancing.h"
+#include "pme_load_balancing.h"

 
 #include <cassert>
 #include <cmath>
 
 #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/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"
 #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 "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 {
 
 /*! \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.
  *
 /*
  * 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.
  * 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 "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
 
 //! 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) 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.
  * 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 "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
  *
 
 /*! \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) 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.
  * 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.
  *
 /*
  * 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.
  * 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).
  * 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:
  *
  *
  * 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
 #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
 #undef computeSplines
 #undef spreadCharges
 #undef CUSTOMIZED_KERNEL_NAME


@@ -72,7 +72,7 @@
 #define computeSplines 1
 #define spreadCharges 0
 #define CUSTOMIZED_KERNEL_NAME(x) pmeSplineKernel
 #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
 #undef computeSplines
 #undef spreadCharges
 #undef CUSTOMIZED_KERNEL_NAME


@@ -81,7 +81,7 @@
 #define computeSplines 0
 #define spreadCharges 1
 #define CUSTOMIZED_KERNEL_NAME(x) pmeSpreadKernel
 #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
 #undef computeSplines
 #undef spreadCharges
 #undef CUSTOMIZED_KERNEL_NAME


@@ -97,14 +97,14 @@
 // gather
 #define overwriteForces 1
 #define CUSTOMIZED_KERNEL_NAME(x) pmeGatherKernel
 // 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
 #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
 
 #undef overwriteForces
 #undef CUSTOMIZED_KERNEL_NAME
 


@@ -121,7 +121,7 @@
 #define gridOrdering YZX
 #define computeEnergyAndVirial 0
 #define CUSTOMIZED_KERNEL_NAME(x) pmeSolveYZXKernel
 #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
 #undef gridOrdering
 #undef computeEnergyAndVirial
 #undef CUSTOMIZED_KERNEL_NAME


@@ -130,7 +130,7 @@
 #define gridOrdering YZX
 #define computeEnergyAndVirial 1
 #define CUSTOMIZED_KERNEL_NAME(x) pmeSolveYZXEnergyKernel
 #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
 #undef gridOrdering
 #undef computeEnergyAndVirial
 #undef CUSTOMIZED_KERNEL_NAME


@@ -139,7 +139,7 @@
 #define gridOrdering XYZ
 #define computeEnergyAndVirial 0
 #define CUSTOMIZED_KERNEL_NAME(x) pmeSolveXYZKernel
 #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
 #undef gridOrdering
 #undef computeEnergyAndVirial
 #undef CUSTOMIZED_KERNEL_NAME


@@ -148,7 +148,7 @@
 #define gridOrdering XYZ
 #define computeEnergyAndVirial 1
 #define CUSTOMIZED_KERNEL_NAME(x) pmeSolveXYZEnergyKernel
 #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
 #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) 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.
  * 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 "gmxpre.h"
 

-#include "pme-redistribute.h"
+#include "pme_redistribute.h"

 
 #include "config.h"
 
 
 #include "config.h"
 


@@ -49,8 +49,8 @@
 #include "gromacs/utility/gmxmpi.h"
 #include "gromacs/utility/smalloc.h"
 
 #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[],
 
 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.
  *
 /*
  * 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.
  * 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
 
 #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);
 
 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.
  *
 /*
  * 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.
  * 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) 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.
  * 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.
  *
 /*
  * 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.
  * 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.
  *  \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:
  *
  *
  * This file's solving kernel specifically expects the following definitions for its flavors:
  *


@@ -49,7 +49,7 @@
  *  \author Aleksei Iupinov <a.yupinov@gmail.com>
  */
 
  *  \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
 #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) 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.
  * 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 "gmxpre.h"
 

-#include "pme-solve.h"
+#include "pme_solve.h"

 
 #include <cmath>
 
 
 #include <cmath>
 


@@ -51,7 +51,7 @@
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/smalloc.h"
 
 #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 */
 
 #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.
  *
 /*
  * 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.
  * 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.
  *
 /*
  * 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.
  * 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) 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.
  * 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 "gmxpre.h"
 

-#include "pme-spline-work.h"
+#include "pme_spline_work.h"

 
 #include "gromacs/simd/simd.h"
 #include "gromacs/utility/alignedallocator.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 "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
 
 
 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.
  *
 /*
  * 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.
  * 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 "gromacs/simd/simd.h"
 

-#include "pme-simd.h"
+#include "pme_simd.h"

 
 struct pme_spline_work
 {
 
 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.
  *
 /*
  * 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.
  * 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).
  *  \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:
  *
  *
  * This file's kernels specifically expect the following definitions:
  *


@@ -51,8 +51,8 @@
  *  \author Aleksei Iupinov <a.yupinov@gmail.com>
  */
 
  *  \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"
 
 /*
 #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) 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.
  * 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 "gmxpre.h"
 

-#include "pme-spread.h"
+#include "pme_spread.h"

 
 #include "config.h"
 
 
 #include "config.h"
 


@@ -52,10 +52,10 @@
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
 #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 */
 
 
 /* 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
 #define PME_SPREAD_SIMD4_ALIGNED
 #define PME_ORDER 4
 #endif

-#include "pme-simd4.h"
+#include "pme_simd4.h"

 #else
                     DO_BSPLINE(4);
 #endif
 #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
 #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
 #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) 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.
  * 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 "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.
 
 /*
  * 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) 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.
  * 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 "gromacs/utility/real.h"
 

-#include "pme-internal.h"
+#include "pme_internal.h"

 
 void
 spread_on_grid(const gmx_pme_t *pme,
 
 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.
  *
 /*
  * 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.
  * 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 <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"
 #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.
  *
 /*
  * 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.
  * 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 <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"
 #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.
  *
 /*
  * 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.
  * 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 <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"
 #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.
  *
 /*
  * 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.
  * 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 <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;
 #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 "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/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"
 #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) 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.
  * 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 <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"
 #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) 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.
  * 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 "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. */
 
 
 /* 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) 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.
  * 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 "gmxpre.h"
 

-#include "gmxfio-xdr.h"
+#include "gmxfio_xdr.h"

 
 #include <cstdio>
 #include <cstring>
 
 #include <cstdio>
 #include <cstring>


@@ -47,7 +47,7 @@
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/smalloc.h"
 
 #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 {
 
 /* 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) 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.
  * 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) 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.
  * 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.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"
 #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/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/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/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"
 #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) 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.
  * 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 <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"
 #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) 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.
  * 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/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"
 #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) 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.
  * 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 <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"
 #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/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"
 #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 <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"
 #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) 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.
  * 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/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"
 #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) 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.
  * 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"
 
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 

-#include "conformation-utilities.h"
+#include "conformation_utilities.h"

 
 #include <cmath>
 
 
 #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) 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.
  * 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) 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.
  * 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 <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"
 #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 <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"
 #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/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"
 #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/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"
 #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/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"
 #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 <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"
 #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 <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"
 #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 <sys/types.h>
 

-#include "gromacs/awh/read-params.h"
+#include "gromacs/awh/read_params.h"

 #include "gromacs/commandline/pargs.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"
 #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/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"
 #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 "gmxpre.h"
 

-#include "insert-molecules.h"
+#include "insert_molecules.h"

 
 #include <algorithm>
 #include <memory>
 
 #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/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"
 #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.
  *
 /*
  * 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.
  * 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/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"
 #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/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/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"
 #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/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"
 #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 <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"
 #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/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"
 #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) 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.
  * 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/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"
 #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/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"
 #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/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"
 #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/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"
 #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
 
 gmx_add_unit_test(GmxPreprocessTests gmxpreprocess-test
     genconf.cpp

-    insert-molecules.cpp
+    insert_molecules.cpp

     readir.cpp
     solvate.cpp
     topdirs.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.
  *
 /*
  * 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.
  * 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 "gmxpre.h"
 

-#include "gromacs/gmxpreprocess/insert-molecules.h"
+#include "gromacs/gmxpreprocess/insert_molecules.h"

 
 #include "testutils/cmdlinetest.h"
 #include "testutils/refdata.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 <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"
 #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"
 
 #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",
 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/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"
 #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/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"
 #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 <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"
 #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 <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"
 #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/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"
 #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/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"
 #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 <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"
 #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.
 } // 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
 gmx_add_libgromacs_sources(
     bonded.cpp
     disre.cpp

-    gpubonded-impl.cpp
+    gpubonded_impl.cpp

     listed_forces.cpp
     listed_forces.cpp

-    listed-internal.cpp
-    manage-threading.cpp
+    listed_internal.cpp
+    manage_threading.cpp

     orires.cpp
     pairs.cpp
     orires.cpp
     pairs.cpp

-    position-restraints.cpp
+    position_restraints.cpp

     restcbt.cpp
     )
 
 if(GMX_USE_CUDA)
     gmx_add_libgromacs_sources(
     restcbt.cpp
     )
 
 if(GMX_USE_CUDA)
     gmx_add_libgromacs_sources(

-       gpubonded-impl.cu
+       gpubonded_impl.cu

        gpubondedkernels.cu
        )
 endif()
        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/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"
 #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 "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
 #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 "gmxpre.h"
 

-#include "gpubonded-impl.h"
+#include "gpubonded_impl.h"

 
 #include "gromacs/gpu_utils/cudautils.cuh"
 #include "gromacs/gpu_utils/devicebuffer.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 "gromacs/topology/ifunc.h"
 #include "gromacs/utility/gmxassert.h"
 

-#include "gpubonded-impl.h"
+#include "gpubonded_impl.h"

 
 #if defined(_MSVC)
 #include <limits>
 
 #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/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"
 #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 "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 

-#include "listed-internal.h"
+#include "listed_internal.h"

 #include "utilities.h"
 
 struct BondedInteractions
 #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 "gmxpre.h"
 

-#include "listed-internal.h"
+#include "listed_internal.h"

 
 #include <cstdlib>
 
 
 #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 "gmxpre.h"
 

-#include "manage-threading.h"
+#include "manage_threading.h"

 
 #include "config.h"
 
 
 #include "config.h"
 


@@ -64,7 +64,7 @@
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/smalloc.h"
 
 #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 */
 #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/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"
 #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 "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
 
 
 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 "gmxpre.h"
 

-#include "position-restraints.h"
+#include "position_restraints.h"

 
 #include <cassert>
 #include <cmath>
 
 #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/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/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"
 #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.
  *
 /*
  * 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.
  * 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 <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"
 #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) 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.
  * 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/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)
 #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/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"
 #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/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"
 #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/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/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/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"
 #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.
  *
 /*
  * 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.
  * 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/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"
 #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/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"
 #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.
  *
 /*
  * 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.
  * 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/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"
 #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) 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.
  * 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/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"
 #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/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"
 #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/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/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"
 #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/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"
 #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/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/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"
 #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/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"
 #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/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"
 #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/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/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"
 #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/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"
 #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/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.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"
 #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/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"
 #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 <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"
 #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.
 #
 #
 # 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.
 # 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
                   $<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>)
                       $<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.
  *
 /*
  * 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.
  * 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.
  *
 /*
  * 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.
  * 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.
  *
 /*
  * 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.
  * 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 <vector>
 

-#include "gromacs/mdtypes/awh-correlation-history.h"
+#include "gromacs/mdtypes/awh_correlation_history.h"

 #include "gromacs/utility/basedefinitions.h"
 
 namespace gmx
 #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.
  *
 /*
  * 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.
  * 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) 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.
  * 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/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/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"
 #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.
  *
 /*
  * 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.
  * 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) 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.
  * 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/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/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"
 #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.
  *
 /*
  * 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.
  * 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.
  *
 /*
  * 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.
  * 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 "abstractsection.h"
 

-#include "options-impl.h"
+#include "options_impl.h"

 
 namespace gmx
 {
 
 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 "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/stringutil.h"
 

-#include "options-impl.h"
+#include "options_impl.h"

 
 namespace gmx
 {
 
 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.
  *
 /*
  * 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.
  * 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 "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
 

-#include "options-impl.h"
+#include "options_impl.h"

 
 namespace gmx
 {
 
 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.
  *
 /*
  * 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.
  * 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 "gromacs/options/options.h"
 #include "gromacs/options/optionsection.h"
 

-#include "options-impl.h"
+#include "options_impl.h"

 
 namespace gmx
 {
 
 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.
  *
 /*
  * 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.
  * 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 "gmxpre.h"
 

-#include "pbc-simd.h"
+#include "pbc_simd.h"

 
 #include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.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.
  *
 /*
  * 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.
  * 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) 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.
  * 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/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"
 #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) 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.
  * 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 <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.
 #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 "gromacs/mdtypes/forceoutput.h"
 #include "gromacs/mdtypes/iforceprovider.h"
 

-#include "restraintmdmodule-impl.h"
+#include "restraintmdmodule_impl.h"

 
 namespace gmx
 {
 
 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.
  *
 /*
  * 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.
  * 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.
  *
 /*
  * 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.
  * 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 "keywords.h"
 #include "mempool.h"
 #include "poscalc.h"

-#include "selectioncollection-impl.h"
+#include "selectioncollection_impl.h"

 #include "selelem.h"
 #include "selmethod.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.
  *
 /*
  * 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.
  * 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 "mempool.h"
 #include "poscalc.h"

-#include "selectioncollection-impl.h"
+#include "selectioncollection_impl.h"

 #include "selelem.h"
 #include "selmethod.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 "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"
 #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.
  *
 /*
  * 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.
  * 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 "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"
 #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 "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"
 #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.
  *
 /*
  * 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.
  * 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.
  *
 /*
  * 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.
  * 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 "gromacs/utility/exceptions.h"
 #include "gromacs/utility/stringutil.h"
 

-#include "selmethod-impl.h"
+#include "selmethod_impl.h"

 #include "symrec.h"
 
 /*! \internal \brief
 #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.
  *
 /*
  * 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.
  * 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.
  *
 /*
  * 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.
  * 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 "gromacs/utility/exceptions.h"
 
 #include "selmethod.h"

-#include "selmethod-impl.h"
+#include "selmethod_impl.h"

 
 /*! \internal
  * \brief
 
 /*! \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.
  *
 /*
  * 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.
  * 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 "selelem.h"
 #include "selmethod.h"

-#include "selmethod-impl.h"
+#include "selmethod_impl.h"

 
 using std::min;
 using std::max;
 
 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.
  *
 /*
  * 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.
  * 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 "gromacs/utility/smalloc.h"
 
 #include "selmethod.h"

-#include "selmethod-impl.h"
+#include "selmethod_impl.h"

 
 /*! \internal \brief
  * Data structure for the merging selection modifiers.
 
 /*! \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.
  *
 /*
  * 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.
  * 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 "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.
 
 /*! \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.
  *
 /*
  * 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.
  * 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 "poscalc.h"
 #include "selelem.h"
 #include "selmethod.h"

-#include "selmethod-impl.h"
+#include "selmethod_impl.h"

 
 /*! \internal \brief
  * Data structure for position keyword evaluation.
 
 /*! \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.
  *
 /*
  * 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.
  * 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 "parsetree.h"
 #include "selelem.h"
 #include "selmethod.h"

-#include "selmethod-impl.h"
+#include "selmethod_impl.h"

 
 /*! \internal
  * \brief
 
 /*! \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.
  *
 /*
  * 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.
  * 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 "gromacs/utility/gmxassert.h"
 
 #include "selmethod.h"

-#include "selmethod-impl.h"
+#include "selmethod_impl.h"

 
 /** Evaluates the \p all selection keyword. */
 static void
 
 /** 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 "gmxpre.h"
 

-#include "report-methods.h"
+#include "report_methods.h"

 
 #include "gromacs/commandline/cmdlineoptionsmodule.h"
 #include "gromacs/fileio/confio.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.
  *
 /*
  * 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.
  * 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.
 #
 #
 # 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.
 # 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
 # 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.
  *
 /*
  * 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.
  * 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 "gmxpre.h"
 

-#include "gromacs/tools/report-methods.h"
+#include "gromacs/tools/report_methods.h"

 
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/gmxpreprocess/grompp.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.
  *
 /*
  * 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.
  * 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 "gromacs/utility/arrayref.h"
 #include "gromacs/utility/gmxassert.h"
 

-#include "analysissettings-impl.h"
+#include "analysissettings_impl.h"

 
 namespace gmx
 {
 
 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.
  *
 /*
  * 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.
  * 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.
  *
 /*
  * 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.
  * 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 "gromacs/utility/smalloc.h"
 #include "gromacs/utility/stringutil.h"
 

-#include "analysissettings-impl.h"
+#include "analysissettings_impl.h"

 
 namespace gmx
 {
 
 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.
  *
 /*
  * 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.
  * 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.
  */
  * 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@";
 
 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.
  *
 /*
  * 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.
  * 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 "config.h"
 

-#include "baseversion-gen.h"
+#include "baseversion_gen.h"

 
 const char *gmx_version()
 {
 
 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.
  *
 /*
  * 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.
  * 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
                   )
 
 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.
  *
 /*
  * 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.
  * 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.
 }  // 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
 {
 
 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.
  *
 /*
  * 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.
  * 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.
  *
 /*
  * 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.
  * 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/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/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"
 
 #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.
 #
 #
 # 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.
 # 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
     filematchers.cpp
     interactivetest.cpp
     loggertest.cpp

-    mpi-printer.cpp
+    mpi_printer.cpp

     mpitest.cpp
     refdata.cpp
     mpitest.cpp
     refdata.cpp

-    refdata-xml.cpp
+    refdata_xml.cpp

     simulationdatabase.cpp
     stdiohelper.cpp
     stringtest.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.
  *
 /*
  * 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.
  * 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 "gmxpre.h"
 

-#include "mpi-printer.h"
+#include "mpi_printer.h"

 
 #include "config.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.
  *
 /*
  * 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.
  * 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 "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"
 #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.
  *
 /*
  * 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.
  * 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 "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"
 
 #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.
  *
 /*
  * 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.
  * 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 "gmxpre.h"
 

-#include "refdata-xml.h"
+#include "refdata_xml.h"

 
 #include <tinyxml2.h>
 
 #include "gromacs/utility/exceptions.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
 #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.
  *
 /*
  * 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.
  * 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 <string>
 

-#include "testutils/refdata-impl.h"
+#include "testutils/refdata_impl.h"

 
 namespace gmx
 {
 
 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 "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"
 #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.
  *
 /*
  * 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.
  * 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.
  *
  *  - 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.
  *
  * 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
  * 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