Improve CUDA codegen flags

- onnly generate PTX for an early and the latest arch (3.5 and 8.0)
- add binary 8.0 and 8.6 targets

diff --git a/api/gmxapi/CMakeLists.txt b/api/gmxapi/CMakeLists.txt
index 1fcf9b69ec88d1e96c6723e59890ffddbf91f8e6..865abe29253db45832529ed5c4e5378f7b7255a2 100644 (file)
--- a/api/gmxapi/CMakeLists.txt
+++ b/api/gmxapi/CMakeLists.txt
@@ -64,17 +64,12 @@ set_target_properties(gmxapi PROPERTIES
 
 if (GMX_LIB_MPI)
     # GROMACS is built against an MPI library.
 
 if (GMX_LIB_MPI)
     # GROMACS is built against an MPI library.

-    # Clarification should be possible with resolution of #3672.

     set(_gmx_mpi_type "library")
     set(_gmx_mpi_type "library")

-    # Ref https://cmake.org/cmake/help/v3.13/module/FindMPI.html#variables-for-using-mpi
-    find_package(MPI COMPONENTS CXX)
-    if (MPI_CXX_FOUND)
-target_link_libraries(gmxapi PRIVATE MPI::MPI_CXX)
-        # If clients also need to link this target, we need to provide help in gmxapi-config.cmake
-        set(_gmxapi_find_dependencies "find_dependency(MPI COMPONENTS CXX)")
-    else()
-        message(FATAL_ERROR "Building gmxapi for MPI-enabled GROMACS, but no MPI toolchain found.")
-    endif ()
+    # TODO: Normative solution with #3672.
+    # Do not target_link_options(gmxapi PRIVATE ${MPI_LINKER_FLAGS})
+    # because the root CMakeLists.txt sets CMAKE_SHARED_LINKER_FLAGS.
+    target_compile_options(gmxapi PUBLIC ${MPI_COMPILE_FLAGS})
+    target_link_libraries(gmxapi PUBLIC ${MPI_CXX_LIBRARIES})

 elseif(GMX_THREAD_MPI)
     # GROMACS is built with its internal thread-MPI implementation.
     set(_gmx_mpi_type "tmpi")
 elseif(GMX_THREAD_MPI)
     # GROMACS is built with its internal thread-MPI implementation.
     set(_gmx_mpi_type "tmpi")

diff --git a/api/nblib/basicdefinitions.h b/api/nblib/basicdefinitions.h
index 41dabd32709734011cd3d048b15dec2e447ce897..ebb4d3f43dcaebaf0d222da17fc6ddf0479197b7 100644 (file)
--- a/api/nblib/basicdefinitions.h
+++ b/api/nblib/basicdefinitions.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) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by

  * Mark Abraham, David van der Spoel, Berk Hess, and 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.


@@ -88,6 +88,11 @@ constexpr const int N_IVEC  = (N_BOX_Z * N_BOX_Y * N_BOX_X);
 //! Needed for generating Bolzmann velocity distribution (kJ/(mol K))
 constexpr const real BOLTZ = (detail::RGAS / detail::KILO); /*  */
 
 //! Needed for generating Bolzmann velocity distribution (kJ/(mol K))
 constexpr const real BOLTZ = (detail::RGAS / detail::KILO); /*  */
 

+#ifndef M_PI
+//! Required work-around for platforms that don't implement POSIX-style cmath header
+#    define M_PI 3.14159265358979323846
+#endif
+

 //! Charge multiplication factor for Coulomb interactions
 constexpr const real ONE_4PI_EPS0 = (1.0 / (4.0 * M_PI * detail::EPSILON0));
 
 //! Charge multiplication factor for Coulomb interactions
 constexpr const real ONE_4PI_EPS0 = (1.0 / (4.0 * M_PI * detail::EPSILON0));
 

diff --git a/cmake/gmxManageNvccConfig.cmake b/cmake/gmxManageNvccConfig.cmake
index 12e54cb40efca94399964c7cff008d92dca0dd38..b5f5663f4c2757ee481d133ef453bdca745072ad 100644 (file)
--- a/cmake/gmxManageNvccConfig.cmake
+++ b/cmake/gmxManageNvccConfig.cmake
@@ -2,7 +2,7 @@
 # This file is part of the GROMACS molecular simulation package.
 #
 # Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
 # This file is part of the GROMACS molecular simulation package.
 #
 # Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.

-# Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by

 # Mark Abraham, David van der Spoel, Berk Hess, and 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.


@@ -101,11 +101,11 @@ if (GMX_CUDA_TARGET_SM OR GMX_CUDA_TARGET_COMPUTE)
 else()
     # Set the CUDA GPU architectures to compile for:
     # - with CUDA >=9.0         CC 7.0 is supported and CC 2.0 is no longer supported
 else()
     # Set the CUDA GPU architectures to compile for:
     # - with CUDA >=9.0         CC 7.0 is supported and CC 2.0 is no longer supported

-    #     => compile sm_30, sm_35, sm_37, sm_50, sm_52, sm_60, sm_61, sm_70 SASS, and compute_70 PTX
+    #     => compile sm_30, sm_35, sm_37, sm_50, sm_52, sm_60, sm_61, sm_70 SASS, and compute_35, compute_70 PTX

     # - with CUDA >=10.0        CC 7.5 is supported
     # - with CUDA >=10.0        CC 7.5 is supported

-    #     => compile sm_30, sm_35, sm_37, sm_50, sm_52, sm_60, sm_61, sm_70, sm_75 SASS, and compute_75 PTX
+    #     => compile sm_30, sm_35, sm_37, sm_50, sm_52, sm_60, sm_61, sm_70, sm_75 SASS, and compute_35, compute_75 PTX

     # - with CUDA >=11.0        CC 8.0 is supported
     # - with CUDA >=11.0        CC 8.0 is supported

-    #     => compile sm_35, sm_37, sm_50, sm_52, sm_60, sm_61, sm_70, sm_75, sm_80 SASS, and compute_80 PTX
+    #     => compile sm_35, sm_37, sm_50, sm_52, sm_60, sm_61, sm_70, sm_75, sm_80 SASS, and compute_35, compute_80 PTX

 
     # First add flags that trigger SASS (binary) code generation for physical arch
     if(CUDA_VERSION VERSION_LESS "11.0")
 
     # First add flags that trigger SASS (binary) code generation for physical arch
     if(CUDA_VERSION VERSION_LESS "11.0")


@@ -118,22 +118,28 @@ else()
     list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_60,code=sm_60")
     list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_61,code=sm_61")
     list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_70,code=sm_70")
     list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_60,code=sm_60")
     list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_61,code=sm_61")
     list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_70,code=sm_70")

+    if(NOT CUDA_VERSION VERSION_LESS "10.0")
+        list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_75,code=sm_75")
+    endif()

     if(NOT CUDA_VERSION VERSION_LESS "11.0")
     if(NOT CUDA_VERSION VERSION_LESS "11.0")

+        list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_80,code=sm_80")

         # Requesting sm or compute 35, 37, or 50 triggers deprecation messages with
         # nvcc 11.0, which we need to suppress for use in CI
         list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-Wno-deprecated-gpu-targets")
     endif()
         # Requesting sm or compute 35, 37, or 50 triggers deprecation messages with
         # nvcc 11.0, which we need to suppress for use in CI
         list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-Wno-deprecated-gpu-targets")
     endif()

+    if(NOT CUDA_VERSION VERSION_LESS "11.1")
+        list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_86,code=sm_86")
+    endif()

 
 

-    # Next add flags that trigger PTX code generation for the newest supported virtual arch
-    # that's useful to JIT to future architectures
+    # Next add flags that trigger PTX code generation for the
+    # newest supported virtual arch that's useful to JIT to future architectures
+    # as well as an older one suitable for JIT-ing to any rare intermediate arch
+    # (like that of Jetson / Drive PX devices)

     list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_35,code=compute_35")
     list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_35,code=compute_35")

-    list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_50,code=compute_50")
-    list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_52,code=compute_52")
-    list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_60,code=compute_60")
-    list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_61,code=compute_61")
-    list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_70,code=compute_70")
-    if(NOT CUDA_VERSION VERSION_LESS "10.0")
-        list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_75,code=compute_75")
+    if(CUDA_VERSION VERSION_LESS "11.0")
+        list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_32,code=compute_32")
+    else()
+        list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_53,code=compute_53")

     endif()
     if(NOT CUDA_VERSION VERSION_LESS "11.0")
         list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_80,code=compute_80")
     endif()
     if(NOT CUDA_VERSION VERSION_LESS "11.0")
         list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_80,code=compute_80")

diff --git a/cmake/gmxTestCompilerProblems.cmake b/cmake/gmxTestCompilerProblems.cmake
index edb8c4714257849e3608ac7a39691016169275c9..620f1767eda7c32b832e6a60faaa169539923fba 100644 (file)
--- a/cmake/gmxTestCompilerProblems.cmake
+++ b/cmake/gmxTestCompilerProblems.cmake
@@ -47,27 +47,27 @@ macro(gmx_test_compiler_problems)
         message(WARNING "The versions of the C and C++ compilers do not match (${CMAKE_C_COMPILER_VERSION} and ${CMAKE_CXX_COMPILER_VERSION}, respectively). Mixing different C/C++ compilers can cause problems.")
     endif()
 
         message(WARNING "The versions of the C and C++ compilers do not match (${CMAKE_C_COMPILER_VERSION} and ${CMAKE_CXX_COMPILER_VERSION}, respectively). Mixing different C/C++ compilers can cause problems.")
     endif()
 

-    # Error if compiler doesn't support required C++14 features.
+    # Error if compiler doesn't support required C++17 features.

     # cmake feature detection is currently inconsistent: gitlab.kitware.com/cmake/cmake/issues/18869
     # cmake feature detection is currently inconsistent: gitlab.kitware.com/cmake/cmake/issues/18869

-    # When we use C++17 we might want to switch to using feature test macros.
+    # We might want to switch to using feature test macros some time.

     if(CMAKE_COMPILER_IS_GNUCXX)
     if(CMAKE_COMPILER_IS_GNUCXX)

-        if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5)
-            set(cxx_required_version "GCC version 5")
+        if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 7)
+            set(cxx_required_version "GCC version 7")

         endif()
     elseif(CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
         if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 19.15)
             set(cxx_required_version "Visual Studio 2017")
         endif()
     elseif(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
         endif()
     elseif(CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
         if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 19.15)
             set(cxx_required_version "Visual Studio 2017")
         endif()
     elseif(CMAKE_CXX_COMPILER_ID MATCHES "Clang")

-        if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 3.6) # For feature complete C++14 only 3.4 is needed.
-            set(cxx_required_version "Clang 3.6")        # But prior version have bugs (e.g. debug symbol support)
+        if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5)
+            set(cxx_required_version "Clang 5")

         endif()
     else()
         endif()
     else()

-        message(WARNING "You are using an unsupported compiler. Please make sure it fully supports C++14.")
+        message(WARNING "You are using an unsupported compiler. Please make sure it fully supports C++17.")

     endif()
     if (cxx_required_version)
         message(FATAL_ERROR "${cxx_required_version} or later required. "
     endif()
     if (cxx_required_version)
         message(FATAL_ERROR "${cxx_required_version} or later required. "

-                            "Earlier versions don't have full C++14 support.")
+                            "Earlier versions don't have full C++17 support.")

     endif()
 
     if (CMAKE_CXX_COMPILER_ID MATCHES "Intel")
     endif()
 
     if (CMAKE_CXX_COMPILER_ID MATCHES "Intel")

diff --git a/docs/reference-manual/plots/GMX_logos/gmx_logo_black.svg b/docs/reference-manual/plots/GMX_logos/gmx_logo_black.svg
index 703166eb70af22bd27d21426545f87cd057b0586..728403c7ea67a6857eef53e181118e2094baba8d 100644 (file)
--- a/docs/reference-manual/plots/GMX_logos/gmx_logo_black.svg
+++ b/docs/reference-manual/plots/GMX_logos/gmx_logo_black.svg
@@ -14,14 +14,14 @@
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-   sodipodi:docname="Gromacs Logo [Blue].svg"
+   sodipodi:docname="gmx_logo_black.svg"

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diff --git a/docs/release-notes/2021/2021.1.rst b/docs/release-notes/2021/2021.1.rst
index 4b884a69f36fa9eb9b694b853ff472924081cfb6..9eb10dae2c77d6be894e25fd730cd5919173cec5 100644 (file)
--- a/docs/release-notes/2021/2021.1.rst
+++ b/docs/release-notes/2021/2021.1.rst
@@ -19,9 +19,34 @@ Fixes where mdrun could behave incorrectly
 Fixes for ``gmx`` tools
 ^^^^^^^^^^^^^^^^^^^^^^^
 
 Fixes for ``gmx`` tools
 ^^^^^^^^^^^^^^^^^^^^^^^
 

+Fix periodic boundary conditions in analysis framework tools
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+There was a bug in the trajectory analysis framework which caused
+molecules that were broken over PBC not to be made whole. This would
+usually lead to obviously incorrect outliers in analysis output.
+
+:issue:`3900`
+
+Fix range checking bug in gmx covar
+"""""""""""""""""""""""""""""""""""
+
+A check was inverted causing range checking to be applied wrong.
+
+:issue:`3902`
+

 Fixes that affect portability
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Fixes that affect portability
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

+Fixed compilation on Cygwin
+"""""""""""""""""""""""""""
+
+A |Gromacs| header file was not including the necessary standard
+header. A problem with the ``M_PI`` math constant defined only by
+POSIX and not by C++ was also worked around.
+
+:issue:`3890`
+

 Miscellaneous
 ^^^^^^^^^^^^^
 Miscellaneous
 ^^^^^^^^^^^^^

-
+* Updated |Gromacs| logos

diff --git a/docs/release-notes/2021/major/miscellaneous.rst b/docs/release-notes/2021/major/miscellaneous.rst
index 91f8cca080fa528083c76d2dd3f0b83960cc83b7..dfa74e3dba3c31f8aedbf15b356520871d58cba4 100644 (file)
--- a/docs/release-notes/2021/major/miscellaneous.rst
+++ b/docs/release-notes/2021/major/miscellaneous.rst
@@ -52,6 +52,7 @@ The environment variables that had exactly the same meaning in OpenCL and CUDA w
 Dysfunctional parts of the QMMM interface has been removed
 """"""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 Dysfunctional parts of the QMMM interface has been removed
 """"""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

-Currently, GROMACS supports QM/MM officially only via MiMiC. All other QM/MM
+Currently, GROMACS supports QM/MM officially only via MiMiC; a new CP2K QM/MM interface is being
+developed within BioExcel. All other QM/MM

 support has been untested and likely dysfunctional for years and has now been removed from .mdp
 input and output, resulting in smaller .mdp output files from grompp.
 support has been untested and likely dysfunctional for years and has now been removed from .mdp
 input and output, resulting in smaller .mdp output files from grompp.

diff --git a/src/external/CMakeLists.txt b/src/external/CMakeLists.txt
index e850736ec45f0a4c378bb7cea7d87b0b29b8c2da..57f73c60d0e3247a737c8a64f3a47f5eeccdd8d1 100644 (file)
--- a/src/external/CMakeLists.txt
+++ b/src/external/CMakeLists.txt
@@ -61,8 +61,9 @@ if(BUILD_TESTING AND GMX_BUILD_UNITTESTS)
             )
     target_compile_definitions(gtest PUBLIC GTEST_LANG_CXX11)
     if (CYGWIN)
             )
     target_compile_definitions(gtest PUBLIC GTEST_LANG_CXX11)
     if (CYGWIN)

-        # Ensure GoogleTest can find POSIX things it needs
-        target_compile_definitions(gtest PRIVATE _POSIX_C_SOURCE=200809L)
+        # Ensure GoogleTest and things that use it can find
+        # POSIX things needed by GoogleTest
+        target_compile_definitions(gtest PUBLIC _POSIX_C_SOURCE=200809L)

     endif()
     gmx_target_warning_suppression(gmock -Wno-deprecated-copy HAVE_NO_DEPRECATED_COPY)
 
     endif()
     gmx_target_warning_suppression(gmock -Wno-deprecated-copy HAVE_NO_DEPRECATED_COPY)
 

diff --git a/src/gromacs/domdec/partition.cpp b/src/gromacs/domdec/partition.cpp
index 06b4937cafcf0a6c98e288a5a8c1664b6c0734de..dca7464ba7813544b4d0aea99718e05943b74028 100644 (file)
--- a/src/gromacs/domdec/partition.cpp
+++ b/src/gromacs/domdec/partition.cpp
@@ -1125,7 +1125,7 @@ static void print_dd_load_av(FILE* fplog, gmx_domdec_t* dd)
     fprintf(fplog, "\n");
     fprintf(stderr, "\n");
 
     fprintf(fplog, "\n");
     fprintf(stderr, "\n");
 

-    if (lossFraction >= DD_PERF_LOSS_WARN)
+    if ((lossFraction >= DD_PERF_LOSS_WARN) && (dd->comm->dlbState != DlbState::offTemporarilyLocked))

     {
         std::string message = gmx::formatString(
                 "NOTE: %.1f %% of the available CPU time was lost due to load imbalance\n"
     {
         std::string message = gmx::formatString(
                 "NOTE: %.1f %% of the available CPU time was lost due to load imbalance\n"


@@ -1133,9 +1133,16 @@ static void print_dd_load_av(FILE* fplog, gmx_domdec_t* dd)
                 lossFraction * 100);
 
         bool hadSuggestion = false;
                 lossFraction * 100);
 
         bool hadSuggestion = false;

-        if (!isDlbOn(comm))
+        if (dd->comm->dlbState == DlbState::offUser)

         {
         {

-            message += "      You might want to use dynamic load balancing (option -dlb.)\n";
+            message += "      You might want to allow dynamic load balancing (option -dlb auto.)\n";
+            hadSuggestion = true;
+        }
+        else if (dd->comm->dlbState == DlbState::offCanTurnOn)
+        {
+            message +=
+                    "      Dynamic load balancing was automatically disabled, but it might be "
+                    "beneficial to manually tuning it on (option -dlb on.)\n";

             hadSuggestion = true;
         }
         else if (dlbWasLimited)
             hadSuggestion = true;
         }
         else if (dlbWasLimited)


@@ -1151,7 +1158,6 @@ static void print_dd_load_av(FILE* fplog, gmx_domdec_t* dd)
                 "      considerable inhomogeneity in the simulated system.",
                 hadSuggestion ? "also " : "");
 
                 "      considerable inhomogeneity in the simulated system.",
                 hadSuggestion ? "also " : "");
 

-

         fprintf(fplog, "%s\n", message.c_str());
         fprintf(stderr, "%s\n", message.c_str());
     }
         fprintf(fplog, "%s\n", message.c_str());
         fprintf(stderr, "%s\n", message.c_str());
     }

diff --git a/src/gromacs/gmxana/gmx_covar.cpp b/src/gromacs/gmxana/gmx_covar.cpp
index a6a07535cac1a49034a085c2fcd2c787c59086b4..33c3fae1bc9bd96a9e3f53ec7756792af671354b 100644 (file)
--- a/src/gromacs/gmxana/gmx_covar.cpp
+++ b/src/gromacs/gmxana/gmx_covar.cpp
@@ -4,7 +4,7 @@
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
  * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
  * 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.

- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by

  * Mark Abraham, David van der Spoel, Berk Hess, and 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.


@@ -73,27 +73,25 @@ namespace
 /*! \brief Throw an error if any element in index exceeds a given number.
  *
  * \param[in] indices to be acessed
 /*! \brief Throw an error if any element in index exceeds a given number.
  *
  * \param[in] indices to be acessed

- * \param[in] largestOkayIndex to be accessed
+ * \param[in] numAtoms to be accessed

  * \param[in] indexUsagePurpose to be more explicit in the error message
  *
  * \param[in] indexUsagePurpose to be more explicit in the error message
  *

- * \throws RangeError if largestOkayIndex is larger than any element in indices
+ * \throws RangeError if any element in indices is larger than or equal numAtoms

  *
  */
  *
  */

-void throwErrorIfIndexOutOfBounds(ArrayRef<const int> indices,
-                                  const int           largestOkayIndex,
-                                  const std::string&  indexUsagePurpose)
+void throwErrorIfIndexOutOfBounds(ArrayRef<const int> indices, const int numAtoms, const std::string& indexUsagePurpose)

 {
     // do nothing if index is empty
 {
     // do nothing if index is empty

-    if (indices.ssize() == 0)
+    if (indices.empty())

     {
         return;
     }
     const int largestIndex = *std::max_element(indices.begin(), indices.end());
     {
         return;
     }
     const int largestIndex = *std::max_element(indices.begin(), indices.end());

-    if (largestIndex < largestOkayIndex)
+    if (largestIndex >= numAtoms)

     {
     {

-        GMX_THROW(RangeError("The provided structure file only contains "
-                             + std::to_string(largestOkayIndex) + " coordinates, but coordinate index "
-                             + std::to_string(largestIndex) + " was requested for " + indexUsagePurpose
+        GMX_THROW(RangeError("The provided structure file only contains " + std::to_string(numAtoms)
+                             + " coordinates, but coordinate index " + std::to_string(largestIndex + 1)
+                             + " was requested for " + indexUsagePurpose

                              + ". Make sure to update structure files "
                                "and index files if you store only a part of your system."));
     }
                              + ". Make sure to update structure files "
                                "and index files if you store only a part of your system."));
     }

diff --git a/src/gromacs/gmxpreprocess/genhydro.cpp b/src/gromacs/gmxpreprocess/genhydro.cpp
index af370d5e719ff270ea3f530b5f19613a715c3151..5ee31602a3bfa2be660374604f57ac2c7cc4d479 100644 (file)
--- a/src/gromacs/gmxpreprocess/genhydro.cpp
+++ b/src/gromacs/gmxpreprocess/genhydro.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) 2013-2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2013-2019,2020,2021, by the GROMACS development team, led by

  * Mark Abraham, David van der Spoel, Berk Hess, and 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.


@@ -80,6 +80,21 @@ static int pdbasearch_atom(const char*              name,
     return search_atom(name, i, pdba, searchtype, bAllowMissing, cyclicBondsIndex);
 }
 
     return search_atom(name, i, pdba, searchtype, bAllowMissing, cyclicBondsIndex);
 }
 

+/*! \brief Return the index of the first atom whose residue index
+ * matches and which has a patch with the given name.
+ *
+ * \param[out] ii      Index of the first atom in the residue that matches,
+ *                       -1 if no match occurs.
+ * \param[out] jj      Index of the patch that matches,
+ *                       unchanged if no match occurs.
+ * \param[in]  name    Name of the desired patch to match
+ * \param[in]  patches The patch database to search
+ * \param[in]  resind  The residue index to match
+ * \param[in]  pdba    The atoms to work with
+ *
+ * \todo The short-circuit logic will be simpler if this returned a
+ * std::pair<int, int> as soon as the first double match is found.
+ */

 static void hacksearch_atom(int*                                            ii,
                             int*                                            jj,
                             const char*                                     name,
 static void hacksearch_atom(int*                                            ii,
                             int*                                            jj,
                             const char*                                     name,


@@ -105,6 +120,10 @@ static void hacksearch_atom(int*                                            ii,
             {
                 *ii = i;
                 *jj = j;
             {
                 *ii = i;
                 *jj = j;

+                if (*ii >= 0)
+                {
+                    break;
+                }

             }
             j++;
         }
             }
             j++;
         }


@@ -220,8 +239,11 @@ static void expand_hackblocks_one(const MoleculePatchDatabase& newPatch,
                 if (singlePatch.tp == 10 && k == 2)
                 {
                     /* This is a water virtual site, not a hydrogen */
                 if (singlePatch.tp == 10 && k == 2)
                 {
                     /* This is a water virtual site, not a hydrogen */

-                    /* Ugly hardcoded name hack */
-                    patch->nname.assign("M");
+                    /* Ugly hardcoded name hack to replace 'H' with 'M' */
+                    GMX_RELEASE_ASSERT(
+                            !patch->nname.empty() && patch->nname[0] == 'H',
+                            "Water virtual site should be named starting with H at this point");
+                    patch->nname[0] = 'M';

                 }
                 else if (singlePatch.tp == 11 && k >= 2)
                 {
                 }
                 else if (singlePatch.tp == 11 && k >= 2)
                 {

diff --git a/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp b/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
index f9bac4c8282411917c0e7fab95b2b0bbd5017e09..fd5fcfc7c69d58ac41f721eb330ecf515c0599ce 100644 (file)
--- a/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
+++ b/src/gromacs/gmxpreprocess/tests/pdb2gmx.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) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by

  * Mark Abraham, David van der Spoel, Berk Hess, and 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.


@@ -65,7 +65,7 @@ using test::CommandLine;
 
 //! Test parameter struct.
 using CommandLineOptionParams =
 
 //! Test parameter struct.
 using CommandLineOptionParams =

-        std::tuple<std::string, std::string, std::string, std::string, std::string, std::string, int>;
+        std::tuple<std::string, std::string, std::string, std::string, std::string, std::string, int, bool>;

 
 /*! \brief Strings containing regular expressions for lines to skip
  * when matching.
 
 /*! \brief Strings containing regular expressions for lines to skip
  * when matching.


@@ -94,6 +94,8 @@ public:
     Pdb2gmxTest()
     {
         int outputFileType = std::get<6>(GetParam());
     Pdb2gmxTest()
     {
         int outputFileType = std::get<6>(GetParam());

+        // If the file type of the output configuration is one
+        // commonly used (ie. pdb, gro), then check its content.

         if (outputFileType == efPDB)
         {
             // If we're writing PDB output, we are interested in
         if (outputFileType == efPDB)
         {
             // If we're writing PDB output, we are interested in


@@ -103,9 +105,9 @@ public:
             ExactTextMatch settings;
             setOutputFile("-o", outputfile.c_str(), TextFileMatch(settings));
         }
             ExactTextMatch settings;
             setOutputFile("-o", outputfile.c_str(), TextFileMatch(settings));
         }

-        else
+        else if (outputFileType == efGRO)

         {
         {

-            setOutputFile("-o", "conf.gro", ConfMatch());
+            setOutputFile("-o", "conf.gro", ConfMatch().matchFullConfiguration(std::get<7>(GetParam())));

         }
         setOutputFile("-p", "topol.top", TextFileMatch(c_textMatcher));
     }
         }
         setOutputFile("-p", "topol.top", TextFileMatch(c_textMatcher));
     }


@@ -151,7 +153,8 @@ INSTANTIATE_TEST_CASE_P(ForOplsaa,
                                                              "fragment2.pdb",
                                                              "fragment3.pdb",
                                                              "fragment4.pdb"),
                                                              "fragment2.pdb",
                                                              "fragment3.pdb",
                                                              "fragment4.pdb"),

-                                           ::testing::Values(efGRO)));
+                                           ::testing::Values(efGRO),
+                                           ::testing::Values(false)));

 #endif
 
 #if GROMOS
 #endif
 
 #if GROMOS


@@ -166,7 +169,8 @@ INSTANTIATE_TEST_CASE_P(ForGromos43a1,
                                                              "fragment2.pdb",
                                                              "fragment3.pdb",
                                                              "fragment4.pdb"),
                                                              "fragment2.pdb",
                                                              "fragment3.pdb",
                                                              "fragment4.pdb"),

-                                           ::testing::Values(efGRO)));
+                                           ::testing::Values(efGRO),
+                                           ::testing::Values(false)));

 
 INSTANTIATE_TEST_CASE_P(ForGromos53a6,
                         Pdb2gmxTest,
 
 INSTANTIATE_TEST_CASE_P(ForGromos53a6,
                         Pdb2gmxTest,


@@ -179,7 +183,8 @@ INSTANTIATE_TEST_CASE_P(ForGromos53a6,
                                                              "fragment2.pdb",
                                                              "fragment3.pdb",
                                                              "fragment4.pdb"),
                                                              "fragment2.pdb",
                                                              "fragment3.pdb",
                                                              "fragment4.pdb"),

-                                           ::testing::Values(efGRO)));
+                                           ::testing::Values(efGRO),
+                                           ::testing::Values(false)));

 #endif
 
 #if AMBER
 #endif
 
 #if AMBER


@@ -194,7 +199,18 @@ INSTANTIATE_TEST_CASE_P(ForAmber99sb_ildn,
                                                              "fragment2.pdb",
                                                              "fragment3.pdb",
                                                              "fragment4.pdb"),
                                                              "fragment2.pdb",
                                                              "fragment3.pdb",
                                                              "fragment4.pdb"),

-                                           ::testing::Values(efGRO)));
+                                           ::testing::Values(efGRO),
+                                           ::testing::Values(false)));
+INSTANTIATE_TEST_CASE_P(ForAmber99sb_ildnWithTip4p,
+                        Pdb2gmxTest,
+                        ::testing::Combine(::testing::Values("amber99sb-ildn"),
+                                           ::testing::Values("tip4p"),
+                                           ::testing::Values("none"),
+                                           ::testing::Values("id_or_ter"),
+                                           ::testing::Values("no"),
+                                           ::testing::Values("tip4p.pdb"),
+                                           ::testing::Values(efGRO),
+                                           ::testing::Values(true)));

 #endif
 
 #if CHARMM
 #endif
 
 #if CHARMM


@@ -209,7 +225,8 @@ INSTANTIATE_TEST_CASE_P(ForCharmm27,
                                                              "fragment2.pdb",
                                                              "fragment3.pdb",
                                                              "fragment4.pdb"),
                                                              "fragment2.pdb",
                                                              "fragment3.pdb",
                                                              "fragment4.pdb"),

-                                           ::testing::Values(efGRO)));
+                                           ::testing::Values(efGRO),
+                                           ::testing::Values(false)));

 
 
 INSTANTIATE_TEST_CASE_P(ChainSep,
 
 
 INSTANTIATE_TEST_CASE_P(ChainSep,


@@ -220,7 +237,8 @@ INSTANTIATE_TEST_CASE_P(ChainSep,
                                            ::testing::Values("id", "ter", "id_or_ter", "id_and_ter"),
                                            ::testing::Values("all", "no"),
                                            ::testing::Values("chainTer.pdb"),
                                            ::testing::Values("id", "ter", "id_or_ter", "id_and_ter"),
                                            ::testing::Values("all", "no"),
                                            ::testing::Values("chainTer.pdb"),

-                                           ::testing::Values(efGRO)));
+                                           ::testing::Values(efGRO),
+                                           ::testing::Values(false)));

 
 INSTANTIATE_TEST_CASE_P(ChainChanges,
                         Pdb2gmxTest,
 
 INSTANTIATE_TEST_CASE_P(ChainChanges,
                         Pdb2gmxTest,


@@ -230,7 +248,8 @@ INSTANTIATE_TEST_CASE_P(ChainChanges,
                                            ::testing::Values("id", "ter", "id_or_ter", "id_and_ter"),
                                            ::testing::Values("no"),
                                            ::testing::Values("two-fragments.pdb"),
                                            ::testing::Values("id", "ter", "id_or_ter", "id_and_ter"),
                                            ::testing::Values("no"),
                                            ::testing::Values("two-fragments.pdb"),

-                                           ::testing::Values(efPDB)));
+                                           ::testing::Values(efPDB),
+                                           ::testing::Values(false)));

 
 INSTANTIATE_TEST_CASE_P(ForCharmm27CyclicSystem,
                         Pdb2gmxTest,
 
 INSTANTIATE_TEST_CASE_P(ForCharmm27CyclicSystem,
                         Pdb2gmxTest,


@@ -241,7 +260,8 @@ INSTANTIATE_TEST_CASE_P(ForCharmm27CyclicSystem,
                                            ::testing::Values("no", "all"),
                                            ::testing::Values("cyclic-rna.pdb",
                                                              "cyclic-protein-small.pdb"),
                                            ::testing::Values("no", "all"),
                                            ::testing::Values("cyclic-rna.pdb",
                                                              "cyclic-protein-small.pdb"),

-                                           ::testing::Values(efGRO)));
+                                           ::testing::Values(efGRO),
+                                           ::testing::Values(false)));

 #endif
 
 } // namespace
 #endif
 
 } // namespace

diff --git a/src/gromacs/gmxpreprocess/tests/refdata/ForAmber99sb_ildnWithTip4p_Pdb2gmxTest_ProducesMatchingTopology_0.xml b/src/gromacs/gmxpreprocess/tests/refdata/ForAmber99sb_ildnWithTip4p_Pdb2gmxTest_ProducesMatchingTopology_0.xml
new file mode 100644 (file)
index 0000000..de032d5
--- /dev/null
+++ b/src/gromacs/gmxpreprocess/tests/refdata/ForAmber99sb_ildnWithTip4p_Pdb2gmxTest_ProducesMatchingTopology_0.xml
@@ -0,0 +1,60 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+  <OutputFiles Name="Files">
+    <File Name="-o">
+      <GroFile Name="Header">
+        <String Name="Title">TIP4p ice to test that MW is handled correctly</String>
+        <Int Name="Number of atoms">8</Int>
+      </GroFile>
+      <String Name="Configuration"><![CDATA[
+    1HO4     OW    1  -2.474  -5.526  -0.497
+    1HO4    HW1    2  -2.393  -5.526  -0.439
+    1HO4    HW2    3  -2.556  -5.526  -0.439
+    1HO4     MW    4  -2.484  -5.527  -0.485
+    2HO4     OW    5  -2.496  -5.242  -0.878
+    2HO4    HW1    6  -2.415  -5.242  -0.820
+    2HO4    HW2    7  -2.496  -5.160  -0.936
+    2HO4     MW    8  -2.482  -5.239  -0.874
+   0.16330   0.36715   0.49637
+]]></String>
+    </File>
+    <File Name="-p">
+      <String Name="Contents"><![CDATA[
+;
+;
+;      This is a standalone topology file
+;
+;      Created by:
+;      
+;      Command line:
+;      Force field was read from the standard GROMACS share directory.
+;
+
+; Include forcefield parameters
+#include "amber99sb-ildn.ff/forcefield.itp"
+
+; Include water topology
+#include "amber99sb-ildn.ff/tip4p.itp"
+
+#ifdef POSRES_WATER
+; Position restraint for each water oxygen
+[ position_restraints ]
+;  i funct       fcx        fcy        fcz
+   1    1       1000       1000       1000
+#endif
+
+; Include topology for ions
+#include "amber99sb-ildn.ff/ions.itp"
+
+[ system ]
+; Name
+TIP4p ice to test that MW is handled correctly
+
+[ molecules ]
+; Compound        #mols
+SOL                 2
+]]></String>
+    </File>
+  </OutputFiles>
+</ReferenceData>

diff --git a/src/gromacs/gmxpreprocess/tests/tip4p.pdb b/src/gromacs/gmxpreprocess/tests/tip4p.pdb
new file mode 100644 (file)
index 0000000..eb55c00
--- /dev/null
+++ b/src/gromacs/gmxpreprocess/tests/tip4p.pdb
@@ -0,0 +1,9 @@
+TITLE     TIP4p ice to test that MW is handled correctly
+ATOM      1  OW  SOL A   1     -24.744 -55.257  -4.969  1.00  1.00      A    O
+ATOM      2  HW1 SOL A   1     -25.692 -55.390  -4.996  1.00  0.00      A    H
+ATOM      3  HW2 SOL A   1     -24.532 -55.232  -4.035  1.00  0.00      A    H
+ATOM      4  MW  SOL A   1     -24.838 -55.271  -4.853  1.00  0.00      A    O
+ATOM      5  OW  SOL A   2     -24.964 -52.416  -8.778  1.00  1.00      A    O
+ATOM      6  HW1 SOL A   2     -24.502 -52.770  -8.018  1.00  0.00      A    H
+ATOM      7  HW2 SOL A   2     -24.314 -51.874  -9.224  1.00  0.00      A    H
+ATOM      8  MW  SOL A   2     -24.822 -52.393  -8.738  1.00  0.00      A    O

diff --git a/src/gromacs/mdlib/stat.h b/src/gromacs/mdlib/stat.h
index d3cf97713abce87ee2e31c8095b5926a31d7ba78..ad7c7657e761a775aa3e930aaa9f4686978c97cc 100644 (file)
--- a/src/gromacs/mdlib/stat.h
+++ b/src/gromacs/mdlib/stat.h
@@ -39,6 +39,8 @@
 #ifndef GMX_MDLIB_STAT_H
 #define GMX_MDLIB_STAT_H
 
 #ifndef GMX_MDLIB_STAT_H
 #define GMX_MDLIB_STAT_H
 

+#include <cstdint>
+

 #include "gromacs/math/vectypes.h"
 
 struct gmx_ekindata_t;
 #include "gromacs/math/vectypes.h"
 
 struct gmx_ekindata_t;

diff --git a/src/gromacs/nbnxm/gpu_types_common.h b/src/gromacs/nbnxm/gpu_types_common.h
index 57d791be2a85f7d4945f9bd1db2173336ee677ee..2d2e90791e9833d227ee3640ab0483086da09da0 100644 (file)
--- a/src/gromacs/nbnxm/gpu_types_common.h
+++ b/src/gromacs/nbnxm/gpu_types_common.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) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by

  * Mark Abraham, David van der Spoel, Berk Hess, and 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.


@@ -212,11 +212,11 @@ struct gpu_plist
     int excl_nalloc;
 
     /* parameter+variables for normal and rolling pruning */
     int excl_nalloc;
 
     /* parameter+variables for normal and rolling pruning */

-    //! true after search, indictes that initial pruning with outer prunning is needed
+    //! true after search, indicates that initial pruning with outer pruning is needed

     bool haveFreshList;
     bool haveFreshList;

-    //! the number of parts/steps over which one cyle of roling pruning takes places
+    //! the number of parts/steps over which one cycle of rolling pruning takes places

     int rollingPruningNumParts;
     int rollingPruningNumParts;

-    //! the next part to which the roling pruning needs to be applied
+    //! the next part to which the rolling pruning needs to be applied

     int rollingPruningPart;
 };
 
     int rollingPruningPart;
 };
 

diff --git a/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp b/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp
index 2a2a394cae417fba976f71d7637425057d8dee48..9fe755c586006afabb0849d592cbd4fece5e83d5 100644 (file)
--- a/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp
+++ b/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp
@@ -191,16 +191,18 @@ void init_plist(gpu_plist* pl)
     pl->excl  = nullptr;
 
     /* size -1 indicates that the respective array hasn't been initialized yet */
     pl->excl  = nullptr;
 
     /* size -1 indicates that the respective array hasn't been initialized yet */

-    pl->na_c          = -1;
-    pl->nsci          = -1;
-    pl->sci_nalloc    = -1;
-    pl->ncj4          = -1;
-    pl->cj4_nalloc    = -1;
-    pl->nimask        = -1;
-    pl->imask_nalloc  = -1;
-    pl->nexcl         = -1;
-    pl->excl_nalloc   = -1;
-    pl->haveFreshList = false;
+    pl->na_c                   = -1;
+    pl->nsci                   = -1;
+    pl->sci_nalloc             = -1;
+    pl->ncj4                   = -1;
+    pl->cj4_nalloc             = -1;
+    pl->nimask                 = -1;
+    pl->imask_nalloc           = -1;
+    pl->nexcl                  = -1;
+    pl->excl_nalloc            = -1;
+    pl->haveFreshList          = false;
+    pl->rollingPruningNumParts = 0;
+    pl->rollingPruningPart     = 0;

 }
 
 void init_timings(gmx_wallclock_gpu_nbnxn_t* t)
 }
 
 void init_timings(gmx_wallclock_gpu_nbnxn_t* t)

diff --git a/src/gromacs/pbcutil/rmpbc.cpp b/src/gromacs/pbcutil/rmpbc.cpp
index ee79717113fd60a3c101a52c99a8484aa7025082..9f8f591dd7e92f6509d05d9afc341c157f192817 100644 (file)
--- a/src/gromacs/pbcutil/rmpbc.cpp
+++ b/src/gromacs/pbcutil/rmpbc.cpp
@@ -4,7 +4,7 @@
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
  * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
  * 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.

- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by

  * Mark Abraham, David van der Spoel, Berk Hess, and 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.


@@ -76,7 +76,8 @@ static t_graph* gmx_rmpbc_get_graph(gmx_rmpbc_t gpbc, PbcType pbcType, int natom
     int            i;
     rmpbc_graph_t* gr;
 
     int            i;
     rmpbc_graph_t* gr;
 

-    if (pbcType == PbcType::No || nullptr == gpbc || nullptr == gpbc->idef || gpbc->idef->ntypes <= 0)
+    if (pbcType == PbcType::No || nullptr == gpbc
+        || (nullptr == gpbc->interactionDefinitions && (nullptr == gpbc->idef || gpbc->idef->ntypes <= 0)))

     {
         return nullptr;
     }
     {
         return nullptr;
     }

diff --git a/src/testutils/conftest.cpp b/src/testutils/conftest.cpp
index 3fd50276cbfc93c058bef27e6c502842c4c94ca5..c9fe48523467e426b889df9df362528f6ec073e7 100644 (file)
--- a/src/testutils/conftest.cpp
+++ b/src/testutils/conftest.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) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by

  * Mark Abraham, David van der Spoel, Berk Hess, and 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.


@@ -48,6 +48,7 @@
 
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/stringutil.h"
 
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/stringutil.h"

+#include "gromacs/utility/textreader.h"

 #include "gromacs/utility/textstream.h"
 
 #include "testutils/refdata.h"
 #include "gromacs/utility/textstream.h"
 
 #include "testutils/refdata.h"


@@ -79,11 +80,11 @@ private:
 
 } // namespace
 
 
 } // namespace
 

-void checkConfFile(TextInputStream* input, TestReferenceChecker* checker, const ConfMatchSettings& /*unused*/)
+void checkConfFile(TextInputStream* input, TestReferenceChecker* checker, const ConfMatchSettings& settings)

 {
 
     TestReferenceChecker groChecker(checker->checkCompound("GroFile", "Header"));
 {
 
     TestReferenceChecker groChecker(checker->checkCompound("GroFile", "Header"));

-    // Just check the first two lines of the output file
+    // Check the first two lines of the output file

     std::string line;
     EXPECT_TRUE(input->readLine(&line));
     line = stripSuffixIfPresent(line, "\n");
     std::string line;
     EXPECT_TRUE(input->readLine(&line));
     line = stripSuffixIfPresent(line, "\n");


@@ -91,6 +92,12 @@ void checkConfFile(TextInputStream* input, TestReferenceChecker* checker, const
     EXPECT_TRUE(input->readLine(&line));
     line = stripSuffixIfPresent(line, "\n");
     groChecker.checkInteger(std::atoi(line.c_str()), "Number of atoms");
     EXPECT_TRUE(input->readLine(&line));
     line = stripSuffixIfPresent(line, "\n");
     groChecker.checkInteger(std::atoi(line.c_str()), "Number of atoms");

+    // Check the full configuration only if required
+    if (settings.matchFullConfiguration)
+    {
+        TextReader reader(input);
+        checker->checkTextBlock(reader.readAll(), "Configuration");
+    }

 }
 
 TextBlockMatcherPointer ConfMatch::createMatcher() const
 }
 
 TextBlockMatcherPointer ConfMatch::createMatcher() const

diff --git a/src/testutils/include/testutils/conftest.h b/src/testutils/include/testutils/conftest.h
index d22033c53790bfc697fb2293077da3e9863bb1ea..144a60f436ef66d9c74cf9d9f85529d13329efc4 100644 (file)
--- a/src/testutils/include/testutils/conftest.h
+++ b/src/testutils/include/testutils/conftest.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) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by

  * Mark Abraham, David van der Spoel, Berk Hess, and 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.


@@ -60,9 +60,8 @@ class TestReferenceChecker;
 
 struct ConfMatchSettings
 {
 
 struct ConfMatchSettings
 {

-    ConfMatchSettings() : tolerance(defaultRealTolerance()) {}
-
-    FloatingPointTolerance tolerance;
+    FloatingPointTolerance tolerance              = defaultRealTolerance();
+    bool                   matchFullConfiguration = false;

 };
 
 /*! \brief
 };
 
 /*! \brief


@@ -96,6 +95,12 @@ public:
         settings_.tolerance = tolerance;
         return *this;
     }
         settings_.tolerance = tolerance;
         return *this;
     }

+    //! Sets whether the full file contents should be matched
+    ConfMatch& matchFullConfiguration(const bool flag)
+    {
+        settings_.matchFullConfiguration = flag;
+        return *this;
+    }

 
     TextBlockMatcherPointer createMatcher() const override;
 
 
     TextBlockMatcherPointer createMatcher() const override;