Merge remote-tracking branch 'origin/release-2021' into merge-2021-into-master

Resolved conflicts:
 - cmake/gmxVersionInfo.cmake
 - docs/CMakeLists.txt
 - python_packaging/src/gmxapi/export_system.cpp
 - python_packaging/src/setup.py
 - src/gromacs/domdec/domdec.cpp
 - src/gromacs/gmxana/gmx_chi.cpp

diff --git a/cmake/gmxVersionInfo.cmake b/cmake/gmxVersionInfo.cmake
index 185f9f0e501690faebe458641fe7e700b5ad5fa0..c4485a330f4951445b192353fb0abcb689a7b7a2 100644 (file)
--- a/cmake/gmxVersionInfo.cmake
+++ b/cmake/gmxVersionInfo.cmake
@@ -263,7 +263,7 @@ set(REGRESSIONTEST_BRANCH "master")
 # build the regressiontests tarball with all the right naming. The
 # naming affects the md5sum that has to go here, and if it isn't right
 # release workflow will report a failure.
-set(REGRESSIONTEST_MD5SUM "62606f5f6ea37f6114b6e9cf58218f13" CACHE INTERNAL "MD5 sum of the regressiontests tarball for this GROMACS version")
+set(REGRESSIONTEST_MD5SUM "93956ea42c4d16fdd541518c05972989" CACHE INTERNAL "MD5 sum of the regressiontests tarball for this GROMACS version")
 
 math(EXPR GMX_VERSION_NUMERIC
      "${GMX_VERSION_MAJOR}*10000 + ${GMX_VERSION_PATCH}")

diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt
index 468c8ed31a43d6c7bcc1a145c76d69f5a9b37591..6eefe6ed5f2788a59b00f363389633587d196dec 100644 (file)
--- a/docs/CMakeLists.txt
+++ b/docs/CMakeLists.txt
@@ -374,6 +374,7 @@ if (SPHINX_FOUND)
         release-notes/2022/major/portability.rst
         release-notes/2022/major/miscellaneous.rst
         release-notes/2022/major/api.rst
+        release-notes/2021/2021.4.rst
         release-notes/2021/2021.3.rst
         release-notes/2021/2021.2.rst
         release-notes/2021/2021.1.rst

diff --git a/docs/reference-manual/analysis/curve-fitting.rst b/docs/reference-manual/analysis/curve-fitting.rst
index dafc3eb2e6be70094ec74ad4f8b318fa38efb194..e3650f8bd942dbcffb4fa5de9bc894fd4dc9d7ed 100644 (file)
--- a/docs/reference-manual/analysis/curve-fitting.rst
+++ b/docs/reference-manual/analysis/curve-fitting.rst
@@ -58,8 +58,8 @@ Under the hood |Gromacs| implements some more fitting functions, namely a
 function to estimate the error in time-correlated data due to Hess \ :ref:`149 <refHess2002a>`:
 
 .. math:: \varepsilon^2(t) =
-          \alpha\tau_1\left(1+\frac{\tau_1}{t}\left(e^{-t/\tau_1}-1\right)\right)
-                + (1-\alpha)\tau_2\left(1+\frac{\tau_2}{t}\left(e^{-t/\tau_2}-1\right)\right)
+          2 \alpha\tau_1\left(1+\frac{\tau_1}{t}\left(e^{-t/\tau_1}-1\right)\right)
+                + 2 (1-\alpha)\tau_2\left(1+\frac{\tau_2}{t}\left(e^{-t/\tau_2}-1\right)\right)
           :label: eqntimecorrerror
 
 where :math:`\tau_1` and :math:`\tau_2` are time constants (with

diff --git a/docs/release-notes/2021/2021.3.rst b/docs/release-notes/2021/2021.3.rst
index a9cccf969c0043e85d35b2c822bb2e5ba10a0022..1ca55184edda04fa11b8112340c27c6204837d97 100644 (file)
--- a/docs/release-notes/2021/2021.3.rst
+++ b/docs/release-notes/2021/2021.3.rst
@@ -1,7 +1,7 @@
 GROMACS 2021.3 release notes
 ----------------------------
 
-This version was released on TODO, 2021. These release notes
+This version was released on August 18th, 2021. These release notes
 document the changes that have taken place in GROMACS since the
 previous 2021.2 version, to fix known issues. It also incorporates all
 fixes made in version 2020.6 and earlier, which you can find described
@@ -16,6 +16,14 @@ in the :ref:`release-notes`.
 Fixes where mdrun could behave incorrectly
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
+Fix mdrun -ddorder pp_pme
+"""""""""""""""""""""""""
+
+When rank ordering PP-PME, mdrun would deadlock during the initialization
+phase.
+
+:issue:`4114`
+
 Fixed gmxapi MD plugin binding
 """"""""""""""""""""""""""""""
 
@@ -24,12 +32,27 @@ simulation through the gmxapi Python interface.
 This meant that restraint potentials would silently fail to be applied with
 gmxapi versions >= 0.1.
 Updates have been applied internally to gmxapi.
+
+The gmxapi 0.2.2 Python package supports the updated GROMACS API and will
+issue errors if a simulation attempts to bind external plugin code with
+a compatible-but-broken API (GROMACS 2021 through 2021.2).
+
 Third party code should not need to be updated, but developers will
 note an additional "null restraint" in
 https://gitlab.com/gromacs/gromacs/-/tree/master/python_packaging/sample_restraint
 (for illustration and testing purposes).
 
-:issue:`4078`
+:issue:`4078` and :issue:`4102`
+
+Fixed multi-rank restarts from checkpoints written by single-rank simulations
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+Currently a single-rank simulation never uses update groups, however a
+multi-rank run can do so. This fix ensures that the atoms within
+update groups always start in the same periodic image, which was not
+guaranteed if the checkpoint was written by a single-rank simulation.
+
+:issue:`4016`
 
 Fixes for ``gmx`` tools
 ^^^^^^^^^^^^^^^^^^^^^^^
@@ -57,6 +80,28 @@ calculate the number of remaining steps correctly.
 
 :issue:`4056`
 
+Fixed dihedral transition counting in gmx chi and gmx angle
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+When a trajectory of only 1 frame is passed, transition counting is
+avoided (formerly it was attempted and crashed).
+
+When a trajectory of multiple frames is passed, transition counting is
+correct (formerly it did not take place).
+
+Fixed possible crash in gmx chi histogramming
+"""""""""""""""""""""""""""""""""""""""""""""
+
+Formerly an invalid reference to a temporary string was used for a
+residue name, which might have caused a crash.
+
+Fixed gmx chi -chi_prod
+"""""""""""""""""""""""
+
+Formerly it could crash or produce garbage results when the number of
+relevant dihedrals differed from the number of residues
+with dihedrals.
+
 Fixes that affect portability
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

diff --git a/docs/release-notes/2021/2021.4.rst b/docs/release-notes/2021/2021.4.rst
new file mode 100644 (file)
index 0000000..f2d3319
--- /dev/null
+++ b/docs/release-notes/2021/2021.4.rst
@@ -0,0 +1,27 @@
+GROMACS 2021.4 release notes
+----------------------------
+
+This version was released on TODO, 2021. These release notes
+document the changes that have taken place in GROMACS since the
+previous 2021.3 version, to fix known issues. It also incorporates all
+fixes made in version 2020.6 and earlier, which you can find described
+in the :ref:`release-notes`.
+
+.. Note to developers!
+   Please use """"""" to underline the individual entries for fixed issues in the subfolders,
+   otherwise the formatting on the webpage is messed up.
+   Also, please use the syntax :issue:`number` to reference issues on GitLab, without the
+   a space between the colon and number!
+
+Fixes where mdrun could behave incorrectly
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Fixes for ``gmx`` tools
+^^^^^^^^^^^^^^^^^^^^^^^
+
+Fixes that affect portability
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Miscellaneous
+^^^^^^^^^^^^^
+

diff --git a/docs/release-notes/index.rst b/docs/release-notes/index.rst
index 0702e8693404a67b8392a99a84ca667a50957771..1b364f73e1cdff792a12c3f495509fa5f686ba42 100644 (file)
--- a/docs/release-notes/index.rst
+++ b/docs/release-notes/index.rst
@@ -31,6 +31,7 @@ Patch releases
 .. toctree::
    :maxdepth: 1
 
+   2021/2021.4
    2021/2021.3
    2021/2021.2
    2021/2021.1

diff --git a/python_packaging/src/CMakeLists.txt b/python_packaging/src/CMakeLists.txt
index 4fb372dc063c7196e27d5fe368e6e16dfee8d9f4..1e8de44d91aa33430df4e52d76d176de38a63826 100644 (file)
--- a/python_packaging/src/CMakeLists.txt
+++ b/python_packaging/src/CMakeLists.txt
@@ -76,9 +76,13 @@ if(POLICY CMP0074) #3.12
 endif()
 
 if(GMXAPI_MASTER_PROJECT)
-    find_package(gmxapi 0.2.1 REQUIRED
+    find_package(gmxapi 0.2 REQUIRED
                  HINTS "$ENV{GROMACS_DIR}"
                  )
+    if (gmxapi_VERSION VERSION_LESS 0.2.1)
+        message(WARNING "Your GROMACS installation does not support custom MD plugins. "
+                "If you need this feature, please install GROMACS 2021.3 or higher.")
+    endif ()
 endif()
 if(gmxapi_FOUND)
     set(_suffix "")
@@ -132,6 +136,12 @@ pybind11_add_module(_gmxapi
                     ${GMXAPI_PYTHON_EXTENSION_SOURCES}
                     )
 
+if (gmxapi_VERSION VERSION_GREATER_EQUAL 0.2.1)
+    target_sources(_gmxapi PRIVATE gmxapi/launch_021.cpp)
+else()
+    target_sources(_gmxapi PRIVATE gmxapi/launch_020.cpp)
+endif()
+
 target_include_directories(_gmxapi PRIVATE
                            ${CMAKE_CURRENT_SOURCE_DIR}/gmxapi
                            ${CMAKE_CURRENT_BINARY_DIR}/gmxapi

diff --git a/python_packaging/src/LICENSE b/python_packaging/src/LICENSE
new file mode 100644 (file)
index 0000000..9840f40
--- /dev/null
+++ b/python_packaging/src/LICENSE
@@ -0,0 +1,459 @@
+                  GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 2.1, February 1999
+
+ Copyright (C) 1991, 1999 Free Software Foundation, Inc.
+ 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+[This is the first released version of the Lesser GPL.  It also counts
+ as the successor of the GNU Library Public License, version 2, hence
+ the version number 2.1.]
+
+                            Preamble
+
+  The licenses for most software are designed to take away your
+freedom to share and change it.  By contrast, the GNU General Public
+Licenses are intended to guarantee your freedom to share and change
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+
+  This license, the Lesser General Public License, applies to some
+specially designated software packages--typically libraries--of the
+Free Software Foundation and other authors who decide to use it.  You
+can use it too, but we suggest you first think carefully about whether
+this license or the ordinary General Public License is the better
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+
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+signed it.  However, nothing else grants you permission to modify or
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+modifying or distributing the Library (or any work based on the
+Library), you indicate your acceptance of this License to do so, and
+all its terms and conditions for copying, distributing or modifying
+the Library or works based on it.
+
+  10. Each time you redistribute the Library (or any work based on the
+Library), the recipient automatically receives a license from the
+original licensor to copy, distribute, link with or modify the Library
+subject to these terms and conditions.  You may not impose any further
+restrictions on the recipients' exercise of the rights granted herein.
+You are not responsible for enforcing compliance by third parties with
+this License.
+
+  11. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues),
+conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License.  If you cannot
+distribute so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you
+may not distribute the Library at all.  For example, if a patent
+license would not permit royalty-free redistribution of the Library by
+all those who receive copies directly or indirectly through you, then
+the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Library.
+
+If any portion of this section is held invalid or unenforceable under any
+particular circumstance, the balance of the section is intended to apply,
+and the section as a whole is intended to apply in other circumstances.
+
+It is not the purpose of this section to induce you to infringe any
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+integrity of the free software distribution system which is
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+generous contributions to the wide range of software distributed
+through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing
+to distribute software through any other system and a licensee cannot
+impose that choice.
+
+This section is intended to make thoroughly clear what is believed to
+be a consequence of the rest of this License.
+
+  12. If the distribution and/or use of the Library is restricted in
+certain countries either by patents or by copyrighted interfaces, the
+original copyright holder who places the Library under this License may add
+an explicit geographical distribution limitation excluding those countries,
+so that distribution is permitted only in or among countries not thus
+excluded.  In such case, this License incorporates the limitation as if
+written in the body of this License.
+
+  13. The Free Software Foundation may publish revised and/or new
+versions of the Lesser General Public License from time to time.
+Such new versions will be similar in spirit to the present version,
+but may differ in detail to address new problems or concerns.
+
+Each version is given a distinguishing version number.  If the Library
+specifies a version number of this License which applies to it and
+"any later version", you have the option of following the terms and
+conditions either of that version or of any later version published by
+the Free Software Foundation.  If the Library does not specify a
+license version number, you may choose any version ever published by
+the Free Software Foundation.
+
+  14. If you wish to incorporate parts of the Library into other free
+programs whose distribution conditions are incompatible with these,
+write to the author to ask for permission.  For software which is
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+Software Foundation; we sometimes make exceptions for this.  Our
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+of all derivatives of our free software and of promoting the sharing
+and reuse of software generally.
+
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+
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+WARRANTY FOR THE LIBRARY, TO THE EXTENT PERMITTED BY APPLICABLE LAW.
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+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
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+SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGES.
+
+                     END OF TERMS AND CONDITIONS
+

diff --git a/python_packaging/src/gmxapi/export_system.cpp b/python_packaging/src/gmxapi/export_system.cpp
index b504ccb9e74599b62bc3af6d1c91e722ecd7b33f..39eeb91d78c3e0b5c0818aeb2e3a394b896290c0 100644 (file)
--- a/python_packaging/src/gmxapi/export_system.cpp
+++ b/python_packaging/src/gmxapi/export_system.cpp
@@ -44,6 +44,7 @@
 #include "gmxapi/session.h"
 #include "gmxapi/status.h"
 #include "gmxapi/system.h"
+#include "gmxapi/version.h"
 
 #include "pycontext.h"
 #include "pysystem.h"
@@ -81,14 +82,7 @@ void export_system(py::module& m)
 
     // Export system container class
     py::class_<System, std::shared_ptr<System>> system(m, "MDSystem");
-    system.def(
-            "launch",
-            [](System* system, std::shared_ptr<PyContext> context) {
-                auto work       = gmxapi::getWork(*system->get());
-                auto newSession = context->launch(*work);
-                return newSession;
-            },
-            "Launch the configured workflow in the provided context.");
+    system.def("launch", &launch, "Launch the configured workflow in the provided context.");
 
     // Module-level function
     m.def("from_tpr",

diff --git a/python_packaging/src/gmxapi/launch_020.cpp b/python_packaging/src/gmxapi/launch_020.cpp
new file mode 100644 (file)
index 0000000..65e5262
--- /dev/null
+++ b/python_packaging/src/gmxapi/launch_020.cpp
@@ -0,0 +1,54 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at 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.
+ */
+/*! \file
+ * \brief Implement Session launcher.
+ *
+ * \ingroup module_python
+ * \author M. Eric Irrgang <ericirrgang@gmail.com>
+ */
+
+#include "pycontext.h"
+#include "pysystem.h"
+
+namespace gmxpy
+{
+
+std::shared_ptr<gmxapi::Session> launch(::gmxapi::System* system, PyContext* context)
+{
+    auto newSession = system->launch(context->get());
+    return newSession;
+}
+
+} // namespace gmxpy

diff --git a/python_packaging/src/gmxapi/launch_021.cpp b/python_packaging/src/gmxapi/launch_021.cpp
new file mode 100644 (file)
index 0000000..44ad5a2
--- /dev/null
+++ b/python_packaging/src/gmxapi/launch_021.cpp
@@ -0,0 +1,55 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at 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.
+ */
+/*! \file
+ * \brief Implement Session launcher.
+ *
+ * \ingroup module_python
+ * \author M. Eric Irrgang <ericirrgang@gmail.com>
+ */
+
+#include "pycontext.h"
+#include "pysystem.h"
+
+namespace gmxpy
+{
+
+std::shared_ptr<gmxapi::Session> launch(::gmxapi::System* system, PyContext* context)
+{
+    auto work       = gmxapi::getWork(*system->get());
+    auto newSession = context->launch(*work);
+    return newSession;
+}
+
+} // namespace gmxpy

diff --git a/python_packaging/src/gmxapi/pycontext.cpp b/python_packaging/src/gmxapi/pycontext.cpp
index a2640301d5f5e4e362e2db84fe573fee9c9e25e7..c77238cebadef29b39397ffce39bb93dea9e8fda 100644 (file)
--- a/python_packaging/src/gmxapi/pycontext.cpp
+++ b/python_packaging/src/gmxapi/pycontext.cpp
@@ -45,7 +45,7 @@
 #include "gmxapi/md.h"
 #include "gmxapi/session.h"
 #include "gmxapi/status.h"
-
+#include "gmxapi/version.h"
 
 namespace py = pybind11;
 
@@ -102,6 +102,10 @@ PyContext::PyContext() :
 
 void PyContext::addMDModule(const pybind11::object& force_object) const
 {
+    if (!::gmxapi::Version::isAtLeast(0, 2, 1))
+    {
+        throw ::gmxapi::NotImplementedError("Feature requires gmxapi 0.2.1 with GROMACS 2021.3.");
+    }
     // If force_object has a bind method, give it a PyCapsule with a pointer
     // to our C++ object.
     if (py::hasattr(force_object, "bind"))

diff --git a/python_packaging/src/gmxapi/pysystem.h b/python_packaging/src/gmxapi/pysystem.h
index 0cafe1ee8499c2a04f31c4cfd4d964f5c079d627..2281df9d0753e6642722282735c04c2590d2b29a 100644 (file)
--- a/python_packaging/src/gmxapi/pysystem.h
+++ b/python_packaging/src/gmxapi/pysystem.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2021, 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.
@@ -53,6 +53,10 @@ namespace gmxpy
 
 std::shared_ptr<gmxapi::System> from_tpr(std::string filename);
 
+class PyContext;
+
+std::shared_ptr<gmxapi::Session> launch(::gmxapi::System* system, PyContext* context);
+
 } // end namespace gmxpy
 
 #endif // header guard

diff --git a/python_packaging/src/setup.py b/python_packaging/src/setup.py
index 27f3408f4cb31e52e04e1b2486fd1b639160fe4c..025aea1c68199c4bef79eda3cd299083d90e225a 100644 (file)
--- a/python_packaging/src/setup.py
+++ b/python_packaging/src/setup.py
@@ -87,7 +87,7 @@ exist in the same location (with different suffixes) only the first one will be
 used when guessing a toolchain, because setup.py does not know which corresponds
 to the gmxapi support library.
 
-If specifying GMXTOOLCHAINDIR and gmxapi_DIR, the tool chain directory must be 
+If specifying GMXTOOLCHAINDIR and gmxapi_DIR, the tool chain directory must be
 located within a subdirectory of gmxapi_DIR.
 
 Refer to project web site for complete documentation.
@@ -157,6 +157,17 @@ cmake_platform_hints = '-DCMAKE_TOOLCHAIN_FILE={}'.format(gmx_toolchain)
 cmake_gmxapi_hint = '-Dgmxapi_ROOT={}'.format(gmxapi_DIR)
 cmake_args = [cmake_platform_hints, cmake_gmxapi_hint]
 
+long_description = """gmxapi provides Python access to GROMACS molecular simulation tools.
+Operations can be connected flexibly to allow high performance simulation and
+analysis with complex control and data flows. Users can define new operations
+in C++ or Python with the same tool kit used to implement this package.
+
+This Python package requires a compatible GROMACS installation with the API
+libraries and headers.
+
+See http://gmxapi.org/ for details on installation and usage.
+"""
+
 setup(
     name='gmxapi',
 
@@ -174,6 +185,7 @@ setup(
     author='M. Eric Irrgang',
     author_email='info@gmxapi.org',
     description='gmxapi Python interface for GROMACS',
+    long_description=long_description,
     license='LGPL',
     url='http://gmxapi.org/',
 

diff --git a/src/gromacs/correlationfunctions/tests/refdata/ExpfitTest_EffnERREST.xml b/src/gromacs/correlationfunctions/tests/refdata/ExpfitTest_EffnERREST.xml
index 5247edc079ae49f1155cd3d4695f550409fd3c5b..d678c31337d57f750ed177a7079ff04223d37fde 100644 (file)
--- a/src/gromacs/correlationfunctions/tests/refdata/ExpfitTest_EffnERREST.xml
+++ b/src/gromacs/correlationfunctions/tests/refdata/ExpfitTest_EffnERREST.xml
@@ -3,8 +3,8 @@
 <ReferenceData>
   <Sequence Name="result">
     <Int Name="Length">3</Int>
-    <Real>0.50082180382778319</Real>
-    <Real>1</Real>
-    <Real>103.32999340041971</Real>
+    <Real>1.2</Real>
+    <Real>0.99</Real>
+    <Real>34.5</Real>
   </Sequence>
 </ReferenceData>

diff --git a/src/gromacs/correlationfunctions/tests/testERREST.xvg b/src/gromacs/correlationfunctions/tests/testERREST.xvg
index 4f28dfc34b37892acb011e3b41ec5d8829e8afa0..7f794647b44819179a47a16f0c6ee6b5d54ed118 100644 (file)
--- a/src/gromacs/correlationfunctions/tests/testERREST.xvg
+++ b/src/gromacs/correlationfunctions/tests/testERREST.xvg
@@ -1,501 +1,503 @@
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+# import numpy as np; t1, a, t2 = 1.2, 0.99, 34.5; t = np.linspace(1, 8001, 501); e2 = 2*a*t1*(1+t1/t*(np.exp(-t/t1)-1)) + 2*(1-a)*t2*(1+t2/t*(np.exp(-t/t2)-1)); np.savetxt('testERREST.xvg', np.array([t, e2]).T, ('%d', '%.7f'), header=open(__file__).readlines()[0])
+# 
+1 0.7738305
+17 2.3534865
+33 2.5354038
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diff --git a/src/gromacs/domdec/domdec.cpp b/src/gromacs/domdec/domdec.cpp
index 3324ca2feae691fa90c8fd2a96446acf9645ea3a..3627ea02d6dba4cf196572d380554b653764b384 100644 (file)
--- a/src/gromacs/domdec/domdec.cpp
+++ b/src/gromacs/domdec/domdec.cpp
@@ -706,7 +706,8 @@ static int ddcoord2simnodeid(const t_commrec* cr, int x, int y, int z)
         }
         else
         {
-            if (cr->dd->comm->ddRankSetup.usePmeOnlyRanks)
+            const DDRankSetup& rankSetup = cr->dd->comm->ddRankSetup;
+            if (rankSetup.rankOrder != DdRankOrder::pp_pme && rankSetup.usePmeOnlyRanks)
             {
                 nodeid = ddindex + gmx_ddcoord2pmeindex(*cr->dd, x, y, z);
             }
@@ -2249,6 +2250,7 @@ static void checkDDGridSetup(const DDGridSetup&   ddGridSetup,
 /*! \brief Set the cell size and interaction limits, as well as the DD grid */
 static DDRankSetup getDDRankSetup(const gmx::MDLogger& mdlog,
                                   int                  numNodes,
+                                  const DdRankOrder    rankOrder,
                                   const DDGridSetup&   ddGridSetup,
                                   const t_inputrec&    ir)
 {
@@ -2261,6 +2263,8 @@ static DDRankSetup getDDRankSetup(const gmx::MDLogger& mdlog,
 
     DDRankSetup ddRankSetup;
 
+    ddRankSetup.rankOrder = rankOrder;
+
     ddRankSetup.numPPRanks = numNodes - ddGridSetup.numPmeOnlyRanks;
     copy_ivec(ddGridSetup.numDomains, ddRankSetup.numPPCells);
 
@@ -2970,7 +2974,8 @@ DomainDecompositionBuilder::Impl::Impl(const MDLogger&                   mdlog,
 
     cr_->npmenodes = ddGridSetup_.numPmeOnlyRanks;
 
-    ddRankSetup_ = getDDRankSetup(mdlog_, cr_->sizeOfDefaultCommunicator, ddGridSetup_, ir_);
+    ddRankSetup_ = getDDRankSetup(
+            mdlog_, cr_->sizeOfDefaultCommunicator, options_.rankOrder, ddGridSetup_, ir_);
 
     /* Generate the group communicator, also decides the duty of each rank */
     cartSetup_ = makeGroupCommunicators(
@@ -3240,3 +3245,42 @@ void dd_init_local_state(const gmx_domdec_t& dd, const t_state* state_global, t_
     init_dfhist_state(state_local, buf[4]);
     state_local->flags = buf[0];
 }
+
+void putUpdateGroupAtomsInSamePeriodicImage(const gmx_domdec_t&      dd,
+                                            const gmx_mtop_t&        mtop,
+                                            const matrix             box,
+                                            gmx::ArrayRef<gmx::RVec> positions)
+{
+    int atomOffset = 0;
+    for (const gmx_molblock_t& molblock : mtop.molblock)
+    {
+        const auto& updateGrouping = dd.comm->systemInfo.updateGroupingsPerMoleculeType[molblock.type];
+
+        for (int mol = 0; mol < molblock.nmol; mol++)
+        {
+            for (int g = 0; g < updateGrouping.numBlocks(); g++)
+            {
+                const auto& block     = updateGrouping.block(g);
+                const int   atomBegin = atomOffset + block.begin();
+                const int   atomEnd   = atomOffset + block.end();
+                for (int a = atomBegin + 1; a < atomEnd; a++)
+                {
+                    // Make sure that atoms in the same update group
+                    // are in the same periodic image after restarts.
+                    for (int d = DIM - 1; d >= 0; d--)
+                    {
+                        while (positions[a][d] - positions[atomBegin][d] > 0.5_real * box[d][d])
+                        {
+                            positions[a] -= box[d];
+                        }
+                        while (positions[a][d] - positions[atomBegin][d] < -0.5_real * box[d][d])
+                        {
+                            positions[a] += box[d];
+                        }
+                    }
+                }
+            }
+            atomOffset += updateGrouping.fullRange().end();
+        }
+    }
+}

diff --git a/src/gromacs/domdec/domdec.h b/src/gromacs/domdec/domdec.h
index 20a7c6994563644e27c5e591c342e5268681a7fb..3fa388684230a4d90ce1406f56da1b07deb66732 100644 (file)
--- a/src/gromacs/domdec/domdec.h
+++ b/src/gromacs/domdec/domdec.h
@@ -291,4 +291,27 @@ void communicateGpuHaloCoordinates(const t_commrec&      cr,
  */
 void communicateGpuHaloForces(const t_commrec& cr, bool accumulateForces);
 
+/*! \brief Wraps the \c positions so that atoms from the same
+ * update group share the same periodic image wrt \c box.
+ *
+ * When DD and update groups are in use, the simulation master rank
+ * should call this to ensure that e.g. when restarting a simulation
+ * that did not use update groups that the coordinates satisfy the new
+ * requirements.
+ *
+ * This function can probably be removed when even single-rank
+ * simulations use domain decomposition, because then the choice of
+ * whether update groups are used is probably going to be the same
+ * regardless of the rank count.
+ *
+ * \param[in]    dd         The DD manager
+ * \param[in]    mtop       The system topology
+ * \param[in]    box        The global system box
+ * \param[in]    positions  The global system positions
+ */
+void putUpdateGroupAtomsInSamePeriodicImage(const gmx_domdec_t&      dd,
+                                            const gmx_mtop_t&        mtop,
+                                            const matrix             box,
+                                            gmx::ArrayRef<gmx::RVec> positions);
+
 #endif

diff --git a/src/gromacs/domdec/domdec_internal.h b/src/gromacs/domdec/domdec_internal.h
index 40e67444615942618f1793650c51de821f04f3da..d82bafa79fa44fe0323352cb3d839b8fcb6cee45 100644 (file)
--- a/src/gromacs/domdec/domdec_internal.h
+++ b/src/gromacs/domdec/domdec_internal.h
@@ -60,6 +60,13 @@ struct t_commrec;
 
 struct BalanceRegion;
 
+namespace gmx
+{
+enum class DdRankOrder : int;
+}
+// namespace
+
+
 //! Indices to communicate in a dimension
 struct gmx_domdec_ind_t
 {
@@ -499,6 +506,9 @@ struct DDSettings
 /*! \brief Information on how the DD ranks are set up */
 struct DDRankSetup
 {
+    /**< The rank ordering */
+    gmx::DdRankOrder rankOrder;
+
     /**< The number of particle-particle (non PME-only) ranks */
     int numPPRanks = 0;
     /**< The DD PP grid */

diff --git a/src/gromacs/gmxana/anadih.cpp b/src/gromacs/gmxana/anadih.cpp
index 6bae98b5599a0f5af104622f6ecbe2e56368a6aa..7238fa320f9bd253ee694eddac64ea6944803329 100644 (file)
--- a/src/gromacs/gmxana/anadih.cpp
+++ b/src/gromacs/gmxana/anadih.cpp
@@ -195,7 +195,7 @@ void low_ana_dih_trans(gmx_bool                bTrans,
     int (*calc_bin)(real, int, real);
     real dt;
 
-    if (1 <= nframes)
+    if (nframes <= 1)
     {
         return;
     }

diff --git a/src/gromacs/gmxana/gmx_chi.cpp b/src/gromacs/gmxana/gmx_chi.cpp
index 0abd978d194e4b0f3c4d20f97105441204848110..deed54bfdf0fb50b9b931a4e6d3ff918c0994a5a 100644 (file)
--- a/src/gromacs/gmxana/gmx_chi.cpp
+++ b/src/gromacs/gmxana/gmx_chi.cpp
@@ -748,7 +748,8 @@ static void histogramming(FILE*                   log,
                     normalize_histo(nbin, his_aa[Dih][i], (360.0 / nbin), normhisto);
                 }
 
-                residue_name = rt->nameFromResidueIndex(i).c_str();
+                std::string residueName = rt->nameFromResidueIndex(i);
+                residue_name            = residueName.c_str();
                 switch (Dih)
                 {
                     case edPhi:
@@ -1555,7 +1556,7 @@ int gmx_chi(int argc, char* argv[])
     }
 
     /* put angles in -M_PI to M_PI ! and correct phase factor for phi and psi
-     * pass nactdih instead of ndih to low_ana_dih_trans and get_chi_product_traj
+     * pass nactdih instead of ndih to low_ana_dih_trans
      * to prevent accessing off end of arrays when maxchi < 5 or 6. */
     nactdih = reset_em_all(nlist, dlist, nf, dih, maxchi);
 
@@ -1682,7 +1683,7 @@ int gmx_chi(int argc, char* argv[])
 
         get_chi_product_traj(dih,
                              nf,
-                             nactdih,
+                             nlist,
                              maxchi,
                              dlist,
                              time,

diff --git a/src/gromacs/mdrun/runner.cpp b/src/gromacs/mdrun/runner.cpp
index e3eb7ff8f227766936c457fa2636eca9d310aa18..2462285bef078b77394308accdff5101000d2387 100644 (file)
--- a/src/gromacs/mdrun/runner.cpp
+++ b/src/gromacs/mdrun/runner.cpp
@@ -1389,6 +1389,19 @@ int Mdrunner::mdrunner()
         ddBuilder.reset(nullptr);
         // Note that local state still does not exist yet.
     }
+    // Ensure that all atoms within the same update group are in the
+    // same periodic image. Otherwise, a simulation that did not use
+    // update groups (e.g. a single-rank simulation) cannot always be
+    // correctly restarted in a way that does use update groups
+    // (e.g. a multi-rank simulation).
+    if (isSimulationMasterRank)
+    {
+        const bool useUpdateGroups = cr->dd ? ddUsesUpdateGroups(*cr->dd) : false;
+        if (useUpdateGroups)
+        {
+            putUpdateGroupAtomsInSamePeriodicImage(*cr->dd, mtop, globalState->box, globalState->x);
+        }
+    }
 
     // The GPU update is decided here because we need to know whether the constraints or
     // SETTLEs can span across the domain borders (i.e. whether or not update groups are