gmxapi-30 Tutorial / working Jupyter notebook examples

Fix typos and bugs so the testing instructions in Dockerfile are true.

Build restraints as static libraries with position independent code to
make the myplugin.so object more portable.

CMakeLists.txt

@@ -99,7 +99,7 @@ endif()
 
 # At some point this may be part of a CMake package with several components for which a single CMAKE_INSTALL_PREFIX does
 # not make sense, so let's manage the install path separately.
-set(GMXPLUGIN_INSTALL_PATH ${GMXPLUGIN_DEFAULT_SITE_PACKAGES}/gmx CACHE PATH
+set(GMXPLUGIN_INSTALL_PATH ${GMXPLUGIN_DEFAULT_SITE_PACKAGES} CACHE PATH
     "Path to Python module install location (site-packages). For an automatically determined install location based on \
     the Python installation, leave undefined or explicitly undefined with -UGMXPLUGIN_INSTALL_PATH and, optionally, set \
     GMXPLUGIN_USER_INSTALL on or off to specify the installation's site-packages directory or the 'user' site-packages \

Dockerfile

@@ -13,7 +13,7 @@
 #     docker run -ti --name restraint_test sample_restraint
 #
 # Test with
-#     docker run --cpus 2 --rm -ti gmxapi/sample_restraint:devel bash -c "cd /home/jovyan/samplerestraint/tests && mpiexec -n 2 python -m mpi4py -m pytest"
+#     docker run --cpus 2 --rm -ti gmxapi/sample_restraint:devel bash -c "cd /home/jovyan/sample_restraint/tests && mpiexec -n 2 python -m mpi4py -m pytest"
 # or replace `gmxapi/sample_restraint:devel` with your local image name
 
 

src/cpp/CMakeLists.txt

@@ -2,9 +2,10 @@
 # unit tests and by the Python module target defined in ../pythonmodule/CMakeLists.txt
 
 # Create a shared object library for a simple restraint.
-add_library(harmonicpotential SHARED
+add_library(harmonicpotential STATIC
             harmonicpotential.h
             harmonicpotential.cpp)
+set_target_properties(harmonicpotential PROPERTIES POSITION_INDEPENDENT_CODE ON)
 
 target_include_directories(harmonicpotential PUBLIC
                            $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
@@ -23,9 +24,10 @@ target_link_libraries(harmonicpotential PRIVATE Gromacs::gmxapi)
 
 
 # Create a shared object library for our restrained ensemble plugin.
-add_library(ensemblepotential SHARED
+add_library(ensemblepotential STATIC
             ensemblepotential.h
             ensemblepotential.cpp)
+set_target_properties(ensemblepotential PROPERTIES POSITION_INDEPENDENT_CODE ON)
 
 target_include_directories(ensemblepotential PUBLIC
                            $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>

src/cpp/ensemblepotential.cpp

@@ -322,6 +322,34 @@ gmx::PotentialPointData EnsembleHarmonic::calculate(gmx::Vector v,
     return output;
 }
 
+std::unique_ptr<ensemble_input_param_type>
+makeEnsembleParams(size_t nbins,
+                   double binWidth,
+                   double minDist,
+                   double maxDist,
+                   const std::vector<double> &experimental,
+                   unsigned int nSamples,
+                   double samplePeriod,
+                   unsigned int nWindows,
+                   double k,
+                   double sigma)
+{
+    using gmx::compat::make_unique;
+    auto params = make_unique<ensemble_input_param_type>();
+    params->nBins = nbins;
+    params->binWidth = binWidth;
+    params->minDist = minDist;
+    params->maxDist = maxDist;
+    params->experimental = experimental;
+    params->nSamples = nSamples;
+    params->samplePeriod = samplePeriod;
+    params->nWindows = nWindows;
+    params->k = k;
+    params->sigma = sigma;
+
+    return params;
+};
+
 EnsembleResourceHandle EnsembleResources::getHandle() const
 {
     auto handle = EnsembleResourceHandle();

src/cpp/ensemblepotential.h

@@ -281,23 +281,7 @@ makeEnsembleParams(size_t nbins,
                    double samplePeriod,
                    unsigned int nWindows,
                    double k,
-                   double sigma)
-{
-    using gmx::compat::make_unique;
-    auto params = make_unique<ensemble_input_param_type>();
-    params->nBins = nbins;
-    params->binWidth = binWidth;
-    params->minDist = minDist;
-    params->maxDist = maxDist;
-    params->experimental = experimental;
-    params->nSamples = nSamples;
-    params->samplePeriod = samplePeriod;
-    params->nWindows = nWindows;
-    params->k = k;
-    params->sigma = sigma;
-
-    return params;
-};
+                   double sigma);
 
 /*!
  * \brief a residue-pair bias calculator for use in restrained-ensemble simulations.