Fix docs, comments, remove non-existing types from swigInputConfig.py

docs-source/usersguide/application/05_add_on_packages.rst

@@ -104,17 +104,6 @@ For more information,  see the OpenMMTools_ website.
 
 .. _OpenMMTools: https://github.com/choderalab/openmmtools
 
-OpenMM-HIP
-**********
-
-This package adds a new platform that is implemented with AMD's HIP framework.
-When running on AMD GPUs, it often has much faster performance than the OpenCL
-platform.  For information about how to install it, see the OpenMM-HIP_ website.
-Once it is installed, the new platform can be selected and used exactly like the
-ones included in the main OpenMM package.
-
-.. _OpenMM-HIP: https://github.com/StreamHPC/openmm-hip
-
 openmmforcefields
 *****************
 

docs-source/usersguide/library/01_introduction.rst

@@ -46,7 +46,7 @@ license.  This is a very permissive license which allows them to be used in
 almost any way, requiring only that you retain the copyright notice and
 disclaimer when distributing them.
 
-The CUDA and OpenCL platforms are distributed under the GNU Lesser General
+The CUDA, HIP, and OpenCL platforms are distributed under the GNU Lesser General
 Public License (LGPL).  This also allows you to use, modify, and distribute them
 in any way you want, but it requires you to also distribute the source code for
 your modifications.  This restriction applies only to modifications to OpenMM
@@ -280,8 +280,8 @@ simulation; it is a fairly generic computational API.  In addition to defining
 the generic classes, OpenMM also defines abstract subclasses of KernelImpl
 corresponding to specific calculations.  For example, there is a class called
 CalcHarmonicBondForceKernel to implement HarmonicBondForce and a class called
-IntegrateLangevinStepKernel to implement LangevinIntegrator.  It is these
-classes for which each Platform must provide a concrete subclass.
+IntegrateLangevinMiddleStepKernel to implement LangevinMiddleIntegrator.  It is
+these classes for which each Platform must provide a concrete subclass.
 
 This architecture is designed to allow easy extensibility.  To support a new
 hardware platform, for example, you create concrete subclasses of all the
@@ -330,6 +330,9 @@ conventional CPUs.
 **CudaPlatform**\ : This platform is implemented using the CUDA language, and
 performs calculations on Nvidia GPUs.
 
+**HipPlatform**\ : This platform is implemented using the HIP language, and
+performs calculations on ROCm-compatible AMD GPUs.
+
 **OpenCLPlatform**\ : This platform is implemented using the OpenCL language,
 and performs calculations on a variety of types of GPUs and CPUs.
 
@@ -343,8 +346,8 @@ The choice of which platform to use for a simulation depends on various factors:
    some older computers.  Also, for simulations that use certain features
    (primarily the various “custom” force classes), it may be faster to use the
    OpenCL platform running on the CPU.
-#. The CUDA platform can only be used with NVIDIA GPUs.  For using an AMD or
-   Intel GPU, use the OpenCL platform.
-#. The AMOEBA force field only works with the CUDA platform, not with the OpenCL
-   platform.  It also works with the Reference and CPU platforms, but the performance
-   is usually too slow to be useful on those platforms.
+#. The CUDA platform can be used with NVIDIA GPUs.  For using an AMD GPU,
+   use the HIP platform (or the OpenCL platform which is usually slower), for
+   using an Intel GPU, use the OpenCL platform.
+#. The AMOEBA force field works with all platforms, but the performance
+   of the Reference and CPU platforms is usually too slow to be useful.

docs-source/usersguide/library/02_compiling.rst

@@ -111,7 +111,7 @@ There are several variables that can be adjusted in the CMake interface:
   any reason CMake is unable to find them, set OPENCL_INCLUDE_DIR to point to
   the directory containing the headers (usually /usr/local/cuda/include on Linux)
   and OPENCL_LIBRARY to point to the library (usually /usr/local/cuda/lib64/libOpenCL.so
-  on Linux).  
+  on Linux).
 
 Configure (press “c”) again.  Adjust any variables that cause an error.
 
@@ -167,12 +167,6 @@ fraction of the time.  These tests will say so in the error message:
     exception: Assertion failure at TestReferenceLangevinIntegrator.cpp:129.  Expected 9.97741,
         found 10.7884 (This test is stochastic and may occasionally fail)
 
-If you get an error message such as :code:`exception: Error launching CUDA compiler: 32512` you need
-to specify the path to the CUDA compiler (nvcc) using the :code:`OPENMM_CUDA_COMPILER` environment
-variable, for example using something like the following::
-
-    OPENMM_CUDA_COMPILER=/<path_to_custom_cuda_dir>/nvcc
-
 Step 3: Install
 ===============
 Install your local build of OpenMM using the following command::
@@ -309,7 +303,7 @@ There are several variables that can be adjusted in the CMake interface:
   the directory containing the headers (usually
   "C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v11.4/include", except
   with the correct version number for the toolkit you installed) and
-  OPENCL_LIBRARY to point to the library (usually "C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v11.4/lib/x64/OpenCL.lib").  
+  OPENCL_LIBRARY to point to the library (usually "C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v11.4/lib/x64/OpenCL.lib").
 
 Press "Configure" again.  Adjust any variables that cause an error.
 
@@ -437,4 +431,4 @@ Step 3: Install local build of openmm
 =====================================
 
 Now we just install our local build of :code:`openmm` as instructed in
-:ref:`compiling-openmm-from-source-linux`
\ No newline at end of file
+:ref:`compiling-openmm-from-source-linux`

libraries/lepton/src/ParsedExpression.cpp

@@ -152,10 +152,10 @@ ExpressionTreeNode ParsedExpression::substituteSimplerExpression(const Expressio
         else
             children[i] = cached->second;
     }
-    
+
     // Collect some info on constant expressions in children
     bool first_const = children.size() > 0 && isConstant(children[0]); // is first child constant?
-    bool second_const = children.size() > 1 && isConstant(children[1]); // is second child constant?   
+    bool second_const = children.size() > 1 && isConstant(children[1]); // is second child constant?
     double first, second; // if yes, value of first and second child
     if (first_const)
         first = getConstantValue(children[0]);
@@ -205,7 +205,7 @@ ExpressionTreeNode ParsedExpression::substituteSimplerExpression(const Expressio
             break;
         }
         case Operation::MULTIPLY:
-        {   
+        {
             if ((first_const && first == 0.0) || (second_const && second == 0.0)) // Multiply by 0
                 return ExpressionTreeNode(new Operation::Constant(0.0));
             if (first_const && first == 1.0) // Multiply by 1
@@ -247,7 +247,7 @@ ExpressionTreeNode ParsedExpression::substituteSimplerExpression(const Expressio
         case Operation::DIVIDE:
         {
             if (children[0] == children[1])
-                return ExpressionTreeNode(new Operation::Constant(1.0)); // Dividing anything from itself is 0
+                return ExpressionTreeNode(new Operation::Constant(1.0)); // Dividing anything by itself is 1
             if (first_const && first == 0.0) // 0 divided by something
                 return ExpressionTreeNode(new Operation::Constant(0.0));
             if (first_const && first == 1.0) // 1 divided by something

wrappers/python/src/swig_doxygen/swigInputConfig.py

@@ -43,21 +43,18 @@ SKIP_METHODS = [('State', 'getPositions'),
                 ('CalcGBSAOBCForceKernel',),
                 ('CalcHarmonicAngleForceKernel',),
                 ('CalcHarmonicBondForceKernel',),
-                ('CalcKineticEnergyKernel',),
                 ('CalcNonbondedForceKernel',),
                 ('CalcPeriodicTorsionForceKernel',),
                 ('CalcRBTorsionForceKernel',),
                 ('ComputationInfo',),
                 ('ConstraintInfo',),
                 ('CudaKernelFactory',),
-                ('CudaStreamFactory',),
+                ('HipKernelFactory',),
                 ('ExceptionInfo',),
                 ('ExclusionInfo',),
                 ('FunctionInfo',),
                 ('GlobalParameterInfo',),
-                ('InitializeForcesKernel',),
                 ('IntegrateBrownianStepKernel',),
-                ('IntegrateLangevinStepKernel',),
                 ('IntegrateNoseHooverStepKernel',),
                 ('IntegrateVariableLangevinStepKernel',),
                 ('IntegrateVariableVerletStepKernel',),
@@ -75,23 +72,19 @@ SKIP_METHODS = [('State', 'getPositions'),
                 ('RBTorsionInfo',),
                 ('RemoveCMMotionKernel',),
                 ('SplineFitter',),
-                ('StreamFactory',),
                 ('TorsionInfo',),
                 ('TorsionTorsionGridInfo',),
                 ('TorsionTorsionInfo',),
                 ('UpdateStateDataKernel',),
-                ('UpdateTimeKernel',),
                 ('VdwInfo',),
                 ('WcaDispersionInfo',),
                 ('Context',  'getIntegrator'),
                 ('Context',  'createCheckpoint'),
                 ('Context',  'loadCheckpoint'),
                 ('CudaPlatform',),
+                ('HipPlatform',),
                 ('Force',    'Force'),
                 ('ParticleParameterInfo',),
-                ('Platform', 'createStream'),
-                ('Platform', 'getDefaultStreamFactory'),
-                ('Platform', 'registerStreamFactory'),
                 ('Platform', 'contextCreated'),
                 ('Platform', 'contextDestroyed'),
                 ('Platform', 'createKernel'),
@@ -113,7 +106,7 @@ SKIP_METHODS = [('State', 'getPositions'),
 
 
 # The build script assumes method args that are non-const references are
-# used to output values. This list gives excpetions to this rule.
+# used to output values. This list gives exceptions to this rule.
 NO_OUTPUT_ARGS = [('LocalEnergyMinimizer', 'minimize', 'context'),
                   ('Platform', 'setPropertyValue', 'context'),
                   ('AmoebaTorsionTorsionForce', 'setTorsionTorsionGrid', 'grid'),