Move example files and update README files

examples/hello/HelloWaterBox.cpp → examples/cpp-examples/HelloWaterBox.cpp

 /* -----------------------------------------------------------------------------
- *              OpenMM(tm) HelloWaterBox example in C++ (June 2009)
+ *                OpenMM HelloWaterBox example in C++ (June 2009)
  * -----------------------------------------------------------------------------
  * This is a complete, self-contained "hello world" example demonstrating 
  * GPU-accelerated simulation of a system with both bonded and nonbonded forces, 

examples/hello/Makefile → examples/cpp-examples/Makefile

 # ----------------------------------------------------------------------
-# Makefile for OpenMM Preview Release 4 workshop "hello world" examples.
+# Makefile for OpenMM "hello world" examples.
 # August 18, 2009
-# See https://simtk.org/home/openmm.
 # ----------------------------------------------------------------------
 # This assumes you have gcc compilers for whatever language you are
 # using: g++ for C++ and C, gfortran for Fortran 95.

examples/hello/NMakefile → examples/cpp-examples/NMakefile

 # ----------------------------------------------------------------------
-# Microsoft NMakefile for OpenMM Preview Release 4 "hello world" examples.
+# Microsoft NMakefile for OpenMM "hello world" examples.
 # August 19, 2009.
-# See https://simtk.org/home/openmm.
 # ----------------------------------------------------------------------
 # This assumes you have gcc compilers for whatever language you are
 # using: cl for C++ and C, ifort for Fortran 95.

examples/cpp-examples/README.md

+## OpenMM C++, C, and Fortran API Examples
+
+These simple "hello world" examples were developed by Christopher Bruns and
+Michael Sherman.  They demonstrate use of the C++, C, and Fortran APIs for
+OpenMM.
+
+### Example Details
+
+Consult the OpenMM user guide for
+[more information on these examples](https://docs.openmm.org/latest/userguide/library/03_tutorials.html),
+as well as
+[use of the C and Fortran API wrappers](https://docs.openmm.org/latest/userguide/library/05_languages_not_cpp.html).
+
+#### `HelloArgon` (C++, C, Fortran 95)
+
+This is the simplest example we could come up with that
+does anything interesting. It is three argon atoms interacting
+in a vacuum via van der Waals forces. It is primarily so you can
+check that you are able to compile, link, and run correctly with
+OpenMM. You will also get a many-frame PDB file generated
+which you can view as an animation in VMD or most other
+molecular viewers.
+
+#### `HelloSodiumChloride` (C++, C, Fortran 95)
+
+This example shows how we recommend using OpenMM so that you
+can call it from an existing molecular dynamics code with
+minimal disruption. The example contains Coulomb and van der
+Waals interactions and implicit solvation in a constant
+temperature simulation.
+
+#### `HelloEthane` (C++ only)
+
+This example shows how to convey bond information to
+OpenMM. It is organized similarly to `HelloSodiumChloride`.
+
+#### `HelloWaterBox` (C++ only)
+
+This example shows use of explicit solvent in a periodic box.
+It is organized like the previous two.
+
+### Building the examples
+
+This directory includes a Makefile suitable for building the  examples under Mac
+or Linux and possibly Cygwin, using the GCC compiler suite.  There is also an
+NMakefile for use with Microsoft's `nmake` program. For Fortran, the Makefile
+expects `gfortran` to be in the path while NMakefile expects `ifort` (Intel
+Fortran).  In the `VisualStudio` subdirectory, there are Visual Studio
+"solutions" for building `HelloArgon` in C++, C, and Fortran. You will have to
+make your own for the other examples or just substitute a different source file
+for HelloArgon.
+
+You must already have the OpenMM binaries installed to build the examples from
+source.  See the
+[user guide](https://docs.openmm.org/latest/userguide/application/01_getting_started.html#installing-openmm)
+for more information.  You may need to slightly edit the Makefile or NMakefile
+to make  it run on your system, depending where you installed OpenMM and  the
+particular requirements of your compiler versions for mixed Fortran/C++
+programming.
+
+Type `make` (or `make default`) to get just one C++ example built
+(`HelloArgon`). Make sure it runs.  To compile all example programs type
+`make all`. That includes Fortran examples though so you will see failures
+unless you have `gfortran` installed (Linux and Mac) or `ifort` installed
+(Windows). However, the C++ and C examples should compile with just `g++` or
+`cl`.  To build just one example, type `make HelloArgonInC` or whatever.
+
+Before you run the executables, remember to add the OpenMM dynamic library
+directory to your library path.  The simplest way to do this is to type the
+following commands:
+
+- For linux (for the bash shell, assuming installation was done in the default
+  location `/usr/local/openmm`):
+  ```bash
+  $ export LD_LIBRARY_PATH=/usr/local/openmm/lib
+  ```
+- For Mac (for the `bash` shell, assuming installation was done in the default
+  location `/usr/local/openmm`):
+  ```bash
+  $ export DYLD_LIBRARY_PATH=/usr/local/openmm/lib
+  ```
+- For Windows (command tool, assuming installation was done in the default
+  location `C:\Program Files\OpenMM`):
+  ```bat
+  C:\> set path=%path%;C:\Program Files\OpenMM\lib
+  ```

examples/extras/README.md

-OpenMM extra utility scripts
-============================
+## OpenMM extra utility scripts
 
 This directory contains standalone utility scripts for use with OpenMM.
 

examples/hello/MakefileNotes.txt

-Instructions for using the Makefile provided.
----------------------------------------------
-
-There is a Makefile for use on Linux and Mac, and an NMakefile
-for use with Microsoft's "nmake" program. For Fortran, the
-Makefile expects gfortran to be in the path while NMakefile
-expects "ifort" (Intel Fortran).
-
-You must already have the OpenMM binaries installed from 
-SimTK.org/home/OpenMM. Pay careful attention to the installation 
-instructions -- if you are hoping to get GPU acceleration you 
-may also have to install appropriate vendor libraries and a driver.
-
-You may need to slightly edit the Makefile or NMakefile to make 
-it run on your system, depending where you installed OpenMM and 
-the particular requirements of your compiler versions for mixed 
-Fortran/C++ programming. 
-
-Type "make" (or "make default") to get just one C++ example built
-(HelloArgon). Make sure it runs.
-
-To compile all example programs type "make all". That includes Fortran
-examples though so you will see failures unless you have gfortran
-installed (Linux and Mac) or ifort installed (Windows). However, 
-the C++ and C examples should compile with just g++ or cl.
-
-To build just one example, type "make HelloArgonInC" or whatever.
-
-Before you run the executables, remember to add the OpenMM dynamic 
-library directory to your library path. 
-
-The simplest way to do this is to type the following commands:
-
-For linux (for the bash shell, assuming installation was done in 
-the default location: /usr/local/openmm): 
-  $ export LD_LIBRARY_PATH=/usr/local/openmm/lib 
-
-For MAC (for the bash shell, assuming installation was done 
-in the default location: /usr/local/openmm):
-  $ export DYLD_LIBRARY_PATH=/usr/local/openmm/lib 
-
-For Windows (command tool, assuming installation was done 
-in the default location: C:/Program Files/OpenMM):
-C:\> set path=%path%;C:\Program Files\OpenMM\lib
-

examples/python-examples/CMakeLists.txt

+# Install Python examples.
+
+INSTALL(FILES simulateAmber.py input.inpcrd input.prmtop DESTINATION examples/python-examples)
+INSTALL(FILES simulateCharmm.py ala_ala_ala.pdb ala_ala_ala.psf charmm22.par charmm22.rtf DESTINATION examples/python-examples)
+INSTALL(FILES simulateGromacs.py input.gro input.top DESTINATION examples/python-examples)
+INSTALL(FILES simulatePdb.py input.pdb DESTINATION examples/python-examples)
+INSTALL(FILES argon-chemical-potential.py DESTINATION examples/python-examples)