"...reference/src/SimTKReference/SimTKOpenMMUtilities.cpp" did not exist on "90f31a686e9d4d3dc6bb2e845cf9c01215932a46"
Commit 0df0cd8b authored by Michael Sherman's avatar Michael Sherman
Browse files

Fix some comments.

parent acf79ffc
...@@ -171,15 +171,16 @@ struct MyOpenMMData_s { ...@@ -171,15 +171,16 @@ struct MyOpenMMData_s {
* INITIALIZE OpenMM DATA STRUCTURES * INITIALIZE OpenMM DATA STRUCTURES
* -------------------------------------------------------------------------- * --------------------------------------------------------------------------
* We take these actions here: * We take these actions here:
* (1) Allocate a MyOpenMMData structure to hang on to OpenMM data structures * (1) Load any available OpenMM plugins, e.g. Cuda and Brook.
* (2) Allocate a MyOpenMMData structure to hang on to OpenMM data structures
* in a manner which is opaque to the caller. * in a manner which is opaque to the caller.
* (2) Allocate the OpenMM objects which persist from call to call.
* (3) Fill the OpenMM::System with the force field parameters we want to * (3) Fill the OpenMM::System with the force field parameters we want to
* use and the particular set of atoms to be simulated. * use and the particular set of atoms to be simulated.
* (4) Create an Integrator and a Context associating the Integrator with * (4) Create an Integrator and a Context associating the Integrator with
* the System. * the System.
* (5) Select the OpenMM platform to be used. * (5) Select the OpenMM platform to be used.
* (6) Return the MyOpenMMData struct and the name of the Platform in use. * (6) Return an opaque pointer to the MyOpenMMData struct and the name
* of the Platform in use.
* *
* Note that this function must understand the calling MD code's molecule and * Note that this function must understand the calling MD code's molecule and
* force field data structures so will need to be customized for each MD code. * force field data structures so will need to be customized for each MD code.
...@@ -222,7 +223,7 @@ myInitializeOpenMM( const MyAtomInfo atoms[], ...@@ -222,7 +223,7 @@ myInitializeOpenMM( const MyAtomInfo atoms[],
* (1) System needs to know the masses. * (1) System needs to know the masses.
* (2) NonbondedForce needs charges,van der Waals properties (in MD units!). * (2) NonbondedForce needs charges,van der Waals properties (in MD units!).
* (3) GBSA needs charge, radius, and scale factor. * (3) GBSA needs charge, radius, and scale factor.
* (3) Collect default positions for initializing the simulation later. */ * (4) Collect default positions for initializing the simulation later. */
initialPosInNm = OpenMM_Vec3Array_create(0); initialPosInNm = OpenMM_Vec3Array_create(0);
for (n=0; *atoms[n].pdb; ++n) { for (n=0; *atoms[n].pdb; ++n) {
const MyAtomInfo* atom = &atoms[n]; const MyAtomInfo* atom = &atoms[n];
......
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