Created Units.h to simplify unit conversions. Also fixed some Doxygen problems.

Doxyfile.in

@@ -75,7 +75,7 @@ WARN_LOGFILE           =
 #---------------------------------------------------------------------------
 # configuration options related to the input files
 #---------------------------------------------------------------------------
-INPUT                  = "@CMAKE_SOURCE_DIR@"
+INPUT                  = "@CMAKE_SOURCE_DIR@/openmmapi" "@CMAKE_SOURCE_DIR@/olla"
 INPUT_ENCODING         = UTF-8
 FILE_PATTERNS          = 
 RECURSIVE              = YES

openmmapi/include/OpenMM.h

@@ -49,6 +49,7 @@
 #include "openmm/RBTorsionForce.h"
 #include "openmm/State.h"
 #include "openmm/System.h"
+#include "openmm/Units.h"
 #include "openmm/Vec3.h"
 #include "openmm/VerletIntegrator.h"
 #include "openmm/Platform.h"

openmmapi/include/openmm/HarmonicAngleForce.h

@@ -64,7 +64,7 @@ public:
      * @param particle1 the index of the first particle forming the angle
      * @param particle2 the index of the second particle forming the angle
      * @param particle3 the index of the third particle forming the angle
-     * @param length    the equilibrium angle, measured in radians
+     * @param angle     the equilibrium angle, measured in radians
      * @param k         the harmonic force constant for the angle
      */
     void addAngle(int particle1, int particle2, int particle3, double angle, double k);
@@ -75,7 +75,7 @@ public:
      * @param particle1 the index of the first particle forming the angle
      * @param particle2 the index of the second particle forming the angle
      * @param particle3 the index of the third particle forming the angle
-     * @param length    the equilibrium angle, measured in radians
+     * @param angle     the equilibrium angle, measured in radians
      * @param k         the harmonic force constant for the angle
      */
     void getAngleParameters(int index, int& particle1, int& particle2, int& particle3, double& angle, double& k) const;
@@ -86,7 +86,7 @@ public:
      * @param particle1 the index of the first particle forming the angle
      * @param particle2 the index of the second particle forming the angle
      * @param particle3 the index of the third particle forming the angle
-     * @param length    the equilibrium angle, measured in radians
+     * @param angle     the equilibrium angle, measured in radians
      * @param k         the harmonic force constant for the angle
      */
     void setAngleParameters(int index, int particle1, int particle2, int particle3, double angle, double k);

openmmapi/include/openmm/Units.h

+#ifndef OPENMM_UNITS_H_
+#define OPENMM_UNITS_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2008 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include <cmath>
+
+/** \file
+ * OpenMM uses the following units everywhere:
+ *
+ * length: nanometers<br/>
+ * time: picoseconds<br/>
+ * mass: atomic mass units (daltons)<br/>
+ * charge: proton charge<br/>
+ * temperature: Kelvin<br/>
+ * angle: radians<br/>
+ * energy: kJ/mol<br/>
+ * force: kJ/mol/nm<br/>
+ *
+ * Because some programs use other units (e.g. Angstroms for length or kcal/mol for energy), this file defines
+ * constants which can be used to convert to and from OpenMM's units.
+ */
+
+namespace OpenMM {
+    /**
+     * The number of nanometers in an Angstrom.
+     */
+    static const double NmPerAngstrom = 0.1;
+    /**
+     * The number of Angstroms in a nanometer.
+     */
+    static const double AngstromsPerNm = 10.0;
+    /**
+     * The number of picoseconds in a femtosecond.
+     */
+    static const double PsPerFs = 0.001;
+    /**
+     * The number of femtoseconds in a picosecond.
+     */
+    static const double FsPerPs = 1000.0;
+    /**
+     * The number of kJ in a kcal.
+     */
+    static const double KJPerKcal = 4.184;
+    /**
+     * The number of kcal in a kJ.
+     */
+    static const double KcalPerKJ = 1.0/4.184;
+    /**
+     * The number of radians in a degree.
+     */
+    static const double RadiansPerDegree = M_PI/180.0;
+    /**
+     * The number of degrees in a radian.
+     */
+    static const double DegreesPerRadian = 180.0/M_PI;
+
+} // namespace OpenMM
+
+#endif /*OPENMM_UNITS_H_*/