Moving the reference code into the platforms folder

platforms/reference/src/SimTKUtilities/Makefile

+# ---------------------------------------------------------------------------------------
+
+include ../makeConfig/Top.mk
+
+# ---------------------------------------------------------------------------------------
+
+# target is gmxGbsa library
+# ld reference is in ../gromacs/vc7.mk
+# include file reference is in ../gromacs/gmxgpu.h
+
+STATIC_LIBRARY      := gmxUtilities
+
+# ---------------------------------------------------------------------------------------
+
+BaseFiles           := $(SimTkBaseFiles)
+IncludeDirectories  := $(SimTkDirectory) $(GromacsIncludeDirectory)
+
+# ---------------------------------------------------------------------------------------
+
+include $(MakeDirectory)/BaseMake.mk
+
+# ---------------------------------------------------------------------------------------

platforms/reference/src/SimTKUtilities/NewOverrideSimTk.cpp

+
+/* Portions copyright (c) 2006 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * 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 <new>
+#include <stdio.h>
+
+// Replacement new/delete w/ Gromac's smalloc() and sfree()
+
+extern "C" {
+#include "smalloc.h" 
+}
+
+/* ---------------------------------------------------------------------------------------
+
+   Override C++ new w/ Gromac's smalloc/sfree (Simbios)
+
+   @param size						bytes to allocate
+
+   @return ptr to allocated memory
+
+   --------------------------------------------------------------------------------------- */
+
+void* operator new( size_t size ){
+
+   void *ptr;
+   smalloc(ptr, (int) size); 
+
+   // (void) fprintf( stdout, "\nGlobal override new called -- size=%u", size );
+   // (void) fflush( stdout );
+
+   return ptr;
+}
+
+/* ---------------------------------------------------------------------------------------
+
+   Override C++ delete w/ Gromac's sfree (Simbios)
+
+   @param ptr						ptr to block to free
+
+   --------------------------------------------------------------------------------------- */
+
+void operator delete( void *ptr ){
+
+   // (void) fprintf( stdout, "\nGlobal override delete called." );
+   // (void) fflush( stdout );
+
+   sfree( ptr ); 
+}

platforms/reference/src/SimTKUtilities/RealTypeSimTk.h

+
+/* Portions copyright (c) 2006 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * 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.
+ */
+
+
+#ifndef __RealSimTk_H_
+#define __RealSimTk_H__
+
+#ifndef RealType
+#define RealType 1
+#endif 
+
+#if RealType == 1 
+#define Real float
+#define SQRT sqrtf
+#define POW  powf
+#define SIN  sinf
+#define COS  cosf
+#define TAN  tanf
+
+// LOG is used in Vishal's gpu code; modifying LOG -> LN 
+#define LN   logf
+
+#define EXP  expf
+#define FABS fabsf
+#define ACOS acosf
+#define ASIN asinf
+#define ATAN atanf
+#else
+#define Real double
+#define SQRT sqrt
+#define POW  pow
+#define SIN  sin
+#define COS  cos
+#define TAN  tan
+
+// LOG is used in Vishal's gpu code; modifying LOG -> LN 
+#define LN   log
+
+#define EXP  exp
+#define FABS fabs
+#define ACOS acos
+#define ASIN asin
+#define ATAN atan
+#endif
+
+#define DOT3(u,v) ((u[0])*(v[0]) + (u[1])*(v[1]) + (u[2])*(v[2]))
+
+#define MATRIXDOT3(u,v) u[0]*v[0] + u[1]*v[1] + u[2]*v[2] + \
+                        u[3]*v[3] + u[4]*v[4] + u[5]*v[5] + \
+                        u[6]*v[6] + u[7]*v[7] + u[8]*v[8]
+
+#define PI                 3.141592653589f
+#define TWO_SIX            1.122462048309372981f
+#define RADIAN            57.29577951308f
+#define RADIAN_TO_DEGREE  57.29577951308f
+#define LOG_TEN            2.302585092994045684f
+#define SQRT_TWO           1.41421356237309504f
+#define RADIAN_INVERSE     0.01745329252f
+#define DEGREE_TO_RADIAN   0.01745329252f
+
+#endif // __RealSimTk_H__

platforms/reference/src/SimTKUtilities/SimTKOpenMMCommon.cpp

+
+/* Portions copyright (c) 2006 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * 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 "SimTKOpenMMCommon.h"
+
+// static settings
+
+// initialization of static data members
+
+const std::string SimTKOpenMMCommon::NotSet                  = std::string( "NotSet" );
+const std::string SimTKOpenMMCommon::Comment                 = std::string( "#" );
+const std::string SimTKOpenMMCommon::Tab                     = std::string( "\t" ); 
+
+const int SimTKOpenMMCommon::DefaultReturn                   = 0;
+const int SimTKOpenMMCommon::ErrorReturn                     = -1;
+const RealOpenMM SimTKOpenMMCommon::BigCutoffValue           = 1.0e+05;
+
+// units
+
+const int SimTKOpenMMCommon::MdUnits                         = 1;
+const int SimTKOpenMMCommon::KcalAngUnits                    = 2;
+
+// specify RealOpenMM number format
+  
+const int SimTKOpenMMCommon::HighStringStreamNumberWidth     = 20;   
+const int SimTKOpenMMCommon::HighStringStreamNumberPrecision = 12;
+
+const RealOpenMM SimTKOpenMMCommon::DegreeToRadians          = (RealOpenMM) 0.017453292;
+

platforms/reference/src/SimTKUtilities/SimTKOpenMMCommon.h

+
+/* Portions copyright (c) 2006 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * 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.
+ */
+
+#ifndef __SimTKOpenMMCommon_H__
+#define __SimTKOpenMMCommon_H__
+
+// include file containing entries commonly used
+
+// STL includes
+
+#include <vector>
+#include <map>
+#include <set>
+#include <string>
+
+// generic c includes
+
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+#include <ctype.h>
+#include <math.h>
+#include <assert.h>
+
+// ---------------------------------------------------------------------------------------
+
+#include "SimTKOpenMMRealType.h"
+#include "SimTKOpenMMWindowLinux.h"
+
+// ---------------------------------------------------------------------------------------
+
+typedef std::vector<int> IntVector;
+typedef IntVector::iterator IntVectorI;
+typedef IntVector::const_iterator IntVectorCI;
+typedef IntVector::reverse_iterator IntVectorRI;
+typedef IntVector::const_reverse_iterator IntVectorCRI;
+
+typedef std::map<int, int> IntIntMap;
+typedef IntIntMap::iterator IntIntMapI;
+typedef IntIntMap::const_iterator IntIntMapCI;
+
+typedef std::set<int> IntSet;
+typedef IntSet::iterator IntSetI;
+typedef IntSet::const_iterator IntSetCI;
+
+typedef std::vector<IntSet> IntSetVector;
+typedef IntSetVector::iterator IntSetVectorI;
+typedef IntSetVector::const_iterator IntSetVectorCI;
+
+typedef std::multiset<int> IntMultiSet;
+typedef IntMultiSet::iterator IntMultiSetI;
+typedef IntMultiSet::const_iterator IntMultiSetCI;
+
+typedef std::vector<std::string> StringVector;
+typedef StringVector::iterator StringVectorI;
+typedef StringVector::const_iterator StringVectorCI;
+
+typedef std::map<std::string, std::string> StringStringMap;
+typedef StringStringMap::iterator StringStringMapI;
+typedef StringStringMap::const_iterator StringStringMapCI;
+
+typedef std::vector<RealOpenMM> RealOpenMMVector;
+typedef RealOpenMMVector::iterator RealOpenMMVectorI;
+typedef RealOpenMMVector::const_iterator RealOpenMMVectorCI;
+
+typedef std::vector<RealOpenMM*> RealOpenMMPtrVector;
+typedef RealOpenMMPtrVector::iterator RealOpenMMPtrVectorI;
+typedef RealOpenMMPtrVector::const_iterator RealOpenMMPtrVectorCI;
+
+typedef std::vector<RealOpenMM**> RealOpenMMPtrPtrVector;
+typedef RealOpenMMPtrPtrVector::iterator RealOpenMMPtrPtrVectorI;
+typedef RealOpenMMPtrPtrVector::const_iterator RealOpenMMPtrPtrVectorCI;
+
+typedef std::map<std::string, RealOpenMM> StringRealOpenMMMap;
+typedef StringRealOpenMMMap::iterator StringRealOpenMMMapI;
+typedef StringRealOpenMMMap::const_iterator StringRealOpenMMMapCI;
+
+typedef std::map<std::string, int> StringIntMap;
+typedef StringIntMap::iterator StringIntMapI;
+typedef StringIntMap::const_iterator StringIntMapCI;
+
+// ---------------------------------------------------------------------------------------
+
+class SimTKOpenMMCommon {
+
+   public:
+
+      static const std::string NotSet;
+      static const RealOpenMM BigCutoffValue;
+      static const std::string Comment;
+      static const std::string Tab;
+      static const std::string YesU;
+      static const std::string YesUl;
+      static const std::string YesL;
+
+      // subroutine returns
+
+      static const int DefaultReturn;
+      static const int ErrorReturn;
+
+      // units
+
+      static const int MdUnits;
+      static const int KcalAngUnits;
+
+      // specify RealOpenMM number format
+  
+      static const int HighStringStreamNumberWidth;
+      static const int HighStringStreamNumberPrecision;
+
+      static const RealOpenMM DegreeToRadians;
+
+      /**---------------------------------------------------------------------------------------
+      
+         Get string w/ minimum desired width
+      
+         @param inputString   input string
+         @param desiredSize   minimum desired size of output string
+         @param spacer        string to append to inputString to get desired width (" ")
+      
+         @return DefaultReturn
+      
+         --------------------------------------------------------------------------------------- */
+      
+      static std::string getSpacedString( const std::string&, int desiredSize = 25,
+                                          const std::string& spacer = " " );
+};
+
+// ---------------------------------------------------------------------------------------
+
+// StringComparisonForMap: used to compare strings in STL maps w/ strings as keys
+
+#ifndef StringComparisonForMapPtrBlcok
+#define StringComparisonForMapPtrBlcok
+
+// above define should be removed once CommonTk is removed
+
+class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > {
+
+   public:
+
+      bool operator()( const std::string* str1, const std::string* str2 ) const {
+         return strcmp( str1->c_str(), str2->c_str() ) < 0;
+      }
+};
+
+class StringComparisonForMap : public std::binary_function< const std::string&, const std::string&, bool > {
+
+   public:
+
+      bool operator()( const std::string& str1, const std::string& str2 ) const {
+         return strcmp( str1.c_str(), str2.c_str() ) < 0;
+      }
+};
+#endif
+
+// ---------------------------------------------------------------------------------------
+
+// Used to compare integers for sorting, ...
+
+int numericCompareI( const void* point1, const void* point2 );
+
+// ---------------------------------------------------------------------------------------
+
+// string-string map and iterator definitions
+
+typedef std::map<std::string, std::string, StringComparisonForMap> StringMap;
+typedef StringMap::iterator StringMapI;
+typedef StringMap::const_iterator StringMapCI;
+
+// string set and iterator definitions
+
+typedef std::set<std::string, StringComparisonForMap> StringSet;
+typedef StringSet::iterator StringSetI;
+typedef StringSet::const_iterator StringSetCI;
+
+// ---------------------------------------------------------------------------------------
+
+#endif // __SimTKOpenMMCommon_H__

platforms/reference/src/SimTKUtilities/SimTKOpenMMGpuUtilities.h

+
+/* Portions copyright (c) 2006 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * 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.
+ */
+
+#ifndef __SimTKOpenMMGpuUtilities_H_
+#define __SimTKOpenMMGpuUtilities_H_
+
+// ---------------------------------------------------------------------------------------
+
+// reserve the option to change between Real and double
+
+#include "SimTKOpenMMRealType.h" 
+#include "SimTKOpenMMCommon.h" 
+
+// ---------------------------------------------------------------------------------------
+
+// class of shared, static utility methods
+
+#include <stdio.h>
+#include <string.h>
+#include <string>
+#include <stdlib.h>
+#include <sstream>
+
+// #include <string>
+
+// ---------------------------------------------------------------------------------------
+
+/**---------------------------------------------------------------------------------------
+
+   Class of static methods to be shared
+   Most methods are standalone 'utility' methods
+
+--------------------------------------------------------------------------------------- */
+
+class SimTKOpenMMGpuUtilities {
+
+   public:
+
+      // dummy constructor/destructor
+
+       SimTKOpenMMGpuUtilities(){};
+      ~SimTKOpenMMGpuUtilities(){};
+
+      /**---------------------------------------------------------------------------------------
+      
+         Helper method to repack RealOpenMM arrays (Simbios)
+      
+         @param numberOfEntries     entries/sub-array
+         @param subarraySize        number of subarrays
+         @param array               array
+      
+         Input array = [subArray_1 subArray_2 subArray_3 ... subArray_Stacked] \n
+                where each subArray_i is 1 x numberOfEntries
+      
+         Output array = [ subArray_1_1 subArray_2_1 subArray_3_1 ... subArray_Stacked_1 \n
+                           subArray_1_2 subArray_2_2 subArray_3_2 ... subArray_Stacked_2 \n
+                           subArray_1_3 subArray_2_3 subArray_3_3 ... subArray_Stacked_3 \n
+                           ... \n
+                           subArray_1_N subArray_2_N subArray_3_N ... subArray_Stacked_N ] \n
+
+         where N = numberOfEntries
+
+         @return SimTKOpenMMCommon::DefaultReturn 
+      
+         --------------------------------------------------------------------------------------- */
+      
+      static int repackArray1( int numberOfEntries, int subarraySize, RealOpenMM* array );
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Copy an array into a packed (e.g., RealOpenMM4 array) (Simbios)
+      
+         Example copy Born radii into last slot of force array
+      
+         @param numberOfEntries     entries/sub-array (no. atoms)
+         @param subarraySize        number of subarrays (4 for RealOpenMM4)
+         @param fullArray           full array (force array in example)
+         @param copySlot            index of slot to copied into (3 in example, since want Born radius in .w slot)
+         @param arrayToCopy         array to copy (Born array)
+      
+         @return SimTKOpenMMCommon::DefaultReturn 
+      
+         --------------------------------------------------------------------------------------- */
+      
+      static int copySubArray( int numberOfEntries, int subarraySize, RealOpenMM* fullArray,
+                               int copySlot, RealOpenMM* arrayToCopy );
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Helper method to repack RealOpenMM arrays (Simbios)
+      
+         @param numberOfEntries     entries/sub-array
+         @param subarraySize        number of subarrays
+         @param array               array
+      
+         Input array = [subArray_1 subArray_2 subArray_3 ... subArray_N] \n
+       
+                where each subArray_i is vector of length M=numberOfEntries \n
+       
+         Output array = [ subArray_1_1 subArray_2_1 subArray_3_1 ... subArray_N_1 \n
+                           subArray_1_2 subArray_2_2 subArray_3_2 ... subArray_N_2 \n
+                           subArray_1_3 subArray_2_3 subArray_3_3 ... subArray_N_3 \n
+                           ... \n
+                           subArray_1_M subArray_2_M subArray_3_M ... subArray_M ] \n
+         where N = numberOfEntries \n
+
+         @return SimTKOpenMMCommon::DefaultReturn 
+      
+         --------------------------------------------------------------------------------------- */
+      
+      static int repackArray( int numberOfEntries, int subarraySize, RealOpenMM* array );
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Helper method to repack RealOpenMM arrays (Simbios)
+      
+         @param numberOfEntries     entries/sub-array
+         @param subarraySize        number of subarrays
+         @param array               repacked output array
+         @param inputArrays         inputArrays[subarraySize][numberOfEntries]
+      
+         Output array = [ inputArrays[0][0]     inputArrays[1][0]    inputArrays[2][0] inputArrays[3][0] \n
+                           inputArrays[0][1]     inputArrays[1][1]    inputArrays[2][1] inputArrays[3][1] \n
+                           inputArrays[0][2]     inputArrays[1][2]    inputArrays[2][2] inputArrays[3][2] \n
+       
+                           ... \n
+                           inputArrays[0][numberOfEntries] ... inputArrays[subarraySize-1][numberOfEntries] \n
+                         ] \n
+         where N = numberOfEntries \n
+      
+      
+         @return SimTKOpenMMCommon::DefaultReturn 
+      
+         --------------------------------------------------------------------------------------- */
+      
+      static int repackArrayOfArrays( int numberOfEntries, int subarraySize,
+                                      RealOpenMM* array, RealOpenMM** inputArrays );
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Collapse 2D array into packed single array (Simbios)
+         Example forces[3][N] -> array of size N containing RealOpenMM3 values 
+      
+         @param numberOfEntries     entries (no. atoms)
+         @param iUnroll             iUnroll
+         @param jUnroll             jUnroll
+         @param arrays              arrays to be merged (dimension is [iUnroll][numberOfEntries/iUnroll]
+         @param mergeArray          output array (if null, then allocated)
+         @param log                 logging file descriptor
+      
+         @return SimTKOpenMMCommon::DefaultReturn 
+      
+         --------------------------------------------------------------------------------------- */
+      
+      static RealOpenMM* collapseArrays( int numberOfEntries, int iUnroll, int jUnroll,
+                                         RealOpenMM** arrays, RealOpenMM* mergeArray, FILE* log );
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Merge 2 arrays based on sentinel value  (Simbios)
+         Overflow array, if present, signals which entries had nonsentinel in both arrays
+      
+         Example   \n
+                   array1 = { 1, 2, 3, s, s, s, 4, 5, s } \n
+                   array2 = { s, s, 6, 8, 9, 3, s, 7, s } \n
+             merge array  = { 1, 2, 3, 8, 9, 3, 4, 5, s } \n
+          overflow array  = { s, s, 6, s, s, s, s, 7, s } \n
+      
+         @param numberOfEntries     entries (no. atoms)
+         @param sentinelValue       sentinel value
+         @param array1              first array
+         @param array2              second array
+         @param mergeArray          output merge array
+         @param overflowArray       output overflow array  (if null, then ignored)
+         @param log                 logging file descriptor
+      
+         @return SimTKOpenMMCommon::DefaultReturn 
+      
+         --------------------------------------------------------------------------------------- */
+      
+      static int mergeArraysBasedSentinelValue( int numberOfEntries,
+                                                RealOpenMM sentinelValue,
+                                                RealOpenMM* array1, RealOpenMM* array2, 
+                                                RealOpenMM* mergeArray, RealOpenMM* overflowArray,
+                                                FILE* log );
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Helper method to store values from CPU loop in position seen in GPU output (Simbios)
+      
+         --------------------------------------------------------------------------------------- */
+      
+      static int storeInGpuFormat( int atomI, int atomJ, int debugAtomJ,
+                                   int jUnroll, int numberOfStreams,
+                                   RealOpenMM** debugStreams, RealOpenMM* RealOpenMMValues[2],
+                                   RealOpenMM unsetDebugValue, bool useUpper, FILE* log );
+
+      /**---------------------------------------------------------------------------------------
+      
+         Helper method to compare cpu and gpu computed arrays
+      
+         @param numberOfAtoms       entries (no. atoms)
+         @param chunkSize           chunk size (usually 3 or 4)
+         @param cpuArray            cpuArray[0-(chunkSize-1)][0,entries-1]
+         @param gpuArray            gpuArray[chunkSize*entries]
+         @param tolerance           check if relative difference is greater
+                                    than this tolerance
+         @param compareColumn       array of size [chunkSize] signalling whether
+                                    column i is to be compared; it may be NULL
+         @param absoluteMin         error if abs(cpu) + abs(gpu) > absoluteMin
+                                    set negative to ignore this condition
+         @param printOn             if not set, then no printing
+         @param header              id header -- optional
+         @param log                 logging file descriptor
+      
+         @return number of failed entries 
+      
+         --------------------------------------------------------------------------------------- */
+      
+      static int compareCpuGpuArrays( int numberOfAtoms, int chunkSize,
+                                      RealOpenMM** cpuArray, RealOpenMM* gpuArray,
+                                      RealOpenMM tolerance,
+                                      int* compareColumn, RealOpenMM absoluteMin,
+                                      int printOn, const char* header, FILE* log );
+
+   // ---------------------------------------------------------------------------------------
+
+};
+   
+// ---------------------------------------------------------------------------------------
+
+#endif // __SimTKOpenMMGpuUtilities_H__

platforms/reference/src/SimTKUtilities/SimTKOpenMMWindowLinux.h

+
+/* Portions copyright (c) 2006 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * 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.
+ */
+
+
+#ifndef __SimTKOpenMMWindowLinux_H_
+#define __SimTKOpenMMWindowLinux_H__
+
+#ifdef WIN32
+#define FOPEN fopen_s
+#else
+#define FOPEN fopen
+#endif
+
+
+#endif // __SimTKOpenMMWindowLinux_H__

platforms/reference/src/SimTKUtilities/SimTk-old-2005.sln

+
+Microsoft Visual Studio Solution File, Format Version 9.00
+# Visual Studio 2005
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "SimTk", "SimTk-old-2005.vcproj", "{82165226-E7AC-4C35-8914-80C31C7B4754}"
+EndProject
+Global
+	GlobalSection(SolutionConfigurationPlatforms) = preSolution
+		Debug|Win32 = Debug|Win32
+		Release|Win32 = Release|Win32
+	EndGlobalSection
+	GlobalSection(ProjectConfigurationPlatforms) = postSolution
+		{82165226-E7AC-4C35-8914-80C31C7B4754}.Debug|Win32.ActiveCfg = Debug|Win32
+		{82165226-E7AC-4C35-8914-80C31C7B4754}.Debug|Win32.Build.0 = Debug|Win32
+		{82165226-E7AC-4C35-8914-80C31C7B4754}.Release|Win32.ActiveCfg = Release|Win32
+		{82165226-E7AC-4C35-8914-80C31C7B4754}.Release|Win32.Build.0 = Release|Win32
+	EndGlobalSection
+	GlobalSection(SolutionProperties) = preSolution
+		HideSolutionNode = FALSE
+	EndGlobalSection
+EndGlobal