Mods

platforms/brook/src/BrookStochasticDynamics.h

+#ifndef OPENMM_BROOK_STOCHASTIC_DYNAMCIS_H_
+#define OPENMM_BROOK_STOCHASTIC_DYNAMCIS_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, Mark Friedrichs                                    *
+ * 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 <vector>
+#include <set>
+
+#include "BrookFloatStreamInternal.h"
+#include "BrookPlatform.h"
+#include "BrookCommon.h"
+
+namespace OpenMM {
+
+/**
+ *
+ * Encapsulates stochastic dynamics algorithm 
+ *
+ */
+
+class BrookStochasticDynamics : public BrookCommon {
+
+   public:
+  
+      // return values
+
+      static const int DefaultReturnValue = 0;
+      static const int ErrorReturnValue   = -1;
+
+      /** 
+       * Constructor
+       * 
+       */
+      
+      BrookStochasticDynamics( );
+  
+      /** 
+       * Destructor
+       * 
+       */
+      
+      ~BrookStochasticDynamics();
+  
+      /**
+       * Get StochasticDynamics atom stream width
+       *
+       * @return atom stream width
+       */
+
+      int getStochasticDynamicsAtomStreamWidth( void ) const; 
+
+      /**
+       * Get StochasticDynamics atom stream height
+       *
+       * @return atom stream height
+       */
+
+      int getStochasticDynamicsAtomStreamHeight( void ) const;
+
+      /**
+       * Get StochasticDynamics atom stream size
+       * 
+       * @return atom stream size
+       */
+
+      int getStochasticDynamicsAtomStreamSize( void ) const; 
+
+      /** 
+       * Update parameters
+       * 
+       * @param  temperature     temperature
+       * @param  friction        friction
+       *
+       * @return   solute dielectric
+       *
+       */
+      
+      int updateParameters( double temperature, double friction );
+      
+      /** 
+       * Get array of StochasticDynamics streams 
+       *
+       * @return  array ofstreams
+       *
+       */
+      
+      BrookFloatStreamInternal** getStreams( void );
+      
+      /* 
+       * Setup of StochasticDynamics parameters
+       *
+       * @param atomParameters        vector of OBC parameters [atomI][0=charge]
+       *                                                       [atomI][1=radius]
+       *                                                       [atomI][2=scaling factor]
+       * @param solventDielectric     solvent dielectric
+       * @param soluteDielectric      solute dielectric
+       * @param platform              Brook platform
+       *
+       * @return nonzero value if error
+       *
+       * */
+      
+      int setup( const std::vector<std::vector<double> >& atomParameters, 
+                 double solventDielectric, double soluteDielectric, const Platform& platform  );
+      
+      /* 
+       * Get contents of object
+       *
+       * @param level of dump
+       *
+       * @return string containing contents
+       *
+       * */
+      
+      std::string getContentsString( int level = 0 ) const;
+
+   private:
+   
+      enum FixedParameters   { GDT, EPH, EMH, EP, EM, B, C, D, V, X, Yv, Yx, MaxFixedParameters };
+      enum TwoDArrayIndicies { X2D, V2D, OldV, xPrime2D, vPrime2D, Max2DArrays };
+      enum OneDArrayIndicies { InverseMasses, Max1DArrays };
+
+      RealOpenMM _fixedParameters[MaxFixedParameters];
+
+      // streams indices
+
+      enum { 
+              SDPC1Stream,
+              SDPC2Stream,
+              SD2XStream,
+              SD1VStream,
+              LastStreamIndex
+           };
+
+      // Atom stream dimensions
+
+      int _sdAtomStreamWidth;
+      int _sdAtomStreamHeight;
+      int _sdAtomStreamSize;
+
+      // inverse masses
+
+      vector<BrookOpenMMFloat>& _inverseMasses;
+
+      // internal streams
+
+      BrookFloatStreamInternal* _sdStreams[LastStreamIndex];
+
+      /* 
+       * Setup of stream dimensions
+       *
+       * @param atomStreamSize        atom stream size
+       * @param atomStreamWidth       atom stream width
+       *
+       * @return ErrorReturnValue if error, else DefaultReturnValue
+       *
+       * */
+      
+      int initializeStreamSizes( int atomStreamSize, int atomStreamWidth );
+
+      /** 
+       * Initialize stream dimensions
+       * 
+       * @param numberOfAtoms             number of atoms
+       * @param platform                  platform
+       *
+       * @return ErrorReturnValue if error, else DefaultReturnValue
+       *
+       */
+      
+      int initializeStreamSizes( int numberOfAtoms, const Platform& platform );
+      
+      /** 
+       * Initialize stream dimensions and streams
+       * 
+       * @param platform                  platform
+       *
+       * @return nonzero value if error
+       *
+       */
+      
+      int initializeStreams( const Platform& platform );
+      
+};
+
+} // namespace OpenMM
+
+#endif /* OPENMM_BROOK_STOCHASTIC_DYNAMCIS_H_ */

platforms/brook/src/gpu/kgbsa.h

+#ifndef __KGBSA_H__
+#define __KGBSA_H__
+
+void kMergeFloat4( 
+      const float repfac, 
+      const float atomStrWidth, 
+      const float pforceStrWidth,
+      const float natoms,
+      const float iUnroll,
+      ::brook::stream stream1, 
+      ::brook::stream stream2, 
+      ::brook::stream outputStream 
+                 );
+
+void kMergeFloat4_4( 
+      const float repfac, 
+      const float atomStrWidth, 
+      const float pforceStrWidth,
+      const float natoms,
+      const float roundNatoms,
+      const float iUnroll,
+      ::brook::stream stream1, 
+      ::brook::stream stream2, 
+      ::brook::stream stream3, 
+      ::brook::stream stream4, 
+      ::brook::stream outputStream 
+                 );
+
+void kMergeFloat4_4X( 
+      const float repfac, 
+      const float atomStrWidth, 
+      const float pforceStrWidth,
+      const float natoms,
+      const float roundNatoms,
+      const float iUnroll,
+      ::brook::stream stream1, 
+      ::brook::stream stream2, 
+      ::brook::stream stream3, 
+      ::brook::stream stream4, 
+      ::brook::stream outputStream 
+                 );
+
+void kCheck( 
+      const float natoms,
+      const float atomStrWidth, 
+      const float pforceStrWidth,
+      const float unroll,
+      ::brook::stream stream1
+                 );
+
+void kAddAndMergeFloat4( 
+      const float repfac, 
+      const float atomStrWidth, 
+      const float pforceStrWidth,
+      const float natoms,
+      const float iUnroll,
+      ::brook::stream inStream, 
+      ::brook::stream stream1, 
+      ::brook::stream stream2, 
+      ::brook::stream outputStream 
+                 );
+
+void kAddAndMergeFloat4_4( 
+      const float repfac, 
+      const float atomStrWidth, 
+      const float pforceStrWidth,
+      const float natoms,
+      const float roundNatoms,
+      const float iUnroll,
+      ::brook::stream inStream, 
+      ::brook::stream stream1, 
+      ::brook::stream stream2, 
+      ::brook::stream stream3, 
+      ::brook::stream stream4, 
+      ::brook::stream outputStream 
+                 );
+
+void kPostObcLoop2( 
+      const float repfac, 
+      const float atomStrWidth, 
+      const float pforceStrWidth,
+      const float natoms,
+      const float roundNatoms,
+      const float iUnroll,
+      const float conversion,
+      const float mergeNonObcForces,
+      ::brook::stream inObcForces, 
+      ::brook::stream nonObcForces, 
+      ::brook::stream stream1, 
+      ::brook::stream stream2, 
+      ::brook::stream stream3, 
+      ::brook::stream stream4, 
+      ::brook::stream atomicRadii,
+      ::brook::stream bornRadii,
+      ::brook::stream obcChain,
+      ::brook::stream outputStream 
+                 );
+
+
+void kPostObcLoop2_nobranch( 
+      const float repfac, 
+      const float atomStrWidth, 
+      const float pforceStrWidth,
+      const float natoms,
+      const float roundNatoms,
+      const float iUnroll,
+      const float conversion,
+      const float mergeNonObcForces,
+      ::brook::stream inObcForces, 
+      ::brook::stream nonObcForces, 
+      ::brook::stream stream1, 
+      ::brook::stream stream2, 
+      ::brook::stream stream3, 
+      ::brook::stream stream4, 
+      ::brook::stream atomicRadii,
+      ::brook::stream bornRadii,
+      ::brook::stream obcChain,
+      ::brook::stream outputStream 
+                 );
+
+void kPreGbsaForce2( 
+      ::brook::stream intermediateForceIn, 
+      ::brook::stream bornRadii, 
+      ::brook::stream bornRadii2Force 
+                 );
+
+void kPreObcForce2( 
+      ::brook::stream intermediateForceIn, 
+      ::brook::stream obcChainForceIn, 
+      ::brook::stream bornRadii, 
+      ::brook::stream bornRadii2Force 
+                 );
+
+void kPostObcLoop1( 
+      const float repfac, 
+      const float atomStrWidth, 
+      const float pforceStrWidth,
+      const float natoms,
+      const float roundNatoms,
+      const float iUnroll,
+      ::brook::stream stream1, 
+      ::brook::stream stream2, 
+      ::brook::stream stream3, 
+      ::brook::stream stream4, 
+      ::brook::stream obcChainForceIn, 
+      ::brook::stream bornRadii, 
+      ::brook::stream outputStream, 
+      ::brook::stream bornRadii2Force 
+                 );
+
+
+void kPostObcLoop1_nobranch( 
+      const float repfac, 
+      const float atomStrWidth, 
+      const float pforceStrWidth,
+      const float natoms,
+      const float roundNatoms,
+      const float iUnroll,
+      ::brook::stream stream1, 
+      ::brook::stream stream2, 
+      ::brook::stream stream3, 
+      ::brook::stream stream4, 
+      ::brook::stream obcChainForceIn, 
+      ::brook::stream bornRadii, 
+      ::brook::stream outputStream, 
+      ::brook::stream bornRadii2Force 
+                 );
+
+void kCopyFloat4( 
+      ::brook::stream stream1, 
+      ::brook::stream stream2
+                 );
+
+void kObcLoop1(
+      const float natoms, 
+      const float roundedUpAtoms, 
+      const float dupfac, 
+      const float strwidth, 
+      const float fstrwidth,
+      const float soluteDielectric,
+      const float solventDielectric,
+      const float includeAce,
+      ::brook::stream posq, 
+      ::brook::stream bornRadii, 
+      ::brook::stream atomicRadii, 
+      ::brook::stream bornForce1,
+      ::brook::stream bornForce2,
+      ::brook::stream bornForce3,
+      ::brook::stream bornForce4
+      );
+
+void kCalculateGbsaForce1_4 (
+      const float natoms, 
+      const float roundedUpAtoms, 
+      const float dupfac, 
+      const float strwidth, 
+      const float fstrwidth,
+      const float soluteDielectric,
+      const float solventDielectric,
+      ::brook::stream posq, 
+      ::brook::stream bornRadii, 
+      ::brook::stream nonpolarForce, 
+      ::brook::stream bornForce1,
+      ::brook::stream bornForce2,
+      ::brook::stream bornForce3,
+      ::brook::stream bornForce4
+      );
+
+void kCalculateGbsaForce1_4X (
+      const float natoms, 
+      const float roundedUpAtoms, 
+      const float dupfac, 
+      const float strwidth, 
+      const float fstrwidth,
+      const float soluteDielectric,
+      const float solventDielectric,
+      ::brook::stream posq, 
+      ::brook::stream bornRadii, 
+      ::brook::stream nonpolarForce, 
+      ::brook::stream bornForce1,
+      ::brook::stream bornForce2,
+      ::brook::stream bornForce3,
+      ::brook::stream bornForce4
+      );
+
+void kCalculateGbsaForce2_4 (
+      float natoms, 
+      float dupfac, 
+      float strwidth, 
+      float fstrwidth,
+      ::brook::stream posq, 
+      ::brook::stream  bornRadii,
+      ::brook::stream vdwRadii, 
+      ::brook::stream volume, 
+      ::brook::stream excludeBlockIndices,
+      ::brook::stream inBornForce,
+      ::brook::stream bornForce1,
+      ::brook::stream bornForce2
+      );
+
+void kCalculateGbsaForce2_4Debug (
+      float natoms, 
+      float dupfac, 
+      float strwidth, 
+      float fstrwidth,
+      const float debugJAtom,
+      const float debugReport,
+      ::brook::stream posq, 
+      ::brook::stream  bornRadii,
+      ::brook::stream vdwRadii, 
+      ::brook::stream volume, 
+      ::brook::stream excludeBlockIndices,
+      ::brook::stream inBornForce,
+      ::brook::stream bornForce1,
+      ::brook::stream bornForce2,
+		::brook::stream debugStream1,
+		::brook::stream debugStream2,
+		::brook::stream debugStream3,
+		::brook::stream debugStream4
+      );
+
+void kCalculateGbsaForce2_4Excl (
+      float natoms, 
+      float dupfac, 
+      float strwidth, 
+      float fstrwidth,
+      ::brook::stream posq, 
+      ::brook::stream  bornRadii,
+      ::brook::stream vdwRadii, 
+      ::brook::stream volume, 
+      ::brook::stream excl,
+      ::brook::stream excludeBlockIndices,
+      ::brook::stream inBornForce,
+      ::brook::stream bornForce1,
+      ::brook::stream bornForce2
+      );
+
+void kCalculateGbsaForce2_4ExclDebug (
+      float natoms, 
+      float dupfac, 
+      float strwidth, 
+      float fstrwidth,
+      const float debugJAtom,
+      const float debugReport,
+      ::brook::stream posq, 
+      ::brook::stream  bornRadii,
+      ::brook::stream vdwRadii, 
+      ::brook::stream volume, 
+      ::brook::stream excl,
+      ::brook::stream excludeBlockIndices,
+      ::brook::stream inBornForce,
+      ::brook::stream bornForce1,
+      ::brook::stream bornForce2,
+		::brook::stream debugStream1,
+		::brook::stream debugStream2,
+		::brook::stream debugStream3,
+		::brook::stream debugStream4
+      );
+
+void kCalculateGbsaForce2_2 (
+      float natoms, 
+      float dupfac, 
+      float strwidth, 
+      float fstrwidth,
+      ::brook::stream posq, 
+      ::brook::stream  bornRadii,
+      ::brook::stream vdwRadii, 
+      ::brook::stream volume, 
+      ::brook::stream excludeBlockIndices,
+      ::brook::stream inBornForce,
+      ::brook::stream bornForce1,
+      ::brook::stream bornForce2
+      );
+
+void kCalculateGbsaForce2_2Debug (
+      float natoms, 
+      float dupfac, 
+      float strwidth, 
+      float fstrwidth,
+      const float debugJAtom,
+      const float debugReport,
+      ::brook::stream posq, 
+      ::brook::stream  bornRadii,
+      ::brook::stream vdwRadii, 
+      ::brook::stream volume, 
+      ::brook::stream excludeBlockIndices,
+      ::brook::stream inBornForce,
+      ::brook::stream bornForce1,
+      ::brook::stream bornForce2,
+		::brook::stream debugStream1,
+		::brook::stream debugStream2,
+		::brook::stream debugStream3,
+		::brook::stream debugStream4
+      );
+
+void kCalculateGbsaForce2_2Excl (
+      float natoms, 
+      float dupfac, 
+      float strwidth, 
+      float fstrwidth,
+      ::brook::stream posq, 
+      ::brook::stream  bornRadii,
+      ::brook::stream vdwRadii, 
+      ::brook::stream volume, 
+      ::brook::stream excl,
+      ::brook::stream excludeBlockIndices,
+      ::brook::stream inBornForce,
+      ::brook::stream bornForce1,
+      ::brook::stream bornForce2
+      );
+
+void kCalculateGbsaForce2_2ExclDebug (
+      float natoms, 
+      float dupfac, 
+      float strwidth, 
+      float fstrwidth,
+      const float debugJAtom,
+      const float debugReport,
+      ::brook::stream posq, 
+      ::brook::stream  bornRadii,
+      ::brook::stream vdwRadii, 
+      ::brook::stream volume, 
+      ::brook::stream excl,
+      ::brook::stream excludeBlockIndices,
+      ::brook::stream inBornForce,
+      ::brook::stream bornForce1,
+      ::brook::stream bornForce2,
+		::brook::stream debugStream1,
+		::brook::stream debugStream2,
+		::brook::stream debugStream3,
+		::brook::stream debugStream4
+      );
+
+void kBornRadii(
+      ::brook::stream gpolNonBonded, 
+      ::brook::stream gPolFixed,
+      ::brook::stream bornRadii
+      );
+
+void kPostGbsaForce2Debug (
+      float natoms, 
+      float dupfac, 
+      float strwidth, 
+      float fstrwidth,
+      const float debugJAtom,
+      const float debugReport,
+      ::brook::stream inBornForce2, 
+		::brook::stream gPolFixed,
+      ::brook::stream  bornRadii,
+		::brook::stream debugStream1,
+		::brook::stream debugStream2,
+		::brook::stream debugStream3,
+		::brook::stream debugStream4
+      );
+
+void kCalculateGbsaForce2_1_4 (
+      float natoms, 
+      float dupfac, 
+      float strwidth, 
+      float fstrwidth,
+      ::brook::stream posq, 
+      ::brook::stream  bornRadii,
+      ::brook::stream vdwRadii, 
+      ::brook::stream volume, 
+      ::brook::stream excludeBlockIndices,
+      ::brook::stream inBornForce,
+      ::brook::stream bornForce1
+      );
+
+void kCalculateGbsaForce2_1_4Debug (
+      float natoms, 
+      float dupfac, 
+      float strwidth, 
+      float fstrwidth,
+      const float debugJAtom,
+      const float debugReport,
+      ::brook::stream posq, 
+      ::brook::stream  bornRadii,
+      ::brook::stream vdwRadii, 
+      ::brook::stream volume, 
+      ::brook::stream excludeBlockIndices,
+      ::brook::stream inBornForce,
+      ::brook::stream bornForce1,
+		::brook::stream debugStream1,
+		::brook::stream debugStream2,
+		::brook::stream debugStream3,
+		::brook::stream debugStream4
+      );
+
+void kCalculateGbsaForce2_1_4Excl (
+      float natoms, 
+      float dupfac, 
+      float strwidth, 
+      float fstrwidth,
+      ::brook::stream posq, 
+      ::brook::stream  bornRadii,
+      ::brook::stream vdwRadii, 
+      ::brook::stream volume, 
+      ::brook::stream excl,
+      ::brook::stream excludeBlockIndices,
+      ::brook::stream inBornForce,
+      ::brook::stream bornForce1
+      );
+
+void kCalculateGbsaForce2_1_4ExclDebug (
+      float natoms, 
+      float dupfac, 
+      float strwidth, 
+      float fstrwidth,
+      const float debugIAtom,
+      const float debugJAtom,
+      const float debugReport,
+      ::brook::stream posq, 
+      ::brook::stream  bornRadii,
+      ::brook::stream vdwRadii, 
+      ::brook::stream volume, 
+      ::brook::stream excl,
+      ::brook::stream excludeBlockIndices,
+      ::brook::stream inBornForce,
+      ::brook::stream bornForce1,
+		::brook::stream debugStream1,
+		::brook::stream debugStream2,
+		::brook::stream debugStream3,
+		::brook::stream debugStream4
+      );
+
+void kObcLoop2(
+      float numberOfAtoms, 
+      float roundNatoms,
+      float duplicationFactor, 
+      float streamWidth, 
+      float fstreamWidth,
+      ::brook::stream posq, 
+      ::brook::stream atomicRadii, 
+      ::brook::stream scaledAtomicRadii, 
+      ::brook::stream bornForceFactor, 
+      ::brook::stream bornForce1,
+      ::brook::stream bornForce2,
+      ::brook::stream bornForce3,
+      ::brook::stream bornForce4
+      );
+
+void kObcBornRadii(
+      float numberOfAtoms, 
+      float streamWidth, 
+      ::brook::stream bornForce, 
+      ::brook::stream atomicRadii, 
+      ::brook::stream bornRadii,
+      ::brook::stream obcChain
+      );
+
+void kAceNonPolar(
+      float soluteDielectric,
+      float solventDielectric,
+      ::brook::stream posq, 
+      ::brook::stream bornRadii, 
+      ::brook::stream vdwRadii, 
+      ::brook::stream bornForce
+      );
+
+void kZeroFloat4( ::brook::stream bornForce );
+void kSetValue4( float value, ::brook::stream bornForce );
+void kSetValue3( float value, ::brook::stream bornForce );
+void kSetValue2( float value, ::brook::stream bornForce );
+void kSetValue1( float value, ::brook::stream bornForce );
+
+void kCopyFloat3To4( ::brook::stream inForce, ::brook::stream outForce );
+
+void kObcLoop2Cdlj4( float numberOfAtoms, float roundedUpAtoms, float duplicationFactor, 
+                     float streamWidth, float fstreamWidth,
+                     float jstreamWidth, float epsfac, 
+                     ::brook::stream posq, 
+                     ::brook::stream atomicRadii,
+                     ::brook::stream scaledAtomicRadii, 
+                     ::brook::stream bornForceFactor,
+                     ::brook::stream isigeps,
+                     ::brook::stream sigma,
+                     ::brook::stream epsilon,
+                     ::brook::stream excl,
+                     ::brook::stream bornForce1,
+                     ::brook::stream bornForce2,
+                     ::brook::stream bornForce3,
+                     ::brook::stream bornForce4 );
+
+#endif //__KGBSA_H__