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Commit 248a01f4 authored by Mark Friedrichs's avatar Mark Friedrichs
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Library to check that forces agree across platforms

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libraries/validate/include/ValidateOpenMM.h 0 → 100644
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#ifndef VALIDATE_OPENMM_H_
#define VALIDATE_OPENMM_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: *
* *
* This program is free software: you can redistribute it and/or modify *
* it under the terms of the GNU Lesser General Public License as published *
* by the Free Software Foundation, either version 3 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* *
* You should have received a copy of the GNU Lesser General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* -------------------------------------------------------------------------- */
#include "OpenMM.h"
#include "../../../platforms/reference/include/ReferencePlatform.h"
#include "openmm/Context.h"
#include "openmm/System.h"
// free-energy plugin includes
//#define INCLUDE_FREE_ENERGY_PLUGIN
#ifdef INCLUDE_FREE_ENERGY_PLUGIN
#include "../../../plugins/freeEnergy/openmmapi/include/OpenMMFreeEnergy.h"
#include "../../../plugins/freeEnergy/openmmapi/include/openmm/freeEnergyKernels.h"
#include "../../../plugins/freeEnergy/platforms/reference/include/ReferenceFreeEnergyPlatform.h"
#endif
#include <sstream>
#include <typeinfo>
#ifdef _MSC_VER
#define isinf !_finite
#define isnan _isnan
#endif
namespace OpenMM {
typedef std::map< std::string, int > StringIntMap;
typedef StringIntMap::iterator StringIntMapI;
typedef StringIntMap::const_iterator StringIntMapCI;
typedef std::map< std::string, double > StringDoubleMap;
typedef StringDoubleMap::iterator StringDoubleMapI;
typedef StringDoubleMap::const_iterator StringDoubleMapCI;
typedef std::map< std::string, unsigned int > StringUIntMap;
typedef StringUIntMap::iterator StringUIntMapI;
typedef StringUIntMap::const_iterator StringUIntMapCI;
typedef std::vector< std::string > StringVector;
typedef StringVector::iterator StringVectorI;
typedef StringVector::const_iterator StringVectorCI;
typedef std::vector< int > IntVector;
typedef IntVector::iterator IntVectorI;
typedef IntVector::const_iterator IntVectorCI;
typedef std::map< std::string, std::vector<std::string> > StringStringVectorMap;
typedef StringStringVectorMap::iterator StringStringVectorMapI;
typedef StringStringVectorMap::const_iterator StringStringVectorMapCI;
/**
* Base class w/ common functionality
*/
class ValidateOpenMM {
public:
ValidateOpenMM( void );
~ValidateOpenMM();
// force names
static const std::string HARMONIC_BOND_FORCE;
static const std::string HARMONIC_ANGLE_FORCE;
static const std::string PERIODIC_TORSION_FORCE;
static const std::string RB_TORSION_FORCE;
static const std::string NB_FORCE;
static const std::string NB_SOFTCORE_FORCE;
static const std::string NB_EXCEPTION_FORCE;
static const std::string NB_EXCEPTION_SOFTCORE_FORCE;
static const std::string GBSA_OBC_FORCE;
static const std::string GBSA_OBC_SOFTCORE_FORCE;
static const std::string GBVI_FORCE;
static const std::string GBVI_SOFTCORE_FORCE;
static const std::string CM_MOTION_REMOVER;
static const std::string ANDERSEN_THERMOSTAT;
static const std::string CUSTOM_BOND_FORCE;
static const std::string CUSTOM_EXTERNAL_FORCE;
static const std::string CUSTOM_NONBONDED_FORCE;
/**
* Return true if input number is nan
*
* @param number number to test
*
* @return true if number is nan
*/
static int isNan( double number );
/**
* Get force name
*
* @param force OpenMM system force
*
* @return force name or "NA" if force is not recognized
*/
std::string getForceName(const Force& force ) const;
/**
* Copy force
*
* @param force OpenMM system force to copy
*
* @return force or NULL if not recognized
*/
Force* copyForce(const Force& force) const;
/**
* Get copy of input system, but omit forces
*
* @param systemToCopy system to copy
*
* @return copy of system but w/o forces
*/
System* copySystemExcludingForces( const System& systemToCopy ) const;
/**
*
* Set the velocities/positions of context2 to those of context1
*
* @param context1 context1
* @param context2 context2
*
* @return 0
*/
void synchContexts( const Context& context1, Context& context2 ) const;
/**
*
* Get log FILE* reference
*
* @return log
*
*/
FILE* getLog( ) const;
/**
*
* Set log FILE* reference
*
* @param log log
*
*/
void setLog( FILE* log );
/**---------------------------------------------------------------------------------------
Copy harmonic bond force
@param forceToCopy force to copy
@param log log file pointer -- may be NULL
@return copy of force
--------------------------------------------------------------------------------------- */
Force* copyHarmonicBondForce( const HarmonicBondForce& forceToCopy, FILE* log = NULL ) const;
/**---------------------------------------------------------------------------------------
Copy harmonic angle
@param forceToCopy force to copy
@param log log file pointer -- may be NULL
@return copy of force
--------------------------------------------------------------------------------------- */
Force* copyHarmonicAngleForce( const HarmonicAngleForce& forceToCopy, FILE* log = NULL ) const;
/**---------------------------------------------------------------------------------------
Copy PeriodicTorsionForce
@param forceToCopy force to copy
@param log log file pointer -- may be NULL
@return copy of force
--------------------------------------------------------------------------------------- */
Force* copyPeriodicTorsionForce( const PeriodicTorsionForce& forceToCopy, FILE* log = NULL ) const;
/**---------------------------------------------------------------------------------------
Copy RBTorsionForce
@param forceToCopy force to copy
@param log log file pointer -- may be NULL
@return copy of force
--------------------------------------------------------------------------------------- */
Force* copyRBTorsionForce( const RBTorsionForce& forceToCopy, FILE* log = NULL ) const;
/**---------------------------------------------------------------------------------------
Copy NonbondedException force
@param forceToCopy force to copy
@param nonbondedForce force to copy execeptions to
@param log log file pointer -- may be NULL
--------------------------------------------------------------------------------------- */
void copyNonbondedExceptions( const NonbondedForce& forceToCopy,
NonbondedForce* nonbondedForce, FILE* log = NULL ) const;
/**---------------------------------------------------------------------------------------
Copy NonbondedSoftcoreExceptions force (free energy plugin force)
@param forceToCopy force to copy
@param nonbondedForce force to copy execeptions to
@param log log file pointer -- may be NULL
--------------------------------------------------------------------------------------- */
#ifdef INCLUDE_FREE_ENERGY_PLUGIN
void copyNonbondedSoftcoreExceptions( const NonbondedSoftcoreForce& forceToCopy,
NonbondedSoftcoreForce* nonbondedForce, FILE* log = NULL ) const;
#endif
/**---------------------------------------------------------------------------------------
Copy NonbondedForce
@param forceToCopy force to copy
@param nonbondedForce force to copy execeptions to
@param log log file pointer -- may be NULL
@return copy of force
--------------------------------------------------------------------------------------- */
Force* copyNonbondedForce( const NonbondedForce& forceToCopy, FILE* log = NULL ) const;
/**---------------------------------------------------------------------------------------
Copy NonbondedSoftcoreForce (free energy plugin force)
@param forceToCopy force to copy
@param nonbondedForce force to copy execeptions to
@param log log file pointer -- may be NULL
@return copy of force
--------------------------------------------------------------------------------------- */
#ifdef INCLUDE_FREE_ENERGY_PLUGIN
Force* copyNonbondedSoftcoreForce( const NonbondedSoftcoreForce& forceToCopy, FILE* log = NULL ) const;
#endif
/**---------------------------------------------------------------------------------------
Copy GBSAOBCForce
@param forceToCopy force to copy
@param log log file pointer -- may be NULL
@return copy of force
--------------------------------------------------------------------------------------- */
Force* copyGBSAOBCForce( const GBSAOBCForce& forceToCopy, FILE* log = NULL ) const;
/**---------------------------------------------------------------------------------------
Copy GBSAOBCSoftcoreForce (free energy plugin force)
@param forceToCopy force to copy
@param log log file pointer -- may be NULL
@return copy of force
--------------------------------------------------------------------------------------- */
#ifdef INCLUDE_FREE_ENERGY_PLUGIN
Force* copyGBSAOBCSoftcoreForce( const GBSAOBCSoftcoreForce& forceToCopy, FILE* log = NULL ) const;
#endif
/**---------------------------------------------------------------------------------------
Copy GBVIForce
@param forceToCopy force to copy
@param log log file pointer -- may be NULL
@return copy of force
--------------------------------------------------------------------------------------- */
Force* copyGBVIForce( const GBVIForce& forceToCopy, FILE* log = NULL ) const;
/**---------------------------------------------------------------------------------------
Copy GBVISoftcoreForce (free energy plugin force)
@param forceToCopy force to copy
@param log log file pointer -- may be NULL
@return copy of force
--------------------------------------------------------------------------------------- */
#ifdef INCLUDE_FREE_ENERGY_PLUGIN
Force* copyGBVISoftcoreForce( const GBVISoftcoreForce& forceToCopy, FILE* log = NULL ) const;
#endif
/**---------------------------------------------------------------------------------------
Copy constraints
@param systemToCopy system whose constraints are to be copied
@param system system to add constraints to
@param log log file pointer -- may be NULL
--------------------------------------------------------------------------------------- */
void copyConstraints( const System& systemToCopy, System* system, FILE* log = NULL ) const;
/**---------------------------------------------------------------------------------------
Get force dependencies
@param forceName force to check if there exist any dependencies
@param returnVector vector of forces the input force is dependent on (example: GBSAOBC force requires Nonbonded force since
on Cuda platofrm they are computed in same loop and hence are inseparable)
--------------------------------------------------------------------------------------- */
void getForceDependencies( std::string forceName, StringVector& returnVector ) const;
/**
* Write masses to parameter file
*
* @param filePtr file to write masses to
* @param system write masses in system
*/
void writeMasses( FILE* filePtr, const System& system ) const;
/**
* Write constraints to parameter file
*
* @param filePtr file to write constraints to
* @param system write constraints in system
*
*/
void writeConstraints( FILE* filePtr, const System& system ) const;
/**
* Write harmonicBondForce parameters to file
*
* @param filePtr file to write forces to
* @param harmonicBondForce write harmonicBondForce parameters
*
*/
void writeHarmonicBondForce( FILE* filePtr, const HarmonicBondForce& harmonicBondForce ) const;
/**
* Write harmonicAngleForce parameters to file
*
* @param filePtr file to write forces to
* @param harmonicAngleForce write harmonicAngleForce parameters
*
*/
void writeHarmonicAngleForce( FILE* filePtr, const HarmonicAngleForce& harmonicAngleForce ) const;
/**
* Write rbTorsionForce parameters to file
*
* @param filePtr file to write forces to
* @param rbTorsionForce write rbTorsionForce parameters
*
*/
void writeRbTorsionForce( FILE* filePtr, const RBTorsionForce& rbTorsionForce ) const;
/**
* Write periodicTorsionForce parameters to file
*
* @param filePtr file to write forces to
* @param periodicTorsionForce write periodicTorsionForce parameters
*
*/
void writePeriodicTorsionForce( FILE* filePtr, const PeriodicTorsionForce& periodicTorsionForce ) const;
/**
* Write nonbonded parameters to file
*
* @param filePtr file to write forces to
* @param nonbondedForce write nonbondedForce parameters
*
*/
void writeNonbondedForce( FILE* filePtr, const NonbondedForce & nonbondedForce ) const;
/**
* Write GBSAOBCForce parameters to file
*
* @param filePtr file to write forces to
* @param gbsaObcForce write gbsaObcForce parameters
*
*/
void writeGbsaObcForce( FILE* filePtr, const GBSAOBCForce& gbsaObcForce ) const;
/**
* Write GBSA GB/VI Force parameters to file
*
* @param filePtr file to write forces to
* @param gbviObcForce write gbviObcForce parameters
*
*/
void writeGBVIForce( FILE* filePtr, const GBVIForce& gbviForce ) const;
#ifdef INCLUDE_FREE_ENERGY_PLUGIN
/**
* Write nonbonded softcore parameters to file
*
* @param filePtr file to write forces to
* @param nonbondedForce write nonbondedForce parameters
*/
void writeNonbondedSoftcoreForce( FILE* filePtr, const NonbondedSoftcoreForce & nonbondedSoftcoreForce ) const;
/**
* Write GBSAOBCSoftcoreForce parameters to file
*
* @param filePtr file to write forces to
* @param gbsaObcForce write gbsaObcForce parameters
*
*/
void writeGbsaObcSoftcoreForce( FILE* filePtr, const GBSAOBCSoftcoreForce& gbsaObcForce ) const;
/**
* Write GBSA GB/VI softcore force parameters to file
*
* @param filePtr file to write forces to
* @param gbviObcForce write gbviObcForce parameters
*
*/
void writeGBVISoftcoreForce( FILE* filePtr, const GBVISoftcoreForce& gbviSoftcoreForce ) const;
#endif
/**
* Write coordinates, velocities, ... to file
*
* @param filePtr file to write Vec3 entries to
* @param vect3Array write array of Vec3
*
*/
void writeVec3( FILE* filePtr, const std::vector<Vec3>& vect3Array ) const;
/**
* Write context info to file (positions, velocities, forces, energies)
*
* @param filePtr file to write entries to
* @param context write context positions, velocities, forces, energies to file
*
*/
void writeContext( FILE* filePtr, const Context& context ) const;
/**
* Write integrator
*
* @param filePtr file to write integrator info to
* @param integrator write integrator info (time step, seed, ... as applicable)
*
*/
void writeIntegrator( FILE* filePtr, const Integrator& integrator ) const;
/**
* Write parameter file
* @param context context whose entries are to be written to file
* @param parameterFileName file name
*
*/
void writeParameterFile( const Context& context, const std::string& parameterFileName ) const;
private:
FILE* _log;
// map of force dependencies (e.g., GBSAObc requires NB force on CudaPlatform)
StringStringVectorMap _forceDependencies;
};
} // namespace OpenMM
#endif /*VALIDATE_OPENMM_H_*/
libraries/validate/include/ValidateOpenMMForces.h 0 → 100644
View file @ 248a01f4
#ifndef VALIDATE_OPENMM_FORCES_H_
#define VALIDATE_OPENMM_FORCES_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: Mark Friedrichs *
* Contributors: *
* *
* This program is free software: you can redistribute it and/or modify *
* it under the terms of the GNU Lesser General Public License as published *
* by the Free Software Foundation, either version 3 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU Lesser General Public License for more details. *
* *
* You should have received a copy of the GNU Lesser General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* -------------------------------------------------------------------------- */
#include "ValidateOpenMM.h"
namespace OpenMM {
typedef std::map< int, int > MapIntInt;
typedef MapIntInt::iterator MapIntIntI;
typedef MapIntInt::const_iterator MapIntIntCI;
// Helper class for ValidateOpenMMForces class used to store force results and facitilitate comparisons of
// resulting forces
class ForceValidationResult {
public:
ForceValidationResult( const Context& context1, const Context& context2, StringUIntMap& forceNamesMap );
~ForceValidationResult();
/**
* Get potential energy at specified platform index (0 || 1)
*
* @return potential energy for spercifed platform
*
* @throws OpenMMException if energyIndex is not 0 or 1
*/
double getPotentialEnergy( int energyIndex ) const;
/**
* Get array of forces at specified platform index (0 || 1)
*
* @return array of force norms
*
* @throws OpenMMException if forceIndex is not 0 or 1
*/
std::vector<double> getForceNorms( int forceIndex ) const;
/**
* Get array of forces at platform index (0 || 1)
*
* @return force array
*
* @throws OpenMMException if forceIndex is not 0 or 1
*/
std::vector<Vec3> getForces( int forceIndex ) const;
/**
* Get maximum delta in force norm
*
* @param maxIndex return atom index of entry with maximum delta norm (optional)
*
* @return max delta in norm of forces
*/
double getMaxDeltaForceNorm( int* maxIndex = NULL ) const;
/**
* Get maximum relative delta in force norm
*
* @param maxIndex return atom index of entry w/ maximum relative delta norm (optional)
*
* @return max relative delta in norm of forces
*/
double getMaxRelativeDeltaForceNorm( int* maxIndex = NULL ) const;
/**
* Get maximum dot product between forces
*
* @param maxIndex return atom index of entry w/ maximum dot product between forces (optional)
*
* @return max dot product between forces
*/
double getMaxDotProduct( int* maxIndex = NULL ) const;
/**
* Get name of force associated w/ computed results
*
* @return force name(s); if more than one force active in computation,
* then names are concatenated and separated by '::' (e.g., 'NB_FORCE::GBSA_OBC_FORCE')
*/
std::string getForceName( void ) const;
/**
* Get platform name
*
* @param index index of platform (0 or 1)
*
* @return platform name
*
* @throws OpenMMException if index is not 0 or 1
*/
std::string getPlatformName( int index ) const;
/**
* Register index of two entries that differ by a specified tolerance
*
* @param index inconsistent index
*
*/
void registerInconsistentForceIndex( int index, int value = 1 );
/**
* Clear list of entries that differ by a specified tolerance
*
*/
void clearInconsistentForceIndexList( void );
/**
* Get list of entries that differ by a specified tolerance
*
*/
void getInconsistentForceIndexList( std::vector<int>& inconsistentIndices ) const;
/**
* Get number of entries in inconsistent index list
*
*/
int getNumberOfInconsistentForceEntries( void ) const;
/**
* Return true if nans were detected
*
* @return true if nans were detected
*/
int nansDetected( void ) const;
/**
* Determine if force norms are valid
*
* @param tolerance tolerance
*/
void compareForceNorms( double tolerance );
/**
* Determine if forces are valid
*
* @param tolerance tolerance
*/
void compareForces( double tolerance );
private:
// computed potential energies and forces fror two platforms
double _potentialEnergies[2];
std::vector<Vec3> _forces[2];
// platform and force names
std::string _platforms[2];
std::vector<std::string> _forceNames;
// force norms and stat entries
std::vector<double> _norms[2];
std::vector<double> _normStatVectors[2];
// map of indicies w/ inconsistent force entries
std::map<int, int> _inconsistentForceIndicies;
// if set, then nans detected
int _nansDetected;
/**
* Calculate norms of vectors
*
*/
void _calculateNorms( void );
/**
* Calculate norms of specified vector
*
*/
void _calculateNormOfForceVector( int forceIndex );
// stat indices
static const int STAT_AVG = 0;
static const int STAT_STD = 1;
static const int STAT_MIN = 2;
static const int STAT_ID1 = 3;
static const int STAT_MAX = 4;
static const int STAT_ID2 = 5;
static const int STAT_CNT = 6;
static const int STAT_END = 7;
/**
* Find vector stats
*
*/
void _findStatsForDouble( const std::vector<double>& array, std::vector<double>& statVector ) const;
};
// Class used to compare forces/potential energies on two platforms
class ValidateOpenMMForces : public ValidateOpenMM {
public:
ValidateOpenMMForces( void );
~ValidateOpenMMForces();
/**
* Validate force/energy by comparing the results between the forces/energies computed on user-provided context platform
* with Reference platform
*
* @param context context reference
* @param summaryString output summary string of results of comparison (optional)
*
* @return number of inconsistent entries
*/
int compareWithReferencePlatform(Context& context, std::string* summaryString = NULL );
/**
* Validate force/energy by comparing the results between the forces/energies computed on two different platforms
*
* @param context context reference
* @param compareForces indices of force to be tested
* @param platform1 first platform to compute forces
* @param platform2 second platform to compute forces
*
* @return ForceValidationResult reference containing results of force/energy computations
* on the two input platforms
*/
ForceValidationResult* compareForce(Context& context, std::vector<int>& compareForces,
Platform& platform1, Platform& platform2 ) const;
/**
* Compare individual forces by comparing calculations across two platforms (platform associated w/ input context and
* comparisonPlatform)
*
* @param context context reference
* @param platform comparsion platform reference
* @param forceValidationResults output vector of ForceValidationResult ptrs (user is responsible for deleting
* individual ForceValidationResult objects)
*/
void compareOpenMMForces(Context& context, Platform& comparisonPlatform, std::vector<ForceValidationResult*>& forceValidationResults ) const;
/**
* Determine if results are consistent
*
* @param forceValidationResults vector of ForceValidationResult ptrs to check if forces are consistent
*/
void checkForInconsistentForceEntries( std::vector<ForceValidationResult*>& forceValidationResults ) const;
/**
* Get total number of force entries that are inconsistent
*
* @param forceValidationResults vector of ForceValidationResult ptrs to check if forces are consistent
*/
int getTotalNumberOfInconsistentForceEntries( std::vector<ForceValidationResult*>& forceValidationResults ) const;
/**
* Get summary string of results
*
* @param forceValidationResults vector of ForceValidationResult ptrs
*/
std::string getSummary( std::vector<ForceValidationResult*>& forceValidationResults ) const;
/**
* Set force tolerance
*
* @param tolerance force tolerance
*/
void setForceTolerance( double tolerance );
/**
* Get force tolerance
*
* @return force tolerance
*/
double getForceTolerance( void ) const;
/*
* Get force tolerance for specified force
*
* @param forceName name of force
*
* @return force tolerance
*
* */
double getForceTolerance( const std::string& forceName ) const;
/*
* Get max errors to print in summary string
*
* @return max errors to print
*
* */
int getMaxErrorsToPrint( void ) const;
/*
* Set max errors to print in summary string
*
* @param maxErrorsToPrint max errors to print
*
* */
void setMaxErrorsToPrint( int maxErrorsToPrint );
/*
* Return true if force is not to be validated (Andersen thermostat, CM motion remover, ...)
*
* @param forceName force name
*
* @return true if force is not currently validated
**/
int isExcludedForce( std::string forceName ) const;
private:
// initialize class entries
void _initialize( void );
/*
* Format output line
*
* @param tab tab
* @param description description
* @param value value
*
* @return string containing contents
*
* */
std::string _getLine( const std::string& tab,
const std::string& description,
const std::string& value ) const;
std::vector<ForceValidationResult*> _forceValidationResults;
// max errors to print
int _maxErrorsToPrint;
// tolerence
double _forceTolerance;
// map of force tolerances to type (name)
StringDoubleMap _forceTolerances;
// forces to be excluded from validation
StringIntMap _forcesToBeExcluded;
};
} // namespace OpenMM
#endif /*VALIDATE_OPENMM_FORCES_H_*/
libraries/validate/src/ValidateOpenMM.cpp 0 → 100644
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libraries/validate/src/ValidateOpenMMForces.cpp 0 → 100644
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