/* -------------------------------------------------------------------------- * * 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) 2009 Stanford University and the Authors. * * Authors: Peter Eastman, 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 . * * -------------------------------------------------------------------------- */ #include "../../../tests/AssertionUtilities.h" #include "openmm/CMMotionRemover.h" #include "openmm/System.h" #include "openmm/Context.h" #include "openmm/LangevinIntegrator.h" #include "openmm/VariableLangevinIntegrator.h" #include "openmm/VerletIntegrator.h" #include "openmm/VariableVerletIntegrator.h" #include "openmm/BrownianIntegrator.h" #include "openmm/AmoebaHarmonicBondForce.h" #include "openmm/AmoebaHarmonicAngleForce.h" #include "openmm/AmoebaHarmonicInPlaneAngleForce.h" #include "openmm/AmoebaTorsionForce.h" #include "openmm/AmoebaPiTorsionForce.h" #include "openmm/AmoebaStretchBendForce.h" #include "openmm/AmoebaOutOfPlaneBendForce.h" #include "openmm/AmoebaTorsionTorsionForce.h" #include "openmm/AmoebaMultipoleForce.h" #include "openmm/AmoebaGeneralizedKirkwoodForce.h" #include "openmm/AmoebaVdwForce.h" #include "openmm/AmoebaWcaDispersionForce.h" #include "openmm/AmoebaUreyBradleyForce.h" #include "openmm/internal/windowsExport.h" #include "openmm/internal/AmoebaWcaDispersionForceImpl.h" #include #include #include #include #include #include #include #include #include extern "C" void registerAmoebaCudaKernelFactories(); // force enums #define MAX_PRINT 5 static std::string AMOEBA_HARMONIC_BOND_FORCE = "AmoebaHarmonicBond"; static std::string AMOEBA_HARMONIC_ANGLE_FORCE = "AmoebaHarmonicAngle"; static std::string AMOEBA_HARMONIC_IN_PLANE_ANGLE_FORCE = "AmoebaHarmonicInPlaneAngle"; static std::string AMOEBA_TORSION_FORCE = "AmoebaTorsion"; static std::string AMOEBA_PI_TORSION_FORCE = "AmoebaPiTorsion"; static std::string AMOEBA_STRETCH_BEND_FORCE = "AmoebaStretchBend"; static std::string AMOEBA_OUT_OF_PLANE_BEND_FORCE = "AmoebaOutOfPlaneBend"; static std::string AMOEBA_TORSION_TORSION_FORCE = "AmoebaTorsionTorsion"; static std::string AMOEBA_MULTIPOLE_FORCE = "AmoebaMultipole"; static std::string AMOEBA_GK_FORCE = "AmoebaGk"; static std::string AMOEBA_GK_CAVITY_FORCE = "AmoebaGkAndCavity"; static std::string AMOEBA_VDW_FORCE = "AmoebaVdw"; static std::string AMOEBA_WCA_DISPERSION_FORCE = "AmoebaWcaDispersion"; static std::string AMOEBA_UREY_BRADLEY_FORCE = "AmoebaUreyBradley"; static std::string ALL_FORCES = "AllForces"; static std::string AMOEBA_MULTIPOLE_ROTATION_MATRICES = "AmoebaMultipoleRotationMatrices"; static std::string AMOEBA_MULTIPOLE_ROTATED = "AmoebaMultipolesRotated"; static std::string AMOEBA_FIXED_E = "AmoebaFixedE"; static std::string AMOEBA_FIXED_E_GK = "AmoebaFixedE_GK"; static std::string AMOEBA_INDUCDED_DIPOLES = "AmoebaInducedDipoles"; static std::string AMOEBA_INDUCDED_DIPOLES_GK = "AmoebaInducedDipoles_GK"; static std::string INCLUDE_OBC_CAVITY_TERM = "includeObcCavityTerm"; static std::string MUTUAL_INDUCED_MAX_ITERATIONS = "mutualInducedMaxIterations"; static std::string MUTUAL_INDUCED_TARGET_EPSILON = "mutualInducedTargetEpsilon"; static std::string APPLY_N2 = "applyN2"; static std::string ZERO_HARMONIC_BOND_IXN = "zeroHarmonicBondIxn"; #define AmoebaHarmonicBondIndex 0 #define AmoebaHarmonicAngleIndex 1 #define AmoebaHarmonicInPlaneAngleIndex 2 #define AmoebaTorsionIndex 3 #define AmoebaPiTorsionIndex 4 #define AmoebaStretchBendIndex 5 #define AmoebaOutOfPlaneBendIndex 6 #define AmoebaTorsionTorsionIndex 7 #define AmoebaMultipoleIndex 8 #define AmoebaVdwIndex 9 #define AmoebaWcaDispersionIndex 10 #define AmoebaObcIndex 11 #define SumIndex 12 #define UreyBradleyIndex 13 #define AmoebaLastIndex 14 #define AngstromToNm 0.1 #define CalToJoule 4.184 const double DegreesToRadians = 3.14159265/180.0; const double RadiansToDegrees = 180/3.14159265; using namespace OpenMM; using namespace std; // the following are used in parsing parameter file typedef std::vector StringVector; typedef StringVector::iterator StringVectorI; typedef StringVector::const_iterator StringVectorCI; typedef std::vector StringVectorVector; typedef std::vector > VectorOfVectors; typedef VectorOfVectors::iterator VectorOfVectorsI; typedef VectorOfVectors::const_iterator VectorOfVectorsCI; typedef std::map< std::string, VectorOfVectors > MapStringVectorOfVectors; typedef MapStringVectorOfVectors::iterator MapStringVectorOfVectorsI; typedef MapStringVectorOfVectors::const_iterator MapStringVectorOfVectorsCI; typedef std::map< std::string, std::string > MapStringString; typedef MapStringString::iterator MapStringStringI; typedef MapStringString::const_iterator MapStringStringCI; typedef std::map< std::string, int > MapStringInt; typedef MapStringInt::iterator MapStringIntI; typedef MapStringInt::const_iterator MapStringIntCI; typedef std::map< std::string, std::vector > MapStringVec3; typedef MapStringVec3::iterator MapStringVec3I; typedef MapStringVec3::const_iterator MapStringVec3CI; typedef std::map< std::string, double > MapStringDouble; typedef MapStringDouble::iterator MapStringDoubleI; typedef MapStringDouble::const_iterator MapStringDoubleCI; typedef std::map< std::string, Force*> MapStringForce; typedef MapStringForce::iterator MapStringForceI; typedef MapStringForce::const_iterator MapStringForceCI; // default return value from methods static const int DefaultReturnValue = 0; static const int LengthUnit = 0; static const int EnergyUnit = 1; static const int ForceUnit = 2; static const int LastUnits = ForceUnit + 1; static const int NoUnitsConversion = 0; static const int KcalA_To_kJNm = 1; /**--------------------------------------------------------------------------------------- * Initialize units * * @param unitType has w/ force name as key and int as value * @param units array * * --------------------------------------------------------------------------------------- */ void setUnits( int unitType, double* units ); /**--------------------------------------------------------------------------------------- Read parameter file @param inputParameterFile input parameter file name @param system system to which forces based on parameters are to be added @param coordinates Vec3 array containing coordinates on output @param velocities Vec3 array containing velocities on output @param inputLog log file pointer -- may be NULL @return number of lines read --------------------------------------------------------------------------------------- */ Integrator* readAmoebaParameterFile( const std::string& inputParameterFile, MapStringInt& forceMap, System& system, std::vector& coordinates, std::vector& velocities, MapStringVec3& forces, MapStringDouble& potentialEnergy, MapStringVectorOfVectors& supplementary, FILE* inputLog ); /**--------------------------------------------------------------------------------------- * Get integrator * * @param integratorName integratorName (VerletIntegrator, BrownianIntegrator, LangevinIntegrator, ...) * @param timeStep time step * @param friction (ps) friction * @param temperature temperature * @param shakeTolerance Shake tolerance * @param errorTolerance Error tolerance * @param randomNumberSeed seed * * @return DefaultReturnValue or ErrorReturnValue * --------------------------------------------------------------------------------------- */ Integrator* getIntegrator( std::string& integratorName, double timeStep, double friction, double temperature, double shakeTolerance, double errorTolerance, int randomNumberSeed, FILE* log ); /**--------------------------------------------------------------------------------------- * Initialize forceMap * * @param forceMap has w/ force name as key and int as value * @param initialValue initial value * * --------------------------------------------------------------------------------------- */ void initializeForceMap( MapStringInt& forceMap, int initialValue ); void testUsingAmoebaTinkerParameterFile( const std::string& amoebaTinkerParameterFileName, MapStringInt& forceMap, double tolerance, FILE* summaryFile, FILE* log ); int OPENMM_EXPORT runTestsUsingAmoebaTinkerParameterFile( MapStringString& argumentMap ); void OPENMM_EXPORT appendInputArgumentsToArgumentMap( int numberOfArguments, char* argv[], MapStringString& argumentMap );