// ******************************************************************************
   //
   // Title:       Force Field X.
   // Description: Force Field X - Software for Molecular Biophysics.
   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2025.
   //
   // This file is part of Force Field X.
   //
   // Force Field X is free software; you can redistribute it and/or modify it
  // under the terms of the GNU General Public License version 3 as published by
  // the Free Software Foundation.
  //
  // Force Field X 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 General Public License for more
  // details.
  //
  // You should have received a copy of the GNU General Public License along with
  // Force Field X; if not, write to the Free Software Foundation, Inc., 59 Temple
  // Place, Suite 330, Boston, MA 02111-1307 USA
  //
  // Linking this library statically or dynamically with other modules is making a
  // combined work based on this library. Thus, the terms and conditions of the
  // GNU General Public License cover the whole combination.
  //
  // As a special exception, the copyright holders of this library give you
  // permission to link this library with independent modules to produce an
  // executable, regardless of the license terms of these independent modules, and
  // to copy and distribute the resulting executable under terms of your choice,
  // provided that you also meet, for each linked independent module, the terms
  // and conditions of the license of that module. An independent module is a
  // module which is not derived from or based on this library. If you modify this
  // library, you may extend this exception to your version of the library, but
  // you are not obligated to do so. If you do not wish to do so, delete this
  // exception statement from your version.
  //
  // ******************************************************************************
  package ffx.potential.openmm;
  
  import edu.uiowa.jopenmm.OpenMM_Vec3;
  import ffx.crystal.Crystal;
  import ffx.numerics.Potential;
  import ffx.openmm.AndersenThermostat;
  import ffx.openmm.CMMotionRemover;
  import ffx.openmm.Force;
  import ffx.openmm.MonteCarloBarostat;
  import ffx.potential.ForceFieldEnergy;
  import ffx.potential.MolecularAssembly;
  import ffx.potential.bonded.Angle;
  import ffx.potential.bonded.Atom;
  import ffx.potential.bonded.Bond;
  import ffx.potential.nonbonded.GeneralizedKirkwood;
  import ffx.potential.nonbonded.ParticleMeshEwald;
  import ffx.potential.nonbonded.VanDerWaals;
  import ffx.potential.nonbonded.VanDerWaalsForm;
  import ffx.potential.nonbonded.implicit.ChandlerCavitation;
  import ffx.potential.nonbonded.implicit.DispersionRegion;
  import ffx.potential.parameters.BondType;
  import ffx.potential.parameters.ForceField;
  import ffx.potential.terms.AnglePotentialEnergy;
  import ffx.potential.terms.BondPotentialEnergy;
  import ffx.utilities.Constants;
  import org.apache.commons.configuration2.CompositeConfiguration;
  
  import javax.annotation.Nullable;
  import java.util.logging.Logger;
  
  import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_NmPerAngstrom;
  import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_Boolean.OpenMM_True;
  import static ffx.potential.parameters.VDWType.VDW_TYPE.LENNARD_JONES;
  import static ffx.utilities.Constants.KCAL_TO_GRAM_ANG2_PER_PS2;
  import static ffx.utilities.Constants.kB;
  import static java.lang.String.format;
  import static org.apache.commons.math3.util.FastMath.cos;
  import static org.apache.commons.math3.util.FastMath.sqrt;
  import static org.apache.commons.math3.util.FastMath.toRadians;
  
  /**
   * Create and manage an OpenMM System.
   *
   * <p>The definition of a System involves four elements:
   *
   * <p>The particles and constraints are defined directly by the System object, while forces are
   * defined by objects that extend the Force class. After creating a System, call addParticle() once
   * for each particle, addConstraint() for each constraint, and addForce() for each Force.
   *
   * <p>In addition, particles may be designated as "virtual sites". These are particles whose
   * positions are computed automatically based on the positions of other particles. To define a
   * virtual site, call setVirtualSite(), passing in a VirtualSite object that defines the rules for
   * computing its position.
   */
  public class OpenMMSystem extends ffx.openmm.System {
  
    private static final Logger logger = Logger.getLogger(OpenMMSystem.class.getName());
  
    /**
     * The OpenMMEnergy instance.
     */
    private final OpenMMEnergy openMMEnergy;
   /**
    * The Force Field in use.
    */
   protected ForceField forceField;
   /**
    * Array of atoms in the system.
    */
   protected Atom[] atoms;
 
   /**
    * This flag indicates bonded force constants and equilibria are updated (e.g. during ManyBody
    * titration).
    */
   protected boolean updateBondedTerms = false;
   /**
    * Fixed charge softcore vdW force boolean.
    */
   protected boolean softcoreCreated = false;
 
   /**
    * OpenMM Custom Bond Force
    */
   protected BondForce bondForce = null;
   /**
    * OpenMM Custom Angle Force
    */
   protected AngleForce angleForce = null;
   /**
    * OpenMM Custom In-Plane Angle Force
    */
   protected InPlaneAngleForce inPlaneAngleForce = null;
   /**
    * OpenMM Custom Stretch-Bend Force
    */
   protected StretchBendForce stretchBendForce = null;
   /**
    * OpenMM Custom Urey-Bradley Force
    */
   protected UreyBradleyForce ureyBradleyForce = null;
   /**
    * OpenMM Custom Out-of-Plane Bend Force
    */
   protected OutOfPlaneBendForce outOfPlaneBendForce = null;
   /**
    * OpenMM Custom Pi-Torsion Force
    */
   protected PiOrbitalTorsionForce piOrbitalTorsionForce = null;
   /**
    * OpenMM AMOEBA Torsion Force.
    */
   protected TorsionForce torsionForce = null;
   /**
    * OpenMM Improper Torsion Force.
    */
   protected ImproperTorsionForce improperTorsionForce = null;
   /**
    * OpenMM Torsion-Torsion Force.
    */
   protected AmoebaTorsionTorsionForce amoebaTorsionTorsionForce = null;
   /**
    * OpenMM Stretch-Torsion Force.
    */
   protected StretchTorsionForce stretchTorsionForce = null;
   /**
    * OpenMM Angle-Torsion Force.
    */
   protected AngleTorsionForce angleTorsionForce = null;
   /**
    * OpenMM Restraint-Torsion Force.
    */
   protected RestrainTorsionsForce restrainTorsionsForce = null;
   /**
    * OpenMM Restrain-Position Force.
    */
   protected RestrainPositionsForce restrainPositionsForce = null;
   /**
    * OpenMM Restrain-Groups Force.
    */
   protected RestrainGroupsForce restrainGroupsForce = null;
   /**
    * OpenMM AMOEBA van der Waals Force.
    */
   protected AmoebaVdwForce amoebaVDWForce = null;
   /**
    * OpenMM AMOEBA Multipole Force.
    */
   protected AmoebaMultipoleForce amoebaMultipoleForce = null;
   /**
    * OpenMM Generalized Kirkwood Force.
    */
   protected AmoebaGeneralizedKirkwoodForce amoebaGeneralizedKirkwoodForce = null;
   /**
    * OpenMM AMOEBA WCA Dispersion Force.
    */
   protected AmoebaWcaDispersionForce amoebaWcaDispersionForce = null;
   /**
    * OpenMM AMOEBA WCA Cavitation Force.
    */
   protected AmoebaGKCavitationForce amoebaGKCavitationForce = null;
   /**
    * OpenMM Custom GB Force.
    */
   protected FixedChargeGBForce fixedChargeGBForce = null;
   /**
    * OpenMM Fixed Charge Non-Bonded Force.
    */
   protected FixedChargeNonbondedForce fixedChargeNonBondedForce = null;
   /**
    * Custom forces to handle alchemical transformations for fixed charge systems.
    */
   protected FixedChargeAlchemicalForces fixedChargeAlchemicalForces = null;
 
   /**
    * OpenMM thermostat. Currently, an Andersen thermostat is supported.
    */
   protected AndersenThermostat andersenThermostat = null;
   /**
    * Barostat to be added if NPT (isothermal-isobaric) dynamics is requested.
    */
   protected MonteCarloBarostat monteCarloBarostat = null;
   /**
    * OpenMM center-of-mass motion remover.
    */
   protected CMMotionRemover cmMotionRemover = null;
 
   /**
    * OpenMMSystem constructor.
    */
   public OpenMMSystem() {
     openMMEnergy = null;
     forceField = null;
     atoms = null;
   }
 
   /**
    * OpenMMSystem constructor.
    *
    * @param openMMEnergy ForceFieldEnergyOpenMM instance.
    */
   public OpenMMSystem(OpenMMEnergy openMMEnergy) {
     this.openMMEnergy = openMMEnergy;
 
     MolecularAssembly molecularAssembly = openMMEnergy.getMolecularAssembly();
     forceField = molecularAssembly.getForceField();
     atoms = molecularAssembly.getAtomArray();
 
     // Load atoms.
     try {
       addAtoms();
     } catch (Exception e) {
       logger.severe(" Atom without mass encountered.");
     }
 
     logger.info(format("\n OpenMM system created with %d atoms.", atoms.length));
   }
 
   /**
    * Get the Potential in use.
    *
    * @return The Potential.
    */
   public Potential getPotential() {
     return openMMEnergy;
   }
 
   /**
    * Get the atoms in the system.
    * @return Array of atoms in the system.
    */
   public Atom[] getAtoms() {
     return atoms;
   }
 
   /**
    * Add forces to the system.
    */
   public void addForces() {
 
     // Set up rigid constraints.
     // These flags need to be set before bonds and angles are created below.
     boolean rigidHydrogen = forceField.getBoolean("RIGID_HYDROGEN", false);
     boolean rigidBonds = forceField.getBoolean("RIGID_BONDS", false);
     boolean rigidHydrogenAngles = forceField.getBoolean("RIGID_HYDROGEN_ANGLES", false);
     if (rigidHydrogen) {
       addHydrogenConstraints();
     }
     if (rigidBonds) {
       addUpBondConstraints();
     }
     if (rigidHydrogenAngles) {
       setUpHydrogenAngleConstraints();
     }
 
     logger.info("\n Bonded Terms\n");
 
     // Add Bond Force.
     if (rigidBonds) {
       logger.info(" Not creating AmoebaBondForce because bonds are constrained.");
     } else {
       bondForce = (BondForce) BondForce.constructForce(openMMEnergy);
       addForce(bondForce);
     }
 
     // Add Angle Force.
     angleForce = (AngleForce) AngleForce.constructForce(openMMEnergy);
     addForce(angleForce);
 
     // Add In-Plane Angle Force.
     inPlaneAngleForce = (InPlaneAngleForce) InPlaneAngleForce.constructForce(openMMEnergy);
     addForce(inPlaneAngleForce);
 
     // Add Stretch-Bend Force.
     stretchBendForce = (StretchBendForce) StretchBendForce.constructForce(openMMEnergy);
     addForce(stretchBendForce);
 
     // Add Urey-Bradley Force.
     ureyBradleyForce = (UreyBradleyForce) UreyBradleyForce.constructForce(openMMEnergy);
     addForce(ureyBradleyForce);
 
     // Out-of Plane Bend Force.
     outOfPlaneBendForce = (OutOfPlaneBendForce) OutOfPlaneBendForce.constructForce(openMMEnergy);
     addForce(outOfPlaneBendForce);
 
     // Add Pi-Torsion Force.
     piOrbitalTorsionForce = (PiOrbitalTorsionForce) PiOrbitalTorsionForce.constructForce(openMMEnergy);
     addForce(piOrbitalTorsionForce);
 
     // Add Torsion Force.
     torsionForce = (TorsionForce) TorsionForce.constructForce(openMMEnergy);
     addForce(torsionForce);
 
     // Add Improper Torsion Force.
     improperTorsionForce = (ImproperTorsionForce) ImproperTorsionForce.constructForce(openMMEnergy);
     addForce(improperTorsionForce);
 
     // Add Stretch-Torsion coupling terms.
     stretchTorsionForce = (StretchTorsionForce) StretchTorsionForce.constructForce(openMMEnergy);
     addForce(stretchTorsionForce);
 
     // Add Angle-Torsion coupling terms.
     angleTorsionForce = (AngleTorsionForce) AngleTorsionForce.constructForce(openMMEnergy);
     addForce(angleTorsionForce);
 
     // Add Torsion-Torsion Force.
     amoebaTorsionTorsionForce = (AmoebaTorsionTorsionForce) AmoebaTorsionTorsionForce.constructForce(openMMEnergy);
     addForce(amoebaTorsionTorsionForce);
 
     if (openMMEnergy.getRestrainMode() == ForceFieldEnergy.RestrainMode.ENERGY) {
       // Add Restrain Positions force.
       restrainPositionsForce = (RestrainPositionsForce) RestrainPositionsForce.constructForce(openMMEnergy);
       addForce(restrainPositionsForce);
 
       // Add Restrain Bonds force for each functional form.
       for (BondType.BondFunction function : BondType.BondFunction.values()) {
         RestrainDistanceForce restrainDistanceForce = (RestrainDistanceForce) RestrainDistanceForce.constructForce(function, openMMEnergy);
         addForce(restrainDistanceForce);
       }
 
       // Add Restrain Torsions force.
       restrainTorsionsForce = (RestrainTorsionsForce) RestrainTorsionsForce.constructForce(openMMEnergy);
       addForce(restrainTorsionsForce);
     }
 
     // Add Restrain Groups force.
     restrainGroupsForce = (RestrainGroupsForce) RestrainGroupsForce.constructForce(openMMEnergy);
     addForce(restrainGroupsForce);
 
     setDefaultPeriodicBoxVectors();
 
     VanDerWaals vdW = openMMEnergy.getVdwNode();
     if (vdW != null) {
       logger.info("\n Non-Bonded Terms");
       VanDerWaalsForm vdwForm = vdW.getVDWForm();
       if (vdwForm.vdwType == LENNARD_JONES) {
         fixedChargeNonBondedForce = (FixedChargeNonbondedForce) FixedChargeNonbondedForce.constructForce(openMMEnergy);
         addForce(fixedChargeNonBondedForce);
         if (fixedChargeNonBondedForce != null) {
           GeneralizedKirkwood gk = openMMEnergy.getGK();
           if (gk != null) {
             fixedChargeGBForce = (FixedChargeGBForce) FixedChargeGBForce.constructForce(openMMEnergy);
             addForce(fixedChargeGBForce);
           }
         }
       } else {
         // Add vdW Force.
         amoebaVDWForce = (AmoebaVdwForce) AmoebaVdwForce.constructForce(openMMEnergy);
         addForce(amoebaVDWForce);
 
         // Add Multipole Force.
         amoebaMultipoleForce = (AmoebaMultipoleForce) AmoebaMultipoleForce.constructForce(openMMEnergy);
         addForce(amoebaMultipoleForce);
 
         // Add Generalized Kirkwood Force.
         GeneralizedKirkwood gk = openMMEnergy.getGK();
         if (gk != null) {
           amoebaGeneralizedKirkwoodForce = (AmoebaGeneralizedKirkwoodForce) AmoebaGeneralizedKirkwoodForce.constructForce(openMMEnergy);
           addForce(amoebaGeneralizedKirkwoodForce);
 
           // Add WCA Dispersion Force.
           DispersionRegion dispersionRegion = gk.getDispersionRegion();
           if (dispersionRegion != null) {
             amoebaWcaDispersionForce = (AmoebaWcaDispersionForce) AmoebaWcaDispersionForce.constructForce(openMMEnergy);
             addForce(amoebaWcaDispersionForce);
           }
 
           // Add a GaussVol Cavitation Force.
           ChandlerCavitation chandlerCavitation = gk.getChandlerCavitation();
           if (chandlerCavitation != null && chandlerCavitation.getGaussVol() != null) {
             amoebaGKCavitationForce = (AmoebaGKCavitationForce) AmoebaGKCavitationForce.constructForce(openMMEnergy);
             addForce(amoebaGKCavitationForce);
           }
         }
       }
     }
   }
 
   /**
    * Remove a force from the OpenMM System.
    * The OpenMM memory associated with the removed Force object is deleted.
    */
   public void removeForce(Force force) {
     if (force != null) {
       removeForce(force.getForceIndex());
     }
   }
 
   /**
    * Add an Andersen thermostat to the system.
    *
    * @param targetTemp Target temperature in Kelvins.
    */
   public void addAndersenThermostatForce(double targetTemp) {
     double collisionFreq = forceField.getDouble("COLLISION_FREQ", 1.0);
     addAndersenThermostatForce(targetTemp, collisionFreq);
   }
 
   /**
    * Add an Andersen thermostat to the system.
    *
    * @param targetTemp    Target temperature in Kelvins.
    * @param collisionFreq Collision frequency in 1/psec.
    */
   public void addAndersenThermostatForce(double targetTemp, double collisionFreq) {
     if (andersenThermostat != null) {
       removeForce(andersenThermostat);
       andersenThermostat = null;
     }
     andersenThermostat = new AndersenThermostat(targetTemp, collisionFreq);
     addForce(andersenThermostat);
     logger.info("\n Adding an Andersen thermostat");
     logger.info(format("  Target Temperature:   %6.2f (K)", targetTemp));
     logger.info(format("  Collision Frequency:  %6.2f (1/psec)", collisionFreq));
   }
 
   /**
    * Adds a force that removes center-of-mass motion.
    */
   public void addCOMMRemoverForce() {
     if (cmMotionRemover != null) {
       removeForce(cmMotionRemover);
       cmMotionRemover = null;
     }
     int frequency = forceField.getInteger("REMOVE-COM-FREQUENCY", 100);
     cmMotionRemover = new CMMotionRemover(frequency);
     int forceGroup = forceField.getInteger("COMM_FORCE_GROUP", 1);
     cmMotionRemover.setForceGroup(forceGroup);
     addForce(cmMotionRemover);
     logger.info("\n Added a Center of Mass Motion Remover");
     logger.info(format("  Frequency:            %6d", frequency));
     logger.info(format("  Force Group:          %6d", forceGroup));
   }
 
   /**
    * Add a Monte Carlo Barostat to the system.
    *
    * @param targetPressure The target pressure (in atm).
    * @param targetTemp     The target temperature.
    * @param frequency      The frequency to apply the barostat.
    */
   public void addMonteCarloBarostatForce(double targetPressure, double targetTemp, int frequency) {
     if (monteCarloBarostat != null) {
       removeForce(monteCarloBarostat);
       monteCarloBarostat = null;
     }
     double pressureInBar = targetPressure * Constants.ATM_TO_BAR;
     monteCarloBarostat = new MonteCarloBarostat(pressureInBar, targetTemp, frequency);
     CompositeConfiguration properties = openMMEnergy.getMolecularAssembly().getProperties();
     if (properties.containsKey("barostat-seed")) {
       int randomSeed = properties.getInt("barostat-seed", 0);
       logger.info(format(" Setting random seed %d for Monte Carlo Barostat", randomSeed));
       monteCarloBarostat.setRandomNumberSeed(randomSeed);
     }
     addForce(monteCarloBarostat);
     logger.info("\n Added a Monte Carlo Barostat");
     logger.info(format("  Target Pressure:      %6.2f (atm)", targetPressure));
     logger.info(format("  Target Temperature:   %6.2f (K)", targetTemp));
     logger.info(format("  MC Move Frequency:    %6d", frequency));
   }
 
   /**
    * Calculate the number of degrees of freedom.
    *
    * @return Number of degrees of freedom.
    */
   public int calculateDegreesOfFreedom() {
     // Begin from the 3 times the number of active atoms.
     int dof = openMMEnergy.getNumberOfVariables();
     // Remove OpenMM constraints.
     dof = dof - getNumConstraints();
     // Remove center of mass motion.
     if (cmMotionRemover != null) {
       dof -= 3;
     }
     return dof;
   }
 
   public double getTemperature(double kineticEnergy) {
     double dof = calculateDegreesOfFreedom();
     return 2.0 * kineticEnergy * KCAL_TO_GRAM_ANG2_PER_PS2 / (kB * dof);
   }
 
   /**
    * Get the ForceField in use.
    *
    * @return ForceField instance.
    */
   public ForceField getForceField() {
     return forceField;
   }
 
   /**
    * Get the Crystal instance.
    *
    * @return the Crystal instance.
    */
   public Crystal getCrystal() {
     return openMMEnergy.getCrystal();
   }
 
   /**
    * Get the number of variables.
    *
    * @return the number of variables.
    */
   public int getNumberOfVariables() {
     return openMMEnergy.getNumberOfVariables();
   }
 
   /**
    * Destroy the system.
    */
   public void free() {
     if (getPointer() != null) {
       logger.fine(" Free OpenMM system.");
       destroy();
       logger.fine(" Free OpenMM system completed.");
     }
   }
 
   public void setUpdateBondedTerms(boolean updateBondedTerms) {
     this.updateBondedTerms = updateBondedTerms;
   }
 
   /**
    * Set the default values of the vectors defining the axes of the periodic box (measured in nm).
    *
    * <p>Any newly created Context will have its box vectors set to these. They will affect any
    * Force added to the System that uses periodic boundary conditions.
    *
    * <p>Triclinic boxes are supported, but the vectors must satisfy certain requirements. In
    * particular, a must point in the x direction, b must point "mostly" in the y direction, and c
    * must point "mostly" in the z direction. See the documentation for details.
    */
   protected void setDefaultPeriodicBoxVectors() {
     Crystal crystal = openMMEnergy.getCrystal();
     if (!crystal.aperiodic()) {
       OpenMM_Vec3 a = new OpenMM_Vec3();
       OpenMM_Vec3 b = new OpenMM_Vec3();
       OpenMM_Vec3 c = new OpenMM_Vec3();
       double[][] Ai = crystal.Ai;
       a.x = Ai[0][0] * OpenMM_NmPerAngstrom;
       a.y = Ai[0][1] * OpenMM_NmPerAngstrom;
       a.z = Ai[0][2] * OpenMM_NmPerAngstrom;
       b.x = Ai[1][0] * OpenMM_NmPerAngstrom;
       b.y = Ai[1][1] * OpenMM_NmPerAngstrom;
       b.z = Ai[1][2] * OpenMM_NmPerAngstrom;
       c.x = Ai[2][0] * OpenMM_NmPerAngstrom;
       c.y = Ai[2][1] * OpenMM_NmPerAngstrom;
       c.z = Ai[2][2] * OpenMM_NmPerAngstrom;
       setDefaultPeriodicBoxVectors(a, b, c);
     }
   }
 
   /**
    * Update parameters if the Use flags and/or Lambda value has changed.
    *
    * @param atoms Atoms in this list are considered.
    */
   public void updateParameters(@Nullable Atom[] atoms) {
     VanDerWaals vanDerWaals = openMMEnergy.getVdwNode();
     if (vanDerWaals != null) {
       boolean vdwLambdaTerm = vanDerWaals.getLambdaTerm();
       if (vdwLambdaTerm) {
         double lambdaVDW = vanDerWaals.getLambda();
         if (fixedChargeNonBondedForce != null) {
           if (!softcoreCreated) {
             fixedChargeAlchemicalForces = new FixedChargeAlchemicalForces(openMMEnergy, fixedChargeNonBondedForce);
             addForce(fixedChargeAlchemicalForces.getFixedChargeSoftcoreForce());
             addForce(fixedChargeAlchemicalForces.getAlchemicalAlchemicalStericsForce());
             addForce(fixedChargeAlchemicalForces.getNonAlchemicalAlchemicalStericsForce());
             // Re-initialize the context.
             openMMEnergy.getContext().reinitialize(OpenMM_True);
             softcoreCreated = true;
           }
           // Update the lambda value.
           openMMEnergy.getContext().setParameter("vdw_lambda", lambdaVDW);
         } else if (amoebaVDWForce != null) {
           // Update the lambda value.
           openMMEnergy.getContext().setParameter("AmoebaVdwLambda", lambdaVDW);
           if (softcoreCreated) {
             ParticleMeshEwald pme = openMMEnergy.getPmeNode();
             // Avoid any updateParametersInContext calls if vdwLambdaTerm is true, but not other alchemical terms.
             if (pme == null || !pme.getLambdaTerm()) {
               return;
             }
           } else {
             softcoreCreated = true;
           }
         }
       }
     }
 
     // Note Stretch-Torsion and Angle-Torsion terms (for nucleic acids)
     // and Torsion-Torsion terms (for protein backbones) are not updated yet.
     if (updateBondedTerms) {
       if (bondForce != null) {
         bondForce.updateForce(openMMEnergy);
       }
       if (angleForce != null) {
         angleForce.updateForce(openMMEnergy);
       }
       if (inPlaneAngleForce != null) {
         inPlaneAngleForce.updateForce(openMMEnergy);
       }
       if (stretchBendForce != null) {
         stretchBendForce.updateForce(openMMEnergy);
       }
       if (ureyBradleyForce != null) {
         ureyBradleyForce.updateForce(openMMEnergy);
       }
       if (outOfPlaneBendForce != null) {
         outOfPlaneBendForce.updateForce(openMMEnergy);
       }
       if (piOrbitalTorsionForce != null) {
         piOrbitalTorsionForce.updateForce(openMMEnergy);
       }
       if (torsionForce != null) {
         torsionForce.updateForce(openMMEnergy);
       }
       if (improperTorsionForce != null) {
         improperTorsionForce.updateForce(openMMEnergy);
       }
     }
 
     if (restrainTorsionsForce != null) {
       restrainTorsionsForce.updateForce(openMMEnergy);
     }
 
     if (atoms == null || atoms.length == 0) {
       return;
     }
 
     // Update fixed charge non-bonded parameters.
     if (fixedChargeNonBondedForce != null) {
       // Need to pass all atoms due to non-bonded exceptions.
       fixedChargeNonBondedForce.updateForce(this.atoms, openMMEnergy);
     }
 
     // Update fixed charge GB parameters.
     if (fixedChargeGBForce != null) {
       fixedChargeGBForce.updateForce(atoms, openMMEnergy);
     }
 
     // Update AMOEBA vdW parameters.
     if (amoebaVDWForce != null) {
       amoebaVDWForce.updateForce(atoms, openMMEnergy);
     }
 
     // Update AMOEBA polarizable multipole parameters.
     if (amoebaMultipoleForce != null) {
       amoebaMultipoleForce.updateForce(atoms, openMMEnergy);
     }
 
     // Update GK force.
     if (amoebaGeneralizedKirkwoodForce != null) {
       amoebaGeneralizedKirkwoodForce.updateForce(atoms, openMMEnergy);
     }
 
     // Update WCA Force.
     if (amoebaWcaDispersionForce != null) {
       amoebaWcaDispersionForce.updateForce(atoms, openMMEnergy);
     }
 
     // Update WCA Force.
     if (amoebaGKCavitationForce != null) {
       amoebaGKCavitationForce.updateForce(atoms, openMMEnergy);
     }
   }
 
   /**
    * Adds atoms from the molecular assembly to the OpenMM System and reports to the user the number
    * of particles added.
    */
   protected void addAtoms() throws Exception {
     for (Atom atom : atoms) {
       double mass = atom.getMass();
       if (mass < 0.0) {
         throw new Exception(" Atom with mass less than 0.");
       }
       if (mass == 0.0) {
         logger.info(format(" Atom %s has zero mass.", atom));
       }
       addParticle(mass);
     }
   }
 
   /**
    * This method sets the mass of inactive atoms to zero.
    *
    * @return Returns true if any inactive atoms were found and set to zero mass.
    */
   public boolean updateAtomMass() {
     int index = 0;
     int inactiveCount = 0;
     for (Atom atom : atoms) {
       double mass = 0.0;
       if (atom.isActive()) {
         mass = atom.getMass();
       } else {
         inactiveCount++;
       }
       setParticleMass(index++, mass);
     }
     if (inactiveCount > 0) {
       logger.fine(format(" Inactive atoms (%d) set to zero mass.", inactiveCount));
       return true;
     }
     return false;
   }
 
   public boolean hasAmoebaCavitationForce() {
     return amoebaGKCavitationForce != null;
   }
 
   /**
    * Add a constraint to every bond.
    */
   protected void addUpBondConstraints() {
     BondPotentialEnergy bondPotentialEnergy = openMMEnergy.getBondPotentialEnergy();
     if (bondPotentialEnergy == null) {
       return;
     }
     Bond[] bonds = bondPotentialEnergy.getBondArray();
     logger.info(" Adding constraints for all bonds.");
     for (Bond bond : bonds) {
       Atom atom1 = bond.getAtom(0);
       Atom atom2 = bond.getAtom(1);
       int iAtom1 = atom1.getXyzIndex() - 1;
       int iAtom2 = atom2.getXyzIndex() - 1;
       addConstraint(iAtom1, iAtom2, bond.bondType.distance * OpenMM_NmPerAngstrom);
     }
   }
 
   /**
    * Add a constraint to every bond that includes a hydrogen atom.
    */
   protected void addHydrogenConstraints() {
     BondPotentialEnergy bondPotentialEnergy = openMMEnergy.getBondPotentialEnergy();
     if (bondPotentialEnergy == null) {
       return;
     }
     Bond[] bonds = bondPotentialEnergy.getBondArray();
     logger.info(" Adding constraints for hydrogen bonds.");
     for (Bond bond : bonds) {
       Atom atom1 = bond.getAtom(0);
       Atom atom2 = bond.getAtom(1);
       if (atom1.isHydrogen() || atom2.isHydrogen()) {
         BondType bondType = bond.bondType;
         int iAtom1 = atom1.getXyzIndex() - 1;
         int iAtom2 = atom2.getXyzIndex() - 1;
         addConstraint(iAtom1, iAtom2, bondType.distance * OpenMM_NmPerAngstrom);
       }
     }
   }
 
   /**
    * Add a constraint to every angle that includes two hydrogen atoms.
    */
   protected void setUpHydrogenAngleConstraints() {
     AnglePotentialEnergy anglePotentialEnergy = openMMEnergy.getAnglePotentialEnergy();
     if (anglePotentialEnergy == null) {
       return;
     }
     Angle[] angles = anglePotentialEnergy.getAngleArray();
     logger.info(" Adding hydrogen angle constraints.");
     for (Angle angle : angles) {
       if (isHydrogenAngle(angle)) {
         Atom atom1 = angle.getAtom(0);
         Atom atom3 = angle.getAtom(2);
 
         // Calculate a "false bond" length between atoms 1 and 3 to constrain the angle using the
         // law of cosines.
         Bond bond1 = angle.getBond(0);
         double distance1 = bond1.bondType.distance;
 
         Bond bond2 = angle.getBond(1);
         double distance2 = bond2.bondType.distance;
 
         // Equilibrium angle value in degrees.
         double angleVal = angle.angleType.angle[angle.nh];
 
         // Law of cosines.
         double falseBondLength = sqrt(
             distance1 * distance1 + distance2 * distance2 - 2.0 * distance1 * distance2 * cos(
                 toRadians(angleVal)));
 
         int iAtom1 = atom1.getXyzIndex() - 1;
         int iAtom3 = atom3.getXyzIndex() - 1;
         addConstraint(iAtom1, iAtom3, falseBondLength * OpenMM_NmPerAngstrom);
       }
     }
   }
 
   /**
    * Check to see if an angle is a hydrogen angle. This method only returns true for hydrogen
    * angles that are less than 160 degrees.
    *
    * @param angle Angle to check.
    * @return boolean indicating whether an angle is a hydrogen angle that is less than 160 degrees.
    */
   protected boolean isHydrogenAngle(Angle angle) {
     if (angle.containsHydrogen()) {
       // Equilibrium angle value in degrees.
       double angleVal = angle.angleType.angle[angle.nh];
       // Make sure angle is less than 160 degrees because greater than 160 degrees will not be
       // constrained
       // well using the law of cosines.
       if (angleVal < 160.0) {
         Atom atom1 = angle.getAtom(0);
         Atom atom2 = angle.getAtom(1);
         Atom atom3 = angle.getAtom(2);
         // Setting constraints only on angles where atom1 or atom3 is a hydrogen while atom2 is
         // not a hydrogen.
         return atom1.isHydrogen() && atom3.isHydrogen() && !atom2.isHydrogen();
       }
     }
     return false;
   }
 }