// ******************************************************************************
   //
   // 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 com.sun.jna.ptr.DoubleByReference;
  import com.sun.jna.ptr.IntByReference;
  import ffx.crystal.Crystal;
  import ffx.openmm.BondArray;
  import ffx.openmm.Force;
  import ffx.openmm.NonbondedForce;
  import ffx.potential.bonded.Atom;
  import ffx.potential.bonded.Bond;
  import ffx.potential.nonbonded.NonbondedCutoff;
  import ffx.potential.nonbonded.ParticleMeshEwald;
  import ffx.potential.nonbonded.VanDerWaals;
  import ffx.potential.nonbonded.VanDerWaalsForm;
  import ffx.potential.parameters.ForceField;
  import ffx.potential.parameters.MultipoleType;
  import ffx.potential.parameters.VDWType;
  import ffx.potential.terms.BondPotentialEnergy;
  
  import java.util.logging.Level;
  import java.util.logging.Logger;
  
  import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_AngstromsPerNm;
  import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_KJPerKcal;
  import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_NmPerAngstrom;
  import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_Boolean.OpenMM_False;
  import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_Boolean.OpenMM_True;
  import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_NonbondedForce_NonbondedMethod.OpenMM_NonbondedForce_NoCutoff;
  import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_NonbondedForce_NonbondedMethod.OpenMM_NonbondedForce_PME;
  import static ffx.potential.parameters.VDWType.EPSILON_RULE.GEOMETRIC;
  import static ffx.potential.parameters.VDWType.RADIUS_RULE.ARITHMETIC;
  import static ffx.potential.parameters.VDWType.RADIUS_SIZE.RADIUS;
  import static ffx.potential.parameters.VDWType.RADIUS_TYPE.R_MIN;
  import static ffx.potential.parameters.VDWType.VDW_TYPE.LENNARD_JONES;
  import static java.lang.String.format;
  import static org.apache.commons.math3.util.FastMath.abs;
  
  /**
   * Define a fixed charge non-bonded force.
   * <p>
   * Uses arithmetic mean to define sigma and geometric mean for epsilon.
   */
  public class FixedChargeNonbondedForce extends NonbondedForce {
  
    private static final Logger logger = Logger.getLogger(FixedChargeNonbondedForce.class.getName());
  
    /**
     * Boolean array, holds charge exclusion list.
     */
    private boolean[] chargeExclusion;
    /**
     * Boolean array, holds van Der Waals exclusion list.
     */
    private boolean[] vdWExclusion;
    /**
     * Double array, holds charge quantity value for exceptions.
     */
    private double[] exceptionChargeProd;
    /**
     * Double array, holds epsilon quantity value for exceptions.
     */
    private double[] exceptionEps;
 
   public FixedChargeNonbondedForce(OpenMMEnergy openMMEnergy) {
     VanDerWaals vdW = openMMEnergy.getVdwNode();
     if (vdW == null) {
       // Free the memory created by the OpenMMNonbondedForce constructor.
       destroy();
       return;
     }
 
     /*
      Only 6-12 LJ with arithmetic mean to define sigma and geometric mean
      for epsilon is supported.
     */
     VanDerWaalsForm vdwForm = vdW.getVDWForm();
     if (vdwForm.vdwType != LENNARD_JONES || vdwForm.radiusRule != ARITHMETIC
         || vdwForm.epsilonRule != GEOMETRIC) {
       logger.info(format(" VDW Type:         %s", vdwForm.vdwType));
       logger.info(format(" VDW Radius Rule:  %s", vdwForm.radiusRule));
       logger.info(format(" VDW Epsilon Rule: %s", vdwForm.epsilonRule));
       logger.log(Level.SEVERE, " Unsupported van der Waals functional form.");
       return;
     }
 
     // OpenMM vdW force requires a diameter (i.e. not radius).
     double radScale = 1.0;
     if (vdwForm.radiusSize == RADIUS) {
       radScale = 2.0;
     }
 
     // OpenMM vdw force requires atomic sigma values (i.e. not r-min).
     if (vdwForm.radiusType == R_MIN) {
       radScale /= 1.122462048309372981;
     }
 
     // Add particles.
     Atom[] atoms = openMMEnergy.getMolecularAssembly().getAtomArray();
     for (Atom atom : atoms) {
       VDWType vdwType = atom.getVDWType();
       double sigma = OpenMM_NmPerAngstrom * vdwType.radius * radScale;
       double eps = OpenMM_KJPerKcal * vdwType.wellDepth;
       double charge = 0.0;
       MultipoleType multipoleType = atom.getMultipoleType();
       if (multipoleType != null && atom.getElectrostatics()) {
         charge = multipoleType.charge;
       }
       addParticle(charge, sigma, eps);
     }
 
     // Define 1-4 scale factors.
     double lj14Scale = vdwForm.getScale14();
     double coulomb14Scale = 1.0 / 1.2;
     ParticleMeshEwald pme = openMMEnergy.getPmeNode();
     if (pme != null) {
       coulomb14Scale = pme.getScale14();
     }
 
     BondPotentialEnergy bondPotentialEnergy = openMMEnergy.getBondPotentialEnergy();
     if (bondPotentialEnergy != null) {
       Bond[] bonds = bondPotentialEnergy.getBondArray();
       BondArray bondArray = new BondArray(0);
       for (Bond bond : bonds) {
         int i1 = bond.getAtom(0).getXyzIndex() - 1;
         int i2 = bond.getAtom(1).getXyzIndex() - 1;
         bondArray.append(i1, i2);
       }
       createExceptionsFromBonds(bondArray, coulomb14Scale, lj14Scale);
       bondArray.destroy();
 
       int num = getNumExceptions();
       chargeExclusion = new boolean[num];
       vdWExclusion = new boolean[num];
       exceptionChargeProd = new double[num];
       exceptionEps = new double[num];
       IntByReference particle1 = new IntByReference();
       IntByReference particle2 = new IntByReference();
       DoubleByReference chargeProd = new DoubleByReference();
       DoubleByReference sigma = new DoubleByReference();
       DoubleByReference eps = new DoubleByReference();
       for (int i = 0; i < num; i++) {
         getExceptionParameters(i, particle1, particle2, chargeProd, sigma, eps);
         if (abs(chargeProd.getValue()) > 0.0) {
           chargeExclusion[i] = false;
           exceptionChargeProd[i] = chargeProd.getValue();
         } else {
           exceptionChargeProd[i] = 0.0;
           chargeExclusion[i] = true;
         }
         if (abs(eps.getValue()) > 0.0) {
           vdWExclusion[i] = false;
           exceptionEps[i] = eps.getValue();
         } else {
           vdWExclusion[i] = true;
           exceptionEps[i] = 0.0;
         }
       }
     }
 
     Crystal crystal = openMMEnergy.getCrystal();
     if (crystal.aperiodic()) {
       setNonbondedMethod(OpenMM_NonbondedForce_NoCutoff);
     } else {
       setNonbondedMethod(OpenMM_NonbondedForce_PME);
       if (pme != null) {
         // Units of the Ewald coefficient are A^-1; Multiply by AngstromsPerNM to convert to (Nm^-1).
         double aEwald = OpenMM_AngstromsPerNm * pme.getEwaldCoefficient();
         int nx = pme.getReciprocalSpace().getXDim();
         int ny = pme.getReciprocalSpace().getYDim();
         int nz = pme.getReciprocalSpace().getZDim();
         setPMEParameters(aEwald, nx, ny, nz);
       }
 
       NonbondedCutoff nonbondedCutoff = vdW.getNonbondedCutoff();
       double off = nonbondedCutoff.off;
       double cut = nonbondedCutoff.cut;
       setCutoffDistance(OpenMM_NmPerAngstrom * off);
       setUseSwitchingFunction(OpenMM_True);
       if (cut == off) {
         logger.warning(" OpenMM does not properly handle cutoffs where cut == off!");
         if (cut == Double.MAX_VALUE || cut == Double.POSITIVE_INFINITY) {
           logger.info(" Detected infinite or max-value cutoff; setting cut to 1E+40 for OpenMM.");
           cut = 1E40;
         } else {
           logger.info(format(" Detected cut %8.4g == off %8.4g; scaling cut to 0.99 of off for OpenMM.", cut, off));
           cut *= 0.99;
         }
       }
       setSwitchingDistance(OpenMM_NmPerAngstrom * cut);
     }
 
     setUseDispersionCorrection(OpenMM_False);
 
     ForceField forceField = openMMEnergy.getMolecularAssembly().getForceField();
     int forceGroup = forceField.getInteger("VDW_FORCE_GROUP", 1);
     int pmeGroup = forceField.getInteger("PME_FORCE_GROUP", 1);
     if (forceGroup != pmeGroup) {
       logger.severe(format(" ERROR: VDW-FORCE-GROUP is %d while PME-FORCE-GROUP is %d. "
               + "This is invalid for fixed-charge force fields with combined non-bonded forces.",
           forceGroup, pmeGroup));
     }
 
     setForceGroup(forceGroup);
     logger.log(Level.INFO, format("  Fixed charge non-bonded force \t%1d", forceGroup));
   }
 
   /**
    * Convenience method to construct an OpenMM Non-Bonded Force.
    *
    * @param openMMEnergy The OpenMM Energy instance that contains the Non-Bonded Force information.
    * @return An OpenMM Non-Bonded Force, or null if there is no vdW information.
    */
   public static Force constructForce(OpenMMEnergy openMMEnergy) {
     VanDerWaals vdW = openMMEnergy.getVdwNode();
     if (vdW == null) {
       // Free the memory created by the OpenMMNonbondedForce constructor.
       return null;
     }
 
     /*
      Only 6-12 LJ with arithmetic mean to define sigma and geometric mean
      for epsilon is supported.
     */
     VanDerWaalsForm vdwForm = vdW.getVDWForm();
     if (vdwForm.vdwType != LENNARD_JONES || vdwForm.radiusRule != ARITHMETIC
         || vdwForm.epsilonRule != GEOMETRIC) {
       logger.info(format(" VDW Type:         %s", vdwForm.vdwType));
       logger.info(format(" VDW Radius Rule:  %s", vdwForm.radiusRule));
       logger.info(format(" VDW Epsilon Rule: %s", vdwForm.epsilonRule));
       logger.log(Level.SEVERE, " Unsupported van der Waals functional form.");
       return null;
     }
 
     return new FixedChargeNonbondedForce(openMMEnergy);
   }
 
   /**
    * Update an existing non-bonded force for the OpenMM System.
    *
    * @param atoms        The Atom array.
    * @param openMMEnergy The OpenMM Energy instance that contains the non-bonded force information.
    */
   public void updateForce(Atom[] atoms, OpenMMEnergy openMMEnergy) {
     VanDerWaals vdW = openMMEnergy.getVdwNode();
     // Only 6-12 LJ with arithmetic mean to define sigma and geometric mean for epsilon is
     // supported.
     VanDerWaalsForm vdwForm = vdW.getVDWForm();
     if (vdwForm.vdwType != LENNARD_JONES || vdwForm.radiusRule != ARITHMETIC
         || vdwForm.epsilonRule != GEOMETRIC) {
       logger.log(Level.SEVERE, " Unsupported van der Waals functional form.");
       return;
     }
 
     // OpenMM vdW force requires a diameter (i.e. not radius).
     double radScale = 1.0;
     if (vdwForm.radiusSize == RADIUS) {
       radScale = 2.0;
     }
 
     // OpenMM vdw force requires atomic sigma values (i.e. not r-min).
     if (vdwForm.radiusType == R_MIN) {
       radScale /= 1.122462048309372981;
     }
 
     // Update parameters.
     for (Atom atom : atoms) {
       int index = atom.getXyzIndex() - 1;
       boolean applyLambda = atom.applyLambda();
 
       double charge = Double.MIN_VALUE;
       MultipoleType multipoleType = atom.getMultipoleType();
       if (multipoleType != null && atom.getElectrostatics()) {
         charge = multipoleType.charge;
       }
 
       VDWType vdwType = atom.getVDWType();
       double sigma = OpenMM_NmPerAngstrom * vdwType.radius * radScale;
       double eps = OpenMM_KJPerKcal * vdwType.wellDepth;
 
       if (applyLambda) {
         boolean vdwLambdaTerm = vdW.getLambdaTerm();
         // If we're using vdwLambdaTerm, this atom's vdW interactions are handled by the Custom Non-Bonded force.
         if (vdwLambdaTerm) {
           eps = 0.0;
         }
         // Always scale the charge by lambdaElec
         double permLambda = openMMEnergy.getPmeNode().getAlchemicalParameters().permLambda;
         charge *= permLambda;
       }
 
       if (!atom.getUse()) {
         eps = 0.0;
         charge = 0.0;
       }
 
       setParticleParameters(index, charge, sigma, eps);
     }
 
     // Update Exceptions.
     IntByReference particle1 = new IntByReference();
     IntByReference particle2 = new IntByReference();
     DoubleByReference chargeProd = new DoubleByReference();
     DoubleByReference sigma = new DoubleByReference();
     DoubleByReference eps = new DoubleByReference();
 
     int numExceptions = getNumExceptions();
     for (int i = 0; i < numExceptions; i++) {
 
       // Only update exceptions.
       if (chargeExclusion[i] && vdWExclusion[i]) {
         continue;
       }
 
       getExceptionParameters(i, particle1, particle2, chargeProd, sigma, eps);
 
       int i1 = particle1.getValue();
       int i2 = particle2.getValue();
 
       double qq = exceptionChargeProd[i];
       double epsilon = exceptionEps[i];
 
       Atom atom1 = atoms[i1];
       Atom atom2 = atoms[i2];
 
       /*
       Note that the minimum epsilon value cannot be zero, or OpenMM may
       report an error that the number of Exceptions has changed.
       */
       double minEpsilon = 1.0e-12;
 
       double lambdaElec = 1.0;
       ParticleMeshEwald pme = openMMEnergy.getPmeNode();
       if (pme != null) {
         lambdaElec = pme.getAlchemicalParameters().permLambda;
       }
 
       boolean vdwLambdaTerm = vdW.getLambdaTerm();
 
       if (lambdaElec < minEpsilon) {
         lambdaElec = minEpsilon;
       }
 
       if (atom1.applyLambda()) {
         qq *= lambdaElec;
         if (vdwLambdaTerm) {
           epsilon = minEpsilon;
         }
       }
       if (atom2.applyLambda()) {
         qq *= lambdaElec;
         if (vdwLambdaTerm) {
           epsilon = minEpsilon;
         }
       }
       if (!atom1.getUse() || !atom2.getUse()) {
         qq = minEpsilon;
         epsilon = minEpsilon;
       }
 
       setExceptionParameters(i, i1, i2, qq, sigma.getValue(), epsilon);
     }
 
     // Update the parameters in the OpenMM Context.
     updateParametersInContext(openMMEnergy.getContext());
   }
 
 }