Examples with Atom ffx.potential.bonded.Atom used on opensource projects

Example 96 with Atom

use of ffx.potential.bonded.Atom in project ffx by mjschnie.

the class ForceFieldEnergy method getdEdXdL.

/**
 * {@inheritDoc}
 *
 * @param gradients
 */
@Override
public void getdEdXdL(double[] gradients) {
    if (!lambdaBondedTerms) {
        if (vanderWaalsTerm) {
            vanderWaals.getdEdXdL(gradients);
        }
        if (multipoleTerm) {
            particleMeshEwald.getdEdXdL(gradients);
        }
        if (restraintBondTerm) {
            for (int i = 0; i < nRestraintBonds; i++) {
                restraintBonds[i].getdEdXdL(gradients);
            }
        }
        if (ncsTerm && ncsRestraint != null) {
            ncsRestraint.getdEdXdL(gradients);
        }
        if (restrainTerm && !coordRestraints.isEmpty()) {
            for (CoordRestraint restraint : coordRestraints) {
                restraint.getdEdXdL(gradients);
            }
        // autoCoordRestraint.getdEdXdL(gradients);
        }
        if (comTerm && comRestraint != null) {
            comRestraint.getdEdXdL(gradients);
        }
        if (lambdaTorsions) {
            double[] grad = new double[3];
            int index = 0;
            for (int i = 0; i < nAtoms; i++) {
                Atom a = atoms[i];
                if (a.isActive()) {
                    a.getLambdaXYZGradient(grad);
                    gradients[index++] += grad[0];
                    gradients[index++] += grad[1];
                    gradients[index++] += grad[2];
                }
            }
        }
    }
}

Example 97 with Atom

use of ffx.potential.bonded.Atom in project ffx by mjschnie.

the class ForceFieldEnergy method energy.

/**
 * <p>
 * energy</p>
 *
 * @param gradient a boolean.
 * @param print a boolean.
 * @return a double.
 */
public double energy(boolean gradient, boolean print) {
    try {
        bondTime = 0;
        angleTime = 0;
        stretchBendTime = 0;
        ureyBradleyTime = 0;
        outOfPlaneBendTime = 0;
        torsionTime = 0;
        piOrbitalTorsionTime = 0;
        torsionTorsionTime = 0;
        improperTorsionTime = 0;
        vanDerWaalsTime = 0;
        electrostaticTime = 0;
        restraintBondTime = 0;
        ncsTime = 0;
        coordRestraintTime = 0;
        totalTime = System.nanoTime();
        // Zero out the potential energy of each bonded term.
        bondEnergy = 0.0;
        angleEnergy = 0.0;
        stretchBendEnergy = 0.0;
        ureyBradleyEnergy = 0.0;
        outOfPlaneBendEnergy = 0.0;
        torsionEnergy = 0.0;
        piOrbitalTorsionEnergy = 0.0;
        torsionTorsionEnergy = 0.0;
        improperTorsionEnergy = 0.0;
        totalBondedEnergy = 0.0;
        // Zero out potential energy of restraint terms
        restraintBondEnergy = 0.0;
        ncsEnergy = 0.0;
        restrainEnergy = 0.0;
        // Zero out bond and angle RMSDs.
        bondRMSD = 0.0;
        angleRMSD = 0.0;
        // Zero out the potential energy of each non-bonded term.
        vanDerWaalsEnergy = 0.0;
        permanentMultipoleEnergy = 0.0;
        permanentRealSpaceEnergy = 0.0;
        permanentSelfEnergy = 0.0;
        permanentReciprocalEnergy = 0.0;
        polarizationEnergy = 0.0;
        inducedRealSpaceEnergy = 0.0;
        inducedSelfEnergy = 0.0;
        inducedReciprocalEnergy = 0.0;
        totalMultipoleEnergy = 0.0;
        totalNonBondedEnergy = 0.0;
        // Zero out the solvation energy.
        solvationEnergy = 0.0;
        // Zero out the relative solvation energy (sequence optimization)
        relativeSolvationEnergy = 0.0;
        nRelativeSolvations = 0;
        esvBias = 0.0;
        // Zero out the total potential energy.
        totalEnergy = 0.0;
        // Zero out the Cartesian coordinate gradient for each atom.
        if (gradient) {
            for (int i = 0; i < nAtoms; i++) {
                atoms[i].setXYZGradient(0.0, 0.0, 0.0);
                atoms[i].setLambdaXYZGradient(0.0, 0.0, 0.0);
            }
        }
        /**
         * Computed the bonded energy terms in parallel.
         */
        try {
            bondedRegion.setGradient(gradient);
            parallelTeam.execute(bondedRegion);
        } catch (RuntimeException ex) {
            logger.warning("Runtime exception during bonded term calculation.");
            throw ex;
        } catch (Exception ex) {
            Utilities.printStackTrace(ex);
            logger.severe(ex.toString());
        }
        if (!lambdaBondedTerms) {
            /**
             * Compute restraint terms.
             */
            if (ncsTerm) {
                ncsTime = -System.nanoTime();
                ncsEnergy = ncsRestraint.residual(gradient, print);
                ncsTime += System.nanoTime();
            }
            if (restrainTerm && !coordRestraints.isEmpty()) {
                coordRestraintTime = -System.nanoTime();
                for (CoordRestraint restraint : coordRestraints) {
                    restrainEnergy += restraint.residual(gradient, print);
                }
                coordRestraintTime += System.nanoTime();
            }
            if (comTerm) {
                comRestraintTime = -System.nanoTime();
                comRestraintEnergy = comRestraint.residual(gradient, print);
                comRestraintTime += System.nanoTime();
            }
            /**
             * Compute non-bonded terms.
             */
            if (vanderWaalsTerm) {
                vanDerWaalsTime = -System.nanoTime();
                vanDerWaalsEnergy = vanderWaals.energy(gradient, print);
                nVanDerWaalInteractions = this.vanderWaals.getInteractions();
                vanDerWaalsTime += System.nanoTime();
            }
            if (multipoleTerm) {
                electrostaticTime = -System.nanoTime();
                totalMultipoleEnergy = particleMeshEwald.energy(gradient, print);
                permanentMultipoleEnergy = particleMeshEwald.getPermanentEnergy();
                permanentRealSpaceEnergy = particleMeshEwald.getPermRealEnergy();
                permanentSelfEnergy = particleMeshEwald.getPermSelfEnergy();
                permanentReciprocalEnergy = particleMeshEwald.getPermRecipEnergy();
                polarizationEnergy = particleMeshEwald.getPolarizationEnergy();
                inducedRealSpaceEnergy = particleMeshEwald.getIndRealEnergy();
                inducedSelfEnergy = particleMeshEwald.getIndSelfEnergy();
                inducedReciprocalEnergy = particleMeshEwald.getIndRecipEnergy();
                nPermanentInteractions = particleMeshEwald.getInteractions();
                solvationEnergy = particleMeshEwald.getGKEnergy();
                nGKInteractions = particleMeshEwald.getGKInteractions();
                electrostaticTime += System.nanoTime();
            }
        }
        if (relativeSolvationTerm) {
            List<Residue> residuesList = molecularAssembly.getResidueList();
            for (Residue residue : residuesList) {
                if (residue instanceof MultiResidue) {
                    Atom refAtom = residue.getSideChainAtoms().get(0);
                    if (refAtom != null && refAtom.getUse()) {
                        /**
                         * Reasonably confident that it should be -=, as we
                         * are trying to penalize residues with strong
                         * solvation energy.
                         */
                        double thisSolvation = relativeSolvation.getSolvationEnergy(residue, false);
                        relativeSolvationEnergy -= thisSolvation;
                        if (thisSolvation != 0) {
                            nRelativeSolvations++;
                        }
                    }
                }
            }
        }
        totalTime = System.nanoTime() - totalTime;
        totalBondedEnergy = bondEnergy + restraintBondEnergy + angleEnergy + stretchBendEnergy + ureyBradleyEnergy + outOfPlaneBendEnergy + torsionEnergy + piOrbitalTorsionEnergy + improperTorsionEnergy + torsionTorsionEnergy + ncsEnergy + restrainEnergy;
        totalNonBondedEnergy = vanDerWaalsEnergy + totalMultipoleEnergy + relativeSolvationEnergy;
        totalEnergy = totalBondedEnergy + totalNonBondedEnergy + solvationEnergy;
        if (esvTerm) {
            esvBias = esvSystem.getBiasEnergy();
            totalEnergy += esvBias;
        }
    } catch (EnergyException ex) {
        if (printOnFailure) {
            File origFile = molecularAssembly.getFile();
            String timeString = LocalDateTime.now().format(DateTimeFormatter.ofPattern("yyyy_MM_dd-HH_mm_ss"));
            String filename = String.format("%s-ERROR-%s.pdb", FilenameUtils.removeExtension(molecularAssembly.getFile().getName()), timeString);
            PotentialsFunctions ef = new PotentialsUtils();
            filename = ef.versionFile(filename);
            logger.info(String.format(" Writing on-error snapshot to file %s", filename));
            ef.saveAsPDB(molecularAssembly, new File(filename));
            molecularAssembly.setFile(origFile);
        }
        if (ex.doCauseSevere()) {
            logger.log(Level.SEVERE, " Error in calculating energies or gradients", ex);
            return 0.0;
        } else {
            // Rethrow exception
            throw ex;
        }
    }
    if (print || printOverride) {
        if (printCompact) {
            logger.info(this.toString());
        } else {
            StringBuilder sb = new StringBuilder();
            if (gradient) {
                sb.append("\n Computed Potential Energy and Atomic Coordinate Gradients\n");
            } else {
                sb.append("\n Computed Potential Energy\n");
            }
            sb.append(this);
            logger.info(sb.toString());
        }
    }
    return totalEnergy;
}

Example 98 with Atom

use of ffx.potential.bonded.Atom in project ffx by mjschnie.

the class ForceFieldEnergy method getCoordinates.

/**
 * {@inheritDoc}
 *
 * @param x
 */
@Override
public double[] getCoordinates(double[] x) {
    int n = getNumberOfVariables();
    if (x == null || x.length < n) {
        x = new double[n];
    }
    int index = 0;
    for (int i = 0; i < nAtoms; i++) {
        Atom a = atoms[i];
        if (a.isActive() && !a.isBackground()) {
            x[index++] = a.getX();
            x[index++] = a.getY();
            x[index++] = a.getZ();
        }
    }
    return x;
}

Example 99 with Atom

use of ffx.potential.bonded.Atom in project ffx by mjschnie.

the class ForceFieldEnergyOpenMM method addGKForce.

private void addGKForce() {
    GeneralizedKirkwood gk = super.getGK();
    amoebaGeneralizedKirkwoodForce = OpenMM_AmoebaGeneralizedKirkwoodForce_create();
    OpenMM_AmoebaGeneralizedKirkwoodForce_setSolventDielectric(amoebaGeneralizedKirkwoodForce, 78.3);
    OpenMM_AmoebaGeneralizedKirkwoodForce_setSoluteDielectric(amoebaGeneralizedKirkwoodForce, 1.0);
    double[] overlapScale = gk.getOverlapScale();
    double[] baseRadii = gk.getBaseRadii();
    Atom[] atoms = molecularAssembly.getAtomArray();
    int nAtoms = atoms.length;
    for (int i = 0; i < nAtoms; i++) {
        MultipoleType multipoleType = atoms[i].getMultipoleType();
        OpenMM_AmoebaGeneralizedKirkwoodForce_addParticle(amoebaGeneralizedKirkwoodForce, multipoleType.charge, OpenMM_NmPerAngstrom * baseRadii[i], overlapScale[i]);
    }
    OpenMM_AmoebaGeneralizedKirkwoodForce_setProbeRadius(amoebaGeneralizedKirkwoodForce, 1.4 * OpenMM_NmPerAngstrom);
    NonPolar nonpolar = gk.getNonPolarModel();
    switch(nonpolar) {
        case BORN_SOLV:
        case BORN_CAV_DISP:
        default:
            // Configure a Born Radii based surface area term.
            double surfaceTension = gk.getSurfaceTension() * OpenMM_KJPerKcal * OpenMM_AngstromsPerNm * OpenMM_AngstromsPerNm;
            OpenMM_AmoebaGeneralizedKirkwoodForce_setIncludeCavityTerm(amoebaGeneralizedKirkwoodForce, OpenMM_True);
            OpenMM_AmoebaGeneralizedKirkwoodForce_setSurfaceAreaFactor(amoebaGeneralizedKirkwoodForce, -surfaceTension);
            break;
        case CAV:
        case CAV_DISP:
        case HYDROPHOBIC_PMF:
        case NONE:
            // This NonPolar model does not use a Born Radii based surface area term.
            OpenMM_AmoebaGeneralizedKirkwoodForce_setIncludeCavityTerm(amoebaGeneralizedKirkwoodForce, OpenMM_False);
            break;
    }
    OpenMM_System_addForce(system, amoebaGeneralizedKirkwoodForce);
    switch(nonpolar) {
        case CAV_DISP:
        case BORN_CAV_DISP:
            addWCAForce();
            break;
        case CAV:
        case HYDROPHOBIC_PMF:
        case BORN_SOLV:
        case NONE:
        default:
    }
    logger.log(Level.INFO, " Added generalized Kirkwood force.");
}

Example 100 with Atom

use of ffx.potential.bonded.Atom in project ffx by mjschnie.

the class ForceFieldEnergyOpenMM method addRestraintBonds.

/**
 * Adds restraint bonds, if any.
 */
private void addRestraintBonds() {
    List<RestraintBond> restraintBonds = super.getRestraintBonds();
    if (restraintBonds != null && !restraintBonds.isEmpty()) {
        // OpenMM's HarmonicBondForce class uses k, not 1/2*k as does FFX.
        double kParameterConversion = BondType.units * 2.0 * OpenMM_KJPerKcal / (OpenMM_NmPerAngstrom * OpenMM_NmPerAngstrom);
        for (RestraintBond rbond : super.getRestraintBonds()) {
            // Is not a valid substitute for a targeting computer.
            PointerByReference theForce;
            BondType bType = rbond.bondType;
            BondType.BondFunction funct = bType.bondFunction;
            if (restraintForces.containsKey(funct)) {
                theForce = restraintForces.get(funct);
            } else {
                theForce = OpenMM_CustomBondForce_create(funct.toMathematicalForm());
                OpenMM_CustomBondForce_addPerBondParameter(theForce, "k");
                OpenMM_CustomBondForce_addPerBondParameter(theForce, "r0");
                if (funct.hasFlatBottom()) {
                    OpenMM_CustomBondForce_addPerBondParameter(theForce, "fb");
                }
                // Wholly untested code.
                switch(funct) {
                    case QUARTIC:
                    case FLAT_BOTTOM_QUARTIC:
                        OpenMM_CustomBondForce_addGlobalParameter(theForce, "cubic", BondType.cubic / OpenMM_NmPerAngstrom);
                        OpenMM_CustomBondForce_addGlobalParameter(theForce, "quartic", BondType.quartic / (OpenMM_NmPerAngstrom * OpenMM_NmPerAngstrom));
                        break;
                    default:
                        break;
                }
                OpenMM_System_addForce(system, theForce);
            }
            double forceConst = bType.forceConstant * kParameterConversion;
            double equilDist = bType.distance * OpenMM_NmPerAngstrom;
            Atom[] ats = rbond.getAtomArray();
            int at1 = ats[0].getXyzIndex() - 1;
            int at2 = ats[1].getXyzIndex() - 1;
            PointerByReference bondParams = OpenMM_DoubleArray_create(0);
            OpenMM_DoubleArray_append(bondParams, forceConst);
            OpenMM_DoubleArray_append(bondParams, equilDist);
            if (funct.hasFlatBottom()) {
                OpenMM_DoubleArray_append(bondParams, bType.flatBottomRadius * OpenMM_NmPerAngstrom);
            }
            OpenMM_CustomBondForce_addBond(theForce, at1, at2, bondParams);
            OpenMM_DoubleArray_destroy(bondParams);
        }
    }
}