vanderwaalsinteractions.java

化学图形处理软件

	/**
	 *  Set the gradient of the MMFF94 Van Der Waals interaction term.
	 *
	 *
	 *@param  coords3d  Current molecule coordinates.
	 */
	public void setGradientMMFF94SumEvdW(GVector coords3d) {

		gradientMMFF94SumEvdW = new GVector(coords3d.getSize());
		if (currentCoordinates.equals(coords3d)) {} 
		else {setFunctionMMFF94SumEvdW(coords3d);}

		setAtomsDistancesFirstOrderDerivative(coords3d);
		for (int l = 0; l < vdwInteractionNumber; l++) {
			vdWEG1[l] = eSK[l] * 7 * Math.pow((1.07 * asteriskR[l]) / (r[l] + 0.07 * asteriskR[l]),6) * 
					1.07 * asteriskR[l] * (-1) * (1/Math.pow((r[l] + 0.07 * asteriskR[l]),2));
			vdWEG2[l] = 1.12 * Math.pow(asteriskR[l],7) * 
					(-1) * (1/Math.pow((Math.pow(r[l],7) + 0.12 * Math.pow(asteriskR[l],7)),2)) * 7 * Math.pow(r[l],6);
		}
		
		double sumGradientEvdW;
		for (int i = 0; i < gradientMMFF94SumEvdW.getSize(); i++) {
			sumGradientEvdW = 0;
			for (int l = 0; l < vdwInteractionNumber; l++) {
				sumGradientEvdW = sumGradientEvdW + vdWEG1[l] * dR[i][l] * vdWE2[l] + vdWE1[l] * vdWEG2[l]  * dR[i][l];
			}
			gradientMMFF94SumEvdW.setElement(i, sumGradientEvdW);
		}
		//logger.debug("gradientMMFF94SumEvdW = " + gradientMMFF94SumEvdW);
	}


	/**
	 *  Get the gradient of the MMFF94 Van Der Waals interaction term.
	 *
	 *
	 *@return           MMFF94 Van Der Waals interaction gradient value.
	 */
	public GVector getGradientMMFF94SumEvdW() {
		return gradientMMFF94SumEvdW;
	}


	/**
	 *  Evaluate a 2nd order error approximation of the gradient, for the Van Der Waals interaction term, given the atoms
	 *  coordinates
	 *
	 *@param  coord3d  Current molecule coordinates.
	 */
	public void set2ndOrderErrorApproximateGradientMMFF94SumEvdW(GVector coord3d) {
		order2ndErrorApproximateGradientMMFF94SumEvdW = new GVector(coord3d.getSize());
		double sigma = Math.pow(0.000000000000001,0.33);
		GVector xplusSigma = new GVector(coord3d.getSize());
		GVector xminusSigma = new GVector(coord3d.getSize());
		double fxplusSigma = 0;
		double fxminusSigma = 0;
		
		for (int m = 0; m < order2ndErrorApproximateGradientMMFF94SumEvdW.getSize(); m++) {
			xplusSigma.set(coord3d);
			xplusSigma.setElement(m,coord3d.getElement(m) + sigma);
			setFunctionMMFF94SumEvdW(xplusSigma);
			fxplusSigma = getFunctionMMFF94SumEvdW();
			xminusSigma.set(coord3d);
			xminusSigma.setElement(m,coord3d.getElement(m) - sigma);
			setFunctionMMFF94SumEvdW(xminusSigma);
			fxminusSigma = getFunctionMMFF94SumEvdW();
			order2ndErrorApproximateGradientMMFF94SumEvdW.setElement(m,(fxplusSigma - fxminusSigma) / (2 * sigma));
		}
			
		//logger.debug("order2ndErrorApproximateGradientMMFF94SumEvdW : " + order2ndErrorApproximateGradientMMFF94SumEvdW);
	}


	/**
	 *  Get the 2nd order error approximate gradient for the Van Der Waals interaction term.
	 *
	 *
	 *@return           Van Der Waals interaction 2nd order error approximate gradient value
	 */
	public GVector get2ndOrderErrorApproximateGradientMMFF94SumEvdW() {
		return order2ndErrorApproximateGradientMMFF94SumEvdW;
	}


	/**
	 *  Evaluate a 5th order error approximation of the gradient, for the Van Der Waals interaction term, given the atoms
	 *  coordinates
	 *
	 *@param  coord3d  Current molecule coordinates.
	 */
	public void set5thOrderErrorApproximateGradientMMFF94SumEvdW(GVector coord3d) {
		order5thErrorApproximateGradientMMFF94SumEvdW = new GVector(coord3d.getSize());
		double sigma = Math.pow(0.000000000000001,0.2);
		GVector xplusSigma = new GVector(coord3d.getSize());
		GVector xminusSigma = new GVector(coord3d.getSize());
		GVector xplus2Sigma = new GVector(coord3d.getSize());
		GVector xminus2Sigma = new GVector(coord3d.getSize());
		double fxplusSigma = 0;
		double fxminusSigma = 0;
		double fxplus2Sigma = 0;
		double fxminus2Sigma = 0;
		
		for (int m=0; m < order5thErrorApproximateGradientMMFF94SumEvdW.getSize(); m++) {
			xplusSigma.set(coord3d);
			xplusSigma.setElement(m,coord3d.getElement(m) + sigma);
			setFunctionMMFF94SumEvdW(xplusSigma);
			fxplusSigma = getFunctionMMFF94SumEvdW();
			xminusSigma.set(coord3d);
			xminusSigma.setElement(m,coord3d.getElement(m) - sigma);
			setFunctionMMFF94SumEvdW(xminusSigma);
			fxminusSigma = getFunctionMMFF94SumEvdW();
			xplus2Sigma.set(coord3d);
			xplus2Sigma.setElement(m,coord3d.getElement(m) + 2 * sigma);
			setFunctionMMFF94SumEvdW(xplus2Sigma);
			fxplus2Sigma = getFunctionMMFF94SumEvdW();
			xminus2Sigma.set(coord3d);
			xminus2Sigma.setElement(m,coord3d.getElement(m) - 2 * sigma);
			setFunctionMMFF94SumEvdW(xminus2Sigma);
			fxminus2Sigma = getFunctionMMFF94SumEvdW();
			order5thErrorApproximateGradientMMFF94SumEvdW.setElement(m, (8 * (fxplusSigma - fxminusSigma) - (fxplus2Sigma - fxminus2Sigma)) / (12 * sigma));
		}
			
		//logger.debug("order5thErrorApproximateGradientMMFF94SumEvdW : " + order5thErrorApproximateGradientMMFF94SumEvdW);
	}


	/**
	 *  Get the 5th order error approximate gradient for the Van Der Waals interaction term.
	 *
	 *@return        Torsion 5th order error approximate gradient value.
	 */
	public GVector get5OrderApproximateGradientMMFF94SumEvdW() {
		return order5thErrorApproximateGradientMMFF94SumEvdW;
	}


	/**
	 *  Evaluate the gradient of the CCG Van Der Waals interaction term.
	 *  
	 *
	 *@param  coords3d  Current molecule coordinates.
	 *@return           CCG Van Der Waals interaction gradient value.
	 */
/*	public GVector gradientMMFF94SumEvdW(GVector coords3d, double[] s) {

		gradientCCGSumEvdWSlaterKirkwood.setSize(molecule.getAtomCount() * 3);
		setAtomDistance(coords3d);
		dR.setSize(molecule.getAtomCount() * 3);

		dterm1.setSize(molecule.getAtomCount() * 3);
		dterm2.setSize(molecule.getAtomCount() * 3);
		
		double c;
		double[] term1 = new double[vdwInteractionNumber];
		double[] term2 = new double[vdwInteractionNumber];
		double sumGradientEvdW;
		for (int i = 0; i < gradientCCGSumEvdWSlaterKirkwood.getSize(); i++) {

			dterm1.setElement(i,1);                 // dterm1 : partial derivative of term1. To change in the future
			dterm2.setElement(i,1);                 // dterm2 : partial derivative of term2. To change in the future
			ds.setElement(i,1);                 // ds : partial derivative of s. To change in the future
			dt.setElement(i,1);                 // dt : partial derivative of t. To change in the future
			dIvdw.setElement(i,1);                 // dIvdw : partial derivative of Ivdw. To change in the future

			sumGradientEvdW = 0;
			for (int l = 0; l < vdwInteractionNumber; l++) {
				
				c = ((1+a) * asteriskR[l]) / (r[l] + a * asteriskR[l]);
				term1[l] = Math.pow(c,nij);
				term2[l] = (nij/mij) * ((1+b) * Math.pow(asteriskR[l],mij) / (Math.pow(r[l],mij) + b * Math.pow(asteriskR[l],mij)))   - (mij + nij)/mij;
				
				sumGradientEvdW = sumGradientEvdW + (deSK.getElement(i) * term1[l] * term2[l] + eSK[l] * (dterm1.getElement(i) * term2[l] + term1[l] * dterm2.getElement(i))) * s[l] * t[l] * ivdw[l] + 
								(eSK[l] * term1[l] * term2[l]) * (ds.getElement(i) * t[l] * ivdw[l] + s[l] * (dt.getElement(i) * ivdw[l] + t[l] * dIvdw.getElement(i)));
			}
			sumGradientEvdW = sumGradientEvdW * 2.51210;
			
			gradientCCGSumEvdWSlaterKirkwood.setElement(i, sumGradientEvdW);
		}
		//logger.debug("gradientCCGSumEvdWSlaterKirkwood = " + gradientCCGSumEvdWSlaterKirkwood);
		return gradientCCGSumEvdWSlaterKirkwood;
	}*/


	/**
	 *  Evaluate the hessian of the CCG Van Der Waals interaction term.
	 *
	 *@param  coords3d  Current molecule coordinates.
	 *@return        Hessian value of the CCG Van Der Waals interaction term.
	 */
/*	public GMatrix hessian(GVector coords3d) {

		double[] forHessian = new double[coords3d.getSize() * coords3d.getSize()];
		setAtomDistance(coords3d);
		double sumHessianEvdW = 0;

		GMatrix ddR = new GMatrix(coords3d.getSize(),coords3d.getSize());
		ddR.setZero();

		for (int i = 0; i < forHessian.length; i++) {
			for (int j = 0; j < vdwInteractionNumber; j++) {
				sumHessianEvdW = sumHessianEvdW + 1;
			}
			forHessian[i] = sumHessianEvdW;
		}

		hessianMMFF94SumEvdW.setSize(coords3d.getSize(), coords3d.getSize());
		hessianMMFF94SumEvdW.set(forHessian); 
		//logger.debug("hessianMMFF94SumEvdW : " + hessianMMFF94SumEvdW);
		return hessianMMFF94SumEvdW;
	}*/


	/**
	 *  Calculate the bond lengths second derivative respect to the cartesian coordinates of the atoms.
	 *
	 *@param  coord3d  Current molecule coordinates.
	 */
	public void setBondLengthsSecondDerivative(GVector coord3d) {
		ddR = new double[coord3d.getSize()][][];
		
		Double forAtomNumber = null;
		int atomNumberi;
		int atomNumberj;
		int coordinatei;
		int coordinatej;
		double ddR1=0;	// ddR[i][j][k] = ddR1 - ddR2
		double ddR2=0;
		
		setAtomsDistancesFirstOrderDerivative(coord3d);
		
		for (int i=0; i<coord3d.getSize(); i++) {
			ddR[i] = new double[coord3d.getSize()][];
			
			forAtomNumber = new Double(i/3);
			
			atomNumberi = forAtomNumber.intValue();
			//logger.debug("atomNumberi = " + atomNumberi);
				
			coordinatei = i % 3;
			//logger.debug("coordinatei = " + coordinatei);
				
			for (int j=0; j<coord3d.getSize(); j++) {
				ddR[i][j] = new double[vdwInteractionNumber];
				
				forAtomNumber = new Double(j/3);

				atomNumberj = forAtomNumber.intValue();
				//logger.debug("atomNumberj = " + atomNumberj);

				coordinatej = j % 3;
				//logger.debug("coordinatej = " + coordinatej);
				
				//logger.debug("atomj : " + molecule.getAtomAt(atomNumberj));
				
				for (int k=0; k < vdwInteractionNumber; k++) {
					
					if ((vdWiAtomPosition[k][0] == atomNumberj) | (vdWiAtomPosition[k][1] == atomNumberj)) {
						if ((vdWiAtomPosition[k][0] == atomNumberi) | (vdWiAtomPosition[k][1] == atomNumberi)) {
					
							// ddR1
							if (vdWiAtomPosition[k][0] == atomNumberj) {
								ddR1 = 1;
							}
							if (vdWiAtomPosition[k][1] == atomNumberj) {
								ddR1 = -1;
							}
							if (vdWiAtomPosition[k][0] == atomNumberi) {
								ddR1 = ddR1 * 1;
							}
							if (vdWiAtomPosition[k][1] == atomNumberi) {
								ddR1 = ddR1 * (-1);
							}
							ddR1 = ddR1 / r[k];

							// ddR2
							switch (coordinatej) {
								case 0: ddR2 = (coord3d.getElement(3 * vdWiAtomPosition[k][0]) - coord3d.getElement(3 * vdWiAtomPosition[k][1]));
									//logger.debug("OK: d1 x");
									break;
								case 1:	ddR2 = (coord3d.getElement(3 * vdWiAtomPosition[k][0] + 1) - coord3d.getElement(3 * vdWiAtomPosition[k][1] + 1));
									//logger.debug("OK: d1 y");
									break;
								case 2:	ddR2 = (coord3d.getElement(3 * vdWiAtomPosition[k][0] + 2) - coord3d.getElement(3 * vdWiAtomPosition[k][1] + 2));
									//logger.debug("OK: d1 z");
									break;
							}
						
							if (vdWiAtomPosition[k][1] == atomNumberj) {
								ddR2 = (-1) * ddR2;
								//logger.debug("OK: bond 1");
							} 
	
							switch (coordinatei) {
								case 0: ddR2 = ddR2 * (coord3d.getElement(3 * vdWiAtomPosition[k][0]) - coord3d.getElement(3 * vdWiAtomPosition[k][1]));
									//logger.debug("OK: have d2 x");
									break;
								case 1:	ddR2 = ddR2 * (coord3d.getElement(3 * vdWiAtomPosition[k][0] + 1) - coord3d.getElement(3 * vdWiAtomPosition[k][1] + 1));
									//logger.debug("OK: have d2 y");
									break;
								case 2: ddR2 = ddR2 * (coord3d.getElement(3 * vdWiAtomPosition[k][0] + 2) - coord3d.getElement(3 * vdWiAtomPosition[k][1] + 2));
									//logger.debug("OK: have d2 z");
									break;
							}
							
							if (vdWiAtomPosition[k][1] == atomNumberi) {
								ddR2 = (-1) * ddR2;
								//logger.debug("OK: d2 bond 1");
							}
							
							ddR2 = ddR2 / Math.pow(r[k],2);
							
							// ddR[i][j][k]
							ddR[i][j][k] = ddR1 - ddR2;
						} else {
							ddR[i][j][k] = 0;
							//logger.debug("OK: 0");
						}
					} else {
						ddR[i][j][k] = 0;
						//logger.debug("OK: 0");
					}
					//logger.debug("bond " + k + " : " + "ddR[" + i + "][" + j + "][" + k + "] = " + ddR[i][j][k]);
				}
			}
		}	
	}


	/**
	 *  Get the bond lengths second derivative respect to the cartesian coordinates of the atoms.
	 *
	 *@return        Bond lengths second derivative value [dimension(3xN)] [bonds Number]
	 */
	 public double[][][] getBondLengthsSecondDerivative() {
		return ddR;
	}


	/**
	 *  Evaluate the second order partial derivative (hessian) for the van der Waals interactions given the atoms coordinates
	 *
	 *@param  coord3d  Current molecule coordinates.
	 */
	public void setHessianMMFF94SumEvdW(GVector coord3d) {
		
		forHessian = new double[coord3d.getSize() * coord3d.getSize()];
		
		if (currentCoordinates.equals(coord3d)) {} 
		else {setFunctionMMFF94SumEvdW(coord3d);}
		
		setBondLengthsSecondDerivative(coord3d);
		
		double sumHessianEvdW;
		int forHessianIndex;
		double vdWEHessian1 = 0;
		double vdWEHessian2 = 0;
		double vdWESD1 = 0;
		double vdWESD2 = 0;
		for (int i = 0; i < coord3d.getSize(); i++) {
			for (int j = 0; j < coord3d.getSize(); j++) {
				sumHessianEvdW = 0;
				for (int k = 0; k < vdwInteractionNumber; k++) {
					vdWESD1 = 89.47 * eSK[k] * Math.pow(asteriskR[k], 7) * (1/Math.pow(r[k] + 0.07 * asteriskR[k], 9)) * dR[i][k];
					vdWESD2 = -7.84 * Math.pow(asteriskR[k],7) * (6 * Math.pow(r[k],5) * dR[i][k] * Math.pow(Math.pow(r[k],7) + 0.12 * Math.pow(asteriskR[k],7),2) - Math.pow(r[k],12) * 14 * (Math.pow(r[k],7) + 0.12 * Math.pow(asteriskR[k],7)) * dR[i][k])/Math.pow(Math.pow(r[k],7) + 0.12 * Math.pow(asteriskR[k],7),4);
					vdWEHessian1 = (vdWESD1 * dR[j][k] + vdWEG1[k] * ddR[i][j][k]) * vdWE2[k] + vdWEG1[k] * (vdWEG2[k] * dR[i][k]);
					vdWEHessian2 = (vdWEG1[k] * dR[i][k]) * (vdWEG2[k]) + (vdWE1[k]) * (vdWESD2 * dR[j][k] + vdWEG2[k] * ddR[i][j][k]);
					sumHessianEvdW = sumHessianEvdW + (vdWEHessian1 + vdWEHessian2);
				}
				forHessianIndex = i*coord3d.getSize()+j;
				forHessian[forHessianIndex] = sumHessianEvdW;
			}
		}
		
		hessianMMFF94SumEvdW = new GMatrix(coord3d.getSize(), coord3d.getSize(), forHessian);
		//logger.debug("hessianMMFF94SumEvdW : " + hessianMMFF94SumEvdW);
	}


	/**
	 *  Get the hessian for the van der Waals interactions.
	 *
	 *@return        Hessian value of the van der Waals interactions term.
	 */
	public GMatrix getHessianMMFF94SumEvdW() {
		return hessianMMFF94SumEvdW;
	}


	/**
	 *  Get the hessian for the van der Waals interactions.
	 *
	 *@return        Hessian value of the van der Waals interactions term.
	 */
	public double[] getForHessianMMFF94SumEvdW() {
		return forHessian;
	}


}