electrostaticinteractions.java

化学图形处理软件

	 *@return           MMFF94 Electrostatic interaction gradient value.
	 */
	public GVector getGradientMMFF94SumEQ() {
		return gradientMMFF94SumEQ;
	}


	/**
	 *  Evaluate a 2nd order error approximation of the gradient, for the Electrostatic interaction term, given the atoms
	 *  coordinates
	 *
	 *@param  coord3d  Current molecule coordinates.
	 */
/*	public void set2ndOrderErrorApproximateGradientMMFF94SumEQ(GVector coord3d) {
		order2ndErrorApproximateGradientMMFF94SumEQ = new GVector(coord3d.getSize());
		double sigma = Math.pow(0.000000000000001,0.33);
		GVector xplusSigma = new GVector(coord3d.getSize());
		GVector xminusSigma = new GVector(coord3d.getSize());
		
		for (int m = 0; m < order2ndErrorApproximateGradientMMFF94SumEQ.getSize(); m++) {
			xplusSigma.set(coord3d);
			xplusSigma.setElement(m,coord3d.getElement(m) + sigma);
			xminusSigma.set(coord3d);
			xminusSigma.setElement(m,coord3d.getElement(m) - sigma);
			order2ndErrorApproximateGradientMMFF94SumEQ.setElement(m,(functionMMFF94SumEQ(xplusSigma) - functionMMFF94SumEQ(xminusSigma)) / (2 * sigma));
		}
			
		//logger.debug("order2ndErrorApproximateGradientMMFF94SumEQ : " + order2ndErrorApproximateGradientMMFF94SumEQ);
	}
*/

	/**
	 *  Get the 2nd order error approximate gradient for the Electrostatic interaction term.
	 *
	 *
	 *@return           Electrostatic interaction 2nd order error approximate gradient value
	 */
/*	public GVector get2ndOrderErrorApproximateGradientMMFF94SumEQ() {
		return order2ndErrorApproximateGradientMMFF94SumEQ;
	}
*/

	/**
	 *  Evaluate a 5th order error approximation of the gradient, for the Electrostatic interaction term, given the atoms
	 *  coordinates
	 *
	 *@param  coords3d  Current molecule coordinates.
	 */
/*	public void set5thOrderErrorApproximateGradientMMFF94SumEQ(GVector coord3d) {
		order5thErrorApproximateGradientMMFF94SumEQ = 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());
		
		for (int m=0; m < order5thErrorApproximateGradientMMFF94SumEQ.getSize(); m++) {
			xplusSigma.set(coord3d);
			xplusSigma.setElement(m,coord3d.getElement(m) + sigma);
			xminusSigma.set(coord3d);
			xminusSigma.setElement(m,coord3d.getElement(m) - sigma);
			xplus2Sigma.set(coord3d);
			xplus2Sigma.setElement(m,coord3d.getElement(m) + 2 * sigma);
			xminus2Sigma.set(coord3d);
			xminus2Sigma.setElement(m,coord3d.getElement(m) - 2 * sigma);
			order5thErrorApproximateGradientMMFF94SumEQ.setElement(m, (8 * (functionMMFF94SumEQ(xplusSigma) - functionMMFF94SumEQ(xminusSigma)) - (functionMMFF94SumEQ(xplus2Sigma) - functionMMFF94SumEQ(xminus2Sigma))) / (12 * sigma));
		}
			
		//logger.debug("order5thErrorApproximateGradientMMFF94SumEQ : " + order5thErrorApproximateGradientMMFF94SumEQ);
	}
*/

	/**
	 *  Get the 5th order error approximate gradient for the Electrostatic interaction term.
	 *
	 *@return        Electrostatic interaction 5th order error approximate gradient value.
	 */
/*	public GVector get5OrderApproximateGradientMMFF94SumEQ() {
		return order5thErrorApproximateGradientMMFF94SumEQ;
	}
*/


	/**
	 *  Calculate the internuclear separation second derivative respect to the cartesian coordinates of the atoms.
	 *
	 *@param  coord3d  Current molecule coordinates.
	 */
	public void setInternuclearSeparationSecondDerivative(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;
		
		setInternuclearSeparationFirstOrderDerivative(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[electrostaticInteractionNumber];
				
				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 < electrostaticInteractionNumber; k++) {
					
					if ((electrostaticInteractionAtomPosition[k][0] == atomNumberj) | (electrostaticInteractionAtomPosition[k][1] == atomNumberj)) {
						if ((electrostaticInteractionAtomPosition[k][0] == atomNumberi) | (electrostaticInteractionAtomPosition[k][1] == atomNumberi)) {
					
							// ddR1
							if (electrostaticInteractionAtomPosition[k][0] == atomNumberj) {
								ddR1 = 1;
							}
							if (electrostaticInteractionAtomPosition[k][1] == atomNumberj) {
								ddR1 = -1;
							}
							if (electrostaticInteractionAtomPosition[k][0] == atomNumberi) {
								ddR1 = ddR1 * 1;
							}
							if (electrostaticInteractionAtomPosition[k][1] == atomNumberi) {
								ddR1 = ddR1 * (-1);
							}
							ddR1 = ddR1 / r[k];

							// ddR2
							switch (coordinatej) {
								case 0: ddR2 = (coord3d.getElement(3 * electrostaticInteractionAtomPosition[k][0]) - coord3d.getElement(3 * electrostaticInteractionAtomPosition[k][1]));
									//logger.debug("OK: d1 x");
									break;
								case 1:	ddR2 = (coord3d.getElement(3 * electrostaticInteractionAtomPosition[k][0] + 1) - coord3d.getElement(3 * electrostaticInteractionAtomPosition[k][1] + 1));
									//logger.debug("OK: d1 y");
									break;
								case 2:	ddR2 = (coord3d.getElement(3 * electrostaticInteractionAtomPosition[k][0] + 2) - coord3d.getElement(3 * electrostaticInteractionAtomPosition[k][1] + 2));
									//logger.debug("OK: d1 z");
									break;
							}
						
							if (electrostaticInteractionAtomPosition[k][1] == atomNumberj) {
								ddR2 = (-1) * ddR2;
								//logger.debug("OK: bond 1");
							} 
	
							switch (coordinatei) {
								case 0: ddR2 = ddR2 * (coord3d.getElement(3 * electrostaticInteractionAtomPosition[k][0]) - coord3d.getElement(3 * electrostaticInteractionAtomPosition[k][1]));
									//logger.debug("OK: have d2 x");
									break;
								case 1:	ddR2 = ddR2 * (coord3d.getElement(3 * electrostaticInteractionAtomPosition[k][0] + 1) - coord3d.getElement(3 * electrostaticInteractionAtomPosition[k][1] + 1));
									//logger.debug("OK: have d2 y");
									break;
								case 2: ddR2 = ddR2 * (coord3d.getElement(3 * electrostaticInteractionAtomPosition[k][0] + 2) - coord3d.getElement(3 * electrostaticInteractionAtomPosition[k][1] + 2));
									//logger.debug("OK: have d2 z");
									break;
							}
							
							if (electrostaticInteractionAtomPosition[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("Electrostatic interactionn " + k + " : " + "ddR[" + i + "][" + j + "][" + k + "] = " + ddR[i][j][k]);
				}
			}
		}	
	}


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


	/**
	 *  Evaluate the second order partial derivative (hessian) for the Electrostatic interaction energy given the atoms coordinates
	 *
	 *@param  coord3d  Current molecule coordinates.
	 */
	public void setHessianMMFF94SumEQ(GVector coord3d) {
		
		forHessian = new double[coord3d.getSize() * coord3d.getSize()];
		
		setInternuclearSeparationSecondDerivative(coord3d);
		
		double sumHessianEQ;
		int forHessianIndex;
		for (int i = 0; i < coord3d.getSize(); i++) {
			for (int j = 0; j < coord3d.getSize(); j++) {
				sumHessianEQ = 0;
				for (int k = 0; k < electrostaticInteractionNumber; k++) {
					sumHessianEQ = sumHessianEQ + (((332.0716 * qi[k] * qj[k] * n * (n+1) / D*Math.pow(r[k]+delta,n+2)) * dR[i][k]) * dR[j][k] 
									+ (-332.0716 * qi[k] * qj[k] * n / D * Math.pow(r[k]+delta,n+1)) * ddR[i][j][k]);
				}
				forHessianIndex = i*coord3d.getSize()+j;
				forHessian[forHessianIndex] = sumHessianEQ;
				//logger.debug("forHessian[forHessianIndex] : " + forHessian[forHessianIndex]);
			}
		}

		hessianMMFF94SumEQ = new GMatrix(coord3d.getSize(), coord3d.getSize(), forHessian);
		//logger.debug("hessianMMFF94SumEQ : " + hessianMMFF94SumEQ);
	}


	/**
	 *  Get the hessian for the Electrostatic interaction energy.
	 *
	 *@return        Hessian value of the Electrostatic interaction term.
	 */
	public GMatrix getHessianMMFF94SumEQ() {
		return hessianMMFF94SumEQ;
	}


	/**
	 *  Get the hessian for the Electrostatic interaction energy.
	 *
	 *@return        Hessian value of the Electrostatic interaction term.
	 */
	public double[] getForHessianMMFF94SumEQ() {
		return forHessian;
	}

}