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[Jmol-commits] SF.net SVN: jmol:[17129] trunk/Jmol/src/org/jmol/minimize
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From: <ha...@us...> - 2012-05-14 22:39:02
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Revision: 17129
http://jmol.svn.sourceforge.net/jmol/?rev=17129&view=rev
Author: hansonr
Date: 2012-05-14 22:38:55 +0000 (Mon, 14 May 2012)
Log Message:
-----------
MMFF -- preliminary parameter setting only for -- all except electrostatic now
set forceField "MMFF"
minimize energy
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/minimize/MinAngle.java
trunk/Jmol/src/org/jmol/minimize/forcefield/Calculations.java
trunk/Jmol/src/org/jmol/minimize/forcefield/CalculationsMMFF.java
trunk/Jmol/src/org/jmol/minimize/forcefield/ForceFieldMMFF.java
Modified: trunk/Jmol/src/org/jmol/minimize/MinAngle.java
===================================================================
--- trunk/Jmol/src/org/jmol/minimize/MinAngle.java 2012-05-14 15:19:52 UTC (rev 17128)
+++ trunk/Jmol/src/org/jmol/minimize/MinAngle.java 2012-05-14 22:38:55 UTC (rev 17129)
@@ -4,6 +4,6 @@
public int sbType;
public Integer sbKey;
MinAngle(int[] data) {
- this.data = data;
+ this.data = data; // ia, ib, ic, iab, ibc
}
}
Modified: trunk/Jmol/src/org/jmol/minimize/forcefield/Calculations.java
===================================================================
--- trunk/Jmol/src/org/jmol/minimize/forcefield/Calculations.java 2012-05-14 15:19:52 UTC (rev 17128)
+++ trunk/Jmol/src/org/jmol/minimize/forcefield/Calculations.java 2012-05-14 22:38:55 UTC (rev 17129)
@@ -125,6 +125,7 @@
}
void appendLogData(String s) {
+ System.out.println("calcultions LOG: " + s);
logData.append(s).append("\n");
}
@@ -447,6 +448,12 @@
+" ATOMS ATOM TYPES VALENCE IDEAL FORCE\n"
+" I J K I J K ANGLE ANGLE CONSTANT ENERGY\n"
+"--------------------------------------------------------------------------";
+ case CALC_STRETCH_BEND:
+ return
+ "\nS T R E T C H B E N D I N G (" + (minAngles.length * 2) + " angles)\n\n"
+ +" ATOMS ATOM TYPES VALENCE IDEAL FORCE\n"
+ +" I J K I J K ANGLE ANGLE CONSTANT ENERGY\n"
+ +"--------------------------------------------------------------------------";
case CALC_TORSION:
return
"\nT O R S I O N A L (" + minTorsions.length + " torsions)\n\n"
@@ -486,6 +493,7 @@
(float)c.delta, (float)c.energy },
new int[] { minAtoms[c.ia].atom.getAtomNumber(), minAtoms[c.ib].atom.getAtomNumber() }});
case CALC_ANGLE:
+ case CALC_STRETCH_BEND:
return TextFormat.sprintf(
"%3d %3d %3d %-5s %-5s %-5s %8.3f %8.3f %8.3f %8.3f",
new Object[] { minAtoms[c.ia].sType, minAtoms[c.ib].sType,
@@ -611,7 +619,7 @@
c.rab = 1.0e-3;
}
- private void setCoords(Calculation c, int n) {
+ void setCoords(Calculation c, int n) {
switch(n) {
case 4:
da.set(minAtoms[c.ia].coord);
Modified: trunk/Jmol/src/org/jmol/minimize/forcefield/CalculationsMMFF.java
===================================================================
--- trunk/Jmol/src/org/jmol/minimize/forcefield/CalculationsMMFF.java 2012-05-14 15:19:52 UTC (rev 17128)
+++ trunk/Jmol/src/org/jmol/minimize/forcefield/CalculationsMMFF.java 2012-05-14 22:38:55 UTC (rev 17129)
@@ -294,12 +294,53 @@
class SBCalc extends Calculation {
- // TODO
void setData(List<Object[]> calc, MinAngle angle) {
+ // not applicable for linear types
+ switch (minAtoms[angle.data[1]].ffType) {
+ case 4:
+ case 53:
+ case 61:
+ return;
+ }
+ double[] data = (double[]) getParameter(angle.sbKey);
+ double[] datakat0 = (double[]) getParameter(angle.key);
+ double[] dataij = (double[]) getParameter(minBonds[angle.data[3]].key);
+ double[] datajk = (double[]) getParameter(minBonds[angle.data[4]].key);
+ if (data == null || datakat0 == null || dataij == null || datajk == null)
+ return;
+ double theta0 = datakat0[1];
+ double r0ij = dataij[1];
+ double r0jk = datajk[1];
+ calc.add(new Object[] { angle.data, new double[] { data[0], theta0, r0ij } });
+ calc.add(new Object[] { new int[] {angle.data[2], angle.data[1], angle.data[0]},
+ new double[] { data[1], theta0, r0jk } });
}
@Override
double compute(Object[] dataIn) {
+ getPointers(dataIn);
+ double k = 2.51210 * dData[0];
+ double t0 = dData[1];
+ double r0_ab = dData[2];
+
+ setBondVariables(this);
+ setAngleVariables(this);
+ double dr_ab = rab - r0_ab;
+ delta = theta * RAD_TO_DEG - t0;
+ // equation 5
+ energy = k * dr_ab * delta;
+
+ if (logging)
+ appendLogData(getDebugLine(CALC_STRETCH_BEND, this));
+
+ if (gradients) {
+ dE = k * dr_ab;
+ addForces(this, 3);
+ setBondVariables(this);
+ dE = k * delta;
+ addForces(this, 2);
+ }
+
return energy;
}
}
@@ -412,18 +453,19 @@
double[] dataB = (double[]) getParameter(b.vdwKey);
if (dataA == null || dataB == null)
return;
+
double alpha_a = dataA[0];
double N_a = dataA[1];
double A_a = dataA[2];
double G_a = dataA[3];
- int DA_a = (int) dataA[4];
+ int DA_a = (int) dataA[4];
+
double alpha_b = dataB[0];
double N_b = dataB[1];
double A_b = dataB[2];
double G_b = dataB[3];
int DA_b = (int) dataB[4];
-
double rs_aa = A_a * Math.pow(alpha_a, 0.25);
double rs_bb = A_b * Math.pow(alpha_b, 0.25);
double gamma = (rs_aa - rs_bb) / (rs_aa + rs_bb);
Modified: trunk/Jmol/src/org/jmol/minimize/forcefield/ForceFieldMMFF.java
===================================================================
--- trunk/Jmol/src/org/jmol/minimize/forcefield/ForceFieldMMFF.java 2012-05-14 15:19:52 UTC (rev 17128)
+++ trunk/Jmol/src/org/jmol/minimize/forcefield/ForceFieldMMFF.java 2012-05-14 22:38:55 UTC (rev 17129)
@@ -50,8 +50,8 @@
public class ForceFieldMMFF extends ForceField {
- private static final int A4_SB = 1;
- private static final int A4_SBDEF = 2;
+ private static final int A4_SB = 125;
+ private static final int A4_SBDEF = 126;
private static final int A4_VDW = 3;
private static final int A4_CHRG = 4;
private static final int KEY_VDW = 0;
@@ -72,7 +72,6 @@
return rawMMFF94Charges;
}
-
/*
* from SMARTS search when calculating partial charges:
*
@@ -681,7 +680,7 @@
private int getRowFor(int i) {
int elemno = minAtoms[i].atom.getElementNumber();
- return (elemno < 3 ? 1 : elemno < 11 ? 2 : elemno < 19 ? 3 : 4);
+ return (elemno < 3 ? 0 : elemno < 11 ? 1 : elemno < 19 ? 2 : elemno < 37 ? 3 : 4);
}
private static Object getFFParams(Integer key) {
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