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[Jmol-commits] SF.net SVN: jmol: [9196] branches/bob-minimize/Jmol/src/org/jmol
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From: <ha...@us...> - 2008-03-25 14:34:13
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Revision: 9196
http://jmol.svn.sourceforge.net/jmol/?rev=9196&view=rev
Author: hansonr
Date: 2008-03-25 07:34:07 -0700 (Tue, 25 Mar 2008)
Log Message:
-----------
bob-minimize
Modified Paths:
--------------
branches/bob-minimize/Jmol/src/org/jmol/minimize/Minimizer.java
branches/bob-minimize/Jmol/src/org/jmol/minimize/forcefield/CalculationsUFF.java
branches/bob-minimize/Jmol/src/org/jmol/minimize/forcefield/ForceField.java
branches/bob-minimize/Jmol/src/org/jmol/viewer/Token.java
Modified: branches/bob-minimize/Jmol/src/org/jmol/minimize/Minimizer.java
===================================================================
--- branches/bob-minimize/Jmol/src/org/jmol/minimize/Minimizer.java 2008-03-25 06:37:55 UTC (rev 9195)
+++ branches/bob-minimize/Jmol/src/org/jmol/minimize/Minimizer.java 2008-03-25 14:34:07 UTC (rev 9196)
@@ -293,14 +293,14 @@
Token.tokenLeftParen,
Token.intToken(1),
Token.tokenComma,
- new Token(Token.identifier, "triple"),
+ new Token(Token.string, "triple"),
Token.tokenRightParen,
Token.tokenOr,
new Token(Token.connected, "connected"),
Token.tokenLeftParen,
Token.intToken(2),
Token.tokenComma,
- new Token(Token.identifier, "double"),
+ new Token(Token.string, "double"),
Token.tokenRightParen,
Token.tokenRightParen,
Token.tokenExpressionEnd},
@@ -313,7 +313,7 @@
Token.tokenLeftParen,
Token.intToken(1),
Token.tokenComma,
- new Token(Token.identifier, "double"),
+ new Token(Token.string, "double"),
Token.tokenRightParen,
Token.tokenExpressionEnd},
};
@@ -512,24 +512,20 @@
//return the new atom coordinates
updateAtomXYZ();
-
+ if (Logger.debugging)
+ pFF.dumpAtomList("F I N A L G E O M E T R Y");
return null;
}
private void updateAtomXYZ() {
if (steps == 0)
return;
- String s = "";
for (int i = 0; i < atomCount; i++) {
MinAtom minAtom = minAtoms[i];
Atom atom = minAtom.atom;
- if (Logger.debugging)
- s = " update " + atom.getInfo() + " was " + atom.x + " " + atom.y + " " + atom.z;
atom.x = (float) minAtom.coord[0];
atom.y = (float) minAtom.coord[1];
atom.z = (float) minAtom.coord[2];
- if (Logger.debugging)
- Logger.info(s + " now " + atom.x + " " + atom.y + " " + atom.z);
}
}
Modified: branches/bob-minimize/Jmol/src/org/jmol/minimize/forcefield/CalculationsUFF.java
===================================================================
--- branches/bob-minimize/Jmol/src/org/jmol/minimize/forcefield/CalculationsUFF.java 2008-03-25 06:37:55 UTC (rev 9195)
+++ branches/bob-minimize/Jmol/src/org/jmol/minimize/forcefield/CalculationsUFF.java 2008-03-25 14:34:07 UTC (rev 9196)
@@ -120,28 +120,6 @@
return true;
}
- void dumpAtomList(String title) {
- Logger.info("\n" + title + "\n\n"
- + " ATOM X Y Z GRAD X Y Z ---------BOND ATOMS--------\n"
- + "---------------------------------------------------------------------------------------");
- for (int i = 0; i < atomCount; i++) {
- MinAtom atom = atoms[i];
- int[] others = atom.getBondedAtomIndexes();
- int[] iVal = new int[others.length + 1];
- iVal[0] = atom.atom.getAtomNumber();
- String s = " ";
- for (int j = 0; j < others.length; j++) {
- s += " %-3i";
- iVal[j + 1] = atoms[others[j]].atom.getAtomNumber();
- }
- Logger.info(TextFormat.sprintf("%-3i %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f" + s, null,
- new float[] { (float) atom.coord[0], (float) atom.coord[1],
- (float) atom.coord[2], (float) atom.gradient[0], (float) atom.gradient[1],
- (float) atom.gradient[2], }, iVal));
- }
- Logger
- .info("-----------------------------------------------------------\n");
- }
private boolean isInvertible(int n) {
switch (n) {
case 6: // C
@@ -262,10 +240,9 @@
// here we fold the 1/2 into the kij from equation 1a
- // Otfherwise, this is equation 6 from the UFF paper.
+ // Otherwise, this is equation 6 from the UFF paper.
-
- kb = (0.5 * KCAL_TO_KJ * 664.12 * parA.dVal[PAR_Z] * parB.dVal[PAR_Z])
+ kb = KCAL332 * parA.dVal[PAR_Z] * parB.dVal[PAR_Z]
/ (r0 * r0 * r0);
calc.addElement(new Object[] {
new int[] { ia, ib },
@@ -324,7 +301,6 @@
double zi = parA.dVal[PAR_Z];
double zk = parC.dVal[PAR_Z];
double theta0 = parB.dVal[PAR_THETA];
- System.out.println(a.atom.getInfo() + " " + zi + " " + b.type + " " + theta0);
double cosT0 = Math.cos(theta0);
double sinT0 = Math.sin(theta0);
double c0, c1, c2;
@@ -961,44 +937,75 @@
}
}
+
+ ///////// REPORTING /////////////
+
+ void dumpAtomList(String title) {
+ String trailer =
+ "----------------------------------------"
+ + "-------------------------------------------------------";
+ Logger.info("\n" + title + "\n\n"
+ + " ATOM X Y Z TYPE GRADX GRADY GRADZ "
+ + "---------BONDED ATOMS--------\n"
+ + trailer);
+ for (int i = 0; i < atomCount; i++) {
+ MinAtom atom = atoms[i];
+ int[] others = atom.getBondedAtomIndexes();
+ int[] iVal = new int[others.length + 1];
+ iVal[0] = atom.atom.getAtomNumber();
+ String s = " ";
+ for (int j = 0; j < others.length; j++) {
+ s += " %3i";
+ iVal[j + 1] = atoms[others[j]].atom.getAtomNumber();
+ }
+ Logger.info(TextFormat.sprintf("%3i %8.3f %8.3f %8.3f %-5s %8.3f %8.3f %8.3f" + s,
+ new String[] { atom.type },
+ new float[] { (float) atom.coord[0], (float) atom.coord[1],
+ (float) atom.coord[2], (float) atom.gradient[0], (float) atom.gradient[1],
+ (float) atom.gradient[2], },
+ iVal));
+ }
+ Logger.info(trailer + "\n");
+ }
+
String getDebugHeader(int iType) {
switch (iType){
case CALC_BOND:
return
"\nB O N D S T R E T C H I N G (" + bondCount + " bonds)\n\n"
- +"ATOMS ATOM TYPES BOND BOND IDEAL FORCE\n"
- +" I J I J TYPE LENGTH LENGTH CONSTANT DELTA ENERGY\n"
+ +" ATOMS ATOM TYPES BOND BOND IDEAL FORCE\n"
+ +" I J I J TYPE LENGTH LENGTH CONSTANT DELTA ENERGY\n"
+"--------------------------------------------------------------------------------";
case CALC_ANGLE:
return
"\nA N G L E B E N D I N G (" + angles.length + " angles)\n\n"
- +" ATOMS ATOM TYPES VALENCE IDEAL FORCE\n"
- +" I J K I J K ANGLE ANGLE CONSTANT ENERGY\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 (" + torsions.length + " torsions)\n\n"
- +" ATOMS ATOM TYPES FORCE TORSION\n"
- +" I J K L I J K L CONSTANT ANGLE ENERGY\n"
- +"--------------------------------------------------------------------------";
+ +" ATOMS ATOM TYPES FORCE TORSION\n"
+ +" I J K L I J K L CONSTANT ANGLE ENERGY\n"
+ +"----------------------------------------------------------------------------";
case CALC_OOP:
return
"\nO U T - O F - P L A N E B E N D I N G\n\n"
- +" ATOMS ATOM TYPES OOP FORCE \n"
- +" I J K L I J K L ANGLE CONSTANT ENERGY\n"
- +"---------------------------------------------------------------------";
+ +" ATOMS ATOM TYPES OOP FORCE \n"
+ +" I J K L I J K L ANGLE CONSTANT ENERGY\n"
+ +"--------------------------------------------------------------------------";
case CALC_VDW:
return
"\nV A N D E R W A A L S\n\n"
- +" ATOMS ATOM TYPES\n"
- +" I J I J Rij kij ENERGY\n"
- +"-------------------------------------------------";
+ +" ATOMS ATOM TYPES\n"
+ +" I J I J Rij kij ENERGY\n"
+ +"-----------------------------------------------";
case CALC_ES:
return
"\nE L E C T R O S T A T I C I N T E R A C T I O N S\n\n"
- +" ATOMS ATOM TYPES\n"
- +" I J I J Rij 332.17*QiQj ENERGY\n"
- +"---------------------------------------------------";
+ +" ATOMS ATOM TYPES QiQj\n"
+ +" I J I J Rij *332.17 ENERGY\n"
+ +"-----------------------------------------------";
}
return "";
}
@@ -1007,7 +1014,7 @@
switch (iType) {
case CALC_BOND:
return TextFormat.sprintf(
- "%-3i %-3i %-5s %-5s %4.2f%8.3f %8.3f %8.3f %8.3f %8.3f",
+ "%3i %3i %-5s %-5s %4.2f%8.3f %8.3f %8.3f %8.3f %8.3f",
new String[] { atoms[c.ia].type, atoms[c.ib].type },
new float[] { (float)c.dData[2]/*rab*/, (float)c.rab,
(float)c.dData[0], (float)c.dData[1],
@@ -1015,7 +1022,7 @@
new int[] { atoms[c.ia].atom.getAtomNumber(), atoms[c.ib].atom.getAtomNumber() });
case CALC_ANGLE:
return TextFormat.sprintf(
- "%-3i %-3i %-3i %-5s %-5s %-5s%8.3f %8.3f %8.3f %8.3f",
+ "%3i %3i %3i %-5s %-5s %-5s %8.3f %8.3f %8.3f %8.3f",
new String[] { atoms[c.ia].type, atoms[c.ib].type,
atoms[c.ic].type },
new float[] { (float)(c.theta * RAD_TO_DEG), (float)c.dData[4] /*THETA0*/,
@@ -1024,7 +1031,7 @@
atoms[c.ic].atom.getAtomNumber()} );
case CALC_TORSION:
return TextFormat.sprintf(
- "%-3i %-3i %-3i %-3i %-5s %-5s %-5s %-5s%6.3f %8.3f %8.3f",
+ "%3i %3i %3i %3i %-5s %-5s %-5s %-5s %8.3f %8.3f %8.3f",
new String[] { atoms[c.ia].type, atoms[c.ib].type,
atoms[c.ic].type, atoms[c.id].type },
new float[] { (float) c.dData[0]/*V*/,
@@ -1033,7 +1040,7 @@
atoms[c.ic].atom.getAtomNumber(), atoms[c.id].atom.getAtomNumber() } );
case CALC_OOP:
return TextFormat.sprintf("" +
- "%-3i %-3i %-3i %-3i %-5s %-5s %-5s %-5s%8.3f %8.3f %8.3f",
+ "%3i %3i %3i %3i %-5s %-5s %-5s %-5s %8.3f %8.3f %8.3f",
new String[] { atoms[c.ia].type, atoms[c.ib].type,
atoms[c.ic].type, atoms[c.id].type },
new float[] { (float)(c.theta * RAD_TO_DEG),
@@ -1041,12 +1048,12 @@
new int[] { atoms[c.ia].atom.getAtomNumber(), atoms[c.ib].atom.getAtomNumber(),
atoms[c.ic].atom.getAtomNumber(), atoms[c.id].atom.getAtomNumber() } );
case CALC_VDW:
- return TextFormat.sprintf("%-3i %-3i %-5s %-5s %8.3f %8.3f %8.3f",
+ return TextFormat.sprintf("%3i %3i %-5s %-5s %6.3f %8.3f %8.3f",
new String[] { atoms[c.iData[0]].type, atoms[c.iData[1]].type },
new float[] { (float)c.rab, (float)c.dData[0]/*kab*/, (float)c.energy},
new int[] { atoms[c.ia].atom.getAtomNumber(), atoms[c.ib].atom.getAtomNumber() } );
case CALC_ES:
- return TextFormat.sprintf("%-3i %-3i %-5s %-5s %8.3f %8.3f %8.3f",
+ return TextFormat.sprintf("%3i %3i %-5s %-5s %6.3f %8.3f %8.3f",
new String[] { atoms[c.iData[0]].type, atoms[c.iData[1]].type },
new float[] { (float)c.rab, (float)c.dData[0]/*qq*/, (float)c.energy },
new int[] { atoms[c.ia].atom.getAtomNumber(), atoms[c.ib].atom.getAtomNumber() });
Modified: branches/bob-minimize/Jmol/src/org/jmol/minimize/forcefield/ForceField.java
===================================================================
--- branches/bob-minimize/Jmol/src/org/jmol/minimize/forcefield/ForceField.java 2008-03-25 06:37:55 UTC (rev 9195)
+++ branches/bob-minimize/Jmol/src/org/jmol/minimize/forcefield/ForceField.java 2008-03-25 14:34:07 UTC (rev 9196)
@@ -391,5 +391,8 @@
return stepCurrent;
}
-
+ public void dumpAtomList(String title) {
+ calc.dumpAtomList(title);
+ }
+
}
Modified: branches/bob-minimize/Jmol/src/org/jmol/viewer/Token.java
===================================================================
--- branches/bob-minimize/Jmol/src/org/jmol/viewer/Token.java 2008-03-25 06:37:55 UTC (rev 9195)
+++ branches/bob-minimize/Jmol/src/org/jmol/viewer/Token.java 2008-03-25 14:34:07 UTC (rev 9196)
@@ -77,7 +77,7 @@
final public static int identifier = 1;
final static int integer = 2;
final static int decimal = 3;
- final static int string = 4;
+ final public static int string = 4;
final static int seqcode = 5;
final static int list = 6;
final public static int point3f = 7;
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