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Jmol: an open-source Java viewer for chemical structures in 3D
/* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* Copyright (C) 2011 The Jmol Development Team
*
* Contact: [email protected]
*
* This library is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public
* License as published by the Free Software Foundation; either
* version 2.1 of the License, or (at your option) any later version.
*
* This library is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
* Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with this library; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
* 02110-1301, USA.
*/
package org.jmol.quantum;
import java.util.Map;
import javajs.util.Lst;
import javajs.util.PT;
import javajs.util.SB;
/**
* Constants and static methods for quantum shells.
*/
public class QS {
public QS() {
//
}
final public static int S = 0;
final public static int P = 1;
final public static int SP = 2;
final public static int DS = 3;
final public static int DC = 4;
final public static int FS = 5;
final public static int FC = 6;
final public static int GS = 7;
final public static int GC = 8;
final public static int HS = 9;
final public static int HC = 10;
final public static int IS = 11;
final public static int IC = 12;
public static int MAX_TYPE_SUPPORTED = FC;
private final static int MAXID = 13;
final public static int[] idSpherical = { S, P, SP, DS, DS, FS, FS, GS, GS, HS, HS, IS, IS};
final public static String[] tags = {"S", "P", "SP", "5D", "D", "7F", "F", "9G", "G", "11H", "H", "13I", "I"};
final public static String[] tags2 = {"S", "X", "SP", "5D", "XX", "7F", "XXX", "9G", "XXXX", "11H", "XXXXX", "13I", "XXXXXX"};
final public static String CANONICAL_DC_LIST = "DXX DYY DZZ DXY DXZ DYZ";
final public static String CANONICAL_DS_LIST = "d0 d1+ d1- d2+ d2-";
final public static String CANONICAL_FC_LIST = "XXX YYY ZZZ XYY XXY XXZ XZZ YZZ YYZ XYZ";
final public static String CANONICAL_FS_LIST = "f0 f1+ f1- f2+ f2- f3+ f3-";
// S("S","S",0,0),
// P("P","X",1,1),
// SP("SP","SP",2,2),
// D_SPHERICAL("5D","5D",3,3),
// D_CARTESIAN("D","XX",4,3),
// F_SPHERICAL("7F","7F",5,5),
// F_CARTESIAN("F","XXX",6,5),
// G_SPHERICAL("9G","9G",7,7),
// G_CARTESIAN("G","XXXX",8,7),
// H_SPHERICAL("11H","11H",9,9),
// H_CARTESIAN("H","XXXXX",10,9),
// I_SPHERICAL("13I","13I",11,11),
// I_CARTESIAN("I","XXXXXX",12,11);
public static boolean isQuantumBasisSupported(char ch) {
return ("SPLDF".indexOf(Character.toUpperCase(ch)) >= 0);
}
public static int[][] getNewDfCoefMap() {
return new int[][] {
new int[1], //0 S 0
new int[3], //1 P
new int[4], // SP
new int[5], //2 D5 3
new int[6], //2 D6
new int[7], //3 F7 5
new int[10], //3 F10
new int[9], //4 G9 7
new int[15], //4 G15
new int[11], //5 H11 9 == 2*5 + 1
new int[21], //5 H21 == (5+1)(5+2)/2 = (n*n+3*n +2)/2 = n(n+3)/2 + 1
new int[13], //6 I13 == 2*6 + 1
new int[28] //6 I28 == (6+1)(6+2)/2
};
}
public static int getItem(int i) {
return (i >= 0 && i < MAXID ? i : -1);
}
public static int getQuantumShellTagID(String tag) {
return (tag.equals("L") ? SP : getQuantumShell(tag));
}
private static int getQuantumShell(String tag) {
for (int i = 0; i < MAXID; i++)
if (tags[i].equals(tag) || tags2[i].equals(tag))
return i;
return -1;
}
final public static int getQuantumShellTagIDSpherical(String tag) {
if (tag.equals("L"))
return SP;
int id = getQuantumShell(tag);
return (id < 0 ? id : idSpherical[id]);
}
final public static String getQuantumShellTag(int id) {
return (id >= 0 && id < MAXID ? tags[id] : "" + id);
}
final public static String getMOString(float[] lc) {
SB sb = new SB();
if (lc.length == 2)
return "" + (int)(lc[0] < 0 ? -lc[1] : lc[1]);
sb.appendC('[');
for (int i = 0; i < lc.length; i += 2) {
if (i > 0)
sb.append(", ");
sb.appendF(lc[i]).append(" ").appendI((int) lc[i + 1]);
}
sb.appendC(']');
return sb.toString();
}
public void setNboLabels(String[] tokens, int nLabels,
Lst> orbitals, int nOrbitals0, String moType) {
for (int i = 0; i < tokens.length; i += nLabels + 2)
if (moType.indexOf(tokens[i]) >= 0) {
for (int j = 0; j < nLabels; j++) {
Map mo = orbitals.get(j + nOrbitals0);
String type = tokens[i + j + 2];
mo.put("type", moType + " " + type);
// TODO: does not account for SOMO
mo.put("occupancy", Float.valueOf(type.indexOf("*") >= 0
|| type.indexOf("(ry)") >= 0 ? 0 : 2));
}
return;
}
}
// Jmol's ordering is based on GAUSSIAN
// We don't modify the coefficients at read time, only create a
// map to send to MOCalculation.
// DS: org.jmol.quantum.MOCalculation expects
// d2z^2-x2-y2, dxz, dyz, dx2-y2, dxy
// DC: org.jmol.quantum.MOCalculation expects
// Dxx Dyy Dzz Dxy Dxz Dyz
// FS: org.jmol.quantum.MOCalculation expects
// as 2z3-3x2z-3y2z
// 4xz2-x3-xy2
// 4yz2-x2y-y3
// x2z-y2z
// xyz
// x3-3xy2
// 3x2y-y3
// FC: org.jmol.quantum.MOCalculation expects
// xxx yyy zzz xyy xxy xxz xzz yzz yyz xyz
// These strings are the equivalents found in the file in Jmol order.
// DO NOT CHANGE THESE. They are in the order the MOCalculate expects.
// Subclassed readers can make their own to match.
/* Molden -- same as Gaussian, so no need to map these:
5D: D 0, D+1, D-1, D+2, D-2
6D: xx, yy, zz, xy, xz, yz
7F: F 0, F+1, F-1, F+2, F-2, F+3, F-3
10F: xxx, yyy, zzz, xyy, xxy, xxz, xzz, yzz, yyz, xyz
9G: G 0, G+1, G-1, G+2, G-2, G+3, G-3, G+4, G-4
15G: xxxx yyyy zzzz xxxy xxxz yyyx yyyz zzzx zzzy,
xxyy xxzz yyzz xxyz yyxz zzxy
*/
public static boolean createDFMap(int[] map, String fileList,
String jmolList, int minLength) {
// say we had line = "251 252 253 254 255" i points here
// Jmol expects list "255 252 253 254 251" pt points here
// we need an array that reads
// [4 0 0 0 -4]
// meaning add that number to the pointer for this coef.
String[] tokens = PT.getTokens(fileList);
boolean isOK = true;
for (int i = 0; i < map.length; i++) {
String key = tokens[i];
if (key.length() >= minLength) {
int pt = jmolList.indexOf(key);
if (pt >= 0) {
pt /= 6;
map[pt] = i - pt;
continue;
}
}
isOK = false;
break;
}
if (!isOK)
map[0] = Integer.MIN_VALUE;
return isOK;
}
}