/* $RCSfile$
* $Author: hansonr $
*
* Copyright (C) 2003-2005 Miguel, Jmol Development, www.jmol.org
*
* Contact: jmol-developers@lists.sf.net
*
* 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 St, Fifth Floor, Boston, MA 02110-1301 USA.
*/
/*
* Copyright (C) 2009 Joerg Meyer, FHI Berlin
*
* Contact: meyer@fhi-berlin.mpg.de
*
* 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 St, Fifth Floor, Boston, MA 02110-1301 USA.
*/
package org.jmol.adapter.readers.xtal;
import javajs.util.PT;
import javajs.util.SB;
import javajs.util.V3;
import org.jmol.adapter.smarter.Atom;
import org.jmol.adapter.smarter.AtomSetCollectionReader;
import org.jmol.util.Vibration;
/**
* Bilbao Crystallographic Database file reader
*
* see, for example, http://www.cryst.ehu.es/cryst/compstru.html Comparison of
* Crystal Structures with the same Symmetry
*
* Note that this reader scrapes HTML. Keys for Bilbao format data are
* a given bit of text such as "High symmetry structure".
* Any changes to that (including capitalization) will cause this reader to fail.
* The space group number is read immediately after the "pre" tag on that line.
*
* filter options include:
*
* HIGH include high-symmetry structure;
*
* preliminary only
*
* @author Bob Hanson
*/
public class BilbaoReader extends AtomSetCollectionReader {
private boolean getHigh;
private boolean getSym;
private boolean normDispl;
private boolean doDisplace;
private String kvec;
private int i0;
private int nAtoms;
private boolean isBCSfile;
@Override
public void initializeReader() throws Exception {
normDispl = !checkFilterKey("NONORM");
doDisplace = isTrajectory;
getSym = true;
getHigh = checkFilterKey("HIGH") && !doDisplace;
asc.vibScale = 1;
appendLoadNote("Bilbao Crystallographic Server\ncryst@wm.lc.ehu.es");
if (rd().indexOf("<") < 0) {
readBilbaoDataFile();
continuing = false;
}
}
@Override
protected boolean checkLine() throws Exception {
if (line.contains(">Bilbao Crystallographic Server<")) {
line = line.substring(line.lastIndexOf(">") + 1).trim();
if (line.length() > 0)
appendLoadNote(line + "\n");
} else if (line.contains("High symmetry structure<")) {
if (getHigh)
readBilbaoFormat("high symmetry", Float.NaN);
} else if (line.contains("Low symmetry structure<")) {
if (!doDisplace)
readBilbaoFormat("low symmetry", Float.NaN);
} else if (line.contains("structure in the subgroup basis<")) {
if (!doDisplace)
readBilbaoFormat("high symmetry in the subgroup basis", Float.NaN);
} else if (line.contains("Low symmetry structure after the origin shift<")) {
readBilbaoFormat("low symmetry after origin shift", Float.NaN);
} else if (line.contains("
Irrep:")) {
readVirtual();
}
return true;
}
private void readBilbaoDataFile() throws Exception {
isBCSfile = true;
checkComment();
while (line != null) {
readBilbaoFormat(null, Float.NaN);
if (rdLine() == null || line.indexOf("##disp-par##") < 0) {
applySymmetryAndSetTrajectory();
} else {
readDisplacements(1);
rdLine();
}
}
}
private boolean checkComment() {
if (!line.startsWith("#") || line.indexOf("disp-par") >= 0)
return false;
if (isBCSfile) {
appendLoadNote(line);
if (line.startsWith("# Title:"))
asc.setAtomSetName(line.substring(8).trim());
}
return true;
}
/*
15
13.800 5.691 9.420 90.0 102.3 90.0
7
Pb 1 4e 0.0000 0.2910 0.2500
Pb 2 8f 0.3170 0.3090 0.3520
P 1 8f 0.5990 0.2410 0.4470
O 1 8f 0.6430 0.0300 0.3920
O 2 8f 0.6340 0.4640 0.3740
O 3 8f 0.6420 0.2800 0.6120
O 4 8f 0.4910 0.2220 0.4200
*/
private void readBilbaoFormat(String title, float fAmp) throws Exception {
setFractionalCoordinates(true);
if (!doGetModel(++modelNumber, title))
return;
asc.newAtomSet();
if (line.startsWith("#"))
rdLine();
if (line.startsWith("Bilbao Crys:")) {
title = line.substring(13).trim();
rdLine();
}
setTitle(title);
int ptPre = line.indexOf("
");
if (ptPre >= 0)
line = line.substring(ptPre + 5);
int intTableNo = parseIntStr(line);
if (intTableNo == 0) {
setSpaceGroupName(line.substring(2));
} else {
while (intTableNo < 0 && rdLine() != null)
intTableNo = parseIntStr(line);
setSpaceGroupName("" + intTableNo);
}
float[] data = new float[6];
fillFloatArray(rdLine(), 0, data);
for (int i = 0; i < 6; i++)
setUnitCellItem(i, data[i]);
i0 = asc.ac;
nAtoms = parseIntStr(rdLine());
for (int i = nAtoms; --i >= 0;) {
String[] tokens = PT.getTokens(rdLine());
if (!getSym && tokens[1].contains("_"))
continue;
if (tokens.length == 3)
addAtomXYZSymName(tokens, 0,"Be", "Be1");
else
addAtomXYZSymName(tokens, 3, tokens[0], tokens[0] + tokens[1]);
}
if (Float.isNaN(fAmp)) {
if (ptPre >= 0)
applySymmetryAndSetTrajectory();
return;
}
line = null;
readDisplacements(fAmp);
}
@Override
public void setSpaceGroupName(String name) {
if (!ignoreFileSpaceGroupName) {
name = "bilbao:" + name;
} else if (sgName.startsWith(":")){
int pt = name.indexOf(':');
if (pt < 0)
pt = name.length();
name = name.substring(0, pt);
SB s = (SB) htParams.get("loadScript");
if (s != null) {
pt = s.indexOf("spacegroup \":");
if (pt > 0)
s.insert(pt + 12, name);
}
name += sgName;
ignoreFileSpaceGroupName = false;
}
super.setSpaceGroupName(name);
}
private void readDisplacements(float fAmp) throws Exception {
/*
##disp-par## Rb1x|x0.000000x|x0.000791x|x-0.001494
##disp-par## Rb1_2x|x0.000000x|x0.000791x|x0.001494
*/
for (int i = 0; i < nAtoms; i++) {
if (line == null)
rdLine();
String[] tokens = PT.split(line, "x|x");
if (getSym || !tokens[0].contains("_"))
asc.atoms[i0 + i].vib = V3.new3(parseFloatStr(tokens[1]),
parseFloatStr(tokens[2]), parseFloatStr(tokens[3]));
line = null;
}
applySymmetryAndSetTrajectory();
// convert the atom vibs to Cartesian displacements
for (int i = asc.ac; --i >= i0;) {
Atom a = asc.atoms[i];
if (a.vib != null) {
Vibration v = new Vibration();
v.setT(a.vib);
a.vib = v;
//v.modDim = Vibration.TYPE_DISPLACEMENT;
asc.getSymmetry().toCartesian(v, true);
v.scale(1 / fAmp);
}
}
appendLoadNote((asc.ac - i0) + " displacements");
}
private void setTitle(String title) {
if (title != null) {
asc.setAtomSetName(title);
appendLoadNote(title);
}
}
private String rdLine() throws Exception {
while (rd() != null && (line.trim().length() == 0 || checkComment())) {
}
return line;
}
/*
with only this symmetry component of the distortion frozen.