Revision: 20109
http://sourceforge.net/p/jmol/code/20109
Author: hansonr
Date: 2014-11-15 17:15:05 +0000 (Sat, 15 Nov 2014)
Log Message:
-----------
Jmol.___JmolVersion="14.3.9_2014.11.15"
new feature: VASP CHGCAR reader
new feature: VASP CHGCAR isosurface reader
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
trunk/Jmol/src/org/jmol/io/JmolUtil.java
trunk/Jmol/src/org/jmol/jvxl/readers/ApbsReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/CastepDensityReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/CubeReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/EfvetReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/JaguarReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/JvxlReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/KinemageReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/MsmsReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/NffReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/ObjReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/PltFormattedReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/Pmesh4Reader.java
trunk/Jmol/src/org/jmol/jvxl/readers/PmeshReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceFileReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/UhbdReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/VolumeFileReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/XplorReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/XsfReader.java
trunk/Jmol/src/org/jmol/util/SimpleUnitCell.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Added Paths:
-----------
trunk/Jmol/src/org/jmol/adapter/readers/xtal/VaspChgcarReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/PeriodicVolumeFileReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/VaspChgcarReader.java
Added: trunk/Jmol/src/org/jmol/adapter/readers/xtal/VaspChgcarReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xtal/VaspChgcarReader.java
(rev 0)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/VaspChgcarReader.java
2014-11-15 17:15:05 UTC (rev 20109)
@@ -0,0 +1,96 @@
+/* $RCSfile$
+ * $Author: hansonr $
+ *
+ * Copyright (C) 2003-2005 Miguel, Jmol Development, www.jmol.org
+ *
+ * Contact: jmol-develop...@lists.sf.net
+ *
+ * Copyright (C) 2009 Piero Canepa, University of Kent, UK
+ *
+ * Contact: pc...@kent.ac.uk or pieremanuele.can...@gmail.com
+ *
+ * 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 org.jmol.adapter.smarter.AtomSetCollectionReader;
+
+/**
+ * http://cms.mpi.univie.ac.at/vasp/vasp/CHGCAR_file.html
+ *
+ * very simple reader of just the header information.
+ *
+ */
+
+public class VaspChgcarReader extends AtomSetCollectionReader {
+
+ @Override
+ protected void initializeReader() {
+ setSpaceGroupName("P1");
+ setFractionalCoordinates(true);
+ }
+
+// Na Cl
+// 5.68452685100000
+// 1.000000 0.000000 0.000000
+// 0.000000 1.000000 0.000000
+// 0.000000 0.000000 1.000000
+// 4 4
+//Direct
+// 0.750000 0.250000 0.250000
+// 0.250000 0.750000 0.250000
+// 0.250000 0.250000 0.750000
+// 0.750000 0.750000 0.750000
+// 0.250000 0.250000 0.250000
+// 0.750000 0.750000 0.250000
+// 0.750000 0.250000 0.750000
+// 0.250000 0.750000 0.750000
+//
+
+ @Override
+ protected boolean checkLine() throws Exception {
+ String[] atomSym = getTokens();
+ float scale = parseFloatStr(rd());
+ float[] unitCellData = new float[9];
+ fillFloatArray(null, 0, unitCellData);
+ for (int i = 0; i < 9; i++)
+ unitCellData[i] *= scale;
+ addPrimitiveLatticeVector(0, unitCellData, 0);
+ addPrimitiveLatticeVector(1, unitCellData, 3);
+ addPrimitiveLatticeVector(2, unitCellData, 6);
+ String[] tokens = getTokensStr(rd());
+ int[] atomCounts = new int[tokens.length];
+ for (int i = tokens.length; --i >= 0;)
+ atomCounts[i] = parseIntStr(tokens[i]);
+ if (atomSym.length != atomCounts.length)
+ atomSym = null;
+ /*String type = */ rd();
+ // type should be "direct"
+ for (int i = 0; i < atomCounts.length; i++)
+ for (int j = atomCounts[i]; --j >= 0;)
+ addAtomXYZSymName(getTokensStr(rd()), 0, (atomSym == null ? "Xx" :
atomSym[i]), null);
+ continuing = false;
+ return false;
+ }
+
+ @Override
+ protected void finalizeSubclassReader() throws Exception {
+ applySymmetryAndSetTrajectory();
+ }
+
+
+}
Property changes on:
trunk/Jmol/src/org/jmol/adapter/readers/xtal/VaspChgcarReader.java
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2014-11-12
19:46:49 UTC (rev 20108)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2014-11-15
17:15:05 UTC (rev 20109)
@@ -54,7 +54,7 @@
"pymol.", ";PyMOL;",
"simple.",
";Alchemy;Ampac;Cube;FoldingXyz;GhemicalMM;HyperChem;Jme;JSON;Mopac;MopacArchive;Tinker;ZMatrix;",
"xtal.",
";Abinit;Aims;Bilbao;Castep;Cgd;Crystal;Dmol;Espresso;Gulp;Jana;Magres;Shelx;Siesta;VaspOutcar;"
+
- "VaspPoscar;Wien2k;Xcrysden;",
+ "VaspPoscar;VaspChgcar;Wien2k;Xcrysden;",
"xml.",
";XmlArgus;XmlCml;XmlChem3d;XmlMolpro;XmlOdyssey;XmlXsd;XmlVasp;XmlQE;",
};
@@ -364,8 +364,10 @@
return "Crystal";
if (checkCastep(lines))
return "Castep";
- if (checkVaspposcar(lines))
+ if (checkVasp(lines, true))
return "VaspPoscar";
+ if (checkVasp(lines, false))
+ return "VaspChgcar";
} else {
if (nLines == 1 && lines[0].length() > 0
&& PT.isDigit(lines[0].charAt(0)))
@@ -456,17 +458,13 @@
return false;
}
- private static boolean checkVaspposcar(String[] lines) {
- String select = lines[8].trim().toLowerCase();
- if (select.contains("direct") || select.contains("cartesian")
- || select.contains("selective"))
- return true;
- String normal = lines[7].trim().toLowerCase();
- if (normal.contains("direct") || normal.contains("cartesian"))
- return true;
- return false;
+ private static boolean checkVasp(String[] lines, boolean isPoscar) {
+ String line = lines[isPoscar ? 7 : 6].toLowerCase();
+ if (isPoscar && line.contains("selective"))
+ line = lines[7].toLowerCase();
+ return (line.contains("direct") || line.contains("cartesian"));
}
-
+
private static boolean checkCrystal(String[] lines) {
String s = lines[1].trim();
if (s.equals("SLAB") ||s.equals("MOLECULE")
Modified: trunk/Jmol/src/org/jmol/io/JmolUtil.java
===================================================================
--- trunk/Jmol/src/org/jmol/io/JmolUtil.java 2014-11-12 19:46:49 UTC (rev
20108)
+++ trunk/Jmol/src/org/jmol/io/JmolUtil.java 2014-11-15 17:15:05 UTC (rev
20109)
@@ -367,7 +367,8 @@
if (nAtoms == Integer.MIN_VALUE)
return (line3.indexOf("+") == 0 ? "Jvxl+" : null);
if (nAtoms >= 0)
- return (line3.length() < 60 ? "Cube": null); //Can't be a Jvxl file; M40
files are > 60 char
+ return (line3.length() >= 60 ? null
+ : line3.indexOf(".") > 0 ? "VaspChgcar" : "Cube"); //Can't be a Jvxl
file; M40 files are > 60 char
nAtoms = -nAtoms;
for (int i = 4 + nAtoms; --i >= 0;)
if ((line = br.readLineWithNewline()) == null)
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/ApbsReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/ApbsReader.java 2014-11-12
19:46:49 UTC (rev 20108)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/ApbsReader.java 2014-11-15
17:15:05 UTC (rev 20109)
@@ -52,10 +52,10 @@
protected void readParameters() throws Exception {
jvxlFileHeaderBuffer = SB.newS(skipComments(false));
while (line != null && line.length() == 0)
- readLine();
+ rd();
jvxlFileHeaderBuffer.append("APBS OpenDx DATA ").append(line).append("\n");
jvxlFileHeaderBuffer.append("see http://apbs.sourceforge.net\n";);
- String atomLine = readLine();
+ String atomLine = rd();
String[] tokens = PT.getTokens(atomLine);
if (tokens.length >= 4) {
volumetricOrigin.set(parseFloatStr(tokens[1]), parseFloatStr(tokens[2]),
@@ -66,7 +66,7 @@
readVoxelVector(0);
readVoxelVector(1);
readVoxelVector(2);
- readLine();
+ rd();
tokens = getTokens();
/* see http://apbs.sourceforge.net/doc/user-guide/index.html#opendx-format
object 2 class gridconnections counts nx ny nz
@@ -75,6 +75,6 @@
*/
for (int i = 0; i < 3; i++)
voxelCounts[i] = parseIntStr(tokens[i + 5]);
- readLine();
+ rd();
}
}
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/CastepDensityReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/CastepDensityReader.java
2014-11-12 19:46:49 UTC (rev 20108)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/CastepDensityReader.java
2014-11-15 17:15:05 UTC (rev 20109)
@@ -25,12 +25,11 @@
import java.io.BufferedReader;
-
import javajs.util.PT;
import javajs.util.SB;
import javajs.util.V3;
-class CastepDensityReader extends VolumeFileReader {
+class CastepDensityReader extends PeriodicVolumeFileReader {
private int nFilePoints;
@@ -43,6 +42,13 @@
isAngstroms = true;
}
+ private int nSkip;
+
+ @Override
+ protected void gotoData(int n, int nPoints) throws Exception {
+ nSkip = n;
+ }
+
/*
*
BEGIN header
@@ -62,16 +68,16 @@
@Override
protected void readParameters() throws Exception {
jvxlFileHeaderBuffer = new SB();
- while (readLine() != null && line.indexOf(".") < 0) {
+ while (rd() != null && line.indexOf(".") < 0) {
// skip front stuff
}
for (int i = 0; i < 3; ++i) {
V3 voxelVector = volumetricVectors[i];
voxelVector.set(parseFloatStr(line), parseFloat(), parseFloat());
- readLine();
+ rd();
}
- nSurfaces = parseIntStr(readLine());
- readLine();
+ nSurfaces = parseIntStr(rd());
+ rd();
voxelCounts[0] = (nPointsX = parseIntStr(line)) + 1;
voxelCounts[1] = (nPointsY = parseInt()) + 1;
voxelCounts[2] = (nPointsZ = parseInt()) + 1;
@@ -82,30 +88,13 @@
if (isAnisotropic)
setVectorAnisotropy(volumetricVectors[i]);
}
- while (readLine().trim().length() > 0) {
+ while (rd().trim().length() > 0) {
//
}
}
- private int nSkip;
-
@Override
- protected void gotoData(int n, int nPoints) throws Exception {
- nSkip = n;
- }
-
- @Override
- protected void readSurfaceData(boolean isMapData) throws Exception {
- initializeSurfaceData();
- voxelData = new float[nPointsX][nPointsY][nPointsZ];
- readLine();
- String[] tokens = getTokens();
- if (nSkip > 0 && tokens.length < 3 + nSurfaces) {
- for (int j = 0; j < nSkip; j++)
- for (int i = 0; i < nFilePoints; i++)
- readLine();
- nSkip = 0;
- }
+ protected void getPeriodicVoxels() throws Exception {
for (int i = 0; i < nFilePoints; i++) {
int x = parseIntStr(line) - 1;
int y = parseInt() - 1;
@@ -113,43 +102,9 @@
if (nSkip > 0)
skipPoints(nSkip);
voxelData[x][y][z] = recordData(parseFloat());
- readLine();
+ rd();
}
- // add in periodic face data
-
- int n;
- n = nPointsX - 1;
- for (int i = 0; i < nPointsY; ++i)
- for (int j = 0; j < nPointsZ; ++j)
- voxelData[n][i][j] = voxelData[0][i][j];
- n = nPointsY - 1;
- for (int i = 0; i < nPointsX; ++i)
- for (int j = 0; j < nPointsZ; ++j)
- voxelData[i][n][j] = voxelData[i][0][j];
- n = nPointsZ - 1;
- for (int i = 0; i < nPointsX; ++i)
- for (int j = 0; j < nPointsY; ++j)
- voxelData[i][j][n] = voxelData[i][j][0];
-
- // for map data, just pick out near points and get rid of voxelData
-
- if (isMapData && volumeData.hasPlane()) {
- volumeData.setVoxelMap();
- for (int x = 0; x < nPointsX; ++x) {
- for (int y = 0; y < nPointsY; ++y) {
- for (int z = 0; z < nPointsZ; ++z) {
- float f = volumeData.getToPlaneParameter();
- if (volumeData.isNearPlane(x, y, z, f))
- volumeData.setVoxelMapValue(x, y, z, voxelData[x][y][z]);
- }
- }
- }
- voxelData = null;
- }
- volumeData.setVoxelDataAsArray(voxelData);
- if (dataMin > params.cutoff)
- params.cutoff = 2 * dataMin;
}
private void skipPoints(int n) {
@@ -166,5 +121,17 @@
}
+ @Override
+ protected void readSkip() throws Exception {
+ rd();
+ String[] tokens = getTokens();
+ if (nSkip > 0 && tokens.length < 3 + nSurfaces) {
+ for (int j = 0; j < nSkip; j++)
+ for (int i = 0; i < nFilePoints; i++)
+ rd();
+ nSkip = 0;
+ }
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/CubeReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/CubeReader.java 2014-11-12
19:46:49 UTC (rev 20108)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/CubeReader.java 2014-11-15
17:15:05 UTC (rev 20109)
@@ -43,9 +43,9 @@
@Override
protected void readParameters() throws Exception {
jvxlFileHeaderBuffer = new SB();
- jvxlFileHeaderBuffer.append(readLine()).appendC('\n');
- jvxlFileHeaderBuffer.append(readLine()).appendC('\n');
- String atomLine = readLine();
+ jvxlFileHeaderBuffer.append(rd()).appendC('\n');
+ jvxlFileHeaderBuffer.append(rd()).appendC('\n');
+ String atomLine = rd();
String[] tokens = PT.getTokensAt(atomLine, 0);
ac = parseIntStr(tokens[0]);
negativeAtomCount = (ac < 0); // MO list
@@ -60,12 +60,12 @@
for (int i = 0; i < 3; ++i)
readVoxelVector(i);
for (int i = 0; i < ac; ++i)
- jvxlFileHeaderBuffer.append(readLine() + "\n");
+ jvxlFileHeaderBuffer.append(rd() + "\n");
if (!negativeAtomCount) {
nSurfaces = 1;
} else {
- readLine();
+ rd();
Logger.info("Reading extra CUBE information line: " + line);
nSurfaces = parseIntStr(line);
}
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/EfvetReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/EfvetReader.java 2014-11-12
19:46:49 UTC (rev 20108)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/EfvetReader.java 2014-11-15
17:15:05 UTC (rev 20109)
@@ -107,7 +107,7 @@
private void getHeader() throws Exception {
skipTo("<efvet", null);
- while(readLine().length() > 0 && line.indexOf(">") < 0)
+ while(rd().length() > 0 && line.indexOf(">") < 0)
jvxlFileHeaderBuffer.append("# " + line + "\n");
Logger.info(jvxlFileHeaderBuffer.toString());
}
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/JaguarReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/JaguarReader.java 2014-11-12
19:46:49 UTC (rev 20108)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/JaguarReader.java 2014-11-15
17:15:05 UTC (rev 20109)
@@ -89,7 +89,7 @@
jvxlFileHeaderBuffer.append("Jaguar data\n");
jvxlFileHeaderBuffer.append("\n");
String atomLine;
- while ((atomLine = readLine()) != null
+ while ((atomLine = rd()) != null
&& atomLine.indexOf("origin=") < 0) {
}
String[] tokens = PT.getTokensAt(atomLine, 0);
@@ -107,7 +107,7 @@
readExtents(1);
readExtents(2);
- tokens = PT.getTokens(readLine());
+ tokens = PT.getTokens(rd());
voxelCounts[0] = parseIntStr(tokens[1]);
voxelCounts[1] = parseIntStr(tokens[2]);
voxelCounts[2] = parseIntStr(tokens[3]);
@@ -129,7 +129,7 @@
// I think, because if you don't use -1 here, then the grid
// distances are the same, but the surface is in the wrong place!
- readLine();
+ rd();
}
@@ -143,7 +143,7 @@
* @exception Exception -- generally a reader issue
*/
private void readExtents(int voxelVectorIndex) throws Exception {
- String[] tokens = PT.getTokens(readLine());
+ String[] tokens = PT.getTokens(rd());
extents[voxelVectorIndex] = parseFloatStr(tokens[voxelVectorIndex + 1]);
}
}
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/JvxlReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/JvxlReader.java 2014-11-12
19:46:49 UTC (rev 20108)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/JvxlReader.java 2014-11-15
17:15:05 UTC (rev 20109)
@@ -61,7 +61,7 @@
if (line == null || line.length() == 0)
line = "Line 1";
jvxlFileHeaderBuffer.append(line).appendC('\n');
- if (readLine() == null || line.length() == 0)
+ if (rd() == null || line.length() == 0)
line = "Line 2";
jvxlFileHeaderBuffer.append(line).appendC('\n');
jvxlFileHeaderBuffer.append(skipComments(false));
@@ -89,7 +89,7 @@
readVoxelVector(1);
readVoxelVector(2);
for (int i = 0; i < ac; ++i)
- jvxlFileHeaderBuffer.append(readLine() + "\n");
+ jvxlFileHeaderBuffer.append(rd() + "\n");
skipComments(true);
Logger.info("Reading extra JVXL information line: " + line);
nSurfaces = parseIntStr(line);
@@ -119,7 +119,7 @@
String str = "";
try {
while (str.length() < nPoints) {
- readLine();
+ rd();
str += JvxlCoder.jvxlDecompressString(line);
}
} catch (Exception e) {
@@ -286,7 +286,7 @@
private void jvxlSkipDataBlock(int nPoints, boolean isInt) throws Exception {
int n = 0;
while (n < nPoints) {
- readLine();
+ rd();
n += (isInt ? countData(line) :
JvxlCoder.jvxlDecompressString(line).length());
}
}
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java 2014-11-12
19:46:49 UTC (rev 20108)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java 2014-11-15
17:15:05 UTC (rev 20109)
@@ -201,7 +201,7 @@
protected void jvxlSkipData(@SuppressWarnings("unused") int nPoints,
@SuppressWarnings("unused") boolean
doSkipColorData)
throws Exception {
- readLine();
+ rd();
xr.skipTag("jvxlSurface");
}
@@ -480,7 +480,7 @@
while (bsVoxelPtr < nPoints) {
nThisValue = parseInt();
if (nThisValue == Integer.MIN_VALUE) {
- readLine();
+ rd();
// note -- does not allow for empty lines;
// must be a continuous block of numbers.
if (line == null || (nThisValue = parseIntStr(line)) ==
Integer.MIN_VALUE) {
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/KinemageReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/KinemageReader.java 2014-11-12
19:46:49 UTC (rev 20108)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/KinemageReader.java 2014-11-15
17:15:05 UTC (rev 20109)
@@ -84,7 +84,7 @@
@Override
protected boolean readVertices() throws Exception {
// also reads polygons
- readLine();
+ rd();
int n0;
while (line != null) {
if (line.length() != 0 && line.charAt(0) == '@') {
@@ -107,7 +107,7 @@
}
}
}
- readLine();
+ rd();
}
return true;
}
@@ -120,7 +120,7 @@
private void readDots() throws Exception {
int[] color = new int[1];
- while (readLine() != null && line.indexOf('@') < 0) {
+ while (rd() != null && line.indexOf('@') < 0) {
int i = getPoint(line, 2, color, true);
if (i < 0)
continue;
@@ -135,7 +135,7 @@
*/
private void readVectors() throws Exception {
int[] color = new int[1];
- while (readLine() != null && line.indexOf('@') < 0) {
+ while (rd() != null && line.indexOf('@') < 0) {
int ia = getPoint(line, 3, color, true);
int ib = getPoint(line.substring(line.lastIndexOf('{')), 2, color,
false);
if (ia < 0 || ib < 0)
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/MsmsReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/MsmsReader.java 2014-11-12
19:46:49 UTC (rev 20108)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/MsmsReader.java 2014-11-15
17:15:05 UTC (rev 20109)
@@ -81,7 +81,7 @@
}
private void skipHeader() throws Exception {
- while (readLine() != null && line.indexOf("#") >= 0) {
+ while (rd() != null && line.indexOf("#") >= 0) {
// skip header
}
tokens = getTokens();
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/NffReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/NffReader.java 2014-11-12 19:46:49 UTC
(rev 20108)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/NffReader.java 2014-11-15 17:15:05 UTC
(rev 20109)
@@ -79,7 +79,7 @@
protected boolean readVerticesAndPolygons() {
int color = 0xFF0000;
try {
- while(readLine() != null) {
+ while(rd() != null) {
if (line.length() == 0)
continue;
String[] tokens = getTokens();
@@ -112,7 +112,7 @@
private final P3 pt = new P3();
private int getVertex() throws Exception {
- Integer i = vertexMap.get(readLine());
+ Integer i = vertexMap.get(rd());
if (i == null) {
String[] tokens = getTokens();
pt.set(parseFloatStr(tokens[0]), parseFloatStr(tokens[1]),
parseFloatStr(tokens[2]));
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/ObjReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/ObjReader.java 2014-11-12 19:46:49 UTC
(rev 20108)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/ObjReader.java 2014-11-15 17:15:05 UTC
(rev 20109)
@@ -100,7 +100,7 @@
// pymol writes a crude file with much re-writing of vertices
BS bsOK = new BS();
- while (readLine() != null) {
+ while (rd() != null) {
if (line.length() < 2 || line.charAt(1) != ' ') {
if (params.readAllData && line.startsWith("usemtl"))
// usemtl k00FF00
Added: trunk/Jmol/src/org/jmol/jvxl/readers/PeriodicVolumeFileReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/PeriodicVolumeFileReader.java
(rev 0)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/PeriodicVolumeFileReader.java
2014-11-15 17:15:05 UTC (rev 20109)
@@ -0,0 +1,52 @@
+package org.jmol.jvxl.readers;
+
+public abstract class PeriodicVolumeFileReader extends VolumeFileReader {
+
+ @Override
+ protected void readSurfaceData(boolean isMapData) throws Exception {
+ initializeSurfaceData();
+ voxelData = new float[nPointsX][nPointsY][nPointsZ];
+ readSkip();
+ getPeriodicVoxels();
+
+ // add in periodic face data
+
+ int n;
+ n = nPointsX - 1;
+ for (int i = 0; i < nPointsY; ++i)
+ for (int j = 0; j < nPointsZ; ++j)
+ voxelData[n][i][j] = voxelData[0][i][j];
+ n = nPointsY - 1;
+ for (int i = 0; i < nPointsX; ++i)
+ for (int j = 0; j < nPointsZ; ++j)
+ voxelData[i][n][j] = voxelData[i][0][j];
+ n = nPointsZ - 1;
+ for (int i = 0; i < nPointsX; ++i)
+ for (int j = 0; j < nPointsY; ++j)
+ voxelData[i][j][n] = voxelData[i][j][0];
+
+ // for map data, just pick out near points and get rid of voxelData
+
+ if (isMapData && volumeData.hasPlane()) {
+ volumeData.setVoxelMap();
+ for (int x = 0; x < nPointsX; ++x) {
+ for (int y = 0; y < nPointsY; ++y) {
+ for (int z = 0; z < nPointsZ; ++z) {
+ float f = volumeData.getToPlaneParameter();
+ if (volumeData.isNearPlane(x, y, z, f))
+ volumeData.setVoxelMapValue(x, y, z, voxelData[x][y][z]);
+ }
+ }
+ }
+ voxelData = null;
+ }
+ volumeData.setVoxelDataAsArray(voxelData);
+
+ if (dataMin > params.cutoff)
+ params.cutoff = 2 * dataMin;
+ }
+
+ protected abstract void getPeriodicVoxels() throws Exception;
+ protected abstract void readSkip() throws Exception;
+
+}
Property changes on:
trunk/Jmol/src/org/jmol/jvxl/readers/PeriodicVolumeFileReader.java
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/PltFormattedReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/PltFormattedReader.java
2014-11-12 19:46:49 UTC (rev 20108)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/PltFormattedReader.java
2014-11-15 17:15:05 UTC (rev 20109)
@@ -62,10 +62,10 @@
@Override
protected void readParameters() throws Exception {
- int n1 = parseIntStr(readLine());
+ int n1 = parseIntStr(rd());
int n2 = parseInt();
//yes, it's "Z Y X", but that doesn't matter. Our loop will be (X (Y (Z)))
- nPointsX = parseIntStr(readLine());
+ nPointsX = parseIntStr(rd());
nPointsY = parseInt();
nPointsZ = parseInt();
jvxlFileHeaderBuffer.append("Plt formatted data (" + n1 + "," + n2 + ") "
@@ -77,7 +77,7 @@
-0.41532E+01 0.78468E+01-0.40155E+01 0.79845E+01-0.38912E+01 0.71088E+01
*/
- float xmin = parseFloatStr(readLine().substring(0, 12));
+ float xmin = parseFloatStr(rd().substring(0, 12));
float xmax = parseFloatRange(line, 12, 24);
float ymin = parseFloatRange(line, 24, 36);
float ymax = parseFloatRange(line, 36, 48);
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/Pmesh4Reader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/Pmesh4Reader.java 2014-11-12
19:46:49 UTC (rev 20108)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/Pmesh4Reader.java 2014-11-15
17:15:05 UTC (rev 20109)
@@ -101,7 +101,7 @@
@Override
void getSurfaceData() throws Exception {
- readLine();
+ rd();
if (readVerticesAndPolygons())
Logger.info(type + " file contains "
+ nVertices + " 4D vertices and " + nPolygons + " polygons for "
@@ -168,7 +168,7 @@
private String nextToken() throws Exception {
while (iToken >= tokens.length) {
iToken = 0;
- readLine();
+ rd();
tokens = getTokens();
}
return tokens[iToken++];
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/PmeshReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/PmeshReader.java 2014-11-12
19:46:49 UTC (rev 20108)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/PmeshReader.java 2014-11-15
17:15:05 UTC (rev 20109)
@@ -309,7 +309,7 @@
private String nextToken() throws Exception {
while (iToken >= tokens.length) {
iToken = 0;
- readLine();
+ rd();
tokens = getTokens();
}
return tokens[iToken++];
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceFileReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceFileReader.java 2014-11-12
19:46:49 UTC (rev 20108)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceFileReader.java 2014-11-15
17:15:05 UTC (rev 20109)
@@ -151,13 +151,13 @@
protected void skipTo(String info, String what) throws Exception {
if (info != null)
- while (readLine().indexOf(info) < 0) {
+ while (rd().indexOf(info) < 0) {
}
if (what != null)
next[0] = line.indexOf(what) + what.length() + 2;
}
- protected String readLine() throws Exception {
+ protected String rd() throws Exception {
line = br.readLine();
if (line != null) {
nBytes += line.length();
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/UhbdReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/UhbdReader.java 2014-11-12
19:46:49 UTC (rev 20108)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/UhbdReader.java 2014-11-15
17:15:05 UTC (rev 20109)
@@ -81,14 +81,14 @@
@Override
protected void readParameters() throws Exception {
- readLine();
+ rd();
// POTENTIAL (kT/e)
jvxlFileHeaderBuffer = SB.newS(line);
jvxlFileHeaderBuffer.append("UHBD format ").append(line).append("\n");
jvxlFileHeaderBuffer.append("see
http://sourceforge.net/p/apbs/code/ci/9527462a39126fb6cd880924b3cc4880ec4b78a9/tree/src/mg/vgrid.c\n";);
- readLine(); // ignored
+ rd(); // ignored
// 1.00000e+00 0.00000e+00 -1 0 161 1 161
- readLine();
+ rd();
// 161 161 161 1.56250e+00-8.79940e+01-6.20705e+01-7.07875e+01
voxelCounts[0] = parseIntStr(line.substring(0, 7));
voxelCounts[1] = parseIntStr(line.substring(7,14));
@@ -101,9 +101,9 @@
volumetricVectors[1].set(0, dx, 0);
volumetricVectors[2].set(dx, 0, 0);
planeCount = voxelCounts[0]*voxelCounts[1];
- readLine(); // ignored
+ rd(); // ignored
// 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
- readLine(); // ignored
+ rd(); // ignored
// 0.00000e+00 0.00000e+00 0 0
}
@@ -112,12 +112,12 @@
@Override
protected float nextVoxel() throws Exception {
if (voxelCount % planeCount == 0) {
- readLine();
+ rd();
// 1 161 161
pt = 0;
}
if (pt%78 == 0) {
- readLine();
+ rd();
// -4.19027e-06 -4.40880e-06 -4.63681e-06 -4.87457e-06 -5.12234e-06
-5.38038e-06
pt = 0;
}
Added: trunk/Jmol/src/org/jmol/jvxl/readers/VaspChgcarReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/VaspChgcarReader.java
(rev 0)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/VaspChgcarReader.java 2014-11-15
17:15:05 UTC (rev 20109)
@@ -0,0 +1,128 @@
+/* $RCSfile$
+ * $Author: hansonr $
+ * $Date: 2007-03-30 11:40:16 -0500 (Fri, 30 Mar 2007) $
+ * $Revision: 7273 $
+ *
+ * Copyright (C) 2007 Miguel, Bob, Jmol Development
+ *
+ * Contact: hans...@stolaf.edu
+ *
+ * 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 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.jvxl.readers;
+
+import java.io.BufferedReader;
+
+import org.jmol.util.SimpleUnitCell;
+
+import javajs.util.SB;
+
+class VaspChgcarReader extends PeriodicVolumeFileReader {
+
+ private float volume;
+
+ VaspChgcarReader(){
+ }
+
+ @Override
+ void init2(SurfaceGenerator sg, BufferedReader br) {
+ init2VFR(sg, br);
+ isAngstroms = true;
+ nSurfaces = 1;
+ canDownsample = isProgressive = false; // for now
+ }
+
+ // pt
+ // 10.0000000000000
+ // 1.000000 0.000000 0.000000
+ // 0.000000 1.000000 0.000000
+ // 0.000000 0.000000 1.000000
+ // 2 4
+ //Direct
+ // 0.080067 0.160200 0.131800
+ // 0.213232 0.160200 0.131800
+ // 0.022723 0.101273 0.060100
+ // 0.022724 0.219127 0.203500
+ // 0.270578 0.101273 0.060100
+ // 0.270577 0.219127 0.203499
+ //
+ // 140 140 140
+ //0.12994340141E+02 0.13765428641E+02 0.14355609008E+02 0.14732384059E+02
0.14873912610E+02
+
+// WRITE(IU,FORM) (((C(NX,NY,NZ),NX=1,NGXC),NY=1,NGYZ),NZ=1,NGZC)
+//
+// The x index is the fastest index, and the z index the slowest index.
+// The file can be read format-free, because at least in new versions,
+// it is guaranteed that spaces separate each number. Please do not forget
+// to divide by the volume before visualizing the file!
+
+ @Override
+ protected void readParameters() throws Exception {
+ jvxlFileHeaderBuffer = new SB();
+ jvxlFileHeaderBuffer.append("Vasp CHGCAR format\n");
+ rd(); // atoms
+ float scale = parseFloatStr(rd());
+ float[] data = new float[15];
+ data[0] = -1;
+ for (int i = 0, pt = 6; i < 3; ++i)
+ volumetricVectors[i].set(data[pt++] = parseFloatStr(rd()) * scale,
+ data[pt++] = parseFloat() * scale, data[pt++] = parseFloat() *
scale);
+ volume = (float) SimpleUnitCell.newA(data).volume;
+ // v0 here will be the slowest, not the fastest
+ while (rd().length() > 2) {
+ }
+ rd();
+ String[] counts = getTokens();
+ for (int i = 0; i < 3; ++i) {
+ volumetricVectors[i]
+ .scale(1f / ((voxelCounts[i] = parseIntStr(counts[i]) + 1) - 1));
+ if (isAnisotropic)
+ setVectorAnisotropy(volumetricVectors[i]);
+ }
+ swapXZ();
+ volumetricOrigin.set(0, 0, 0);
+ }
+
+ private int pt;
+
+ @Override
+ protected float nextVoxel() throws Exception {
+ if ((pt++)%5 == 0) {
+ rd();
+ next[0] = 0;
+ }
+ return parseFloat() / volume;
+ }
+
+ @Override
+ protected void getPeriodicVoxels() throws Exception {
+ int ni = voxelCounts[0] - 1;
+ int nj = voxelCounts[1] - 1;
+ int nk = voxelCounts[2] - 1;
+ for (int i = 0; i < ni; i++)
+ for (int j = 0; j < nj; j++)
+ for (int k = 0; k < nk; k++)
+ voxelData[i][j][k] = recordData(nextVoxel());
+ }
+
+ @Override
+ protected void readSkip() throws Exception {
+ // n/a
+ }
+
+
+}
+
+
Property changes on: trunk/Jmol/src/org/jmol/jvxl/readers/VaspChgcarReader.java
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/VolumeFileReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/VolumeFileReader.java 2014-11-12
19:46:49 UTC (rev 20108)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/VolumeFileReader.java 2014-11-15
17:15:05 UTC (rev 20109)
@@ -174,14 +174,14 @@
protected String skipComments(boolean allowBlankLines) throws Exception {
SB sb = new SB();
- while (readLine() != null
+ while (rd() != null
&& (allowBlankLines && line.length() == 0 || line.indexOf("#") == 0))
sb.append(line).appendC('\n');
return sb.toString();
}
protected void readVoxelVector(int voxelVectorIndex) throws Exception {
- readLine();
+ rd();
V3 voxelVector = volumetricVectors[voxelVectorIndex];
if ((voxelCounts[voxelVectorIndex] = parseIntStr(line)) ==
Integer.MIN_VALUE) //unreadable
next[0] = line.indexOf(" ");
@@ -469,7 +469,7 @@
protected float nextVoxel() throws Exception {
float voxelValue = parseFloat();
if (Float.isNaN(voxelValue)) {
- while (readLine() != null && Float.isNaN(voxelValue =
parseFloatStr(line))) {
+ while (rd() != null && Float.isNaN(voxelValue = parseFloatStr(line))) {
}
if (line == null) {
if (!endOfData)
@@ -500,7 +500,7 @@
protected void skipDataVFR(int nPoints) throws Exception {
int iV = 0;
while (iV < nPoints)
- iV += countData(readLine());
+ iV += countData(rd());
}
private int countData(String str) {
@@ -612,4 +612,14 @@
volumetricVectors[2].scale(scale);
}
+ protected void swapXZ() {
+ V3 v = volumetricVectors[0];
+ volumetricVectors[0] = volumetricVectors[2];
+ volumetricVectors[2] = v;
+ int n = voxelCounts[0];
+ voxelCounts[0] = voxelCounts[2];
+ voxelCounts[2] = n;
+ params.insideOut = !params.insideOut;
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/XplorReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/XplorReader.java 2014-11-12
19:46:49 UTC (rev 20108)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/XplorReader.java 2014-11-15
17:15:05 UTC (rev 20109)
@@ -155,9 +155,9 @@
private String getLine() throws Exception {
- readLine();
+ rd();
while (line != null && (line.length() == 0 || line.indexOf("REMARKS") >= 0
|| line.indexOf("XPLOR:") >= 0))
- readLine();
+ rd();
return line;
}
@@ -167,14 +167,14 @@
@Override
protected float nextVoxel() throws Exception {
if (linePt >= line.length()) {
- readLine();
+ rd();
//System.out.println(nRead + " " + line);
linePt = 0;
if ((nRead % nBlock) == 0) {
//if (Logger.debugging)
//Logger.info("XplorReader: block " + line + " min/max "
//+ dataMin + "/" + dataMax);
- readLine();
+ rd();
}
}
if (line == null)
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/XsfReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/XsfReader.java 2014-11-12 19:46:49 UTC
(rev 20108)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/XsfReader.java 2014-11-15 17:15:05 UTC
(rev 20109)
@@ -54,7 +54,7 @@
isAngstroms = true;
String beginKey = "BEGIN_DATAGRID_3D";
nSurfaces = 1;
- while (readLine() != null && line.indexOf(beginKey) < 0) {
+ while (rd() != null && line.indexOf(beginKey) < 0) {
Logger.info(line);
if (line.indexOf("Fermi Energy:") >= 0) {
isBXSF = true;
@@ -69,14 +69,14 @@
if (needCutoff)
params.cutoff = 0.05f;
if (isBXSF)
- nSurfaces = parseIntStr(readLine());
- voxelCounts[0] = parseIntStr(readLine());
+ nSurfaces = parseIntStr(rd());
+ voxelCounts[0] = parseIntStr(rd());
voxelCounts[1] = parseInt();
voxelCounts[2] = parseInt();
- volumetricOrigin.set(parseFloatStr(readLine()), parseFloat(),
parseFloat());
+ volumetricOrigin.set(parseFloatStr(rd()), parseFloat(), parseFloat());
// SPANNING vectors here.
for (int i = 0; i < 3; ++i) {
- volumetricVectors[i].set(parseFloatStr(readLine()), parseFloat(),
+ volumetricVectors[i].set(parseFloatStr(rd()), parseFloat(),
parseFloat());
volumetricVectors[i].scale(1.0f / (voxelCounts[i] - 1));
}
@@ -92,13 +92,7 @@
} else {
// data are slowest-z
// reversed order -- so we just reverse the vectors
- V3 v = volumetricVectors[0];
- volumetricVectors[0] = volumetricVectors[2];
- volumetricVectors[2] = v;
- int n = voxelCounts[0];
- voxelCounts[0] = voxelCounts[2];
- voxelCounts[2] = n;
- params.insideOut = !params.insideOut;
+ swapXZ();
}
}
@@ -109,7 +103,7 @@
if (n > 0)
Logger.info("skipping " + n + " data sets, " + nPoints + " points each");
if (isBXSF)
- Logger.info(readLine()); //"BAND: <n>" line
+ Logger.info(rd()); //"BAND: <n>" line
for (int i = 0; i < n; i++)
skipData(nPoints);
}
@@ -118,7 +112,7 @@
protected void skipData(int nPoints) throws Exception {
skipDataVFR(nPoints);
if (isBXSF)
- Logger.info(readLine()); //"BAND: <n>" line
+ Logger.info(rd()); //"BAND: <n>" line
}
}
Modified: trunk/Jmol/src/org/jmol/util/SimpleUnitCell.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/SimpleUnitCell.java 2014-11-12 19:46:49 UTC
(rev 20108)
+++ trunk/Jmol/src/org/jmol/util/SimpleUnitCell.java 2014-11-15 17:15:05 UTC
(rev 20109)
@@ -46,6 +46,7 @@
protected float[] notionalUnitcell; //6 parameters + optional 16 matrix items
public M4 matrixCartesianToFractional;
public M4 matrixFractionalToCartesian;
+ public double volume;
protected final static float toRadians = (float) Math.PI * 2 / 360;
@@ -58,7 +59,6 @@
protected double cosAlpha, sinAlpha;
protected double cosBeta, sinBeta;
protected double cosGamma, sinGamma;
- protected double volume;
protected double cA_, cB_;
protected double a_;
protected double b_, c_;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-12 19:46:49 UTC
(rev 20108)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-15 17:15:05 UTC
(rev 20109)
@@ -15,8 +15,13 @@
TODO: design and implement sidechain mutation -- MUTATE command ?
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
-Jmol.___JmolVersion="14.3.9_2014.11.12"
+Jmol.___JmolVersion="14.3.9_2014.11.15"
+new feature: VASP CHGCAR reader
+new feature: VASP CHGCAR isosurface reader
+
+JmolVersion="14.3.9_2014.11.12"
+
bug fix: Molden reader fails to read orbitals if [GEOCONV] is present
JmolVersion="14.3.9_2014.11.11"
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