Revision: 20114
http://sourceforge.net/p/jmol/code/20114
Author: hansonr
Date: 2014-11-19 11:47:35 +0000 (Wed, 19 Nov 2014)
Log Message:
-----------
Added Paths:
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branches/v14_2/Jmol/src/org/jmol/adapter/readers/xtal/VaspChgcarReader.java
branches/v14_2/Jmol/src/org/jmol/jvxl/readers/PeriodicVolumeFileReader.java
branches/v14_2/Jmol/src/org/jmol/jvxl/readers/VaspChgcarReader.java
Added:
branches/v14_2/Jmol/src/org/jmol/adapter/readers/xtal/VaspChgcarReader.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/adapter/readers/xtal/VaspChgcarReader.java
(rev 0)
+++ branches/v14_2/Jmol/src/org/jmol/adapter/readers/xtal/VaspChgcarReader.java
2014-11-19 11:47:35 UTC (rev 20114)
@@ -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:
branches/v14_2/Jmol/src/org/jmol/adapter/readers/xtal/VaspChgcarReader.java
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Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Added:
branches/v14_2/Jmol/src/org/jmol/jvxl/readers/PeriodicVolumeFileReader.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/jvxl/readers/PeriodicVolumeFileReader.java
(rev 0)
+++ branches/v14_2/Jmol/src/org/jmol/jvxl/readers/PeriodicVolumeFileReader.java
2014-11-19 11:47:35 UTC (rev 20114)
@@ -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:
branches/v14_2/Jmol/src/org/jmol/jvxl/readers/PeriodicVolumeFileReader.java
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Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Added: branches/v14_2/Jmol/src/org/jmol/jvxl/readers/VaspChgcarReader.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/jvxl/readers/VaspChgcarReader.java
(rev 0)
+++ branches/v14_2/Jmol/src/org/jmol/jvxl/readers/VaspChgcarReader.java
2014-11-19 11:47:35 UTC (rev 20114)
@@ -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:
branches/v14_2/Jmol/src/org/jmol/jvxl/readers/VaspChgcarReader.java
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
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