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[Jmol-commits] SF.net SVN: jmol:[14877] trunk/Jmol/src/org/jmol/adapter
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From: <ha...@us...> - 2010-12-22 18:39:43
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Revision: 14877
http://jmol.svn.sourceforge.net/jmol/?rev=14877&view=rev
Author: hansonr
Date: 2010-12-22 18:39:37 +0000 (Wed, 22 Dec 2010)
Log Message:
-----------
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/xtal/EspressoReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xtal/EspressoReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xtal/EspressoReader.java 2010-12-22 18:27:53 UTC (rev 14876)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/EspressoReader.java 2010-12-22 18:39:37 UTC (rev 14877)
@@ -33,13 +33,13 @@
if (line.contains("lattice parameter (a_0)")) {
readAparam();
} else if (line.contains("crystal axes:")) {
- readIntialCellParam();
+ readCellParam(false);
} else if (line.contains("Cartesian axes")) {
readInitialAtomic();
} else if (line.contains("! total energy")) {
readEnergy();
} else if (line.contains("CELL_PARAMETERS")) {
- readCellParam();
+ readCellParam(true);
} else if (line.contains("ATOMIC_POSITIONS")) {
readAtomic();
} else if(line.contains("End") && line.contains(" Geometry Optimization")){
@@ -52,8 +52,8 @@
private float aPar;
private void readAparam() throws Exception {
- String[] tokens = getTokens(line.substring(line.indexOf("=") + 1));
- aPar = parseFloat(tokens[0]) * ANGSTROMS_PER_BOHR;
+ String[] tokens = getTokens();
+ aPar = parseFloat(tokens[4]) * ANGSTROMS_PER_BOHR;
}
/*
@@ -69,71 +69,30 @@
*/
- private float a, b, c, alpha, beta, gamma;
-
- private void readIntialCellParam() throws Exception {
- readLine();
- String[] tokens = getTokens();
- float x, y, z;
- for (int n = 0; n < 3; n++) {
- if (tokens.length >= 3) {
- x = parseFloat(tokens[3]) * aPar;
- y = parseFloat(tokens[4]) * aPar;
- z = parseFloat(tokens[5]) * aPar;
- abc[n] = new Vector3f(x, y, z);
- }
- tokens = getTokens(readLine());
- }
- a = abc[0].length();
- b = abc[1].length();
- c = abc[2].length();
- alpha = (float) Math.toDegrees(abc[1].angle(abc[2]));
- beta = (float) Math.toDegrees(abc[2].angle(abc[0]));
- gamma = (float) Math.toDegrees(abc[0].angle(abc[1]));
- setCell();
- }
-
-
-/*
+ /*
CELL_PARAMETERS (alat= 17.62853047)
1.019135101 0.000000000 0.000000000
-0.509567550 0.882596887 0.000000000
0.000000000 0.000000000 0.737221415
-*/ private void readCellParam() throws Exception {
- aPar = parseFloat(line.substring(line.indexOf("=") + 1, line
- .lastIndexOf(")") - 1))
- * ANGSTROMS_PER_BOHR;
- String[] tokens = getTokens();
- float x, y, z;
- for (int n = 0; n < 3; n++) {
- if (tokens.length >= 3) {
- x = parseFloat(tokens[0]) * aPar;
- y = parseFloat(tokens[1]) * aPar;
- z = parseFloat(tokens[2]) * aPar;
- abc[n] = new Vector3f(x, y, z);
- }
- tokens = getTokens(readLine());
+*/
+
+ float[] cellParams;
+
+ private void readCellParam(boolean andAPar) throws Exception {
+ int i0 = (andAPar ? 0 : 3);
+ if (andAPar)
+ aPar = parseFloat(line.substring(line.indexOf("=") + 1)) * ANGSTROMS_PER_BOHR;
+ cellParams = new float[9];
+ for (int n = 0, i = 0; n < 3; n++) {
+ String[] tokens = getTokens(readLine());
+ cellParams[i++] = parseFloat(tokens[i0]) * aPar;
+ cellParams[i++] = parseFloat(tokens[i0 + 1]) * aPar;
+ cellParams[i++] = parseFloat(tokens[i0 + 2]) * aPar;
}
- a = abc[0].length();
- b = abc[1].length();
- c = abc[2].length();
- alpha = (float) Math.toDegrees(abc[1].angle(abc[2]));
- beta = (float) Math.toDegrees(abc[2].angle(abc[0]));
- gamma = (float) Math.toDegrees(abc[0].angle(abc[1]));
-
-
- applySymmetryAndSetTrajectory();
- setSpaceGroupName("P1");
- setFractionalCoordinates(true);
- setCell();
}
-
- private void setCell() throws Exception {
- setUnitCell(a, b, c, alpha, beta, gamma);
- applySymmetryAndSetTrajectory();
- }
-
+
+
/*
Cartesian axes
@@ -150,20 +109,33 @@
10 Ca tau( 10) = ( 0.1171775 -0.2203283 -0.1867815 )
*/
private void readInitialAtomic() throws Exception {
+ setCellParams();
discardLines(2);
while (readLine() != null && line.length() > 1) {
String[] tokens = getTokens();
Atom atom = atomSetCollection.addNewAtom();
atom.atomName = tokens[1];
- // here the cordinates are a_lat there fore expressed on base of cube of side a
- float x = parseFloat(tokens[6])* aPar;
- float y = parseFloat(tokens[7])* aPar;
- float z = parseFloat(tokens[8])* aPar;
+ // here the coordinates are a_lat there fore expressed on base of cube of side a
+ float x = parseFloat(tokens[6]) * aPar;
+ float y = parseFloat(tokens[7]) * aPar;
+ float z = parseFloat(tokens[8]) * aPar;
setAtomCoord(atom, x, y, z);
-
}
}
+ private void setCellParams() throws Exception {
+ if (!doGetModel(++modelNumber))
+ return;
+ applySymmetryAndSetTrajectory();
+ atomSetCollection.newAtomSet();
+ if (cellParams != null) {
+ setFractionalCoordinates(true);
+ addPrimitiveLatticeVector(0, cellParams, 0);
+ addPrimitiveLatticeVector(1, cellParams, 3);
+ addPrimitiveLatticeVector(2, cellParams, 6);
+ }
+ }
+
private void readAtomic() throws Exception {
/*
@@ -181,6 +153,7 @@
if(endOptimization){
condition = 22;
}
+ setCellParams();
while (readLine() != null && line.length() > condition){
String[] tokens = getTokens();
Atom atom = atomSetCollection.addNewAtom();
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2010-12-22 18:27:53 UTC (rev 14876)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2010-12-22 18:39:37 UTC (rev 14877)
@@ -685,7 +685,7 @@
return true;
if (lines[i].contains("http://www.quantum-espresso.org"))
return true;
- if (lines[i].contains("Program PWSCF v"))
+ if (lines[i].contains("Program PWSCF"))
return true;
if (lines[i].contains("PHONON "))
return true;
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