Revision: 20150
http://sourceforge.net/p/jmol/code/20150
Author: hansonr
Date: 2014-11-28 22:52:14 +0000 (Fri, 28 Nov 2014)
Log Message:
-----------
not-so-useful NBO archive reader
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/quantum/GenNBOReader.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/quantum/GenNBOReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/quantum/GenNBOReader.java
2014-11-28 21:24:05 UTC (rev 20149)
+++ trunk/Jmol/src/org/jmol/adapter/readers/quantum/GenNBOReader.java
2014-11-28 22:52:14 UTC (rev 20150)
@@ -198,18 +198,15 @@
*
---------------------------------------------------------------------------
* 36 90 162
*
---------------------------------------------------------------------------
- * 6 -2.992884000 -1.750577000 1.960024000 6 -2.378528000 -1.339374000
- * 0.620578000
+ * 6 -2.992884000 -1.750577000 1.960024000
+ * 6 -2.378528000 -1.339374000 0.620578000
*/
private boolean readFile31() throws Exception {
String data = getFileData(".31");
BufferedReader readerSave = reader;
reader = Rdr.getBR(data);
- if (!readData31(null, null))
- return false;
- reader = readerSave;
- return true;
+ return (readData31(null, null) && (reader = readerSave) != null);
}
private void readFile46() throws Exception {
@@ -255,7 +252,123 @@
// 301 307 310 304 302 303 306 309 308 305
+//
+// private boolean readData47() throws Exception {
+// readFile47();
+// discardLinesUntilContains("$BASIS");
+// int[] centers = getIntData();
+// int[] labels = getIntData();
+//
+// discardLinesUntilContains("NSHELL =");
+// shellCount = parseIntStr(line.substring(8));
+// gaussianCount = parseIntStr(rd().substring(8));
+// rd();
+// int[] ncomp = getIntData();
+// int[] nprim = getIntData();
+// int[] nptr = getIntData();
+//
+//
+// // read basis functions
+// shells = new Lst<int[]>();
+// gaussians = AU.newFloat2(gaussianCount);
+// for (int i = 0; i < gaussianCount; i++)
+// gaussians[i] = new float[6];
+// nOrbitals = 0;
+// int ptCenter = 0;
+// for (int i = 0; i < shellCount; i++) {
+// int[] slater = new int[4];
+// int nc = ncomp[i];
+// slater[0] = centers[ptCenter] - 1;
+// line = "";
+// for (int ii = 0; ii < nc; ii++)
+// line += labels[ptCenter++] + " ";
+// if (!fillSlater(slater, nc, nptr[i], nprim[i]))
+// return false;
+// }
+// getAlphasAndExponents();
+// return true;
+// }
+//private int[] getIntData() throws Exception {
+//if (line.indexOf("=") < 0)
+// rd();
+//String s = line.substring(line.indexOf("=") + 1);
+//line = "";
+//while (rd().indexOf("=") < 0 && line.indexOf("$") < 0)
+// s += line;
+//String[] tokens = getTokensStr(s);
+//int[] f = new int[tokens.length];
+//for (int i = f.length; --i >= 0;)
+// f[i] = parseIntStr(tokens[i]);
+//return f;
+//}
+
+ private boolean fillSlater(int[] slater, int n, int pt, int ng) {
+ nOrbitals += n;
+ switch (n) {
+ case 1:
+ slater[1] = JmolAdapter.SHELL_S;
+ break;
+ case 3:
+ if (!getDFMap(line, JmolAdapter.SHELL_P, P_LIST, 3))
+ return false;
+ slater[1] = JmolAdapter.SHELL_P;
+ break;
+ case 4:
+ if (!getDFMap(line, JmolAdapter.SHELL_SP, SP_LIST, 1))
+ return false;
+ slater[1] = JmolAdapter.SHELL_SP;
+ break;
+ case 5:
+ if (!getDFMap(line, JmolAdapter.SHELL_D_SPHERICAL, DS_LIST, 3))
+ return false;
+ slater[1] = JmolAdapter.SHELL_D_SPHERICAL;
+ break;
+ case 6:
+ if (!getDFMap(line, JmolAdapter.SHELL_D_CARTESIAN, DC_LIST, 3))
+ return false;
+ slater[1] = JmolAdapter.SHELL_D_CARTESIAN;
+ break;
+ case 7:
+ if (!getDFMap(line, JmolAdapter.SHELL_F_SPHERICAL, FS_LIST, 3))
+ return false;
+ slater[1] = JmolAdapter.SHELL_F_SPHERICAL;
+ break;
+ case 10:
+ if (!getDFMap(line, JmolAdapter.SHELL_F_CARTESIAN, FC_LIST, 3))
+ return false;
+ slater[1] = JmolAdapter.SHELL_F_CARTESIAN;
+ break;
+ }
+ slater[2] = pt; // gaussian list pointer
+ slater[3] = ng; // number of gaussians
+ shells.addLast(slater);
+ return true;
+ }
+
+ private void getAlphasAndExponents() throws Exception {
+ for (int j = 0; j < 5; j++) {
+ rd();
+ line = line.substring(line.indexOf("=") + 1);
+ float[] temp = fillFloatArray(null, 0, new float[gaussianCount]);
+ for (int i = 0; i < gaussianCount; i++) {
+ gaussians[i][j] = temp[i];
+ if (j > 1)
+ gaussians[i][5] += temp[i];
+ }
+ }
+ // GenNBO lists S, P, D, F, G orbital coefficients separately
+ // we need all of them in [1] if [1] is zero (not S or SP)
+ for (int i = 0; i < gaussianCount; i++) {
+ if (gaussians[i][1] == 0)
+ gaussians[i][1] = gaussians[i][5];
+ }
+ if (Logger.debugging) {
+ Logger.debug(shells.size() + " slater shells read");
+ Logger.debug(gaussians.length + " gaussian primitives read");
+ }
+ }
+
private boolean readData31(String line1, String line2) throws Exception {
if (line1 == null)
line1 = rd();
@@ -295,69 +408,13 @@
int[] slater = new int[4];
slater[0] = parseIntStr(tokens[0]) - 1; // atom pointer; 1-based
int n = parseIntStr(tokens[1]);
- nOrbitals += n;
+ int pt = parseIntStr(tokens[2]) - 1; // gaussian list pointer
+ int ng = parseIntStr(tokens[3]); // number of gaussians
line = rd().trim();
- switch (n) {
- case 1:
- slater[1] = JmolAdapter.SHELL_S;
- break;
- case 3:
- if (!getDFMap(line, JmolAdapter.SHELL_P, P_LIST, 3))
- return false;
- slater[1] = JmolAdapter.SHELL_P;
- break;
- case 4:
- if (!getDFMap(line, JmolAdapter.SHELL_SP, SP_LIST, 1))
- return false;
- slater[1] = JmolAdapter.SHELL_SP;
- break;
- case 5:
- if (!getDFMap(line, JmolAdapter.SHELL_D_SPHERICAL, DS_LIST, 3))
- return false;
- slater[1] = JmolAdapter.SHELL_D_SPHERICAL;
- break;
- case 6:
- if (!getDFMap(line, JmolAdapter.SHELL_D_CARTESIAN, DC_LIST, 3))
- return false;
- slater[1] = JmolAdapter.SHELL_D_CARTESIAN;
- break;
- case 7:
- if (!getDFMap(line, JmolAdapter.SHELL_F_SPHERICAL, FS_LIST, 3))
- return false;
- slater[1] = JmolAdapter.SHELL_F_SPHERICAL;
- break;
- case 10:
- if (!getDFMap(line, JmolAdapter.SHELL_F_CARTESIAN, FC_LIST, 3))
- return false;
- slater[1] = JmolAdapter.SHELL_F_CARTESIAN;
- break;
- }
- slater[2] = parseIntStr(tokens[2]) - 1; // gaussian list pointer
- slater[3] = parseIntStr(tokens[3]); // number of gaussians
- shells.addLast(slater);
+ if (!fillSlater(slater, n, pt, ng))
+ return false;
}
-
- // get alphas and exponents
-
- for (int j = 0; j < 5; j++) {
- rd();
- float[] temp = fillFloatArray(null, 0, new float[gaussianCount]);
- for (int i = 0; i < gaussianCount; i++) {
- gaussians[i][j] = temp[i];
- if (j > 1)
- gaussians[i][5] += temp[i];
- }
- }
- // GenNBO lists S, P, D, F, G orbital coefficients separately
- // we need all of them in [1] if [1] is zero (not S or SP)
- for (int i = 0; i < gaussianCount; i++) {
- if (gaussians[i][1] == 0)
- gaussians[i][1] = gaussians[i][5];
- }
- if (Logger.debugging) {
- Logger.debug(shells.size() + " slater shells read");
- Logger.debug(gaussians.length + " gaussian primitives read");
- }
+ getAlphasAndExponents();
return true;
}
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