Revision: 18491
http://sourceforge.net/p/jmol/code/18491
Author: hansonr
Date: 2013-07-24 11:28:50 +0000 (Wed, 24 Jul 2013)
Log Message:
-----------
NWChem fix
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/quantum/NWChemReader.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/quantum/NWChemReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/quantum/NWChemReader.java
2013-07-24 03:22:39 UTC (rev 18490)
+++ trunk/Jmol/src/org/jmol/adapter/readers/quantum/NWChemReader.java
2013-07-24 11:28:50 UTC (rev 18491)
@@ -28,6 +28,7 @@
import java.util.Hashtable;
import java.util.Map;
+import java.util.Map.Entry;
import org.jmol.adapter.smarter.Atom;
import org.jmol.adapter.smarter.SmarterJmolAdapter;
@@ -85,11 +86,10 @@
private boolean inInput;
private JmolList<String> atomTypes;
- private boolean readROHFonly;
+ private Map<String, JmolList<String>> htMOs = new Hashtable<String,
JmolList<String>>();
@Override
protected void initializeReader() {
- readROHFonly = (filter != null && filter.indexOf("ROHF") >= 0);
calculationType = "(NWCHEM)"; // normalization is different for NWCHEM
}
@@ -104,6 +104,9 @@
if (line.trim().startsWith("NWChem")) {
// currently only keep track of whether I am in the input module or not.
inInput = (line.indexOf("NWChem Input Module") >= 0);
+ if (inInput) {
+ checkMOs();
+ }
}
if (line.startsWith(" Step")) {
@@ -160,42 +163,35 @@
if (line.startsWith(" Mulliken analysis of the total density")) {
// only do this if I have read an atom set in this task/step
- if (equivalentAtomSets == 0)
- return true;
- readPartialCharges();
+ if (equivalentAtomSets != 0)
+ readPartialCharges();
return true;
}
+
if (line.contains("Basis \"ao basis\"") && doReadMolecularOrbitals) {
return readBasis();
}
- if (line.contains("Final Molecular Orbital Analysis")) {
- if (equivalentAtomSets == 0)
- return true;
- return readMolecularOrbitalAnalysis(true);
+
+ if (line.contains("Molecular Orbital Analysis")) {
+ if (equivalentAtomSets != 0)
+ readMOs();
+ return true;
}
+// if (!readROHFonly && line.contains("Final MO vectors")) {
+// if (equivalentAtomSets == 0)
+// return true;
+// return readMolecularOrbitalVectors();
+// }
- if (line.contains("Final Alpha Molecular Orbital Analysis")) {
- if (equivalentAtomSets == 0)
- return true;
- alphaBeta = "alpha ";
- return readMolecularOrbitalAnalysis(true);
- }
-
- if (line.contains("Final Beta Molecular Orbital Analysis")) {
- if (equivalentAtomSets == 0)
- return true;
- return readMolecularOrbitalAnalysis(false);
- }
-
- if (!readROHFonly && line.contains("Final MO vectors")) {
- if (equivalentAtomSets == 0)
- return true;
- return readMolecularOrbitalVectors();
- }
-
return true;
}
+ @Override
+ protected void finalizeReader() throws Exception {
+ checkMOs();
+ finalizeReaderASCR();
+ }
+
private void init() {
haveEnergy = false;
haveAt = false;
@@ -684,7 +680,6 @@
gaussianCount = 0;
shellCount = 0;
nBasisFunctions = 0;
-
boolean isD6F10 = (line.indexOf("cartesian") >= 0);
if (isD6F10) {
getDFMap(DC_LIST, JmolAdapter.SHELL_D_CARTESIAN, CANONICAL_DC_LIST, 3);
@@ -807,62 +802,62 @@
*
*/
- private Map<Integer, Map<String, Object>> moInfo;
int moCount;
- private boolean readMolecularOrbitalAnalysis(boolean doClear) throws
Exception {
+ // get just the LAST MO definition of each type.
+ private boolean readMOs() throws Exception {
+ JmolList<String> lines = new JmolList<String>();
+ htMOs.put(line, lines);
+ lines.addLast(line);
+ int nblank = 0;
+ while (nblank != 2 && readLine() != null) {
+ lines.addLast(line);
+ if (line.length() < 2)
+ nblank++;
+ else
+ nblank = 0;
+ }
+ return true;
+ }
+ private void checkMOs() throws Exception {
if (shells == null)
- return true;
- int moCount = 0;
- boolean isBeta = false;
- if (doClear && !readROHFonly) {
- moInfo = new Hashtable<Integer, Map<String, Object>>();
- }
- while (line != null) {
- while ((line.length() < 3 || line.charAt(1) == ' ')
- && line.indexOf("Final") < 0) {
- readLine();
- }
+ return;
+ for (Entry<String, JmolList<String>> entry : htMOs.entrySet()) {
+ line = entry.getKey();
+ alphaBeta = line.substring(0, line.indexOf("Final")).trim() + " ";
+ int moCount = 0;
+ if (!filterMO())
+ continue;
+ JmolList<String> list = entry.getValue();
+ int n = list.size();
Logger.info(line);
- if (line.indexOf("Final") >= 0) {
- if (line.indexOf("MO") >= 0)
+ for (int i = 3; i < n; i++) {
+ while (i < n && ((line = list.get(i)).length() < 2
+ || line.charAt(1) != 'V'))
+ i++;
+ if (i == n)
break;
- if (line.indexOf("Final Beta") >= 0) {
- isBeta = true;
- }
- readLine();
- continue;
- }
- if (line.charAt(1) != 'V')
- break;
- line = line.replace('=', ' ');
- // Vector 9 Occ=2.000000D+00 E=-1.152419D+00 Symmetry=a1
- String[] tokens = getTokens();
- int iMo = parseIntStr(tokens[1]);
- float occupancy = parseFloatStr(tokens[3]);
- float energy = parseFloatStr(tokens[5]);
- String symmetry = (tokens.length > 7 ? tokens[7] : null);
- Map<String, Object> mo = new Hashtable<String, Object>();
- mo.put("occupancy", Float.valueOf(occupancy));
- mo.put("energy", Float.valueOf(energy));
- if (symmetry != null)
- mo.put("symmetry", symmetry);
- float[] coefs = null;
- if (readROHFonly) {
+ line = line.replace('=', ' ');
+ // Vector 9 Occ=2.000000D+00 E=-1.152419D+00 Symmetry=a1
+ String[] tokens = getTokens();
+ float occupancy = parseFloatStr(tokens[3]);
+ float energy = parseFloatStr(tokens[5]);
+ String symmetry = (tokens.length > 7 ? tokens[7] : null);
+ Map<String, Object> mo = new Hashtable<String, Object>();
+ mo.put("occupancy", Float.valueOf(occupancy));
+ mo.put("energy", Float.valueOf(energy));
+ if (symmetry != null)
+ mo.put("symmetry", symmetry);
+ float[] coefs = null;
setMO(mo);
- mo.put("type", "ROHF " + (++moCount));
+ mo.put("type", alphaBeta + (++moCount));
coefs = new float[nBasisFunctions];
mo.put("coefficients", coefs);
- } else {
- moInfo.put(Integer.valueOf(isBeta ? -iMo : iMo), mo);
- }
-
- readLines(3);
- // 68 2.509000 5 C py 39 -2.096777 3 C
pz
- while (readLine() != null && line.length() > 3) {
- if (readROHFonly) {
+ i += 3;
+ // 68 2.509000 5 C py 39 -2.096777 3 C
pz
+ while ((line = list.get(++i)) != null && line.length() > 3) {
tokens = getTokens();
coefs[parseIntStr(tokens[0]) - 1] = parseFloatStr(tokens[1]);
int pt = tokens.length / 2;
@@ -872,12 +867,14 @@
}
}
energyUnits = "a.u.";
- if (readROHFonly)
- setMOData(false);
- return false;
+ setMOData(true);
+ shells = null;
+ htMOs.clear();
}
/*
+ *
+ * OLD format? I do not have any examples of these files.
Final MO vectors
----------------
@@ -896,75 +893,75 @@
1 -0.00000 -0.00000 0.02285 -0.00000 -0.00000 0.00000
*/
- private boolean readMolecularOrbitalVectors() throws Exception {
+// private boolean readMolecularOrbitalVectors() throws Exception {
+//
+// if (shells == null)
+// return true;
+// Map<String, Object>[] mos = null;
+// JmolList<String>[] data = null;
+// int iListed = 0;
+// int ptOffset = -1;
+// int fieldSize = 0;
+// int nThisLine = 0;
+// readLines(5);
+// boolean isBeta = false;
+// boolean betaOnly = !filterMO();
+// while (readLine() != null) {
+// if (parseIntStr(line) != iListed + 1) {
+// if (line.indexOf("beta") < 0)
+// break;
+// alphaBeta = "beta ";
+// if (!filterMO())
+// break;
+// isBeta = true;
+// iListed = 0;
+// readLine();
+// continue;
+// }
+//
+// readLine();
+// String[] tokens = getTokens();
+// if (Logger.debugging) {
+// Logger.debug(tokens.length + " --- " + line);
+// }
+// nThisLine = tokens.length;
+// ptOffset = 6;
+// fieldSize = 12;
+// mos = ArrayUtil.createArrayOfHashtable(nThisLine);
+// data = ArrayUtil.createArrayOfArrayList(nThisLine);
+// for (int i = 0; i < nThisLine; i++) {
+// mos[i] = new Hashtable<String, Object>();
+// data[i] = new JmolList<String>();
+// }
+//
+// while (readLine() != null && line.length() > 0)
+// for (int i = 0, pt = ptOffset; i < nThisLine; i++, pt += fieldSize)
+// data[i].addLast(line.substring(pt, pt + fieldSize).trim());
+//
+// for (int iMo = 0; iMo < nThisLine; iMo++) {
+// float[] coefs = new float[data[iMo].size()];
+// int iCoeff = 0;
+// while (iCoeff < coefs.length) {
+// coefs[iCoeff] = parseFloatStr(data[iMo].get(iCoeff));
+// iCoeff++;
+// }
+// mos[iMo].put("coefficients", coefs);
+// mos[iMo].put("type", alphaBeta + " " + (++iListed));
+// ++moCount;
+// Map<String, Object> mo = (moInfo == null ? null : moInfo.get(Integer
+// .valueOf(isBeta ? -iListed : iListed)));
+// if (mo != null)
+// mos[iMo].putAll(mo);
+// if (!betaOnly || isBeta)
+// setMO(mos[iMo]);
+// }
+// line = "";
+// }
+// energyUnits = "a.u.";
+// setMOData(false);
+// return true;
+// }
- if (shells == null)
- return true;
- Map<String, Object>[] mos = null;
- JmolList<String>[] data = null;
- int iListed = 0;
- int ptOffset = -1;
- int fieldSize = 0;
- int nThisLine = 0;
- readLines(5);
- boolean isBeta = false;
- boolean betaOnly = !filterMO();
- while (readLine() != null) {
- if (parseIntStr(line) != iListed + 1) {
- if (line.indexOf("beta") < 0)
- break;
- alphaBeta = "beta ";
- if (!filterMO())
- break;
- isBeta = true;
- iListed = 0;
- readLine();
- continue;
- }
-
- readLine();
- String[] tokens = getTokens();
- if (Logger.debugging) {
- Logger.debug(tokens.length + " --- " + line);
- }
- nThisLine = tokens.length;
- ptOffset = 6;
- fieldSize = 12;
- mos = ArrayUtil.createArrayOfHashtable(nThisLine);
- data = ArrayUtil.createArrayOfArrayList(nThisLine);
- for (int i = 0; i < nThisLine; i++) {
- mos[i] = new Hashtable<String, Object>();
- data[i] = new JmolList<String>();
- }
-
- while (readLine() != null && line.length() > 0)
- for (int i = 0, pt = ptOffset; i < nThisLine; i++, pt += fieldSize)
- data[i].addLast(line.substring(pt, pt + fieldSize).trim());
-
- for (int iMo = 0; iMo < nThisLine; iMo++) {
- float[] coefs = new float[data[iMo].size()];
- int iCoeff = 0;
- while (iCoeff < coefs.length) {
- coefs[iCoeff] = parseFloatStr(data[iMo].get(iCoeff));
- iCoeff++;
- }
- mos[iMo].put("coefficients", coefs);
- mos[iMo].put("type", alphaBeta + " " + (++iListed));
- ++moCount;
- Map<String, Object> mo = (moInfo == null ? null : moInfo.get(Integer
- .valueOf(isBeta ? -iListed : iListed)));
- if (mo != null)
- mos[iMo].putAll(mo);
- if (!betaOnly || isBeta)
- setMO(mos[iMo]);
- }
- line = "";
- }
- energyUnits = "a.u.";
- setMOData(false);
- return true;
- }
-
/*
------------------------------------------------------------
EAF file 0: "./CeO2-ECP-RHF.aoints.0" size=19922944 bytes
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