Revision: 20616
http://sourceforge.net/p/jmol/code/20616
Author: hansonr
Date: 2015-07-02 17:18:02 +0000 (Thu, 02 Jul 2015)
Log Message:
-----------
load NBO CH3CH3 working, but still have a run-away NBOServe.exe
Modified Paths:
--------------
branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialog.java
branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialogConfig.java
branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialogRun.java
branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialogSearch.java
branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBOService.java
Modified: branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialog.java
===================================================================
--- branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialog.java
2015-07-01 19:31:54 UTC (rev 20615)
+++ branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialog.java
2015-07-02 17:18:02 UTC (rev 20616)
@@ -104,13 +104,8 @@
modules.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
- if (nboService != null) {
- nboService.closeProcess();
- nboService.startProcess(false);
- while (!nboService.restartIfNecessary()) {
- // continue forever?
- }
- }
+ if (nboService != null)
+ nboService.restart();
switch (modules.getSelectedIndex()) {
case 0:
openPanel('m');
Modified:
branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialogConfig.java
===================================================================
--- branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialogConfig.java
2015-07-01 19:31:54 UTC (rev 20615)
+++ branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialogConfig.java
2015-07-02 17:18:02 UTC (rev 20616)
@@ -235,9 +235,8 @@
}
protected void connectPressed() {
- nboService.closeProcess();
+ String err = nboService.restart();
nboReport(null);
- String err = nboService.startProcess(false);
if (err == null) {
nboReport("NBOServe successfully connected");
} else {
@@ -372,11 +371,6 @@
sb.append(s);
}
- String getFileData(String fileName) {
- return vwr.getFileAsString4(fileName, Integer.MAX_VALUE,
- false, false, false, "nbo");
- }
-
protected JTextField tfFolder, tfName, tfExt;
protected int jmolAtomCount;
protected File inputFile;
Modified: branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialogRun.java
===================================================================
--- branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialogRun.java
2015-07-01 19:31:54 UTC (rev 20615)
+++ branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialogRun.java
2015-07-02 17:18:02 UTC (rev 20616)
@@ -175,7 +175,7 @@
protected void getParams(File inputFile) {
newParams = params = "";
- String data = getFileData(inputFile.toString());
+ String data = nboService.getFileData(inputFile.toString());
int n = data.length();
String sep = (data.indexOf("\r") >= 0 ? "\n\r" : "\n");
String[] tokens = PT.split(data, "$END");
Modified:
branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialogSearch.java
===================================================================
--- branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialogSearch.java
2015-07-01 19:31:54 UTC (rev 20615)
+++ branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBODialogSearch.java
2015-07-02 17:18:02 UTC (rev 20616)
@@ -925,11 +925,7 @@
private void done() {
try {
labelAt();
- nboService.closeProcess();
- nboService.startProcess(false);
- while (!nboService.restartIfNecessary()) {
- // continue forever?
- }
+ nboService.restart();
rawCmd("");
} catch (Exception e) {
e.printStackTrace();
Modified: branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBOService.java
===================================================================
--- branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBOService.java
2015-07-01 19:31:54 UTC (rev 20615)
+++ branches/nbo/Jmol/src/org/openscience/jmol/app/nbo/NBOService.java
2015-07-02 17:18:02 UTC (rev 20616)
@@ -46,9 +46,90 @@
*
* TODO: figure out how to manage time-consuming asynchronous requests
*
+ *
*/
public class NBOService {
+ /// BH: observations:
+ //
+ // 1) NBOServe creates jmol_infile.txt, jmol_molfile.txt, and
jmol_outfile.txt.
+ //
+ // 2) Of these three, jmol_outfile is locked for writing during NBOServe
sessions
+ // and stays locked until the program finishes.
+ //
+ //
+ // 3) When View starts up, a new jmol_outfile is created, and it can be
deleted.
+ //
+ // 4) The process of View...Browse... leads to the following:
+ //
+ // 07/02/2015 09:04 AM 20 jmol_infile.txt
+ // 07/02/2015 09:04 AM 429 jmol_outfile.txt
+ // 07/02/2015 09:05 AM 95 v_test1435845900375.txt
+ // 07/02/2015 09:05 AM 11 fort.106
+ // 07/02/2015 09:05 AM 0 v_test1435845900375.txtDONE
+ //
+ // v_test... is
+ //
+ // GLOBAL C_PATH C:\temp
+ // GLOBAL I_KEYWORD 6
+ // GLOBAL C_JOBSTEM ch3nh2
+ // GLOBAL I_BAS_1 6
+ // CMD LABEL
+ //
+ // jmol_infile.txt is:
+ //
+ // 1 1 2
+ //
+ // jmol_outfile.txt is:
+
+ // DATA " "
+ // 1 1 2
+ // NBOServe: NATURAL BOND ORBITAL PROGRAM SUITE
+ // _______________________________________________
+ // (1) NBOModel:
+ // Create & edit molecular model and input files
+ // (2) NBORun:
+ // Launch NBO analysis for chosen archive (.47) file
+ // (3) NBOView:
+ // Display NBO orbitals in 1D/2D/3D imagery
+ // (4) NBOSearch:
+ // Search NBO output interactively
+ // Your choice (1-4), (H)elp, e(X)it, or (D)ir reset?
+ // END ""
+ //
+ // fort.106 is
+ //
+ // END ""
+ //
+ // note that the actual label information came back only over sysout.
+ //
+ // requesting a 3D view (raytrace) produces the following files:
+ //
+ // 07/02/2015 09:13 AM 97 v_test1435846433040.txt
+ // 07/02/2015 09:13 AM 0 v_test1435846433040.txtDONE
+ // 07/02/2015 09:14 AM 59 v_test1435846446147.txt
+ // 07/02/2015 09:14 AM 480,029 ch3nh2.bmp (in c:\temp)
+ // 07/02/2015 09:14 AM 0 v_test1435846446147.txtDONE
+ // 07/02/2015 09:14 AM 2 jmol_outfile.txt
+ // 07/02/2015 09:14 AM 121 jmol_molfile.txt
+ // 07/02/2015 09:14 AM 5,552 raytrace.rt
+
+ // the first v_test is:
+ //
+ // GLOBAL C_PATH C:\temp
+ // GLOBAL C_JOBSTEM ch3nh2
+ // GLOBAL I_BAS_1 6
+ // GLOBAL SIGN +1
+ // CMD PROFILE 10
+ //
+ // and the second is:
+ //
+ // GLOBAL C_PATH C:\temp
+ // GLOBAL C_JOBSTEM ch3nh2
+ // CMD VIEW 1
+
+
+
// modes of operation
// NOTE: There was a problem in that View and Raw were both 4 here
@@ -81,6 +162,7 @@
private boolean inData;
protected boolean inRequest, isWorking;
String serverPath;
+ String serverDir;
String workingPath;
private boolean nboSync;
@@ -110,6 +192,7 @@
*/
private void setServerPath(String path) {
serverPath = path;
+ serverDir = new File(serverPath).getParent() + "/";
}
/**
@@ -152,8 +235,6 @@
serverMode = MODE_ERR;
}
String nboAction = (String) info.get("action");
- if (nboAction == null)
- System.out.println("HOH");
String s;
switch (serverMode) {
case MODE_MODEL:
@@ -176,13 +257,13 @@
break;
}
if (s != null) {
+ if (nboSync) {
+ clearServerFile("fort.106");
+ clearServerFile("jmol_molfile.txt");
+ }
sendToNBO(serverMode, s);
if (nboSync) {
- try {
- nboServer.waitFor();
- } catch (InterruptedException e) {
- return false;
- }
+ waitFor(serverMode);
}
ok = true;
}
@@ -193,12 +274,54 @@
return ok;
}
+ private boolean waitFor(int mode) {
+ String fname = serverDir + (mode == MODE_MODEL ? "jmol_molfile.txt" :
"fort.106");
+ File f = new File(fname);
+ for (int i = 0; i < 200; i++) { // 2 seconds allowed
+ if (f.exists()) {
+ switch (mode) {
+ case MODE_MODEL:
+ String dataCmd = fixNBOModel(getFileData(fname));
+ Logger.info(dataCmd);
+ sbRet.append(dataCmd + ";rotate best;");
+ break;
+ case MODE_RAW:
+ // sbRet already created?
+ break;
+ }
+ break;
+ }
+ try {
+ Thread.sleep(10);
+ } catch (InterruptedException e) {
+ return false;
+ }
+ }
+ return true;
+// try {
+// nboServer.waitFor();
+// return true;
+// } catch (InterruptedException e) {
+// return false;
+// }
+ }
+
+ private boolean clearServerFile(String fname) {
+ File f = new File(serverDir + fname);
+ try {
+ f.delete();
+ } catch (Exception e) {
+ return false;
+ }
+ return true;
+ }
+
/**
* @param mode
* @param s
*/
private void sendToNBO(int mode, String s) {
- s = (mode == MODE_RAW ? s : mode + "\r\n" + s + "\r\n"
+ s = (mode == MODE_RAW ? s : "\r\n" + mode + "\r\n" + s + "\r\nexit\r\n"
+ (nboSync ? "x\r\n" : ""));
sendCmd(s);
}
@@ -222,8 +345,7 @@
} else if (line.startsWith("DATA ")) {
if (line.startsWith("DATA \"model")) {
sbRet.setLength(0);
- nboModel = PT.getQuotedStringAt(line, 0);
- line += " NBO " + nboModel;
+ line = fixNBOModel(line);
}
inData = (line.indexOf("exit") < 0);
if (inData)
@@ -251,6 +373,19 @@
nboDialog.nboReport(line);
}
+ /**
+ * fixes DATA line to include a title
+ *
+ * @param line
+ * @return line or full data block
+ */
+ private String fixNBOModel(String line) {
+ nboModel = PT.getQuotedStringAt(line, 0);
+ String s = " NBO " + nboModel;
+ int pt = line.indexOf("\n");
+ return (pt < 0 ? line + s : line.substring(0, pt) + s +
line.substring(pt));
+ }
+
String startProcess(boolean sync) {
try {
System.out.println("starting NBO process sync=" + sync);
@@ -372,6 +507,12 @@
nboServer = null;
}
+ String restart() {
+ closeProcess();
+ return startProcess(false);
+ }
+
+
public boolean restartIfNecessary() {
if (nboServer == null)
startProcess(false);
@@ -383,7 +524,7 @@
vwr.script(script);
}
- private Object lock = "";
+ private Object lock = "jmol_lock";
synchronized String runScriptNow(String script) {
synchronized (lock) {
@@ -410,9 +551,16 @@
}
}
- private Object nbo = "";
+ private Object nbo = "nbo_lock";
+ /**
+ * The interface for ALL communication with NBOServe from NBODialog.
+ *
+ * @param cmd
+ * @param data
+ * @param doWait
+ */
protected void rawCmdNew(String cmd, SB data, boolean doWait) {
synchronized (nbo) {
String fname = null;
@@ -422,7 +570,7 @@
Logger.info("issuing\n" + cmd);
} else {
fname = cmd + "_test" + System.currentTimeMillis() + ".txt";
- cmdFile = new File(new File(serverPath).getParent() + "/" + fname);
+ cmdFile = new File(serverDir + fname);
Logger.info("issuing " + fname + "\n" + data);
writeToFile(data.toString(), cmdFile);
cmd = "<" + fname + ">";
@@ -445,7 +593,7 @@
}
}
if (cmdFile != null) {
- cmdFile = new File(new File(serverPath).getParent() + "/" + fname +
"DONE");
+ cmdFile = new File(serverDir + fname + "DONE");
writeToFile("", cmdFile);
}
@@ -466,5 +614,10 @@
Logger.info(s.length() + " bytes written to " + file);
}
+ String getFileData(String fileName) {
+ return vwr.getFileAsString4(fileName, Integer.MAX_VALUE,
+ false, false, false, "nbo");
+ }
+
}
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