Merge pull request #2 from zfalls/release9

r9

Author: zfalls

AUTHORS

@@ -0,0 +1,33 @@
+* Enhancements / New features:
+** Added support for the LSF and LoadLeveler queuing systems.
+** Added support for the SIESTA program package.
+** Incorporated the XtalComp library for duplicate structure removal (niching).
+** Added the "mitosis" function, which increases the local order of structures in the initial generation by replicating a unit cell to create a supercell for constructing the starting structure.
+** Customizable polling interval for updating remote queue information.
+** Automatic removal of remote working files (optional).
+** Optional removal of unnecessary files for VASP calculations.
+** Option to rank all current structures and export structures to a new subdirectory as .cml, CONTCAR, or .got.
+** New option to replace a failing structure with a new offspring.
+** Ability to “inject” (seed) a structure mid-run.
+** Minimum atomic separation now specified as a fraction of the sum of atomic radii, with a hard minimum.
+** Set a final number of structures to be generated before termination of the search.
+** Changing the minimum and maximum cell vectors now directly influences the minimum and maximum volume for the cell.
+
+* Bug fixes:
+** Numerous misc bug-fixes.
+
+* Documentation:
+** New program website
+   - http://xtalopt.github.io/
+** New landing page for user tutorials
+   - http://xtalopt.github.io/tut.html
+** New landing page for user docs
+   - http://xtalopt.github.io/api/html/annotated.html
+
+* Maintenance:
+** More server-friendly method of fetching queue data.
+** Support for GULP shell/core calculations added.
+** Submission of remote calculations is throttled to ease DRMS load.
+** Fix compilation against Qt 4.6.3 and 4.8.0.
+** Bundled libssh library removed, now an optional dependency.
+** Added option to use command-line ssh/scp interfaces when libssh is unavailable or Kerberos authentication is needed.

ChangeLogs/ChangeLog.r9

@@ -1,4 +1,4 @@
-XtalOpt
+XtalOpt - r9
 =========
 
 XtalOpt searches for the global minimum of a crystal structure's
@@ -20,3 +20,22 @@ http://xtalopt.github.io/tut.html
 #License
 
 GPL v2 or later. See COPYING.
+
+#Authors
+
+All contributors, in alphabetical order:
+
+- Patrick Avery <[email protected]>
+- Zackary Falls <[email protected]>
+- David Lonie <[email protected]>
+
+
+=========
+Included sources from various projects are found under:
+
+- src/spglib   http://spglib.sourceforge.net/
+- src/libssh   http://www.libssh.org/
+
+These files, other than some minor modifications for interoperability
+with XtalOpt/libglobalsearch, are the works of the copyright holders
+specified in the source files.

INSTALL

@@ -79,7 +79,7 @@ bool SSHConnectionLibSSH::isConnected()
 
   // Set a three timeout, check every 50 ms for new data.
   int bytesAvail;
-  int timeout = 3000;
+  int timeout = 15000;
   do {
     // Poll for number of bytes available
     bytesAvail = channel_poll(m_shell, 0);
@@ -117,7 +117,7 @@ bool SSHConnectionLibSSH::isConnected()
                              0)) > 0) {
     ossout.write(buffer,len);
     // Poll for number of bytes available using a 1 second timeout in case the stack is full.
-    timeout = 1000;
+    timeout = 10000;
     do {
       bytesAvail = channel_poll(m_shell, 0);
       if (bytesAvail == SSH_ERROR) {
@@ -155,7 +155,7 @@ bool SSHConnectionLibSSH::isConnected()
   int exitcode;
   // Set a timeout of 1 seconds and check every 50 ms. It takes execute a litte
   // bit of time to work, so 1 second will end up being a few seconds...
-  int timeout = 1000;
+  int timeout = 10000;
   bool success;
   bool printWarning = false;
   do {
@@ -225,7 +225,7 @@ bool SSHConnectionLibSSH::connectSession(bool throwExceptions)
   int verbosity = SSH_LOG_NOLOG;
   //int verbosity = SSH_LOG_PROTOCOL;
   //int verbosity = SSH_LOG_PACKET;
-  int timeout = 5; // timeout in sec
+  int timeout = 15; // timeout in sec
 
   ssh_options_set(m_session, SSH_OPTIONS_HOST, m_host.toStdString().c_str());
   ssh_options_set(m_session, SSH_OPTIONS_LOG_VERBOSITY, &verbosity);
@@ -448,7 +448,7 @@ bool SSHConnectionLibSSH::_execute(const QString &command,
   channel_close(channel);
 
   // 5 second timeout
-  int timeout = 5;
+  int timeout = 15;
   while (channel_get_exit_status(channel) == -1 && timeout >= 0) {
     qDebug() << "Waiting for server to close channel...";
     GS_SLEEP(1);
@@ -1060,7 +1060,7 @@ bool SSHConnectionLibSSH::addKeyToKnownHosts(const QString &host, unsigned int p
 
   // Set options
   int verbosity = SSH_LOG_NOLOG;
-  int timeout = 5; // timeout in sec
+  int timeout = 15; // timeout in sec
 
   ssh_options_set(session, SSH_OPTIONS_HOST, host.toStdString().c_str());
   ssh_options_set(session, SSH_OPTIONS_LOG_VERBOSITY, &verbosity);

README.md

@@ -695,7 +695,7 @@ namespace XtalOpt {
               .arg(locpath_s));
       }
     }
-    xtal->moveToThread(m_tracker->thread());
+//    xtal->moveToThread(m_tracker->thread());
     xtal->setupConnections();
     xtal->setFileName(locpath_s);
     xtal->setRempath(rempath_s);