--- trunk/src/minimizers/MinimizerParameterSet.cpp	2005/01/12 22:41:40	246
+++ branches/heatflux/src/minimizers/MinimizerParameterSet.cpp	2012/01/27 19:07:19	1670
@@ -1,4 +1,4 @@
- /*
+/*
  * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
  *
  * The University of Notre Dame grants you ("Licensee") a
@@ -6,19 +6,10 @@
  * redistribute this software in source and binary code form, provided
  * that the following conditions are met:
  *
- * 1. Acknowledgement of the program authors must be made in any
- *    publication of scientific results based in part on use of the
- *    program.  An acceptable form of acknowledgement is citation of
- *    the article in which the program was described (Matthew
- *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
- *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
- *    Parallel Simulation Engine for Molecular Dynamics,"
- *    J. Comput. Chem. 26, pp. 252-271 (2005))
- *
- * 2. Redistributions of source code must retain the above copyright
+ * 1. Redistributions of source code must retain the above copyright
  *    notice, this list of conditions and the following disclaimer.
  *
- * 3. Redistributions in binary form must reproduce the above copyright
+ * 2. Redistributions in binary form must reproduce the above copyright
  *    notice, this list of conditions and the following disclaimer in the
  *    documentation and/or other materials provided with the
  *    distribution.
@@ -37,61 +28,70 @@
  * arising out of the use of or inability to use software, even if the
  * University of Notre Dame has been advised of the possibility of
  * such damages.
+ *
+ * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
+ * research, please cite the appropriate papers when you publish your
+ * work.  Good starting points are:
+ *                                                                      
+ * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
+ * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
+ * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
+ * [4]  Vardeman & Gezelter, in progress (2009).                        
  */
  
 #include "minimizers/MinimizerParameterSet.hpp"
 
-namespace oopse {
+namespace OpenMD {
 
-MinimizerParameterSet::MinimizerParameterSet(SimInfo* info) : defaultTolerance(1.0e-8) {
+  MinimizerParameterSet::MinimizerParameterSet(SimInfo* info) : defaultTolerance(1.0e-8) {
     setDefaultParameter();
 
     Globals* globals = info->getSimParams();
 
     if (globals->haveMinimizer()){
-        setFTol(globals->getMinFTol());
+      setFTol(globals->getMinimizerFTol());
     }
 
-    if (globals->haveMinGTol()){
-        setGTol(globals->getMinGTol());
+    if (globals->haveMinimizerGTol()){
+      setGTol(globals->getMinimizerGTol());
     }
 
-    if (globals->haveMinMaxIter()){
-        setMaxIteration(globals->getMinMaxIter());
+    if (globals->haveMinimizerMaxIter()){
+      setMaxIteration(globals->getMinimizerMaxIter());
     }
 
-    if (globals->haveMinWriteFrq()){
-        setMaxIteration(globals->getMinMaxIter());
+    if (globals->haveMinimizerWriteFreq()){
+      setMaxIteration(globals->getMinimizerMaxIter());
     }
 
-    if (globals->haveMinWriteFrq()){
-        setWriteFrq(globals->getMinWriteFrq());
+    if (globals->haveMinimizerWriteFreq()){
+      setWriteFreq(globals->getMinimizerWriteFreq());
     }
     
-    if (globals->haveMinStepSize()){
-        setStepSize(globals->getMinStepSize());
+    if (globals->haveMinimizerStepSize()){
+      setStepSize(globals->getMinimizerStepSize());
     }
 
-    if (globals->haveMinLSMaxIter()){
-        setLineSearchMaxIteration(globals->getMinLSMaxIter());
+    if (globals->haveMinimizerLSMaxIter()){
+      setLineSearchMaxIteration(globals->getMinimizerLSMaxIter());
     }    
 
-    if (globals->haveMinLSTol()){
-        setLineSearchTol(globals->getMinLSTol());
+    if (globals->haveMinimizerLSTol()){
+      setLineSearchTol(globals->getMinimizerLSTol());
     }
 
-}
+  }
 
-void MinimizerParameterSet::setDefaultParameter() {
+  void MinimizerParameterSet::setDefaultParameter() {
     maxIteration = 200;
     stepSize = 0.01;
     stepTol = defaultTolerance;
     fTol = defaultTolerance;
     gTol = defaultTolerance;
-    writeFrq = maxIteration;
+    writeFreq = maxIteration;
     lsMaxIteration = 50;
     lsTol = defaultTolerance;
-}
+  }