--- trunk/OOPSE-2.0/src/brains/Thermo.hpp	2004/09/24 16:27:58	1492
+++ trunk/OOPSE-2.0/src/brains/Thermo.hpp	2005/01/12 22:41:40	1930
@@ -1,48 +1,77 @@
-#ifndef __THERMO_H__
-#define __THERMO_H__
+ /*
+ * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
+ *
+ * The University of Notre Dame grants you ("Licensee") a
+ * non-exclusive, royalty free, license to use, modify and
+ * 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
+ *    notice, this list of conditions and the following disclaimer.
+ *
+ * 3. 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.
+ *
+ * This software is provided "AS IS," without a warranty of any
+ * kind. All express or implied conditions, representations and
+ * warranties, including any implied warranty of merchantability,
+ * fitness for a particular purpose or non-infringement, are hereby
+ * excluded.  The University of Notre Dame and its licensors shall not
+ * be liable for any damages suffered by licensee as a result of
+ * using, modifying or distributing the software or its
+ * derivatives. In no event will the University of Notre Dame or its
+ * licensors be liable for any lost revenue, profit or data, or for
+ * direct, indirect, special, consequential, incidental or punitive
+ * damages, however caused and regardless of the theory of liability,
+ * 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.
+ */
+ 
+#ifndef BRAINS_THERMO_HPP
+#define BRAINS_THERMO_HPP
 
 #include "primitives/Atom.hpp"
-#include "primitives/SRI.hpp"
 #include "brains/SimInfo.hpp"
 #include "math/randomSPRNG.hpp"
 
+namespace oopse {
+
 class Thermo{
 
-public:
-  
-  Thermo( SimInfo* the_info );
-  ~Thermo();
+    public:
 
-  // note: all the following energies are in kcal/mol
+        Thermo( SimInfo* info) : info_(info) {}
 
-  double getKinetic(); // the total kinetic energy 
-  double getPotential(); // the total potential energy
-  double getTotalE(); // gets the total energy
+        // note: all the following energies are in kcal/mol
 
-  double getTemperature(); // gives the instant temp. in K
+        double getKinetic(); // the total kinetic energy 
+        double getPotential(); // the total potential energy
+        double getTotalE(); // gets the total energy
 
-  double getPressure(); // gives the instant pressure in atm;
-  double getPressureX(); // gives the instant pressure in atm;
-  double getPressureY(); // gives the instant pressure in atm;
-  double getPressureZ(); // gives the instant pressure in atm;
+        double getTemperature(); // gives the instant temp. in K
 
-  void   getPressureTensor(double press[3][3]); // gives the pressure 
-                                                // tensor in 
-                                                // amu*fs^-2*Ang^-1
-  double getVolume();   // gives the volume in Ang^3 
+        double getPressure(); // gives the instant pressure in atm;
 
-  int getNDF();    // get the number of degrees of freedom in the system
-  int getNDFraw(); // get the number of raw degrees of freedom in the system
-                   // i.e. don't subtract constraints or system COM.
-  
-  void velocitize(); // set the temperature to the target temp in SimInfo
-                     // NOTE: srand48 should be seeded before calling.
-  void getCOMVel(double vdrift[3]);
-  void getCOM(double COM[3]);
-  void removeCOMdrift();
+        Mat3x3d getPressureTensor(); // gives the pressure  tensor in amu*fs^-2*Ang^-1
+        double getVolume();   // gives the volume in Ang^3 
 
-private:
-  SimInfo* info;
-  gaussianSPRNG *gaussStream;
+        void saveStat();
+        
+    private:
+        SimInfo* info_;
 };
+
+} //end namespace oopse
 #endif