applications/sequentialProps/DensityAnalyzer.cpp

/*
 * 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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 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.
 *
 * 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.
 *
 * 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, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#include <algorithm>
#include <functional>
#include "applications/sequentialProps/DensityAnalyzer.hpp"
#include "utils/simError.h"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/NumericConstant.hpp"
namespace OpenMD {

  DensityAnalyzer::DensityAnalyzer(SimInfo* info, const std::string& filename, 
                                   const std::string& sele)
    : SequentialAnalyzer(info, filename), selectionScript_(sele), 
      evaluator_(info), seleMan_(info)   {
    
    setOutputName(getPrefix(filename) + ".dens");
    
    evaluator_.loadScriptString(sele);
    
    if (!evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.evaluate());
    }            
  }

  void DensityAnalyzer::doFrame() {
    Molecule* mol;
    RigidBody* rb;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;
    
    if (evaluator_.isDynamic()) {
        seleMan_.setSelectionSet(evaluator_.evaluate());
    }
        
    unsigned int count = seleMan_.getSelectionCount();
    
    values_.push_back( count );
  }
}


Revision:	2024
Committed:	Thu Oct 16 19:13:51 2014 UTC (10 years, 6 months ago) by gezelter
File size:	3254 byte(s)
Log Message:	Added Radial and Z-projected velocity autocorrelation functions Started to add SequentialProps program Mucking about with angular restraint potentials
#	User	Rev	Content
1	gezelter	2024	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Redistributions of source code must retain the above copyright
10			* notice, this list of conditions and the following disclaimer.
11			*
12			* 2. Redistributions in binary form must reproduce the above copyright
13			* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31			*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39			* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41			*/
42
43			#include <algorithm>
44			#include <functional>
45			#include "applications/sequentialProps/DensityAnalyzer.hpp"
46			#include "utils/simError.h"
47			#include "io/DumpReader.hpp"
48			#include "primitives/Molecule.hpp"
49			#include "utils/NumericConstant.hpp"
50			namespace OpenMD {
51
52			DensityAnalyzer::DensityAnalyzer(SimInfo* info, const std::string& filename,
53			const std::string& sele)
54			: SequentialAnalyzer(info, filename), selectionScript_(sele),
55			evaluator_(info), seleMan_(info) {
56
57			setOutputName(getPrefix(filename) + ".dens");
58
59			evaluator_.loadScriptString(sele);
60
61			if (!evaluator_.isDynamic()) {
62			seleMan_.setSelectionSet(evaluator_.evaluate());
63			}
64			}
65
66			void DensityAnalyzer::doFrame() {
67			Molecule* mol;
68			RigidBody* rb;
69			SimInfo::MoleculeIterator mi;
70			Molecule::RigidBodyIterator rbIter;
71
72			if (evaluator_.isDynamic()) {
73			seleMan_.setSelectionSet(evaluator_.evaluate());
74			}
75
76			unsigned int count = seleMan_.getSelectionCount();
77
78			values_.push_back( count );
79			}
80			}
81
82