applications/sequentialProps/SequentialAnalyzer.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/SequentialAnalyzer.hpp"
#include "utils/simError.h"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "utils/NumericConstant.hpp"
namespace OpenMD {

  void SequentialAnalyzer::doSequence() {

    preSequence();

    Molecule* mol;
    RigidBody* rb;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;
    
    DumpReader reader(info_, dumpFilename_); 
    int nFrames = reader.getNFrames();
  
    storageLayout_ = info_->getStorageLayout();

    for (int i = 0; i < nFrames; i += step_) {
      reader.readFrame(i);
      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
      times_.push_back( currentSnapshot_->getTime() );
      
      if (storageLayout_ & DataStorage::dslPosition) {
        for (mol = info_->beginMolecule(mi); mol != NULL; 
             mol = info_->nextMolecule(mi)) {
          
          //change the positions of atoms which belong to the rigidbodies
          for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
               rb = mol->nextRigidBody(rbIter)) {
            rb->updateAtoms();
          }
        }        
      }
      
      if (storageLayout_ & DataStorage::dslVelocity) {
        for (mol = info_->beginMolecule(mi); mol != NULL; 
             mol = info_->nextMolecule(mi)) {
          
          //change the positions of atoms which belong to the rigidbodies
          for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
             rb = mol->nextRigidBody(rbIter)) {
            rb->updateAtomVel();
          }
        }      
      }    
            
      doFrame();
    }   

    postSequence();
    writeSequence();   
  }
  
  void SequentialAnalyzer::writeSequence() {
    std::ofstream ofs(outputFilename_.c_str(), std::ios::binary);

    if (ofs.is_open()) {

      ofs << "#" << getSequenceType() << "\n";
      ofs << "#extra information: " << extra_ << "\n";
      ofs << "#time\tvalue\n";

      for (unsigned int i = 0; i < times_.size(); ++i) {
        ofs << times_[i] << "\t" << values_[i] << "\n";
      }
      
    } else {
      sprintf(painCave.errMsg,
              "SequentialAnalyzer::writeCorrelate Error: fail to open %s\n", 
              outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();        
    }
    
    ofs.close();    
  }

}


Revision:	2024
Committed:	Thu Oct 16 19:13:51 2014 UTC (10 years, 6 months ago) by gezelter
File size:	4576 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/SequentialAnalyzer.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			void SequentialAnalyzer::doSequence() {
53
54			preSequence();
55
56			Molecule* mol;
57			RigidBody* rb;
58			SimInfo::MoleculeIterator mi;
59			Molecule::RigidBodyIterator rbIter;
60
61			DumpReader reader(info_, dumpFilename_);
62			int nFrames = reader.getNFrames();
63
64			storageLayout_ = info_->getStorageLayout();
65
66			for (int i = 0; i < nFrames; i += step_) {
67			reader.readFrame(i);
68			currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
69			times_.push_back( currentSnapshot_->getTime() );
70
71			if (storageLayout_ & DataStorage::dslPosition) {
72			for (mol = info_->beginMolecule(mi); mol != NULL;
73			mol = info_->nextMolecule(mi)) {
74
75			//change the positions of atoms which belong to the rigidbodies
76			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
77			rb = mol->nextRigidBody(rbIter)) {
78			rb->updateAtoms();
79			}
80			}
81			}
82
83			if (storageLayout_ & DataStorage::dslVelocity) {
84			for (mol = info_->beginMolecule(mi); mol != NULL;
85			mol = info_->nextMolecule(mi)) {
86
87			//change the positions of atoms which belong to the rigidbodies
88			for (rb = mol->beginRigidBody(rbIter); rb != NULL;
89			rb = mol->nextRigidBody(rbIter)) {
90			rb->updateAtomVel();
91			}
92			}
93			}
94
95			doFrame();
96			}
97
98			postSequence();
99			writeSequence();
100			}
101
102			void SequentialAnalyzer::writeSequence() {
103			std::ofstream ofs(outputFilename_.c_str(), std::ios::binary);
104
105			if (ofs.is_open()) {
106
107			ofs << "#" << getSequenceType() << "\n";
108			ofs << "#extra information: " << extra_ << "\n";
109			ofs << "#time\tvalue\n";
110
111			for (unsigned int i = 0; i < times_.size(); ++i) {
112			ofs << times_[i] << "\t" << values_[i] << "\n";
113			}
114
115			} else {
116			sprintf(painCave.errMsg,
117			"SequentialAnalyzer::writeCorrelate Error: fail to open %s\n",
118			outputFilename_.c_str());
119			painCave.isFatal = 1;
120			simError();
121			}
122
123			ofs.close();
124			}
125
126			}
127
128