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
#	Content
1	/*
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