applications/dynamicProps/FreqFlucCorrFunc.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 "applications/dynamicProps/FreqFlucCorrFunc.hpp"
#include "primitives/Atom.hpp"
#include "types/MultipoleAdapter.hpp"
#include "utils/simError.h"

namespace OpenMD {
  FreqFlucCorrFunc::FreqFlucCorrFunc(SimInfo* info, const std::string& filename,
                                     const std::string& sele1, 
                                     const std::string& sele2, 
                                     long long int memSize)
    : ParticleTimeCorrFunc(info, filename, sele1, sele2,  
                           DataStorage::dslElectricField | 
                           DataStorage::dslAmat | DataStorage::dslDipole, 
                           memSize){
    
    setCorrFuncType("FreqFluc Correlation Function");
    setOutputName(getPrefix(dumpFilename_) + ".ffcorr");
    
  }

  RealType FreqFlucCorrFunc::calcCorrVal(int frame1, int frame2, 
                                         StuntDouble* sd1,  StuntDouble* sd2) {

    Vector3d e1;    
    Vector3d u1;
    Vector3d e2;    
    Vector3d u2;

    e1 = sd1->getElectricField(frame1);
    
    if (sd1->isRigidBody()) {
      u1 = sd1->getA(frame1).getRow(2);
    } else {
      AtomType* at = static_cast<Atom*>(sd1)->getAtomType();
      MultipoleAdapter ma = MultipoleAdapter(at);
      
      if (ma.isDipole()) {
        u1 = sd1->getDipole(frame1);
      }
    }

    e2 = sd2->getElectricField(frame2);
    
    if (sd2->isRigidBody()) {
      u2 = sd2->getA(frame2).getRow(2);
    } else {
      AtomType* at = static_cast<Atom*>(sd2)->getAtomType();
      MultipoleAdapter ma = MultipoleAdapter(at);
      
      if (ma.isDipole()) {
        u2 = sd2->getDipole(frame2);
      }
    }
    
    return (dot(u1, e1) - mean_) * (dot(u2, e2) - mean_);
  }


  void FreqFlucCorrFunc::validateSelection(const SelectionManager& seleMan) {
    StuntDouble* sd;
    int i;    
    for (sd = seleMan1_.beginSelected(i); sd != NULL; 
         sd = seleMan1_.nextSelected(i)) {

      if (!sd->isRigidBody()) {

        AtomType* at = static_cast<Atom*>(sd)->getAtomType();
        MultipoleAdapter ma = MultipoleAdapter(at);
        
        if (!ma.isDipole()) {
          sprintf(painCave.errMsg,
                  "FreqFlucCorrFunc::validateSelection Error: selection is not a RigidBody or does\n"
                  "\tnot have a dipole\n");
          painCave.isFatal = 1;
          simError();        
        }
      }
    }    
  }

  void FreqFlucCorrFunc::preCorrelate() {
    mean_ = 0.0;
    RealType sum(0.0);
    int count(0);
    StuntDouble* sd1;
    Vector3d e1;
    Vector3d u1;
    int ii;
    std::cerr << "preCorrelating to compute mean values\n";
    // dump files can be enormous, so read them in block-by-block:
    int nblocks = bsMan_->getNBlocks();
    bool firsttime = true;
    for (int i = 0; i < nblocks; ++i) {
      bsMan_->loadBlock(i);
      assert(bsMan_->isBlockActive(i));      
      SnapshotBlock block1 = bsMan_->getSnapshotBlock(i);
      for (int j = block1.first; j < block1.second; ++j) {

        // go snapshot-by-snapshot through this block:
        Snapshot* snap = bsMan_->getSnapshot(j);
        
        // update the positions and velocities of the atoms belonging
        // to rigid bodies:
        
        updateFrame(j);        
        for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL; sd1 = seleMan1_.nextSelected(ii)) {
          e1 = sd1->getElectricField(j);
          
          if (sd1->isRigidBody()) {
            u1 = sd1->getA(j).getRow(2);
          } else {
            AtomType* at = static_cast<Atom*>(sd1)->getAtomType();
            MultipoleAdapter ma = MultipoleAdapter(at);
            
            if (ma.isDipole()) {
              u1 = sd1->getDipole(j);
            }
          }

          RealType value = dot(u1, e1);

          sum += value;                         
          count++;
        }
      }
      bsMan_->unloadBlock(i);
    }

    mean_ = sum / RealType(count);
    std::cerr << "done with preCorrelation\n";
  }
}


Revision:	2004
Committed:	Tue Jun 3 16:51:43 2014 UTC (11 years, 2 months ago) by gezelter
File size:	6180 byte(s)
Log Message:	Added an unload block
#	User	Rev	Content
1	gezelter	2003	/*
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 "applications/dynamicProps/FreqFlucCorrFunc.hpp"
44			#include "primitives/Atom.hpp"
45			#include "types/MultipoleAdapter.hpp"
46			#include "utils/simError.h"
47
48			namespace OpenMD {
49	gezelter	2004	FreqFlucCorrFunc::FreqFlucCorrFunc(SimInfo* info, const std::string& filename,
50			const std::string& sele1,
51			const std::string& sele2,
52	gezelter	2003	long long int memSize)
53	gezelter	2004	: ParticleTimeCorrFunc(info, filename, sele1, sele2,
54			DataStorage::dslElectricField \|
55			DataStorage::dslAmat \| DataStorage::dslDipole,
56			memSize){
57	gezelter	2003
58			setCorrFuncType("FreqFluc Correlation Function");
59			setOutputName(getPrefix(dumpFilename_) + ".ffcorr");
60
61			}
62
63	gezelter	2004	RealType FreqFlucCorrFunc::calcCorrVal(int frame1, int frame2,
64			StuntDouble* sd1, StuntDouble* sd2) {
65	gezelter	2003
66			Vector3d e1;
67			Vector3d u1;
68			Vector3d e2;
69			Vector3d u2;
70
71			e1 = sd1->getElectricField(frame1);
72
73			if (sd1->isRigidBody()) {
74			u1 = sd1->getA(frame1).getRow(2);
75			} else {
76			AtomType* at = static_cast<Atom*>(sd1)->getAtomType();
77			MultipoleAdapter ma = MultipoleAdapter(at);
78
79			if (ma.isDipole()) {
80			u1 = sd1->getDipole(frame1);
81			}
82			}
83
84			e2 = sd2->getElectricField(frame2);
85
86			if (sd2->isRigidBody()) {
87			u2 = sd2->getA(frame2).getRow(2);
88			} else {
89			AtomType* at = static_cast<Atom*>(sd2)->getAtomType();
90			MultipoleAdapter ma = MultipoleAdapter(at);
91
92			if (ma.isDipole()) {
93			u2 = sd2->getDipole(frame2);
94			}
95			}
96
97			return (dot(u1, e1) - mean_) * (dot(u2, e2) - mean_);
98			}
99
100
101			void FreqFlucCorrFunc::validateSelection(const SelectionManager& seleMan) {
102			StuntDouble* sd;
103			int i;
104			for (sd = seleMan1_.beginSelected(i); sd != NULL;
105			sd = seleMan1_.nextSelected(i)) {
106
107			if (!sd->isRigidBody()) {
108
109			AtomType* at = static_cast<Atom*>(sd)->getAtomType();
110			MultipoleAdapter ma = MultipoleAdapter(at);
111
112			if (!ma.isDipole()) {
113			sprintf(painCave.errMsg,
114			"FreqFlucCorrFunc::validateSelection Error: selection is not a RigidBody or does\n"
115			"\tnot have a dipole\n");
116			painCave.isFatal = 1;
117			simError();
118			}
119			}
120			}
121			}
122
123			void FreqFlucCorrFunc::preCorrelate() {
124			mean_ = 0.0;
125			RealType sum(0.0);
126			int count(0);
127			StuntDouble* sd1;
128			Vector3d e1;
129			Vector3d u1;
130			int ii;
131			std::cerr << "preCorrelating to compute mean values\n";
132			// dump files can be enormous, so read them in block-by-block:
133			int nblocks = bsMan_->getNBlocks();
134			bool firsttime = true;
135			for (int i = 0; i < nblocks; ++i) {
136			bsMan_->loadBlock(i);
137			assert(bsMan_->isBlockActive(i));
138			SnapshotBlock block1 = bsMan_->getSnapshotBlock(i);
139			for (int j = block1.first; j < block1.second; ++j) {
140
141			// go snapshot-by-snapshot through this block:
142			Snapshot* snap = bsMan_->getSnapshot(j);
143
144			// update the positions and velocities of the atoms belonging
145			// to rigid bodies:
146
147			updateFrame(j);
148			for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL; sd1 = seleMan1_.nextSelected(ii)) {
149			e1 = sd1->getElectricField(j);
150
151			if (sd1->isRigidBody()) {
152			u1 = sd1->getA(j).getRow(2);
153			} else {
154			AtomType* at = static_cast<Atom*>(sd1)->getAtomType();
155			MultipoleAdapter ma = MultipoleAdapter(at);
156
157			if (ma.isDipole()) {
158			u1 = sd1->getDipole(j);
159			}
160			}
161
162			RealType value = dot(u1, e1);
163
164			sum += value;
165			count++;
166			}
167			}
168	gezelter	2004	bsMan_->unloadBlock(i);
169	gezelter	2003	}
170
171			mean_ = sum / RealType(count);
172			std::cerr << "done with preCorrelation\n";
173			}
174			}
175
176