applications/staticProps/GofAngle2.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, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#include <algorithm>
#include <fstream>
#include "applications/staticProps/GofAngle2.hpp"
#include "utils/simError.h"

namespace OpenMD {

  GofAngle2::GofAngle2(SimInfo* info, const std::string& filename, const std::string& sele1, 
                       const std::string& sele2, int nangleBins)
    : RadialDistrFunc(info, filename, sele1, sele2), nAngleBins_(nangleBins) {

      setOutputName(getPrefix(filename) + ".gto");

      deltaCosAngle_ = 2.0 / nAngleBins_;

      histogram_.resize(nAngleBins_);
      avgGofr_.resize(nAngleBins_);
      for (int i = 0 ; i < nAngleBins_; ++i) {
        histogram_[i].resize(nAngleBins_);
        avgGofr_[i].resize(nAngleBins_);
      }    

    }


  void GofAngle2::preProcess() {

    for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
      std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
    }
  }

  void GofAngle2::initializeHistogram() {
    npairs_ = 0;
    for (unsigned int i = 0; i < histogram_.size(); ++i)
      std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
  }


  void GofAngle2::processHistogram() {

    //std::for_each(avgGofr_.begin(), avgGofr_.end(), std::plus<std::vector<int>>)

  }

  void GofAngle2::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {

    if (sd1 == sd2) {
      return;
    }

    Vector3d pos1 = sd1->getPos();
    Vector3d pos2 = sd2->getPos();
    Vector3d r12 = pos1 - pos2;
    if (usePeriodicBoundaryConditions_) 
      currentSnapshot_->wrapVector(r12);
    Vector3d dipole1 = sd1->getElectroFrame().getColumn(2);
    Vector3d dipole2 = sd2->getElectroFrame().getColumn(2);
    
    r12.normalize();
    dipole1.normalize();    
    dipole2.normalize();    
    

    RealType cosAngle1 = dot(r12, dipole1);
    RealType cosAngle2 = dot(dipole1, dipole2);

    RealType halfBin = (nAngleBins_ - 1) * 0.5;
    int angleBin1 = halfBin * (cosAngle1 + 1.0);
    int angleBin2 = halfBin * (cosAngle2 + 1.0);

    ++histogram_[angleBin1][angleBin2];    
    ++npairs_;
  }

  void GofAngle2::writeRdf() {
    std::ofstream rdfStream(outputFilename_.c_str());
    if (rdfStream.is_open()) {
      rdfStream << "#radial distribution function\n";
      rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
      rdfStream << "selection2: (" << selectionScript2_ << ")\n";
      rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n";
      for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
        RealType cosAngle1 = -1.0 + (i + 0.5)*deltaCosAngle_;

        for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) {
          RealType cosAngle2 = -1.0 + (j + 0.5)*deltaCosAngle_;
          rdfStream <<avgGofr_[i][j]/nProcessed_ << "\t";
        }

        rdfStream << "\n";
      }
        
    } else {

      sprintf(painCave.errMsg, "GofAngle2: unable to open %s\n", outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();  
    }

    rdfStream.close();
  }

}
Revision:	1785
Committed:	Wed Aug 22 18:43:27 2012 UTC (12 years, 8 months ago) by jmichalk
File size:	5071 byte(s)
Log Message:	Trunk: The changes in this commit are confined to applications/staticProps and for the most part deal with a misspelling of initialize. The one other change took place in StaticProps.cpp and deals with the default treatment of sele2. It had previously been set to 'select all' which seems to go against what would be desired by not specifying it with regard to proper operations of many of the analysis programs ( g of r's especially)
#	User	Rev	Content
1	tim	310	/*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	310	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	310	* 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	gezelter	1390	*
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, 24107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	310	*/
42
43			#include <algorithm>
44			#include <fstream>
45	tim	311	#include "applications/staticProps/GofAngle2.hpp"
46	tim	310	#include "utils/simError.h"
47
48	gezelter	1390	namespace OpenMD {
49	tim	310
50	gezelter	507	GofAngle2::GofAngle2(SimInfo* info, const std::string& filename, const std::string& sele1,
51			const std::string& sele2, int nangleBins)
52	tim	354	: RadialDistrFunc(info, filename, sele1, sele2), nAngleBins_(nangleBins) {
53	tim	310
54	gezelter	507	setOutputName(getPrefix(filename) + ".gto");
55	tim	354
56	gezelter	507	deltaCosAngle_ = 2.0 / nAngleBins_;
57	tim	354
58	gezelter	507	histogram_.resize(nAngleBins_);
59			avgGofr_.resize(nAngleBins_);
60			for (int i = 0 ; i < nAngleBins_; ++i) {
61	tim	354	histogram_[i].resize(nAngleBins_);
62			avgGofr_[i].resize(nAngleBins_);
63	gezelter	507	}
64	tim	354
65	gezelter	507	}
66	tim	310
67
68	gezelter	507	void GofAngle2::preProcess() {
69	tim	310
70	gezelter	1782	for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
71	gezelter	507	std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
72	tim	310	}
73	gezelter	507	}
74	tim	310
75	jmichalk	1785	void GofAngle2::initializeHistogram() {
76	tim	310	npairs_ = 0;
77	gezelter	1782	for (unsigned int i = 0; i < histogram_.size(); ++i)
78	gezelter	507	std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
79			}
80	tim	310
81
82	gezelter	507	void GofAngle2::processHistogram() {
83	tim	310
84			//std::for_each(avgGofr_.begin(), avgGofr_.end(), std::plus<std::vector<int>>)
85
86	gezelter	507	}
87	tim	310
88	gezelter	507	void GofAngle2::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
89	tim	310
90			if (sd1 == sd2) {
91	gezelter	507	return;
92	tim	310	}
93
94			Vector3d pos1 = sd1->getPos();
95			Vector3d pos2 = sd2->getPos();
96			Vector3d r12 = pos1 - pos2;
97	gezelter	1078	if (usePeriodicBoundaryConditions_)
98			currentSnapshot_->wrapVector(r12);
99	tim	310	Vector3d dipole1 = sd1->getElectroFrame().getColumn(2);
100			Vector3d dipole2 = sd2->getElectroFrame().getColumn(2);
101
102			r12.normalize();
103			dipole1.normalize();
104			dipole2.normalize();
105
106
107	tim	963	RealType cosAngle1 = dot(r12, dipole1);
108			RealType cosAngle2 = dot(dipole1, dipole2);
109	tim	310
110	tim	963	RealType halfBin = (nAngleBins_ - 1) * 0.5;
111	tim	310	int angleBin1 = halfBin * (cosAngle1 + 1.0);
112	gezelter	1041	int angleBin2 = halfBin * (cosAngle2 + 1.0);
113	tim	310
114	gezelter	1041	++histogram_[angleBin1][angleBin2];
115	tim	310	++npairs_;
116	gezelter	507	}
117	tim	310
118	gezelter	507	void GofAngle2::writeRdf() {
119	tim	310	std::ofstream rdfStream(outputFilename_.c_str());
120			if (rdfStream.is_open()) {
121	gezelter	507	rdfStream << "#radial distribution function\n";
122			rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
123			rdfStream << "selection2: (" << selectionScript2_ << ")\n";
124			rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n";
125	gezelter	1782	for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
126	tim	963	RealType cosAngle1 = -1.0 + (i + 0.5)*deltaCosAngle_;
127	tim	310
128	gezelter	1782	for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) {
129	tim	963	RealType cosAngle2 = -1.0 + (j + 0.5)*deltaCosAngle_;
130	gezelter	507	rdfStream <<avgGofr_[i][j]/nProcessed_ << "\t";
131			}
132	tim	360
133	gezelter	507	rdfStream << "\n";
134			}
135	tim	310
136			} else {
137
138	gezelter	507	sprintf(painCave.errMsg, "GofAngle2: unable to open %s\n", outputFilename_.c_str());
139			painCave.isFatal = 1;
140			simError();
141	tim	310	}
142
143			rdfStream.close();
144	gezelter	507	}
145	tim	310
146			}