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]  Vardeman & Gezelter, in progress (2009).                        
 */

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

  void GofAngle2::initalizeHistogram() {
    npairs_ = 0;
    for (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 (int i = 0; i < avgGofr_.size(); ++i) {
        RealType cosAngle1 = -1.0 + (i + 0.5)*deltaCosAngle_;

        for(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:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (14 years, 9 months ago) by chuckv
File size:	4968 byte(s)
Log Message:	Creating busticated version of OpenMD
#	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			* [4] Vardeman & Gezelter, in progress (2009).
40	tim	310	*/
41
42			#include <algorithm>
43			#include <fstream>
44	tim	311	#include "applications/staticProps/GofAngle2.hpp"
45	tim	310	#include "utils/simError.h"
46
47	gezelter	1390	namespace OpenMD {
48	tim	310
49	gezelter	507	GofAngle2::GofAngle2(SimInfo* info, const std::string& filename, const std::string& sele1,
50			const std::string& sele2, int nangleBins)
51	tim	354	: RadialDistrFunc(info, filename, sele1, sele2), nAngleBins_(nangleBins) {
52	tim	310
53	gezelter	507	setOutputName(getPrefix(filename) + ".gto");
54	tim	354
55	gezelter	507	deltaCosAngle_ = 2.0 / nAngleBins_;
56	tim	354
57	gezelter	507	histogram_.resize(nAngleBins_);
58			avgGofr_.resize(nAngleBins_);
59			for (int i = 0 ; i < nAngleBins_; ++i) {
60	tim	354	histogram_[i].resize(nAngleBins_);
61			avgGofr_[i].resize(nAngleBins_);
62	gezelter	507	}
63	tim	354
64	gezelter	507	}
65	tim	310
66
67	gezelter	507	void GofAngle2::preProcess() {
68	tim	310
69			for (int i = 0; i < avgGofr_.size(); ++i) {
70	gezelter	507	std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
71	tim	310	}
72	gezelter	507	}
73	tim	310
74	gezelter	507	void GofAngle2::initalizeHistogram() {
75	tim	310	npairs_ = 0;
76			for (int i = 0; i < histogram_.size(); ++i)
77	gezelter	507	std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
78			}
79	tim	310
80
81	gezelter	507	void GofAngle2::processHistogram() {
82	tim	310
83			//std::for_each(avgGofr_.begin(), avgGofr_.end(), std::plus<std::vector<int>>)
84
85	gezelter	507	}
86	tim	310
87	gezelter	507	void GofAngle2::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
88	tim	310
89			if (sd1 == sd2) {
90	gezelter	507	return;
91	tim	310	}
92
93			Vector3d pos1 = sd1->getPos();
94			Vector3d pos2 = sd2->getPos();
95			Vector3d r12 = pos1 - pos2;
96	gezelter	1078	if (usePeriodicBoundaryConditions_)
97			currentSnapshot_->wrapVector(r12);
98	tim	310	Vector3d dipole1 = sd1->getElectroFrame().getColumn(2);
99			Vector3d dipole2 = sd2->getElectroFrame().getColumn(2);
100
101			r12.normalize();
102			dipole1.normalize();
103			dipole2.normalize();
104
105
106	tim	963	RealType cosAngle1 = dot(r12, dipole1);
107			RealType cosAngle2 = dot(dipole1, dipole2);
108	tim	310
109	tim	963	RealType halfBin = (nAngleBins_ - 1) * 0.5;
110	tim	310	int angleBin1 = halfBin * (cosAngle1 + 1.0);
111	gezelter	1041	int angleBin2 = halfBin * (cosAngle2 + 1.0);
112	tim	310
113	gezelter	1041	++histogram_[angleBin1][angleBin2];
114	tim	310	++npairs_;
115	gezelter	507	}
116	tim	310
117	gezelter	507	void GofAngle2::writeRdf() {
118	tim	310	std::ofstream rdfStream(outputFilename_.c_str());
119			if (rdfStream.is_open()) {
120	gezelter	507	rdfStream << "#radial distribution function\n";
121			rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
122			rdfStream << "selection2: (" << selectionScript2_ << ")\n";
123			rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n";
124			for (int i = 0; i < avgGofr_.size(); ++i) {
125	tim	963	RealType cosAngle1 = -1.0 + (i + 0.5)*deltaCosAngle_;
126	tim	310
127	gezelter	507	for(int j = 0; j < avgGofr_[i].size(); ++j) {
128	tim	963	RealType cosAngle2 = -1.0 + (j + 0.5)*deltaCosAngle_;
129	gezelter	507	rdfStream <<avgGofr_[i][j]/nProcessed_ << "\t";
130			}
131	tim	360
132	gezelter	507	rdfStream << "\n";
133			}
134	tim	310
135			} else {
136
137	gezelter	507	sprintf(painCave.errMsg, "GofAngle2: unable to open %s\n", outputFilename_.c_str());
138			painCave.isFatal = 1;
139			simError();
140	tim	310	}
141
142			rdfStream.close();
143	gezelter	507	}
144	tim	310
145			}