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, 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 <fstream>
#include "applications/staticProps/GofAngle2.hpp"
#include "primitives/Atom.hpp"
#include "types/MultipoleAdapter.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);

    AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType();
    AtomType* atype2 = static_cast<Atom*>(sd2)->getAtomType();
    MultipoleAdapter ma1 = MultipoleAdapter(atype1);
    MultipoleAdapter ma2 = MultipoleAdapter(atype2);

    Vector3d dipole1, dipole2;
    if (ma1.isDipole())         
        dipole1 = sd1->getDipole();
    else
        dipole1 = sd1->getA().transpose() * V3Z;

    if (ma2.isDipole())         
        dipole2 = sd2->getDipole();
    else
        dipole2 = sd2->getA().transpose() * V3Z;
    
    r12.normalize();
    dipole1.normalize();    
    dipole2.normalize();    
    

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

    RealType halfBin = (nAngleBins_ - 1) * 0.5;
    int angleBin1 = int(halfBin * (cosAngle1 + 1.0));
    int angleBin2 = int(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:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (11 years, 10 months ago) by gezelter
File size:	5565 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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	gezelter	1879	#include "primitives/Atom.hpp"
47			#include "types/MultipoleAdapter.hpp"
48	tim	310	#include "utils/simError.h"
49
50	gezelter	1390	namespace OpenMD {
51	tim	310
52	gezelter	507	GofAngle2::GofAngle2(SimInfo* info, const std::string& filename, const std::string& sele1,
53			const std::string& sele2, int nangleBins)
54	tim	354	: RadialDistrFunc(info, filename, sele1, sele2), nAngleBins_(nangleBins) {
55	tim	310
56	gezelter	507	setOutputName(getPrefix(filename) + ".gto");
57	tim	354
58	gezelter	507	deltaCosAngle_ = 2.0 / nAngleBins_;
59	tim	354
60	gezelter	507	histogram_.resize(nAngleBins_);
61			avgGofr_.resize(nAngleBins_);
62			for (int i = 0 ; i < nAngleBins_; ++i) {
63	tim	354	histogram_[i].resize(nAngleBins_);
64			avgGofr_[i].resize(nAngleBins_);
65	gezelter	507	}
66	tim	354
67	gezelter	507	}
68	tim	310
69
70	gezelter	507	void GofAngle2::preProcess() {
71	tim	310
72	gezelter	1782	for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
73	gezelter	507	std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
74	tim	310	}
75	gezelter	507	}
76	tim	310
77	jmichalk	1785	void GofAngle2::initializeHistogram() {
78	tim	310	npairs_ = 0;
79	gezelter	1782	for (unsigned int i = 0; i < histogram_.size(); ++i)
80	gezelter	507	std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
81			}
82	tim	310
83
84	gezelter	507	void GofAngle2::processHistogram() {
85	tim	310
86			//std::for_each(avgGofr_.begin(), avgGofr_.end(), std::plus<std::vector<int>>)
87
88	gezelter	507	}
89	tim	310
90	gezelter	507	void GofAngle2::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
91	tim	310
92			if (sd1 == sd2) {
93	gezelter	507	return;
94	tim	310	}
95
96			Vector3d pos1 = sd1->getPos();
97			Vector3d pos2 = sd2->getPos();
98			Vector3d r12 = pos1 - pos2;
99	gezelter	1078	if (usePeriodicBoundaryConditions_)
100			currentSnapshot_->wrapVector(r12);
101	gezelter	1879
102			AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType();
103			AtomType* atype2 = static_cast<Atom*>(sd2)->getAtomType();
104			MultipoleAdapter ma1 = MultipoleAdapter(atype1);
105			MultipoleAdapter ma2 = MultipoleAdapter(atype2);
106
107			Vector3d dipole1, dipole2;
108			if (ma1.isDipole())
109			dipole1 = sd1->getDipole();
110			else
111			dipole1 = sd1->getA().transpose() * V3Z;
112
113			if (ma2.isDipole())
114			dipole2 = sd2->getDipole();
115			else
116			dipole2 = sd2->getA().transpose() * V3Z;
117	tim	310
118			r12.normalize();
119			dipole1.normalize();
120			dipole2.normalize();
121
122
123	tim	963	RealType cosAngle1 = dot(r12, dipole1);
124			RealType cosAngle2 = dot(dipole1, dipole2);
125	tim	310
126	tim	963	RealType halfBin = (nAngleBins_ - 1) * 0.5;
127	gezelter	1790	int angleBin1 = int(halfBin * (cosAngle1 + 1.0));
128			int angleBin2 = int(halfBin * (cosAngle2 + 1.0));
129	tim	310
130	gezelter	1041	++histogram_[angleBin1][angleBin2];
131	tim	310	++npairs_;
132	gezelter	507	}
133	tim	310
134	gezelter	507	void GofAngle2::writeRdf() {
135	tim	310	std::ofstream rdfStream(outputFilename_.c_str());
136			if (rdfStream.is_open()) {
137	gezelter	507	rdfStream << "#radial distribution function\n";
138			rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
139			rdfStream << "selection2: (" << selectionScript2_ << ")\n";
140			rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n";
141	gezelter	1782	for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
142	gezelter	1796	// RealType cosAngle1 = -1.0 + (i + 0.5)*deltaCosAngle_;
143
144	gezelter	1782	for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) {
145	gezelter	1796	// RealType cosAngle2 = -1.0 + (j + 0.5)*deltaCosAngle_;
146	gezelter	507	rdfStream <<avgGofr_[i][j]/nProcessed_ << "\t";
147			}
148	tim	360
149	gezelter	507	rdfStream << "\n";
150			}
151	tim	310
152			} else {
153
154	gezelter	507	sprintf(painCave.errMsg, "GofAngle2: unable to open %s\n", outputFilename_.c_str());
155			painCave.isFatal = 1;
156			simError();
157	tim	310	}
158
159			rdfStream.close();
160	gezelter	507	}
161	tim	310
162			}