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 "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:	1798
Committed:	Thu Sep 13 14:10:11 2012 UTC (12 years, 7 months ago) by gezelter
File size:	5564 byte(s)
Log Message:	Merged trunk changes into the development branch
#	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, 24107 (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 <fstream>
45	#include "applications/staticProps/GofAngle2.hpp"
46	#include "primitives/Atom.hpp"
47	#include "types/MultipoleAdapter.hpp"
48	#include "utils/simError.h"
49
50	namespace OpenMD {
51
52	GofAngle2::GofAngle2(SimInfo* info, const std::string& filename, const std::string& sele1,
53	const std::string& sele2, int nangleBins)
54	: RadialDistrFunc(info, filename, sele1, sele2), nAngleBins_(nangleBins) {
55
56	setOutputName(getPrefix(filename) + ".gto");
57
58	deltaCosAngle_ = 2.0 / nAngleBins_;
59
60	histogram_.resize(nAngleBins_);
61	avgGofr_.resize(nAngleBins_);
62	for (int i = 0 ; i < nAngleBins_; ++i) {
63	histogram_[i].resize(nAngleBins_);
64	avgGofr_[i].resize(nAngleBins_);
65	}
66
67	}
68
69
70	void GofAngle2::preProcess() {
71
72	for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
73	std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
74	}
75	}
76
77	void GofAngle2::initializeHistogram() {
78	npairs_ = 0;
79	for (unsigned int i = 0; i < histogram_.size(); ++i)
80	std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
81	}
82
83
84	void GofAngle2::processHistogram() {
85
86	//std::for_each(avgGofr_.begin(), avgGofr_.end(), std::plus<std::vector<int>>)
87
88	}
89
90	void GofAngle2::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
91
92	if (sd1 == sd2) {
93	return;
94	}
95
96	Vector3d pos1 = sd1->getPos();
97	Vector3d pos2 = sd2->getPos();
98	Vector3d r12 = pos1 - pos2;
99	if (usePeriodicBoundaryConditions_)
100	currentSnapshot_->wrapVector(r12);
101
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
118	r12.normalize();
119	dipole1.normalize();
120	dipole2.normalize();
121
122
123	RealType cosAngle1 = dot(r12, dipole1);
124	RealType cosAngle2 = dot(dipole1, dipole2);
125
126	RealType halfBin = (nAngleBins_ - 1) * 0.5;
127	int angleBin1 = int(halfBin * (cosAngle1 + 1.0));
128	int angleBin2 = int(halfBin * (cosAngle2 + 1.0));
129
130	++histogram_[angleBin1][angleBin2];
131	++npairs_;
132	}
133
134	void GofAngle2::writeRdf() {
135	std::ofstream rdfStream(outputFilename_.c_str());
136	if (rdfStream.is_open()) {
137	rdfStream << "#radial distribution function\n";
138	rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
139	rdfStream << "selection2: (" << selectionScript2_ << ")\n";
140	rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n";
141	for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
142	// RealType cosAngle1 = -1.0 + (i + 0.5)*deltaCosAngle_;
143
144	for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) {
145	// RealType cosAngle2 = -1.0 + (j + 0.5)*deltaCosAngle_;
146	rdfStream <<avgGofr_[i][j]/nProcessed_ << "\t";
147	}
148
149	rdfStream << "\n";
150	}
151
152	} else {
153
154	sprintf(painCave.errMsg, "GofAngle2: unable to open %s\n", outputFilename_.c_str());
155	painCave.isFatal = 1;
156	simError();
157	}
158
159	rdfStream.close();
160	}
161
162	}