applications/staticProps/pAngle.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).
 * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
 */

/* Calculates Rho(theta) */

#include <algorithm>
#include <fstream>
#include "applications/staticProps/pAngle.hpp"
#include "utils/simError.h"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "brains/Thermo.hpp"

namespace OpenMD {
  
  pAngle::pAngle(SimInfo* info, const std::string& filename, 
                 const std::string& sele, int nthetabins)
    : StaticAnalyser(info, filename), selectionScript_(sele),  
      evaluator_(info), seleMan_(info), nThetaBins_(nthetabins){
    
    evaluator_.loadScriptString(sele);
    if (!evaluator_.isDynamic()) {
      seleMan_.setSelectionSet(evaluator_.evaluate());
    }            
    
    count_.resize(nThetaBins_);
    histogram_.resize(nThetaBins_);
    
    setOutputName(getPrefix(filename) + ".pAngle");
  }
  
  void pAngle::process() {
    Molecule* mol;
    RigidBody* rb;
    StuntDouble* sd;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;
    int i;

    Thermo thermo(info_);
    DumpReader reader(info_, dumpFilename_);    
    int nFrames = reader.getNFrames();
    nProcessed_ = nFrames/step_;

    std::fill(histogram_.begin(), histogram_.end(), 0.0);
    std::fill(count_.begin(), count_.end(), 0);
    
    for (int istep = 0; istep < nFrames; istep += step_) {
      reader.readFrame(istep);
      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();

      for (mol = info_->beginMolecule(mi); mol != NULL; 
           mol = info_->nextMolecule(mi)) {
        //change the positions of atoms which belong to the rigidbodies
        for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
             rb = mol->nextRigidBody(rbIter)) {
          rb->updateAtoms();
        }
      }
      
      Vector3d CenterOfMass = thermo.getCom();      

      if  (evaluator_.isDynamic()) {
        seleMan_.setSelectionSet(evaluator_.evaluate());
      }
      
      for (sd = seleMan_.beginSelected(i); sd != NULL; 
           sd = seleMan_.nextSelected(i)) {
        
        Vector3d pos = sd->getPos();
        
        Vector3d r1 = CenterOfMass - pos;
        // only do this if the stunt double actually has a vector associated
        // with it
        if (sd->isDirectional()) {
          Vector3d dipole = sd->getA().getColumn(2);
          RealType distance = r1.length();
          
          dipole.normalize();
          r1.normalize();
          RealType cosangle = dot(r1, dipole);
                          
          int binNo = int(nThetaBins_ * (1.0 + cosangle) / 2.0);
          count_[binNo]++;
        }
        
      }
    }
    processHistogram();
    writeProbs();
    
  }
  
  void pAngle::processHistogram() {
    
    int atot = 0;
    for(unsigned int i = 0; i < count_.size(); ++i) 
      atot += count_[i];
    
    for(unsigned int i = 0; i < count_.size(); ++i) {
      histogram_[i] = double(count_[i] / double(atot));
    }    
  }
  
  
  void pAngle::writeProbs() {

    std::ofstream rdfStream(outputFilename_.c_str());
    if (rdfStream.is_open()) {
      rdfStream << "#pAngle\n";
      rdfStream << "#nFrames:\t" << nProcessed_ << "\n";
      rdfStream << "#selection: (" << selectionScript_ << ")\n";
      rdfStream << "#cos(theta)\tp(cos(theta))\n";
      RealType dct = 2.0 / histogram_.size();
      for (unsigned int i = 0; i < histogram_.size(); ++i) {
        RealType ct = -1.0 + (2.0 * i + 1) / (histogram_.size());
        rdfStream << ct << "\t" << histogram_[i]/dct << "\n";
      }
      
    } else {
      
      sprintf(painCave.errMsg, "pAngle: 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:	5855 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	* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
41	*/
42
43	/* Calculates Rho(theta) */
44
45	#include <algorithm>
46	#include <fstream>
47	#include "applications/staticProps/pAngle.hpp"
48	#include "utils/simError.h"
49	#include "io/DumpReader.hpp"
50	#include "primitives/Molecule.hpp"
51	#include "brains/Thermo.hpp"
52
53	namespace OpenMD {
54
55	pAngle::pAngle(SimInfo* info, const std::string& filename,
56	const std::string& sele, int nthetabins)
57	: StaticAnalyser(info, filename), selectionScript_(sele),
58	evaluator_(info), seleMan_(info), nThetaBins_(nthetabins){
59
60	evaluator_.loadScriptString(sele);
61	if (!evaluator_.isDynamic()) {
62	seleMan_.setSelectionSet(evaluator_.evaluate());
63	}
64
65	count_.resize(nThetaBins_);
66	histogram_.resize(nThetaBins_);
67
68	setOutputName(getPrefix(filename) + ".pAngle");
69	}
70
71	void pAngle::process() {
72	Molecule* mol;
73	RigidBody* rb;
74	StuntDouble* sd;
75	SimInfo::MoleculeIterator mi;
76	Molecule::RigidBodyIterator rbIter;
77	int i;
78
79	Thermo thermo(info_);
80	DumpReader reader(info_, dumpFilename_);
81	int nFrames = reader.getNFrames();
82	nProcessed_ = nFrames/step_;
83
84	std::fill(histogram_.begin(), histogram_.end(), 0.0);
85	std::fill(count_.begin(), count_.end(), 0);
86
87	for (int istep = 0; istep < nFrames; istep += step_) {
88	reader.readFrame(istep);
89	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
90
91	for (mol = info_->beginMolecule(mi); mol != NULL;
92	mol = info_->nextMolecule(mi)) {
93	//change the positions of atoms which belong to the rigidbodies
94	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
95	rb = mol->nextRigidBody(rbIter)) {
96	rb->updateAtoms();
97	}
98	}
99
100	Vector3d CenterOfMass = thermo.getCom();
101
102	if (evaluator_.isDynamic()) {
103	seleMan_.setSelectionSet(evaluator_.evaluate());
104	}
105
106	for (sd = seleMan_.beginSelected(i); sd != NULL;
107	sd = seleMan_.nextSelected(i)) {
108
109	Vector3d pos = sd->getPos();
110
111	Vector3d r1 = CenterOfMass - pos;
112	// only do this if the stunt double actually has a vector associated
113	// with it
114	if (sd->isDirectional()) {
115	Vector3d dipole = sd->getA().getColumn(2);
116	RealType distance = r1.length();
117
118	dipole.normalize();
119	r1.normalize();
120	RealType cosangle = dot(r1, dipole);
121
122	int binNo = int(nThetaBins_ * (1.0 + cosangle) / 2.0);
123	count_[binNo]++;
124	}
125
126	}
127	}
128	processHistogram();
129	writeProbs();
130
131	}
132
133	void pAngle::processHistogram() {
134
135	int atot = 0;
136	for(unsigned int i = 0; i < count_.size(); ++i)
137	atot += count_[i];
138
139	for(unsigned int i = 0; i < count_.size(); ++i) {
140	histogram_[i] = double(count_[i] / double(atot));
141	}
142	}
143
144
145	void pAngle::writeProbs() {
146
147	std::ofstream rdfStream(outputFilename_.c_str());
148	if (rdfStream.is_open()) {
149	rdfStream << "#pAngle\n";
150	rdfStream << "#nFrames:\t" << nProcessed_ << "\n";
151	rdfStream << "#selection: (" << selectionScript_ << ")\n";
152	rdfStream << "#cos(theta)\tp(cos(theta))\n";
153	RealType dct = 2.0 / histogram_.size();
154	for (unsigned int i = 0; i < histogram_.size(); ++i) {
155	RealType ct = -1.0 + (2.0 * i + 1) / (histogram_.size());
156	rdfStream << ct << "\t" << histogram_[i]/dct << "\n";
157	}
158
159	} else {
160
161	sprintf(painCave.errMsg, "pAngle: unable to open %s\n", outputFilename_.c_str());
162	painCave.isFatal = 1;
163	simError();
164	}
165
166	rdfStream.close();
167	}
168
169	}
170