applications/staticProps/GofZ.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/GofZ.hpp"
#include "utils/simError.h"

namespace OpenMD {

  GofZ::GofZ(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, int nrbins)
    : RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins){

      deltaZ_ = len_ /nRBins_;
      rC_ = len_ / 2.0;
    
      histogram_.resize(nRBins_);
      avgGofz_.resize(nRBins_);

      setOutputName(getPrefix(filename) + ".gofz");
    }


  void GofZ::preProcess() {
    std::fill(avgGofz_.begin(), avgGofz_.end(), 0.0);    
  }

  void GofZ::initializeHistogram() {
    std::fill(histogram_.begin(), histogram_.end(), 0);
  }


  void GofZ::processHistogram() {

    int nPairs = getNPairs();
    RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
    RealType pairDensity = nPairs /volume * 2.0;
    RealType pairConstant = ( 2.0 * NumericConstant::PI * pairDensity );

    for(unsigned int i = 0 ; i < histogram_.size(); ++i){

      RealType zLower = i * deltaZ_;
      RealType zUpper = zLower + deltaZ_;
      RealType cylSlice = (zUpper - zLower)*rC_*rC_;
      RealType nIdeal = cylSlice * pairConstant;

      avgGofz_[i] += histogram_[i] / nIdeal;    
    }

  }

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

    RealType thisZ;

    if (sd1 == sd2) {
      return;
    }
    
    Vector3d pos1 = sd1->getPos();
    Vector3d pos2 = sd2->getPos();
    Vector3d r12 = pos2 - pos1;
    if (usePeriodicBoundaryConditions_)
      currentSnapshot_->wrapVector(r12);

    RealType distance = r12.length();
    RealType z2 = r12.z()*r12.z();
    RealType xydist = sqrt(distance*distance - z2);

    if (xydist < rC_) {
      thisZ = abs(r12.z());
      int whichBin = thisZ / deltaZ_;
      histogram_[whichBin] += 2;
    }
  }


  void GofZ::writeRdf() {
    std::ofstream rdfStream(outputFilename_.c_str());
    if (rdfStream.is_open()) {
      rdfStream << "#z-separation distribution function\n";
      rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
      rdfStream << "selection2: (" << selectionScript2_ << ")\n";
      rdfStream << "#r\tcorrValue\n";
      for (unsigned int i = 0; i < avgGofz_.size(); ++i) {
        RealType z = deltaZ_ * (i + 0.5);
        rdfStream << z << "\t" << avgGofz_[i]/nProcessed_ << "\n";
      }
        
    } else {

      sprintf(painCave.errMsg, "GofZ: 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:	4767 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)
#	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/GofZ.hpp"
46	#include "utils/simError.h"
47
48	namespace OpenMD {
49
50	GofZ::GofZ(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, int nrbins)
51	: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins){
52
53	deltaZ_ = len_ /nRBins_;
54	rC_ = len_ / 2.0;
55
56	histogram_.resize(nRBins_);
57	avgGofz_.resize(nRBins_);
58
59	setOutputName(getPrefix(filename) + ".gofz");
60	}
61
62
63	void GofZ::preProcess() {
64	std::fill(avgGofz_.begin(), avgGofz_.end(), 0.0);
65	}
66
67	void GofZ::initializeHistogram() {
68	std::fill(histogram_.begin(), histogram_.end(), 0);
69	}
70
71
72	void GofZ::processHistogram() {
73
74	int nPairs = getNPairs();
75	RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
76	RealType pairDensity = nPairs /volume * 2.0;
77	RealType pairConstant = ( 2.0 * NumericConstant::PI * pairDensity );
78
79	for(unsigned int i = 0 ; i < histogram_.size(); ++i){
80
81	RealType zLower = i * deltaZ_;
82	RealType zUpper = zLower + deltaZ_;
83	RealType cylSlice = (zUpper - zLower)rC_rC_;
84	RealType nIdeal = cylSlice * pairConstant;
85
86	avgGofz_[i] += histogram_[i] / nIdeal;
87	}
88
89	}
90
91	void GofZ::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
92
93	RealType thisZ;
94
95	if (sd1 == sd2) {
96	return;
97	}
98
99	Vector3d pos1 = sd1->getPos();
100	Vector3d pos2 = sd2->getPos();
101	Vector3d r12 = pos2 - pos1;
102	if (usePeriodicBoundaryConditions_)
103	currentSnapshot_->wrapVector(r12);
104
105	RealType distance = r12.length();
106	RealType z2 = r12.z()*r12.z();
107	RealType xydist = sqrt(distance*distance - z2);
108
109	if (xydist < rC_) {
110	thisZ = abs(r12.z());
111	int whichBin = thisZ / deltaZ_;
112	histogram_[whichBin] += 2;
113	}
114	}
115
116
117	void GofZ::writeRdf() {
118	std::ofstream rdfStream(outputFilename_.c_str());
119	if (rdfStream.is_open()) {
120	rdfStream << "#z-separation distribution function\n";
121	rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
122	rdfStream << "selection2: (" << selectionScript2_ << ")\n";
123	rdfStream << "#r\tcorrValue\n";
124	for (unsigned int i = 0; i < avgGofz_.size(); ++i) {
125	RealType z = deltaZ_ * (i + 0.5);
126	rdfStream << z << "\t" << avgGofz_[i]/nProcessed_ << "\n";
127	}
128
129	} else {
130
131	sprintf(painCave.errMsg, "GofZ: unable to open %s\n", outputFilename_.c_str());
132	painCave.isFatal = 1;
133	simError();
134	}
135
136	rdfStream.close();
137	}
138
139	}
140