applications/staticProps/GofXyz.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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */

#include <algorithm>
#include <fstream>
#include "applications/staticProps/GofXyz.hpp"
#include "utils/simError.h"
#include "primitives/Molecule.hpp"
namespace oopse {

  GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, const std::string& sele3, RealType len, int nrbins)
    : RadialDistrFunc(info, filename, sele1, sele2), evaluator3_(info), seleMan3_(info), len_(len), halfLen_(len/2), nRBins_(nrbins) {
      setOutputName(getPrefix(filename) + ".gxyz");

      evaluator3_.loadScriptString(sele3);
      if (!evaluator3_.isDynamic()) {
        seleMan3_.setSelectionSet(evaluator3_.evaluate());
      }    

      deltaR_ =  len_ / nRBins_;
    
      histogram_.resize(nRBins_);
      for (int i = 0 ; i < nRBins_; ++i) {
        histogram_[i].resize(nRBins_);
        for(int j = 0; j < nRBins_; ++j) {
          histogram_[i][j].resize(nRBins_);
        }
      }   
   
    }


  void GofXyz::preProcess() {
    for (int i = 0 ; i < nRBins_; ++i) {
      histogram_[i].resize(nRBins_);
      for(int j = 0; j < nRBins_; ++j) {
        std::fill(histogram_[i][j].begin(), histogram_[i][j].end(), 0);
      }
    }   
  }


  void GofXyz::initalizeHistogram() {
    //calculate the center of mass of the molecule of selected stuntdouble in selection1

    if (!evaluator3_.isDynamic()) {
      seleMan3_.setSelectionSet(evaluator3_.evaluate());
    }    

    assert(seleMan1_.getSelectionCount() == seleMan3_.getSelectionCount());
    
    //dipole direction of selection3 and position of selection3 will be used to determine the y-z plane
    //v1 = s3 -s1, 
    //z = origin.dipole
    //x = v1 X z
    //y = z X x 
    rotMats_.clear();

    int i;
    int j;
    StuntDouble* sd1;
    StuntDouble* sd3;
    
    for (sd1 = seleMan1_.beginSelected(i), sd3 = seleMan3_.beginSelected(j); 
         sd1 != NULL, sd3 != NULL;
         sd1 = seleMan1_.nextSelected(i), sd3 = seleMan3_.nextSelected(j)) {

      Vector3d r3 =sd3->getPos();
      Vector3d r1 = sd1->getPos();
      Vector3d v1 =  r3 - r1;
      if (usePeriodicBoundaryConditions_)
        info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
      Vector3d zaxis = sd1->getElectroFrame().getColumn(2);
      Vector3d xaxis = cross(v1, zaxis);
      Vector3d yaxis = cross(zaxis, xaxis);

      xaxis.normalize();
      yaxis.normalize();
      zaxis.normalize();

      RotMat3x3d rotMat;
      rotMat.setRow(0, xaxis);
      rotMat.setRow(1, yaxis);
      rotMat.setRow(2, zaxis);
        
      rotMats_.insert(std::map<int, RotMat3x3d>::value_type(sd1->getGlobalIndex(), rotMat));
    }

  }

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

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

    std::map<int, RotMat3x3d>::iterator i = rotMats_.find(sd1->getGlobalIndex());
    assert(i != rotMats_.end());
    
    Vector3d newR12 = i->second * r12;
    // x, y and z's possible values range -halfLen_ to halfLen_
    int xbin = (newR12.x()+ halfLen_) / deltaR_;
    int ybin = (newR12.y() + halfLen_) / deltaR_;
    int zbin = (newR12.z() + halfLen_) / deltaR_;

    if (xbin < nRBins_ && xbin >=0 &&
        ybin < nRBins_ && ybin >= 0 &&
        zbin < nRBins_ && zbin >=0 ) {
      ++histogram_[xbin][ybin][zbin];
    }
    
  }

  void GofXyz::writeRdf() {
    std::ofstream rdfStream(outputFilename_.c_str(), std::ios::binary);
    if (rdfStream.is_open()) {
      //rdfStream << "#g(x, y, z)\n";
      //rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
      //rdfStream << "selection2: (" << selectionScript2_ << ")\n";
      //rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
      for (int i = 0; i < histogram_.size(); ++i) {
 
        for(int j = 0; j < histogram_[i].size(); ++j) {
 
          for(int k = 0;k < histogram_[i][j].size(); ++k) {
            rdfStream.write(reinterpret_cast<char *>(&histogram_[i][j][k] ), sizeof(histogram_[i][j][k] ));
          }
        }
      }
        
    } else {

      sprintf(painCave.errMsg, "GofXyz: unable to open %s\n", outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();  
    }

    rdfStream.close();
  }

}
Revision:	3054
Committed:	Wed Oct 18 21:58:48 2006 UTC (17 years, 9 months ago) by gezelter
File size:	6370 byte(s)
Log Message:	fixing a wrapVector problem in staticProps, also making Shifted force and electrostatic damping the default behavior
#	User	Rev	Content
1	tim	1994	/*
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. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#include <algorithm>
43			#include <fstream>
44			#include "applications/staticProps/GofXyz.hpp"
45			#include "utils/simError.h"
46	tim	2045	#include "primitives/Molecule.hpp"
47	tim	1994	namespace oopse {
48
49	tim	2759	GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, const std::string& sele3, RealType len, int nrbins)
50	tim	2053	: RadialDistrFunc(info, filename, sele1, sele2), evaluator3_(info), seleMan3_(info), len_(len), halfLen_(len/2), nRBins_(nrbins) {
51	gezelter	2204	setOutputName(getPrefix(filename) + ".gxyz");
52	tim	1994
53	gezelter	2204	evaluator3_.loadScriptString(sele3);
54			if (!evaluator3_.isDynamic()) {
55	tim	2053	seleMan3_.setSelectionSet(evaluator3_.evaluate());
56	gezelter	2204	}
57	tim	2053
58	gezelter	2204	deltaR_ = len_ / nRBins_;
59	tim	2038
60	gezelter	2204	histogram_.resize(nRBins_);
61			for (int i = 0 ; i < nRBins_; ++i) {
62	tim	2038	histogram_[i].resize(nRBins_);
63			for(int j = 0; j < nRBins_; ++j) {
64	gezelter	2204	histogram_[i][j].resize(nRBins_);
65	tim	2038	}
66	gezelter	2204	}
67	tim	2053
68	gezelter	2204	}
69	tim	1994
70
71	gezelter	2204	void GofXyz::preProcess() {
72	tim	2045	for (int i = 0 ; i < nRBins_; ++i) {
73	gezelter	2204	histogram_[i].resize(nRBins_);
74			for(int j = 0; j < nRBins_; ++j) {
75			std::fill(histogram_[i][j].begin(), histogram_[i][j].end(), 0);
76			}
77	tim	2045	}
78	gezelter	2204	}
79	tim	1994
80	tim	2045
81	gezelter	2204	void GofXyz::initalizeHistogram() {
82	tim	2045	//calculate the center of mass of the molecule of selected stuntdouble in selection1
83	tim	1994
84	tim	2053	if (!evaluator3_.isDynamic()) {
85	gezelter	2204	seleMan3_.setSelectionSet(evaluator3_.evaluate());
86	tim	2053	}
87
88			assert(seleMan1_.getSelectionCount() == seleMan3_.getSelectionCount());
89
90			//dipole direction of selection3 and position of selection3 will be used to determine the y-z plane
91			//v1 = s3 -s1,
92			//z = origin.dipole
93	tim	2045	//x = v1 X z
94			//y = z X x
95	tim	2053	rotMats_.clear();
96	tim	1994
97	tim	2045	int i;
98	tim	2053	int j;
99			StuntDouble* sd1;
100			StuntDouble* sd3;
101
102			for (sd1 = seleMan1_.beginSelected(i), sd3 = seleMan3_.beginSelected(j);
103	gezelter	2204	sd1 != NULL, sd3 != NULL;
104			sd1 = seleMan1_.nextSelected(i), sd3 = seleMan3_.nextSelected(j)) {
105	tim	2053
106	gezelter	2204	Vector3d r3 =sd3->getPos();
107			Vector3d r1 = sd1->getPos();
108			Vector3d v1 = r3 - r1;
109	gezelter	3054	if (usePeriodicBoundaryConditions_)
110			info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
111	gezelter	2204	Vector3d zaxis = sd1->getElectroFrame().getColumn(2);
112			Vector3d xaxis = cross(v1, zaxis);
113			Vector3d yaxis = cross(zaxis, xaxis);
114	tim	2053
115	gezelter	2204	xaxis.normalize();
116			yaxis.normalize();
117			zaxis.normalize();
118	tim	2053
119	gezelter	2204	RotMat3x3d rotMat;
120			rotMat.setRow(0, xaxis);
121			rotMat.setRow(1, yaxis);
122			rotMat.setRow(2, zaxis);
123	tim	2053
124	gezelter	2204	rotMats_.insert(std::map<int, RotMat3x3d>::value_type(sd1->getGlobalIndex(), rotMat));
125	tim	2045	}
126	tim	1994
127	gezelter	2204	}
128	tim	1994
129	gezelter	2204	void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
130	tim	1994
131			Vector3d pos1 = sd1->getPos();
132			Vector3d pos2 = sd2->getPos();
133	tim	2045	Vector3d r12 = pos2 - pos1;
134	gezelter	3054	if (usePeriodicBoundaryConditions_)
135			currentSnapshot_->wrapVector(r12);
136	tim	1994
137	tim	2053	std::map<int, RotMat3x3d>::iterator i = rotMats_.find(sd1->getGlobalIndex());
138			assert(i != rotMats_.end());
139	tim	2045
140	tim	2053	Vector3d newR12 = i->second * r12;
141	tim	2048	// x, y and z's possible values range -halfLen_ to halfLen_
142	tim	2053	int xbin = (newR12.x()+ halfLen_) / deltaR_;
143			int ybin = (newR12.y() + halfLen_) / deltaR_;
144			int zbin = (newR12.z() + halfLen_) / deltaR_;
145	tim	2045
146	tim	2049	if (xbin < nRBins_ && xbin >=0 &&
147			ybin < nRBins_ && ybin >= 0 &&
148			zbin < nRBins_ && zbin >=0 ) {
149	gezelter	2204	++histogram_[xbin][ybin][zbin];
150	tim	2045	}
151	tim	1994
152	gezelter	2204	}
153	tim	1994
154	gezelter	2204	void GofXyz::writeRdf() {
155	tim	2046	std::ofstream rdfStream(outputFilename_.c_str(), std::ios::binary);
156	tim	1994	if (rdfStream.is_open()) {
157	gezelter	2204	//rdfStream << "#g(x, y, z)\n";
158			//rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
159			//rdfStream << "selection2: (" << selectionScript2_ << ")\n";
160			//rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
161			for (int i = 0; i < histogram_.size(); ++i) {
162	tim	2045
163	gezelter	2204	for(int j = 0; j < histogram_[i].size(); ++j) {
164	tim	2045
165	gezelter	2204	for(int k = 0;k < histogram_[i][j].size(); ++k) {
166			rdfStream.write(reinterpret_cast<char *>(&histogram_[i][j][k] ), sizeof(histogram_[i][j][k] ));
167			}
168			}
169			}
170	tim	1994
171			} else {
172
173	gezelter	2204	sprintf(painCave.errMsg, "GofXyz: unable to open %s\n", outputFilename_.c_str());
174			painCave.isFatal = 1;
175			simError();
176	tim	1994	}
177
178			rdfStream.close();
179	gezelter	2204	}
180	tim	1994
181			}