src/brains/Snapshot.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.
 */
  
/**
 * @file Snapshot.cpp
 * @author tlin
 * @date 11/11/2004
 * @time 10:56am
 * @version 1.0
 */

#include "brains/Snapshot.hpp"
#include "utils/NumericConstant.hpp"
#include "utils/simError.h"
#include "utils/Utility.hpp"
namespace oopse {

  void  Snapshot::setHmat(const Mat3x3d& m) {
    hmat_ = m;
    invHmat_ = hmat_.inverse();
    
    //prepare fortran Hmat 
    RealType fortranHmat[9];
    RealType fortranInvHmat[9];
    hmat_.getArray(fortranHmat);
    invHmat_.getArray(fortranInvHmat);

    //determine whether the box is orthoTolerance or not
    int oldOrthoRhombic = orthoRhombic_;
    
    RealType smallDiag = fabs(hmat_(0, 0));
    if(smallDiag > fabs(hmat_(1, 1))) smallDiag = fabs(hmat_(1, 1));
    if(smallDiag > fabs(hmat_(2, 2))) smallDiag = fabs(hmat_(2, 2));    
    RealType tol = smallDiag * orthoTolerance_;

    orthoRhombic_ = 1;

    for (int i = 0; i < 3; i++ ) {
      for (int j = 0 ; j < 3; j++) {
        if (i != j) {
          if (orthoRhombic_) {
            if ( fabs(hmat_(i, j)) >= tol)
              orthoRhombic_ = 0;
          }        
        }
      }
    }

    if( oldOrthoRhombic != orthoRhombic_ ){

      if( orthoRhombic_ ) {
        sprintf( painCave.errMsg,
                 "OOPSE is switching from the default Non-Orthorhombic\n"
                 "\tto the faster Orthorhombic periodic boundary computations.\n"
                 "\tThis is usually a good thing, but if you want the\n"
                 "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
                 "\tvariable ( currently set to %G ) smaller.\n",
                 orthoTolerance_);
        painCave.severity = OOPSE_INFO;
        simError();
      }
      else {
        sprintf( painCave.errMsg,
                 "OOPSE is switching from the faster Orthorhombic to the more\n"
                 "\tflexible Non-Orthorhombic periodic boundary computations.\n"
                 "\tThis is usually because the box has deformed under\n"
                 "\tNPTf integration. If you want to live on the edge with\n"
                 "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
                 "\tvariable ( currently set to %G ) larger.\n",
                 orthoTolerance_);
        painCave.severity = OOPSE_WARNING;
        simError();
      }
    }    

    //notify fortran simulation box has changed
    setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_);
  }


  void Snapshot::wrapVector(Vector3d& pos) {

    int i;
    Vector3d scaled;

    if( !orthoRhombic_ ){

      // calc the scaled coordinates.
      scaled = invHmat_* pos;

      // wrap the scaled coordinates
      for (i = 0; i < 3; ++i) {
        scaled[i] -= roundMe(scaled[i]);
      }

      // calc the wrapped real coordinates from the wrapped scaled coordinates
      pos = hmat_ * scaled;    

    } else {//if it is orthoRhombic, we could improve efficiency by only caculating the diagonal element
    
      // calc the scaled coordinates.
      for (i=0; i<3; i++) {
        scaled[i] = pos[i] * invHmat_(i, i);
      }
        
      // wrap the scaled coordinates
      for (i = 0; i < 3; ++i) {
        scaled[i] -= roundMe(scaled[i]);
      }

      // calc the wrapped real coordinates from the wrapped scaled coordinates
      for (i=0; i<3; i++) {
        pos[i] = scaled[i] * hmat_(i, i);
      }
        
    }

  }

  Vector3d Snapshot::getCOM() {
    if( !hasCOM_ ) {
      sprintf( painCave.errMsg, "COM was requested before COM was computed!\n");
      painCave.severity = OOPSE_ERROR;
      simError();
    }
    return COM_;
  }
  
  Vector3d Snapshot::getCOMvel() {
    if( !hasCOM_ ) {
      sprintf( painCave.errMsg, "COMvel was requested before COM was computed!\n");
      painCave.severity = OOPSE_ERROR;
      simError();
    }
    return COMvel_;
  }
  
  Vector3d Snapshot::getCOMw() {
    if( !hasCOM_ ) {
      sprintf( painCave.errMsg, "COMw was requested before COM was computed!\n");
      painCave.severity = OOPSE_ERROR;
      simError();
    }
    return COMw_;
  }
 
}
  
Revision:	3102
Committed:	Fri Dec 29 21:43:18 2006 UTC (17 years, 8 months ago) by gezelter
File size:	5843 byte(s)
Log Message:	Adding the ability to compute Center of Mass properties on reading in a dump file. DumpReader must be told if it needs to do this, however.
#	User	Rev	Content
1	gezelter	2204	/*
2	gezelter	1930	* 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	gezelter	2204	/**
43			* @file Snapshot.cpp
44			* @author tlin
45			* @date 11/11/2004
46			* @time 10:56am
47			* @version 1.0
48			*/
49	gezelter	1930
50			#include "brains/Snapshot.hpp"
51			#include "utils/NumericConstant.hpp"
52			#include "utils/simError.h"
53			#include "utils/Utility.hpp"
54			namespace oopse {
55
56	gezelter	2204	void Snapshot::setHmat(const Mat3x3d& m) {
57	gezelter	1930	hmat_ = m;
58			invHmat_ = hmat_.inverse();
59
60			//prepare fortran Hmat
61	tim	2759	RealType fortranHmat[9];
62			RealType fortranInvHmat[9];
63	gezelter	1930	hmat_.getArray(fortranHmat);
64			invHmat_.getArray(fortranInvHmat);
65
66			//determine whether the box is orthoTolerance or not
67			int oldOrthoRhombic = orthoRhombic_;
68
69	tim	2759	RealType smallDiag = fabs(hmat_(0, 0));
70	gezelter	1930	if(smallDiag > fabs(hmat_(1, 1))) smallDiag = fabs(hmat_(1, 1));
71			if(smallDiag > fabs(hmat_(2, 2))) smallDiag = fabs(hmat_(2, 2));
72	gezelter	2970	RealType tol = smallDiag * orthoTolerance_;
73	gezelter	1930
74			orthoRhombic_ = 1;
75
76			for (int i = 0; i < 3; i++ ) {
77	gezelter	2204	for (int j = 0 ; j < 3; j++) {
78			if (i != j) {
79			if (orthoRhombic_) {
80			if ( fabs(hmat_(i, j)) >= tol)
81			orthoRhombic_ = 0;
82			}
83			}
84			}
85	gezelter	1930	}
86
87			if( oldOrthoRhombic != orthoRhombic_ ){
88
89	gezelter	2204	if( orthoRhombic_ ) {
90			sprintf( painCave.errMsg,
91			"OOPSE is switching from the default Non-Orthorhombic\n"
92			"\tto the faster Orthorhombic periodic boundary computations.\n"
93	gezelter	2593	"\tThis is usually a good thing, but if you want the\n"
94	gezelter	2204	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
95			"\tvariable ( currently set to %G ) smaller.\n",
96	gezelter	2970	orthoTolerance_);
97	gezelter	2204	painCave.severity = OOPSE_INFO;
98			simError();
99			}
100			else {
101			sprintf( painCave.errMsg,
102			"OOPSE is switching from the faster Orthorhombic to the more\n"
103			"\tflexible Non-Orthorhombic periodic boundary computations.\n"
104			"\tThis is usually because the box has deformed under\n"
105	gezelter	2593	"\tNPTf integration. If you want to live on the edge with\n"
106	gezelter	2204	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
107			"\tvariable ( currently set to %G ) larger.\n",
108	gezelter	2970	orthoTolerance_);
109	gezelter	2204	painCave.severity = OOPSE_WARNING;
110			simError();
111			}
112	gezelter	1930	}
113
114			//notify fortran simulation box has changed
115			setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_);
116	gezelter	2204	}
117	gezelter	1930
118
119	gezelter	2204	void Snapshot::wrapVector(Vector3d& pos) {
120	gezelter	1930
121			int i;
122			Vector3d scaled;
123
124			if( !orthoRhombic_ ){
125
126	gezelter	2204	// calc the scaled coordinates.
127			scaled = invHmat_* pos;
128	gezelter	1930
129	gezelter	2204	// wrap the scaled coordinates
130			for (i = 0; i < 3; ++i) {
131			scaled[i] -= roundMe(scaled[i]);
132			}
133	gezelter	1930
134	gezelter	2204	// calc the wrapped real coordinates from the wrapped scaled coordinates
135			pos = hmat_ * scaled;
136	gezelter	1930
137			} else {//if it is orthoRhombic, we could improve efficiency by only caculating the diagonal element
138
139	gezelter	2204	// calc the scaled coordinates.
140			for (i=0; i<3; i++) {
141			scaled[i] = pos[i] * invHmat_(i, i);
142			}
143	gezelter	1930
144	gezelter	2204	// wrap the scaled coordinates
145			for (i = 0; i < 3; ++i) {
146			scaled[i] -= roundMe(scaled[i]);
147			}
148	gezelter	1930
149	gezelter	2204	// calc the wrapped real coordinates from the wrapped scaled coordinates
150			for (i=0; i<3; i++) {
151			pos[i] = scaled[i] * hmat_(i, i);
152			}
153	gezelter	1930
154			}
155
156	gezelter	2204	}
157	gezelter	1930
158	gezelter	3102	Vector3d Snapshot::getCOM() {
159			if( !hasCOM_ ) {
160			sprintf( painCave.errMsg, "COM was requested before COM was computed!\n");
161			painCave.severity = OOPSE_ERROR;
162			simError();
163			}
164			return COM_;
165			}
166
167			Vector3d Snapshot::getCOMvel() {
168			if( !hasCOM_ ) {
169			sprintf( painCave.errMsg, "COMvel was requested before COM was computed!\n");
170			painCave.severity = OOPSE_ERROR;
171			simError();
172			}
173			return COMvel_;
174			}
175
176			Vector3d Snapshot::getCOMw() {
177			if( !hasCOM_ ) {
178			sprintf( painCave.errMsg, "COMw was requested before COM was computed!\n");
179			painCave.severity = OOPSE_ERROR;
180			simError();
181			}
182			return COMw_;
183			}
184
185	gezelter	1930	}
186