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);
      }
        
    }

  }

}
  
Revision:	1021
Committed:	Wed Aug 2 19:40:39 2006 UTC (19 years, 2 months ago) by gezelter
File size:	5169 byte(s)
Log Message:	starting change of file formats
#	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. 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	/**
43	* @file Snapshot.cpp
44	* @author tlin
45	* @date 11/11/2004
46	* @time 10:56am
47	* @version 1.0
48	*/
49
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	void Snapshot::setHmat(const Mat3x3d& m) {
57	hmat_ = m;
58	invHmat_ = hmat_.inverse();
59
60	//prepare fortran Hmat
61	RealType fortranHmat[9];
62	RealType fortranInvHmat[9];
63	hmat_.getArray(fortranHmat);
64	invHmat_.getArray(fortranInvHmat);
65
66	//determine whether the box is orthoTolerance or not
67	int oldOrthoRhombic = orthoRhombic_;
68
69	RealType smallDiag = fabs(hmat_(0, 0));
70	if(smallDiag > fabs(hmat_(1, 1))) smallDiag = fabs(hmat_(1, 1));
71	if(smallDiag > fabs(hmat_(2, 2))) smallDiag = fabs(hmat_(2, 2));
72	RealType tol = smallDiag * orthoTolerance_;
73
74	orthoRhombic_ = 1;
75
76	for (int i = 0; i < 3; i++ ) {
77	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	}
86
87	if( oldOrthoRhombic != orthoRhombic_ ){
88
89	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	"\tThis is usually a good thing, but if you want the\n"
94	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
95	"\tvariable ( currently set to %G ) smaller.\n",
96	orthoTolerance_);
97	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	"\tNPTf integration. If you want to live on the edge with\n"
106	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
107	"\tvariable ( currently set to %G ) larger.\n",
108	orthoTolerance_);
109	painCave.severity = OOPSE_WARNING;
110	simError();
111	}
112	}
113
114	//notify fortran simulation box has changed
115	setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_);
116	}
117
118
119	void Snapshot::wrapVector(Vector3d& pos) {
120
121	int i;
122	Vector3d scaled;
123
124	if( !orthoRhombic_ ){
125
126	// calc the scaled coordinates.
127	scaled = invHmat_* pos;
128
129	// wrap the scaled coordinates
130	for (i = 0; i < 3; ++i) {
131	scaled[i] -= roundMe(scaled[i]);
132	}
133
134	// calc the wrapped real coordinates from the wrapped scaled coordinates
135	pos = hmat_ * scaled;
136
137	} else {//if it is orthoRhombic, we could improve efficiency by only caculating the diagonal element
138
139	// calc the scaled coordinates.
140	for (i=0; i<3; i++) {
141	scaled[i] = pos[i] * invHmat_(i, i);
142	}
143
144	// wrap the scaled coordinates
145	for (i = 0; i < 3; ++i) {
146	scaled[i] -= roundMe(scaled[i]);
147	}
148
149	// 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
154	}
155
156	}
157
158	}
159