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. 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).
 */
  
/**
 * @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"
#include <cstdio>

namespace OpenMD {

  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,
                 "OpenMD 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 = OPENMD_INFO;
        simError();
      }
      else {
        sprintf( painCave.errMsg,
                 "OpenMD 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 = OPENMD_WARNING;
        simError();
      }
    }    

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


  void Snapshot::wrapVector(Vector3d& pos) {
    
    Vector3d scaled = scaleVector(pos);
    
    for (int i = 0; i < 3; i++) 
      scaled[i] -= roundMe(scaled[i]);

    if( !orthoRhombic_ )
      pos = hmat_ * scaled;    
    else {

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

  inline Vector3d Snapshot::scaleVector(Vector3d& pos) {   
    
    Vector3d scaled;

    if( !orthoRhombic_ )
      scaled = invHmat_* pos;
    else {
      // calc the scaled coordinates.
      for (int i=0; i<3; i++) 
        scaled[i] = pos[i] * invHmat_(i, i);
    }

    return scaled;
  }
  
  Vector3d Snapshot::getCOM() {
    if( !hasCOM_ ) {
      sprintf( painCave.errMsg, "COM was requested before COM was computed!\n");
      painCave.severity = OPENMD_ERROR;
      simError();
    }
    return COM_;
  }
  
  Vector3d Snapshot::getCOMvel() {
    if( !hasCOM_ ) {
      sprintf( painCave.errMsg, "COMvel was requested before COM was computed!\n");
      painCave.severity = OPENMD_ERROR;
      simError();
    }
    return COMvel_;
  }
  
  Vector3d Snapshot::getCOMw() {
    if( !hasCOM_ ) {
      sprintf( painCave.errMsg, "COMw was requested before COM was computed!\n");
      painCave.severity = OPENMD_ERROR;
      simError();
    }
    return COMw_;
  }
}
  
Revision:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	5770 byte(s)
Log Message:	updated copyright notices
#	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	/**
44	* @file Snapshot.cpp
45	* @author tlin
46	* @date 11/11/2004
47	* @time 10:56am
48	* @version 1.0
49	*/
50
51	#include "brains/Snapshot.hpp"
52	#include "utils/NumericConstant.hpp"
53	#include "utils/simError.h"
54	#include "utils/Utility.hpp"
55	#include <cstdio>
56
57	namespace OpenMD {
58
59	void Snapshot::setHmat(const Mat3x3d& m) {
60	hmat_ = m;
61	invHmat_ = hmat_.inverse();
62
63	//prepare fortran Hmat
64	RealType fortranHmat[9];
65	RealType fortranInvHmat[9];
66	hmat_.getArray(fortranHmat);
67	invHmat_.getArray(fortranInvHmat);
68
69	//determine whether the box is orthoTolerance or not
70	int oldOrthoRhombic = orthoRhombic_;
71
72	RealType smallDiag = fabs(hmat_(0, 0));
73	if(smallDiag > fabs(hmat_(1, 1))) smallDiag = fabs(hmat_(1, 1));
74	if(smallDiag > fabs(hmat_(2, 2))) smallDiag = fabs(hmat_(2, 2));
75	RealType tol = smallDiag * orthoTolerance_;
76
77	orthoRhombic_ = 1;
78
79	for (int i = 0; i < 3; i++ ) {
80	for (int j = 0 ; j < 3; j++) {
81	if (i != j) {
82	if (orthoRhombic_) {
83	if ( fabs(hmat_(i, j)) >= tol)
84	orthoRhombic_ = 0;
85	}
86	}
87	}
88	}
89
90	if( oldOrthoRhombic != orthoRhombic_ ){
91
92	if( orthoRhombic_ ) {
93	sprintf( painCave.errMsg,
94	"OpenMD is switching from the default Non-Orthorhombic\n"
95	"\tto the faster Orthorhombic periodic boundary computations.\n"
96	"\tThis is usually a good thing, but if you want the\n"
97	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
98	"\tvariable ( currently set to %G ) smaller.\n",
99	orthoTolerance_);
100	painCave.severity = OPENMD_INFO;
101	simError();
102	}
103	else {
104	sprintf( painCave.errMsg,
105	"OpenMD is switching from the faster Orthorhombic to the more\n"
106	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
107	"\tThis is usually because the box has deformed under\n"
108	"\tNPTf integration. If you want to live on the edge with\n"
109	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
110	"\tvariable ( currently set to %G ) larger.\n",
111	orthoTolerance_);
112	painCave.severity = OPENMD_WARNING;
113	simError();
114	}
115	}
116
117	//notify fortran simulation box has changed
118	// setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_);
119	}
120
121
122	void Snapshot::wrapVector(Vector3d& pos) {
123
124	Vector3d scaled = scaleVector(pos);
125
126	for (int i = 0; i < 3; i++)
127	scaled[i] -= roundMe(scaled[i]);
128
129	if( !orthoRhombic_ )
130	pos = hmat_ * scaled;
131	else {
132
133	// calc the wrapped real coordinates from the wrapped scaled coordinates
134	for (int i=0; i<3; i++) {
135	pos[i] = scaled[i] * hmat_(i, i);
136	}
137	}
138	}
139
140	inline Vector3d Snapshot::scaleVector(Vector3d& pos) {
141
142	Vector3d scaled;
143
144	if( !orthoRhombic_ )
145	scaled = invHmat_* pos;
146	else {
147	// calc the scaled coordinates.
148	for (int i=0; i<3; i++)
149	scaled[i] = pos[i] * invHmat_(i, i);
150	}
151
152	return scaled;
153	}
154
155	Vector3d Snapshot::getCOM() {
156	if( !hasCOM_ ) {
157	sprintf( painCave.errMsg, "COM was requested before COM was computed!\n");
158	painCave.severity = OPENMD_ERROR;
159	simError();
160	}
161	return COM_;
162	}
163
164	Vector3d Snapshot::getCOMvel() {
165	if( !hasCOM_ ) {
166	sprintf( painCave.errMsg, "COMvel was requested before COM was computed!\n");
167	painCave.severity = OPENMD_ERROR;
168	simError();
169	}
170	return COMvel_;
171	}
172
173	Vector3d Snapshot::getCOMw() {
174	if( !hasCOM_ ) {
175	sprintf( painCave.errMsg, "COMw was requested before COM was computed!\n");
176	painCave.severity = OPENMD_ERROR;
177	simError();
178	}
179	return COMw_;
180	}
181	}
182