src/brains/SnapShot.cpp

/*
 * Copyright (C) 2000-2004  Object Oriented Parallel Simulation Engine (OOPSE) project
 * 
 * Contact: oopse@oopse.org
 * 
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 */
 
 /**
  * @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) {
    const double orthoTolerance = NumericConstant::epsilon;
    hmat_ = m;
    invHmat_ = hmat_.inverse();
    
    //prepare fortran Hmat 
    double fortranHmat[9];
    double fortranInvHmat[9];
    hmat_.getArray(fortranHmat);
    invHmat_.getArray(fortranInvHmat);

    //determine whether the box is orthoTolerance or not
    int oldOrthoRhombic = orthoRhombic_;
    
    double 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));    
    double 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 wan't 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 wan't 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:	1869
Committed:	Wed Dec 8 20:37:47 2004 UTC (20 years, 10 months ago) by tim
File size:	4693 byte(s)
Log Message:	fix a parsing bug in ElectroStaticAtomTypesSectionParser
#	User	Rev	Content
1	tim	1727	/*
2			* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project
3			*
4			* Contact: oopse@oopse.org
5			*
6			* This program is free software; you can redistribute it and/or
7			* modify it under the terms of the GNU Lesser General Public License
8			* as published by the Free Software Foundation; either version 2.1
9			* of the License, or (at your option) any later version.
10			* All we ask is that proper credit is given for our work, which includes
11			* - but is not limited to - adding the above copyright notice to the beginning
12			* of your source code files, and to any copyright notice that you may distribute
13			* with programs based on this work.
14			*
15			* This program is distributed in the hope that it will be useful,
16			* but WITHOUT ANY WARRANTY; without even the implied warranty of
17			* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18			* GNU Lesser General Public License for more details.
19			*
20			* You should have received a copy of the GNU Lesser General Public License
21			* along with this program; if not, write to the Free Software
22			* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
23			*
24			*/
25
26			/**
27			* @file Snapshot.cpp
28			* @author tlin
29			* @date 11/11/2004
30			* @time 10:56am
31			* @version 1.0
32			*/
33
34			#include "brains/Snapshot.hpp"
35	tim	1869	#include "utils/NumericConstant.hpp"
36			#include "utils/simError.h"
37	tim	1727	#include "utils/Utility.hpp"
38	tim	1804	namespace oopse {
39
40	tim	1869	void Snapshot::setHmat(const Mat3x3d& m) {
41			const double orthoTolerance = NumericConstant::epsilon;
42			hmat_ = m;
43			invHmat_ = hmat_.inverse();
44
45			//prepare fortran Hmat
46			double fortranHmat[9];
47			double fortranInvHmat[9];
48			hmat_.getArray(fortranHmat);
49			invHmat_.getArray(fortranInvHmat);
50
51			//determine whether the box is orthoTolerance or not
52			int oldOrthoRhombic = orthoRhombic_;
53
54			double smallDiag = fabs(hmat_(0, 0));
55			if(smallDiag > fabs(hmat_(1, 1))) smallDiag = fabs(hmat_(1, 1));
56			if(smallDiag > fabs(hmat_(2, 2))) smallDiag = fabs(hmat_(2, 2));
57			double tol = smallDiag * orthoTolerance;
58
59			orthoRhombic_ = 1;
60
61			for (int i = 0; i < 3; i++ ) {
62			for (int j = 0 ; j < 3; j++) {
63			if (i != j) {
64			if (orthoRhombic_) {
65			if ( fabs(hmat_(i, j)) >= tol)
66			orthoRhombic_ = 0;
67			}
68			}
69			}
70			}
71
72			if( oldOrthoRhombic != orthoRhombic_ ){
73
74			if( orthoRhombic_ ) {
75			sprintf( painCave.errMsg,
76			"OOPSE is switching from the default Non-Orthorhombic\n"
77			"\tto the faster Orthorhombic periodic boundary computations.\n"
78			"\tThis is usually a good thing, but if you wan't the\n"
79			"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
80			"\tvariable ( currently set to %G ) smaller.\n",
81			orthoTolerance);
82			painCave.severity = OOPSE_INFO;
83			simError();
84			}
85			else {
86			sprintf( painCave.errMsg,
87			"OOPSE is switching from the faster Orthorhombic to the more\n"
88			"\tflexible Non-Orthorhombic periodic boundary computations.\n"
89			"\tThis is usually because the box has deformed under\n"
90			"\tNPTf integration. If you wan't to live on the edge with\n"
91			"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
92			"\tvariable ( currently set to %G ) larger.\n",
93			orthoTolerance);
94			painCave.severity = OOPSE_WARNING;
95			simError();
96			}
97			}
98
99			//notify fortran simulation box has changed
100			setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_);
101			}
102
103
104	tim	1727	void Snapshot::wrapVector(Vector3d& pos) {
105
106			int i;
107	tim	1765	Vector3d scaled;
108	tim	1727
109			if( !orthoRhombic_ ){
110
111			// calc the scaled coordinates.
112			scaled = invHmat_* pos;
113
114			// wrap the scaled coordinates
115			for (i = 0; i < 3; ++i) {
116			scaled[i] -= roundMe(scaled[i]);
117			}
118
119			// calc the wrapped real coordinates from the wrapped scaled coordinates
120			pos = hmat_ * scaled;
121
122			} else {//if it is orthoRhombic, we could improve efficiency by only caculating the diagonal element
123
124			// calc the scaled coordinates.
125			for (i=0; i<3; i++) {
126			scaled[i] = pos[i] * invHmat_(i, i);
127			}
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			for (i=0; i<3; i++) {
136			pos[i] = scaled[i] * hmat_(i, i);
137			}
138
139			}
140
141			}
142
143			}
144