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root/OpenMD/branches/development/src/brains/Snapshot.cpp

Comparing:
trunk/src/brains/Snapshot.cpp (file contents), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/brains/Snapshot.cpp (file contents), Revision 1715 by gezelter, Tue May 22 21:55:31 2012 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	Line 6 | Line 6
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
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 37 | Line 28
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	<	*/
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	<	namespace oopse {
55	>	#include <cstdio>
56
57	<	void  Snapshot::setHmat(const Mat3x3d& m) {
57	<	const double orthoTolerance = NumericConstant::epsilon;
58	<	hmat_ = m;
59	<	invHmat_ = hmat_.inverse();
60	<
61	<	//prepare fortran Hmat
62	<	double fortranHmat[9];
63	<	double fortranInvHmat[9];
64	<	hmat_.getArray(fortranHmat);
65	<	invHmat_.getArray(fortranInvHmat);
57	>	namespace OpenMD {
58
59	+	void  Snapshot::setHmat(const Mat3x3d& m) {
60	+	frameData.hmat = m;
61	+	frameData.invHmat = frameData.hmat.inverse();
62	+
63		//determine whether the box is orthoTolerance or not
64	<	int oldOrthoRhombic = orthoRhombic_;
64	>	bool oldOrthoRhombic = frameData.orthoRhombic;
65
66	<	double smallDiag = fabs(hmat_(0, 0));
67	<	if(smallDiag > fabs(hmat_(1, 1))) smallDiag = fabs(hmat_(1, 1));
68	<	if(smallDiag > fabs(hmat_(2, 2))) smallDiag = fabs(hmat_(2, 2));
69	<	double tol = smallDiag * orthoTolerance;
66	>	RealType smallDiag = fabs(frameData.hmat(0, 0));
67	>	if(smallDiag > fabs(frameData.hmat(1, 1))) smallDiag = fabs(frameData.hmat(1, 1));
68	>	if(smallDiag > fabs(frameData.hmat(2, 2))) smallDiag = fabs(frameData.hmat(2, 2));
69	>	RealType tol = smallDiag * orthoTolerance_;
70
71	<	orthoRhombic_ = 1;
71	>	frameData.orthoRhombic = true;
72
73		for (int i = 0; i < 3; i++ ) {
74	<	for (int j = 0 ; j < 3; j++) {
75	<	if (i != j) {
76	<	if (orthoRhombic_) {
77	<	if ( fabs(hmat_(i, j)) >= tol)
78	<	orthoRhombic_ = 0;
79	<	}
80	<	}
81	<	}
74	>	for (int j = 0 ; j < 3; j++) {
75	>	if (i != j) {
76	>	if (frameData.orthoRhombic) {
77	>	if ( fabs(frameData.hmat(i, j)) >= tol)
78	>	frameData.orthoRhombic = false;
79	>	}
80	>	}
81	>	}
82		}
83
84	<	if( oldOrthoRhombic != orthoRhombic_ ){
84	>	if( oldOrthoRhombic != frameData.orthoRhombic){
85
86	<	if( orthoRhombic_ ) {
87	<	sprintf( painCave.errMsg,
88	<	"OOPSE is switching from the default Non-Orthorhombic\n"
89	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
90	<	"\tThis is usually a good thing, but if you wan't the\n"
91	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
92	<	"\tvariable ( currently set to %G ) smaller.\n",
93	<	orthoTolerance);
94	<	painCave.severity = OOPSE_INFO;
95	<	simError();
96	<	}
97	<	else {
98	<	sprintf( painCave.errMsg,
99	<	"OOPSE is switching from the faster Orthorhombic to the more\n"
100	<	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
101	<	"\tThis is usually because the box has deformed under\n"
102	<	"\tNPTf integration. If you wan't to live on the edge with\n"
103	<	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
104	<	"\tvariable ( currently set to %G ) larger.\n",
105	<	orthoTolerance);
106	<	painCave.severity = OOPSE_WARNING;
107	<	simError();
108	<	}
86	>	if( frameData.orthoRhombic ) {
87	>	sprintf( painCave.errMsg,
88	>	"OpenMD is switching from the default Non-Orthorhombic\n"
89	>	"\tto the faster Orthorhombic periodic boundary computations.\n"
90	>	"\tThis is usually a good thing, but if you want the\n"
91	>	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
92	>	"\tvariable ( currently set to %G ) smaller.\n",
93	>	orthoTolerance_);
94	>	painCave.severity = OPENMD_INFO;
95	>	simError();
96	>	}
97	>	else {
98	>	sprintf( painCave.errMsg,
99	>	"OpenMD is switching from the faster Orthorhombic to the more\n"
100	>	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
101	>	"\tThis is usually because the box has deformed under\n"
102	>	"\tNPTf integration. If you want to live on the edge with\n"
103	>	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
104	>	"\tvariable ( currently set to %G ) larger.\n",
105	>	orthoTolerance_);
106	>	painCave.severity = OPENMD_WARNING;
107	>	simError();
108	>	}
109		}
110	+	}
111
115	–	//notify fortran simulation box has changed
116	–	setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_);
117	–	}
112
113	+	void Snapshot::wrapVector(Vector3d& pos) {
114	+
115	+	Vector3d scaled = scaleVector(pos);
116	+
117	+	for (int i = 0; i < 3; i++)
118	+	scaled[i] -= roundMe(scaled[i]);
119
120	<	void Snapshot::wrapVector(Vector3d& pos) {
120	>	if( !frameData.orthoRhombic )
121	>	pos = frameData.hmat * scaled;
122	>	else {
123
124	<	int i;
125	<	Vector3d scaled;
124	>	// calc the wrapped real coordinates from the wrapped scaled coordinates
125	>	for (int i=0; i<3; i++) {
126	>	pos[i] = scaled[i] * frameData.hmat(i, i);
127	>	}
128	>	}
129	>	}
130
131	<	if( !orthoRhombic_ ){
126	<
127	<	// calc the scaled coordinates.
128	<	scaled = invHmat_* pos;
129	<
130	<	// wrap the scaled coordinates
131	<	for (i = 0; i < 3; ++i) {
132	<	scaled[i] -= roundMe(scaled[i]);
133	<	}
134	<
135	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
136	<	pos = hmat_ * scaled;
137	<
138	<	} else {//if it is orthoRhombic, we could improve efficiency by only caculating the diagonal element
131	>	inline Vector3d Snapshot::scaleVector(Vector3d& pos) {
132
133	<	// calc the scaled coordinates.
141	<	for (i=0; i<3; i++) {
142	<	scaled[i] = pos[i] * invHmat_(i, i);
143	<	}
144	<
145	<	// wrap the scaled coordinates
146	<	for (i = 0; i < 3; ++i) {
147	<	scaled[i] -= roundMe(scaled[i]);
148	<	}
133	>	Vector3d scaled;
134
135	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
136	<	for (i=0; i<3; i++) {
137	<	pos[i] = scaled[i] * hmat_(i, i);
138	<	}
139	<
135	>	if( !frameData.orthoRhombic )
136	>	scaled = frameData.invHmat * pos;
137	>	else {
138	>	// calc the scaled coordinates.
139	>	for (int i=0; i<3; i++)
140	>	scaled[i] = pos[i] * frameData.invHmat(i, i);
141		}
142
143	+	return scaled;
144	+	}
145	+
146	+	Vector3d Snapshot::getCOM() {
147	+	if( !hasCOM_ ) {
148	+	sprintf( painCave.errMsg, "COM was requested before COM was computed!\n");
149	+	painCave.severity = OPENMD_ERROR;
150	+	simError();
151	+	}
152	+	return frameData.COM;
153	+	}
154	+
155	+	Vector3d Snapshot::getCOMvel() {
156	+	if( !hasCOM_ ) {
157	+	sprintf( painCave.errMsg, "COMvel was requested before COM was computed!\n");
158	+	painCave.severity = OPENMD_ERROR;
159	+	simError();
160	+	}
161	+	return frameData.COMvel;
162	+	}
163	+
164	+	Vector3d Snapshot::getCOMw() {
165	+	if( !hasCOM_ ) {
166	+	sprintf( painCave.errMsg, "COMw was requested before COM was computed!\n");
167	+	painCave.severity = OPENMD_ERROR;
168	+	simError();
169	+	}
170	+	return frameData.COMw;
171	+	}
172		}
158	–
159	–	}
173

Comparing:
trunk/src/brains/Snapshot.cpp (property svn:keywords), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/brains/Snapshot.cpp (property svn:keywords), Revision 1715 by gezelter, Tue May 22 21:55:31 2012 UTC

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