src/primitives/DirectionalAtom.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.
 */
 
#include "primitives/DirectionalAtom.hpp"
#include "utils/simError.h"
namespace oopse {
  
  DirectionalAtom::DirectionalAtom(DirectionalAtomType* dAtomType) 
    : Atom(dAtomType){
    objType_= otDAtom;
    if (dAtomType->isMultipole()) {
      electroBodyFrame_ = dAtomType->getElectroBodyFrame();
    }
    
    // Check if one of the diagonal inertia tensor of this directional
    // atom is zero:
    int nLinearAxis = 0;
    Mat3x3d inertiaTensor = getI();
    for (int i = 0; i < 3; i++) {    
      if (fabs(inertiaTensor(i, i)) < oopse::epsilon) {
        linear_ = true;
        linearAxis_ = i;
        ++ nLinearAxis;
      }
    }

    if (nLinearAxis > 1) {
      sprintf( painCave.errMsg,
               "Directional Atom warning.\n"
               "\tOOPSE found more than one axis in this directional atom with a vanishing \n"
               "\tmoment of inertia.");
      painCave.isFatal = 0;
      simError();
    }    
  }
  
  Mat3x3d DirectionalAtom::getI() {
    return static_cast<DirectionalAtomType*>(getAtomType())->getI();
  }    
  
  void DirectionalAtom::setPrevA(const RotMat3x3d& a) {
    ((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a;
    if (atomType_->isMultipole()) {
      ((snapshotMan_->getPrevSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_;
    }
  }
  
  
  void DirectionalAtom::setA(const RotMat3x3d& a) {
    ((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a;
    
    if (atomType_->isMultipole()) {
      ((snapshotMan_->getCurrentSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_;
    }
  }    
  
  void DirectionalAtom::setA(const RotMat3x3d& a, int snapshotNo) {
    ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a;
    
    if (atomType_->isMultipole()) {
      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_;    
    }
  }    
  
  void DirectionalAtom::rotateBy(const RotMat3x3d& m) {
    setA(m *getA());
  }
  
  std::vector<RealType> DirectionalAtom::getGrad() {
    std::vector<RealType> grad(6, 0.0);
    Vector3d force;
    Vector3d torque;
    Vector3d myEuler;
    RealType phi, theta, psi;
    RealType cphi, sphi, ctheta, stheta;
    Vector3d ephi;
    Vector3d etheta;
    Vector3d epsi;
    
    force = getFrc();
    torque =getTrq();
    myEuler = getA().toEulerAngles();
    
    phi = myEuler[0];
    theta = myEuler[1];
    psi = myEuler[2];
    
    cphi = cos(phi);
    sphi = sin(phi);
    ctheta = cos(theta);
    stheta = sin(theta);
    
    // get unit vectors along the phi, theta and psi rotation axes
    
    ephi[0] = 0.0;
    ephi[1] = 0.0;
    ephi[2] = 1.0;
    
    etheta[0] = cphi;
    etheta[1] = sphi;
    etheta[2] = 0.0;
    
    epsi[0] = stheta * cphi;
    epsi[1] = stheta * sphi;
    epsi[2] = ctheta;
    
    //gradient is equal to -force
    for (int j = 0 ; j<3; j++)
      grad[j] = -force[j];
    
    for (int j = 0; j < 3; j++ ) {      
      grad[3] -= torque[j]*ephi[j];
      grad[4] -= torque[j]*etheta[j];
      grad[5] -= torque[j]*epsi[j];      
    }
    
    return grad;
  }    
  
  void DirectionalAtom::accept(BaseVisitor* v) {
    v->visit(this);
  }
}

Revision:	1211
Committed:	Wed Jan 23 16:38:22 2008 UTC (17 years, 9 months ago) by gezelter
File size:	5367 byte(s)
Log Message:	A few formatting changes to prettify the code
#	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	#include "primitives/DirectionalAtom.hpp"
43	#include "utils/simError.h"
44	namespace oopse {
45
46	DirectionalAtom::DirectionalAtom(DirectionalAtomType* dAtomType)
47	: Atom(dAtomType){
48	objType_= otDAtom;
49	if (dAtomType->isMultipole()) {
50	electroBodyFrame_ = dAtomType->getElectroBodyFrame();
51	}
52
53	// Check if one of the diagonal inertia tensor of this directional
54	// atom is zero:
55	int nLinearAxis = 0;
56	Mat3x3d inertiaTensor = getI();
57	for (int i = 0; i < 3; i++) {
58	if (fabs(inertiaTensor(i, i)) < oopse::epsilon) {
59	linear_ = true;
60	linearAxis_ = i;
61	++ nLinearAxis;
62	}
63	}
64
65	if (nLinearAxis > 1) {
66	sprintf( painCave.errMsg,
67	"Directional Atom warning.\n"
68	"\tOOPSE found more than one axis in this directional atom with a vanishing \n"
69	"\tmoment of inertia.");
70	painCave.isFatal = 0;
71	simError();
72	}
73	}
74
75	Mat3x3d DirectionalAtom::getI() {
76	return static_cast<DirectionalAtomType*>(getAtomType())->getI();
77	}
78
79	void DirectionalAtom::setPrevA(const RotMat3x3d& a) {
80	((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a;
81	if (atomType_->isMultipole()) {
82	((snapshotMan_->getPrevSnapshot())->storage_).electroFrame[localIndex_] = a.transpose() electroBodyFrame_;
83	}
84	}
85
86
87	void DirectionalAtom::setA(const RotMat3x3d& a) {
88	((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a;
89
90	if (atomType_->isMultipole()) {
91	((snapshotMan_->getCurrentSnapshot())->storage_).electroFrame[localIndex_] = a.transpose() electroBodyFrame_;
92	}
93	}
94
95	void DirectionalAtom::setA(const RotMat3x3d& a, int snapshotNo) {
96	((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a;
97
98	if (atomType_->isMultipole()) {
99	((snapshotMan_->getSnapshot(snapshotNo))->storage_).electroFrame[localIndex_] = a.transpose() electroBodyFrame_;
100	}
101	}
102
103	void DirectionalAtom::rotateBy(const RotMat3x3d& m) {
104	setA(m *getA());
105	}
106
107	std::vector<RealType> DirectionalAtom::getGrad() {
108	std::vector<RealType> grad(6, 0.0);
109	Vector3d force;
110	Vector3d torque;
111	Vector3d myEuler;
112	RealType phi, theta, psi;
113	RealType cphi, sphi, ctheta, stheta;
114	Vector3d ephi;
115	Vector3d etheta;
116	Vector3d epsi;
117
118	force = getFrc();
119	torque =getTrq();
120	myEuler = getA().toEulerAngles();
121
122	phi = myEuler[0];
123	theta = myEuler[1];
124	psi = myEuler[2];
125
126	cphi = cos(phi);
127	sphi = sin(phi);
128	ctheta = cos(theta);
129	stheta = sin(theta);
130
131	// get unit vectors along the phi, theta and psi rotation axes
132
133	ephi[0] = 0.0;
134	ephi[1] = 0.0;
135	ephi[2] = 1.0;
136
137	etheta[0] = cphi;
138	etheta[1] = sphi;
139	etheta[2] = 0.0;
140
141	epsi[0] = stheta * cphi;
142	epsi[1] = stheta * sphi;
143	epsi[2] = ctheta;
144
145	//gradient is equal to -force
146	for (int j = 0 ; j<3; j++)
147	grad[j] = -force[j];
148
149	for (int j = 0; j < 3; j++ ) {
150	grad[3] -= torque[j]*ephi[j];
151	grad[4] -= torque[j]*etheta[j];
152	grad[5] -= torque[j]*epsi[j];
153	}
154
155	return grad;
156	}
157
158	void DirectionalAtom::accept(BaseVisitor* v) {
159	v->visit(this);
160	}
161	}
162