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 error.\n"
                 "\tOOPSE found more than one axis in this directional atom with a vanishing \n"
                 "\tmoment of inertia.");
        painCave.isFatal = 1;
        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<double> DirectionalAtom::getGrad() {
    std::vector<double> grad(6, 0.0);
    Vector3d force;
    Vector3d torque;
    Vector3d myEuler;
    double phi, theta, psi;
    double 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:	642
Committed:	Mon Oct 3 15:54:23 2005 UTC (20 years, 1 month ago) by tim
File size:	5274 byte(s)
Log Message:	fix a bug in projecting the inertia tensor of directional atom in rigibody into rigidbody's body frame (previous commit is wrong)
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	tim	3	#include "primitives/DirectionalAtom.hpp"
43	tim	273	#include "utils/simError.h"
44	gezelter	246	namespace oopse {
45	gezelter	2
46	gezelter	507	DirectionalAtom::DirectionalAtom(DirectionalAtomType* dAtomType)
47			: Atom(dAtomType){
48			objType_= otDAtom;
49			if (dAtomType->isMultipole()) {
50	gezelter	246	electroBodyFrame_ = dAtomType->getElectroBodyFrame();
51	gezelter	507	}
52	tim	273
53	gezelter	507	//check if one of the diagonal inertia tensor of this directional atom is zero
54			int nLinearAxis = 0;
55			Mat3x3d inertiaTensor = getI();
56			for (int i = 0; i < 3; i++) {
57	tim	273	if (fabs(inertiaTensor(i, i)) < oopse::epsilon) {
58	gezelter	507	linear_ = true;
59			linearAxis_ = i;
60			++ nLinearAxis;
61	tim	273	}
62	gezelter	507	}
63	tim	273
64	gezelter	507	if (nLinearAxis > 1) {
65	tim	273	sprintf( painCave.errMsg,
66	gezelter	507	"Directional Atom error.\n"
67			"\tOOPSE found more than one axis in this directional atom with a vanishing \n"
68			"\tmoment of inertia.");
69	tim	273	painCave.isFatal = 1;
70			simError();
71	gezelter	507	}
72
73	tim	273	}
74	gezelter	2
75	gezelter	507	Mat3x3d DirectionalAtom::getI() {
76	gezelter	246	return static_cast<DirectionalAtomType*>(getAtomType())->getI();
77	gezelter	507	}
78	gezelter	2
79	gezelter	507	void DirectionalAtom::setPrevA(const RotMat3x3d& a) {
80	gezelter	246	((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a;
81			if (atomType_->isMultipole()) {
82	gezelter	507	((snapshotMan_->getPrevSnapshot())->storage_).electroFrame[localIndex_] = a.transpose() electroBodyFrame_;
83	gezelter	205	}
84	gezelter	507	}
85	gezelter	2
86	gezelter	246
87	gezelter	507	void DirectionalAtom::setA(const RotMat3x3d& a) {
88	gezelter	246	((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a;
89	gezelter	2
90	gezelter	246	if (atomType_->isMultipole()) {
91	gezelter	507	((snapshotMan_->getCurrentSnapshot())->storage_).electroFrame[localIndex_] = a.transpose() electroBodyFrame_;
92	gezelter	2	}
93	gezelter	507	}
94	gezelter	2
95	gezelter	507	void DirectionalAtom::setA(const RotMat3x3d& a, int snapshotNo) {
96	gezelter	246	((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a;
97	gezelter	2
98	gezelter	246	if (atomType_->isMultipole()) {
99	gezelter	507	((snapshotMan_->getSnapshot(snapshotNo))->storage_).electroFrame[localIndex_] = a.transpose() electroBodyFrame_;
100	gezelter	2	}
101	gezelter	507	}
102	gezelter	2
103	gezelter	507	void DirectionalAtom::rotateBy(const RotMat3x3d& m) {
104	gezelter	246	setA(m *getA());
105	gezelter	507	}
106	gezelter	2
107	gezelter	507	std::vector<double> DirectionalAtom::getGrad() {
108	gezelter	246	std::vector<double> grad(6, 0.0);
109			Vector3d force;
110			Vector3d torque;
111			Vector3d myEuler;
112			double phi, theta, psi;
113			double cphi, sphi, ctheta, stheta;
114			Vector3d ephi;
115			Vector3d etheta;
116			Vector3d epsi;
117	gezelter	2
118	gezelter	246	force = getFrc();
119			torque =getTrq();
120			myEuler = getA().toEulerAngles();
121	gezelter	2
122	gezelter	246	phi = myEuler[0];
123			theta = myEuler[1];
124			psi = myEuler[2];
125	gezelter	2
126	gezelter	246	cphi = cos(phi);
127			sphi = sin(phi);
128			ctheta = cos(theta);
129			stheta = sin(theta);
130	gezelter	2
131	gezelter	246	// get unit vectors along the phi, theta and psi rotation axes
132	gezelter	2
133	gezelter	246	ephi[0] = 0.0;
134			ephi[1] = 0.0;
135			ephi[2] = 1.0;
136	gezelter	2
137	gezelter	246	etheta[0] = cphi;
138			etheta[1] = sphi;
139			etheta[2] = 0.0;
140	gezelter	2
141	gezelter	246	epsi[0] = stheta * cphi;
142			epsi[1] = stheta * sphi;
143			epsi[2] = ctheta;
144	gezelter	2
145	gezelter	246	//gradient is equal to -force
146			for (int j = 0 ; j<3; j++)
147	gezelter	507	grad[j] = -force[j];
148	gezelter	2
149	gezelter	246	for (int j = 0; j < 3; j++ ) {
150	gezelter	2
151	tim	642	grad[3] -= torque[j]*ephi[j];
152			grad[4] -= torque[j]*etheta[j];
153			grad[5] -= torque[j]*epsi[j];
154	gezelter	2
155	gezelter	246	}
156	gezelter	2
157	gezelter	246	return grad;
158	gezelter	507	}
159	gezelter	2
160	gezelter	507	void DirectionalAtom::accept(BaseVisitor* v) {
161	gezelter	246	v->visit(this);
162	gezelter	507	}
163	gezelter	2
164			}
165