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] = -sphi;
    etheta[1] =  cphi;
    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:	3520
Committed:	Mon Sep 7 16:31:51 2009 UTC (15 years, 7 months ago) by cli2
File size:	5370 byte(s)
Log Message:	Added new restraint infrastructure Added MolecularRestraints Added ObjectRestraints Added RestraintStamp Updated thermodynamic integration to use ObjectRestraints Added Quaternion mathematics for twist swing decompositions Significantly updated RestWriter and RestReader to use dump-like files Added selections for x, y, and z coordinates of atoms Removed monolithic Restraints class Fixed a few bugs in gradients of Euler angles in DirectionalAtom and RigidBody Added some rotational capabilities to prinicpalAxisCalculator
#	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] = -sphi;
138	etheta[1] = cphi;
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