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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#include "primitives/DirectionalAtom.hpp"
#include "types/DirectionalAdapter.hpp"
#include "types/MultipoleAdapter.hpp"
#include "utils/simError.h"
namespace OpenMD {
  
  DirectionalAtom::DirectionalAtom(AtomType* dAtomType) 
    : Atom(dAtomType) {
    objType_= otDAtom;

    DirectionalAdapter da = DirectionalAdapter(dAtomType);
    I_ = da.getI();

    MultipoleAdapter ma = MultipoleAdapter(dAtomType);
    if (ma.isDipole()) {
      dipole_ = ma.getDipole();
    }
    if (ma.isQuadrupole()) {
      quadrupole_ = ma.getQuadrupole();
    }

    // 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)) < OpenMD::epsilon) {
        linear_ = true;
        linearAxis_ = i;
        ++ nLinearAxis;
      }
    }

    if (nLinearAxis > 1) {
      sprintf( painCave.errMsg,
               "Directional Atom warning.\n"
               "\tOpenMD found more than one axis in this directional atom with a vanishing \n"
               "\tmoment of inertia.");
      painCave.isFatal = 0;
      simError();
    }    
  }
  
  Mat3x3d DirectionalAtom::getI() {
    return I_;     
  }    
  
  void DirectionalAtom::setPrevA(const RotMat3x3d& a) {
    ((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a;

    if (atomType_->isMultipole()) {
      RotMat3x3d atrans = a.transpose();
      
      if (atomType_->isDipole()) {
        ((snapshotMan_->getPrevSnapshot())->*storage_).dipole[localIndex_] = atrans * dipole_;
      }

      if (atomType_->isQuadrupole()) {
        ((snapshotMan_->getPrevSnapshot())->*storage_).quadrupole[localIndex_] = atrans * quadrupole_ * a;
      }
    }
  }
  
  
  void DirectionalAtom::setA(const RotMat3x3d& a) {
    ((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a;
 
    if (atomType_->isMultipole()) {
      RotMat3x3d atrans = a.transpose();
      
      if (atomType_->isDipole()) {
        ((snapshotMan_->getCurrentSnapshot())->*storage_).dipole[localIndex_] = atrans * dipole_;
      }

      if (atomType_->isQuadrupole()) {
        ((snapshotMan_->getCurrentSnapshot())->*storage_).quadrupole[localIndex_] = atrans * quadrupole_ * a;
      }
    }
   
  }    
  
  void DirectionalAtom::setA(const RotMat3x3d& a, int snapshotNo) {
    ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a;

    if (atomType_->isMultipole()) {
      RotMat3x3d atrans = a.transpose();
      
      if (atomType_->isDipole()) {
        ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).dipole[localIndex_] = atrans * dipole_;
      }

      if (atomType_->isQuadrupole()) {
        ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).quadrupole[localIndex_] = atrans * quadrupole_ * a;
      }
    }

  }    
  
  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;
    // RealType 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;
    
    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:	1798
Committed:	Thu Sep 13 14:10:11 2012 UTC (12 years, 7 months ago) by gezelter
File size:	6441 byte(s)
Log Message:	Merged trunk changes into the development branch
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
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	gezelter	1390	*
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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43	tim	3	#include "primitives/DirectionalAtom.hpp"
44	gezelter	1710	#include "types/DirectionalAdapter.hpp"
45			#include "types/MultipoleAdapter.hpp"
46	tim	273	#include "utils/simError.h"
47	gezelter	1390	namespace OpenMD {
48	gezelter	1211
49	gezelter	1710	DirectionalAtom::DirectionalAtom(AtomType* dAtomType)
50			: Atom(dAtomType) {
51	gezelter	1211	objType_= otDAtom;
52	gezelter	1710
53			DirectionalAdapter da = DirectionalAdapter(dAtomType);
54			I_ = da.getI();
55
56			MultipoleAdapter ma = MultipoleAdapter(dAtomType);
57	gezelter	1787	if (ma.isDipole()) {
58			dipole_ = ma.getDipole();
59	gezelter	1211	}
60	gezelter	1787	if (ma.isQuadrupole()) {
61			quadrupole_ = ma.getQuadrupole();
62			}
63	gezelter	1710
64	gezelter	1211	// Check if one of the diagonal inertia tensor of this directional
65			// atom is zero:
66			int nLinearAxis = 0;
67			Mat3x3d inertiaTensor = getI();
68			for (int i = 0; i < 3; i++) {
69	gezelter	1390	if (fabs(inertiaTensor(i, i)) < OpenMD::epsilon) {
70	gezelter	1211	linear_ = true;
71			linearAxis_ = i;
72			++ nLinearAxis;
73	gezelter	507	}
74	tim	273	}
75	gezelter	2
76	gezelter	1211	if (nLinearAxis > 1) {
77			sprintf( painCave.errMsg,
78			"Directional Atom warning.\n"
79	gezelter	1390	"\tOpenMD found more than one axis in this directional atom with a vanishing \n"
80	gezelter	1211	"\tmoment of inertia.");
81			painCave.isFatal = 0;
82			simError();
83			}
84			}
85
86	gezelter	507	Mat3x3d DirectionalAtom::getI() {
87	gezelter	1710	return I_;
88	gezelter	507	}
89	gezelter	1211
90	gezelter	507	void DirectionalAtom::setPrevA(const RotMat3x3d& a) {
91	gezelter	246	((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a;
92	gezelter	1787
93	gezelter	246	if (atomType_->isMultipole()) {
94	gezelter	1787	RotMat3x3d atrans = a.transpose();
95
96			if (atomType_->isDipole()) {
97			((snapshotMan_->getPrevSnapshot())->storage_).dipole[localIndex_] = atrans dipole_;
98			}
99
100			if (atomType_->isQuadrupole()) {
101			((snapshotMan_->getPrevSnapshot())->storage_).quadrupole[localIndex_] = atrans quadrupole_ * a;
102			}
103	gezelter	205	}
104	gezelter	507	}
105	gezelter	1211
106
107	gezelter	507	void DirectionalAtom::setA(const RotMat3x3d& a) {
108	gezelter	246	((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a;
109	gezelter	1787
110	gezelter	246	if (atomType_->isMultipole()) {
111	gezelter	1787	RotMat3x3d atrans = a.transpose();
112
113			if (atomType_->isDipole()) {
114			((snapshotMan_->getCurrentSnapshot())->storage_).dipole[localIndex_] = atrans dipole_;
115			}
116
117			if (atomType_->isQuadrupole()) {
118			((snapshotMan_->getCurrentSnapshot())->storage_).quadrupole[localIndex_] = atrans quadrupole_ * a;
119			}
120	gezelter	2	}
121	gezelter	1787
122	gezelter	507	}
123	gezelter	1211
124	gezelter	507	void DirectionalAtom::setA(const RotMat3x3d& a, int snapshotNo) {
125	gezelter	246	((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a;
126	gezelter	1787
127	gezelter	246	if (atomType_->isMultipole()) {
128	gezelter	1787	RotMat3x3d atrans = a.transpose();
129
130			if (atomType_->isDipole()) {
131			((snapshotMan_->getSnapshot(snapshotNo))->storage_).dipole[localIndex_] = atrans dipole_;
132			}
133
134			if (atomType_->isQuadrupole()) {
135			((snapshotMan_->getSnapshot(snapshotNo))->storage_).quadrupole[localIndex_] = atrans quadrupole_ * a;
136			}
137	gezelter	2	}
138	gezelter	1787
139	gezelter	507	}
140	gezelter	1211
141	gezelter	507	void DirectionalAtom::rotateBy(const RotMat3x3d& m) {
142	gezelter	246	setA(m *getA());
143	gezelter	507	}
144	gezelter	1211
145	tim	963	std::vector<RealType> DirectionalAtom::getGrad() {
146			std::vector<RealType> grad(6, 0.0);
147	gezelter	246	Vector3d force;
148			Vector3d torque;
149			Vector3d myEuler;
150	gezelter	1798	RealType phi, theta;
151			// RealType psi;
152	tim	963	RealType cphi, sphi, ctheta, stheta;
153	gezelter	246	Vector3d ephi;
154			Vector3d etheta;
155			Vector3d epsi;
156	gezelter	1211
157	gezelter	246	force = getFrc();
158			torque =getTrq();
159			myEuler = getA().toEulerAngles();
160	gezelter	1211
161	gezelter	246	phi = myEuler[0];
162			theta = myEuler[1];
163	gezelter	1798	// psi = myEuler[2];
164	gezelter	1211
165	gezelter	246	cphi = cos(phi);
166			sphi = sin(phi);
167			ctheta = cos(theta);
168			stheta = sin(theta);
169	gezelter	1211
170	gezelter	246	// get unit vectors along the phi, theta and psi rotation axes
171	gezelter	1211
172	gezelter	246	ephi[0] = 0.0;
173			ephi[1] = 0.0;
174			ephi[2] = 1.0;
175	gezelter	1211
176	gezelter	1424	//etheta[0] = -sphi;
177			//etheta[1] = cphi;
178			//etheta[2] = 0.0;
179	gezelter	1211
180	gezelter	1424	etheta[0] = cphi;
181			etheta[1] = sphi;
182			etheta[2] = 0.0;
183
184	gezelter	246	epsi[0] = stheta * cphi;
185			epsi[1] = stheta * sphi;
186			epsi[2] = ctheta;
187	gezelter	1211
188	gezelter	246	//gradient is equal to -force
189			for (int j = 0 ; j<3; j++)
190	gezelter	507	grad[j] = -force[j];
191	gezelter	1211
192			for (int j = 0; j < 3; j++ ) {
193	tim	642	grad[3] -= torque[j]*ephi[j];
194			grad[4] -= torque[j]*etheta[j];
195	gezelter	1211	grad[5] -= torque[j]*epsi[j];
196	gezelter	246	}
197	gezelter	2
198	gezelter	246	return grad;
199	gezelter	507	}
200	gezelter	1211
201	gezelter	507	void DirectionalAtom::accept(BaseVisitor* v) {
202	gezelter	246	v->visit(this);
203	gezelter	1211	}
204	gezelter	2	}
205