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.isMultipole()) {
      electroBodyFrame_ = ma.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)) < 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()) {
      ((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;
    
    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:	1710
Committed:	Fri May 18 21:44:02 2012 UTC (12 years, 11 months ago) by gezelter
File size:	5691 byte(s)
Log Message:	Added an adapter layer between the AtomType and the rest of the code to handle the bolt-on capabilities of new types. Fixed a long-standing bug in how storageLayout was being set to the maximum possible value. Started to add infrastructure for Polarizable and fluc-Q calculations.
#	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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
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.
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	*
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	#include "primitives/DirectionalAtom.hpp"
44	#include "types/DirectionalAdapter.hpp"
45	#include "types/MultipoleAdapter.hpp"
46	#include "utils/simError.h"
47	namespace OpenMD {
48
49	DirectionalAtom::DirectionalAtom(AtomType* dAtomType)
50	: Atom(dAtomType) {
51	objType_= otDAtom;
52
53	DirectionalAdapter da = DirectionalAdapter(dAtomType);
54	I_ = da.getI();
55
56	MultipoleAdapter ma = MultipoleAdapter(dAtomType);
57	if (ma.isMultipole()) {
58	electroBodyFrame_ = ma.getElectroBodyFrame();
59	}
60
61	// Check if one of the diagonal inertia tensor of this directional
62	// atom is zero:
63	int nLinearAxis = 0;
64	Mat3x3d inertiaTensor = getI();
65	for (int i = 0; i < 3; i++) {
66	if (fabs(inertiaTensor(i, i)) < OpenMD::epsilon) {
67	linear_ = true;
68	linearAxis_ = i;
69	++ nLinearAxis;
70	}
71	}
72
73	if (nLinearAxis > 1) {
74	sprintf( painCave.errMsg,
75	"Directional Atom warning.\n"
76	"\tOpenMD found more than one axis in this directional atom with a vanishing \n"
77	"\tmoment of inertia.");
78	painCave.isFatal = 0;
79	simError();
80	}
81	}
82
83	Mat3x3d DirectionalAtom::getI() {
84	return I_;
85	}
86
87	void DirectionalAtom::setPrevA(const RotMat3x3d& a) {
88	((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a;
89	if (atomType_->isMultipole()) {
90	((snapshotMan_->getPrevSnapshot())->storage_).electroFrame[localIndex_] = a.transpose() electroBodyFrame_;
91	}
92	}
93
94
95	void DirectionalAtom::setA(const RotMat3x3d& a) {
96	((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a;
97
98	if (atomType_->isMultipole()) {
99	((snapshotMan_->getCurrentSnapshot())->storage_).electroFrame[localIndex_] = a.transpose() electroBodyFrame_;
100	}
101	}
102
103	void DirectionalAtom::setA(const RotMat3x3d& a, int snapshotNo) {
104	((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a;
105
106	if (atomType_->isMultipole()) {
107	((snapshotMan_->getSnapshot(snapshotNo))->storage_).electroFrame[localIndex_] = a.transpose() electroBodyFrame_;
108	}
109	}
110
111	void DirectionalAtom::rotateBy(const RotMat3x3d& m) {
112	setA(m *getA());
113	}
114
115	std::vector<RealType> DirectionalAtom::getGrad() {
116	std::vector<RealType> grad(6, 0.0);
117	Vector3d force;
118	Vector3d torque;
119	Vector3d myEuler;
120	RealType phi, theta, psi;
121	RealType cphi, sphi, ctheta, stheta;
122	Vector3d ephi;
123	Vector3d etheta;
124	Vector3d epsi;
125
126	force = getFrc();
127	torque =getTrq();
128	myEuler = getA().toEulerAngles();
129
130	phi = myEuler[0];
131	theta = myEuler[1];
132	psi = myEuler[2];
133
134	cphi = cos(phi);
135	sphi = sin(phi);
136	ctheta = cos(theta);
137	stheta = sin(theta);
138
139	// get unit vectors along the phi, theta and psi rotation axes
140
141	ephi[0] = 0.0;
142	ephi[1] = 0.0;
143	ephi[2] = 1.0;
144
145	//etheta[0] = -sphi;
146	//etheta[1] = cphi;
147	//etheta[2] = 0.0;
148
149	etheta[0] = cphi;
150	etheta[1] = sphi;
151	etheta[2] = 0.0;
152
153	epsi[0] = stheta * cphi;
154	epsi[1] = stheta * sphi;
155	epsi[2] = ctheta;
156
157	//gradient is equal to -force
158	for (int j = 0 ; j<3; j++)
159	grad[j] = -force[j];
160
161	for (int j = 0; j < 3; j++ ) {
162	grad[3] -= torque[j]*ephi[j];
163	grad[4] -= torque[j]*etheta[j];
164	grad[5] -= torque[j]*epsi[j];
165	}
166
167	return grad;
168	}
169
170	void DirectionalAtom::accept(BaseVisitor* v) {
171	v->visit(this);
172	}
173	}
174